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Slade, M. B., A. C. M. Chang, et al. (1995). Plasmid vectors for cellular slime moulds of the genus Dictyostelium. USA: 35 pages/20 claims.
	The present invention relates generally to the fields of molecular biology and the production of recombinant protein using cellular slime moulds of the genus Dictyostelium. Most particularly, the present invention relates to novel strains of the genus Dictyostelium, recombinant plasmids for use with strains of the genus Dictyostelium, and polypeptides which facilitate the extrachromosomal replication of such plasmids in strains of the genus Dictyostelium. In particular, the present invention provides a polypeptide which facilitates the extrachromosomal replication of a recombinant plasmid in Dictyostelium spp in which the recombinant plasmid includes an origin of replication derived from a Ddp2-like plasmid but which lacks functional genes for extrachromosomal replication in wild type Dictyostelium spp. The extrachromosomal replicating plasmid constructed in accordance with the present invention are suitable for carrying a wide variety of genes and promoter sequences for control production of recombinant proteins by the biotechnology industry. 


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Atkinson, P. R. and L. K. Foster (1996). Method for removing N-terminal dipeptides from precursor polypeptides with immobilized dipeptidylaminopeptidase from Dictyostelium discoideum. USA, Eli Lilly and Company: 17 pages/20 claims.
	A method for removing dipeptides from the amino terminus of precursor polypeptides to produce a polypeptide product is presented which comprises contacting the precursor polypeptide for sufficient time to remove the dipeptide with an immobilized dipeptidylaminopeptidase (dDAP) from the slime mold, Dictyostelium discoideum, which has a mass of about 225 kilodaltons and a pH optimum of about 3.5. The precursor polypeptides may be made recombinantly and may be analogs of naturally occurring polypeptides. 


Atkinson, P. R., M. D. Hilton, et al. (1996). Method for removing N-terminal dipeptides from precursor polypeptides with dipeptidylaminopeptidase from Dictyostelium discoideum. USA, Eli Lilly and Company: 12 pages/22 claims.
	A method for removing dipeptides from the amino terminus of precursor polypeptides to produce a polypeptide product is presented which comprises contacting the precursor polypeptide for sufficient time to remove the dipeptide with a dipeptidylaminopeptidase (dDAP) from the slime mold, Dictyostelium descoideum, which has a mass of about 225 kilodaltons and a pH optimum of about 3.5. The precursor polypeptides may be made recombinantly and may be analogs of naturally occurring polypeptides. 


Atkinson, P. R., M. D. Hilton, et al. (1996). Dictyostelium dipeptidylaminopeptidase. USA, Eli Lilly and Company: 11 pages/14 claims.
	A dipeptidylaminopeptidase (dDAP enzyme) and a method for isolating it from the culture medium of the cellular slime mold, Dictyostelium discoideum have been presented. The isolated dDAP enzyme has a pH optimum of about 3.5 and a mass of about 225 kDA. The dDAP enzyme has an activity which is somewhat similar to both DAP-I and DAP-III from this organism. Methods for using the dDAP enzyme to remove dipeptides from the N-terminus of recombinantly produced precursor proteins or peptides are also presented. 


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Chae, S. C. and Y. Maeda (1998). "Cloning and sequence analysis of the cDNA encoding the elongation factor-1beta of Dictyostelium discoideum." Biochim. Biophys. Acta 1383: 1-3.
	
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Clements, C. H. (1998). The role of actin tyrosine phosphorylation in spore dormancy, and germination of Dictyostelium discoideum. Windsor, ON (Canada), University of Windsor: 102.
	
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de Vet, E. C. J. M. and H. van den Bosch (1998). "Nucleotide sequence of alkyl-dihydroxyacetonephosphate synthase cDNA from Dictyostelium discoideum." Biochem. Biophys. Res. Commun. 252: 629-633.
	
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Detterbeck, A. (1998). Untersuchungen der Musterbildung in Dictyostelium discoideum mit Reportern verschiedener Halbwertzeit. Munich, Ludwig-Maximilians Univ.
	
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Edelstein-Keshet, L. and G. B. Ermentrout (1998). "Models for the length distributions of actin filaments: I. Simple polymerization and fragmentation." Bull. Math. Biol. 60: 449-475.
	
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Ermentrout, G. B. and L. Edelstein-Keshet (1998). "Models for the length distributions of actin filaments: II. Polymerization and fragmentation by gelsolin acting together." Bull. Math. Biol. 60: 477-503.
	
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Fasel, N. J. and C. D. Reymond (1998). Dictyostelid expression vector and method for expressing a desired protein. USA, RMF Dictagene S.A.: 11 pages/27 claims.
	The invention relates to recombinant DNA molecules comprising a Dictyostelium discoideum homologous promoter region, a heterologous DNA sequence with a Dictyostelium discoideum homologous peptide sequence capable of functioning as a leader peptide sequence positioned upstream thereof and in proper reading frame therewith, and a Dictyostelium discoideum homologous termination region, the heterologous DNA sequence encoding the desired functional polypeptide or intermediate thereof, said DNA sequence being positioned downstream from the promoter region and said termination region being positioned downstream from the DNA sequence. The invention also provides recombinant dictyostelid hosts as well as methods for preparing recombinant DNA molecules of the invention and for expressing recombinant polypeptides encoded by said recombinant DNA molecules in dictyostelid hosts. The invention in particular relates to the expression of the CS protein of Plasmodium falciparum. 

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Fukui, Y. (1998). Microinjection into Dictyostelium amoebae. Cell Biology - A Laboratory Handbook (2nd Edition). J. E. Celis. San Diego, CA, Ac. Press: 31-36.
	
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Gale, K. E. (1998). The acid-activatable cysteine proteinases of the Dictyosteliaceae and other lower eukaryotes. Windsor, ON (Canada), University of Windsor: 126.
	
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Gisser, J. M. (1998). Interactions among a group of related proteins in the cellular slime mold Dictyostelium discoideum. Montreal, QU (Canada), Concordia University: 81.
	
Golstein, P. (1998). Cell death in us and others. Science. 281: 1283.
	
Gomer, R. H. (1998). "Antisense: a key tool for cell and developmental studies in Dictyostelium." Genetic Engin. 20: 135-141.
	
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Gregg, K. Y. (1998). Pattern formation in Polysphondylium pallidum. Princeton, NJ, Princeton University: 134.
	
Hagiwara, H. (1998). "Dictyostelids in Pakistan. III. Dictyostelium aureocephalum Hagiwara and Dictyostelium macrocephalum Hagiwara, Yeh et Chien." Bull. Natl. Sci. Mus. Tokyo, Ser. B 24: 77-80.
	
Hagiwara, H. (1998). "Dictyostelids in Japan XI. Distyostelium giganteum Singh." Bull. Natl. Sci. Mus. Tokyo, Ser. B 24: 81-84.
	
Hagiwara, H. (1998). "Altitudinal distribution of dictyostelids on Mt. Sobo, Kyushu, Japan." Mem. Natl. Sci. Mus. Tokyo 30: 93-99.
	
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Han, Y. H. and S. O. Kang (1998). "Cloning of a cDNA encoding a new calcium-binding protein from Dictyostelium discoideum and its developmental regulation." FEBS Lett. 441: 302-306.
	
Han, Z. and R. A. Firtel (1998). "The homeobox-containing gene Wariai regulates anterior-posterior patterning and cell-type homeostasis in Dictyostelium." Development 125: 313-325.
	
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Hellsten, M. and U. P. Roos (1998). "The actomyosin cytoskeleton of amoebae of the cellular slime molds Acrasis rosea and Protostelium mycophaga: structure, biochemical properties, and function." Fungal Genet. Biol. 24: 123-145.
	
Holmes, K. C. (1998). "A powerful stroke." Nature Struct. Biol. 5: 940-942.
	
Huang, H. J. and C. Pears (1998). "Generation of genomic mini-libraries by Tag DNA polymerase modification of genomic fragments." BioTechniques 24: 566-568.
	
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Iijima, M., H. Shimizu, et al. (1998). "A Dictyostelium discoideum homologue to Tcp-1 is essential for growth and development." Gene 213: 101-106.
	
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Inouye, K. (1998). Cytosolic pH and cell movement measurement in Dictyostelium. Single cell techniques in signal transduction research. B. van Duijn and A. Wiltink. Heidelberg, Springer Verlag: 375-397.
	
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Iwamoto, M., M. Pi, et al. (1998). "A ribosomal protein gene cluster is encoded in the mitochondrial DNA of Dictyostelium discoideum: UGA termination codons and similarity of gene order to Acanthamoeba castellanii." Curr. Genet. 33: 304-310.
	
Jaffe, L. F. and R. Creton (1998). "On the conservation of calcium wave speeds." Cell Calcium 24: 1-8.
	
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Jiang, Y. (1998). Cellular pattern formation. Notre Dame, IN, University of Notre Dame: 302.
	
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Kay, R. R. (1998). "The biosynthesis of differentiation-inducing factor, a chlorinated signal molecule regulating Dictyostelium development." J. Biol. Chem. 273: 2669-2675.
	
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Kishi, Y., C. Clements, et al. (1998). "High levels of actin tyrosine phosphorylation: correlation with the dormant state of Dictyostelium spores." J. Cell Sci. 111: 2923-2932.
	
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Koonce, M. P. and D. A. Knecht (1998). "Cytoplasmic dynein heavy chain is an essential gene product in Dictyostelium." Cell Motil. Cytoskel. 39: 63-72.
	
Kosaka, C., M. Khosla, et al. (1998). "Negative influence of RasG on chemoattractant-induced ERK2 phosphorylation in Dictyostelium." Biochim. Biophys. Acta 1402: 1-5.
	
Kubohara, Y., K. Kabeya, et al. (1998). "Effects of DIF-1, an anti-tumor agent isolated from Dictyostelium discoideum, on rat gastric mucosal RGM-1 and leptomeningeal cells." Zool. Sci. 15: 713-721.
	
Kuhlman, P. A. and C. R. Bagshaw (1998). "ATPase kinetics of the Dictyostelium discoideum myosin II motor domain." J. Muscle Res. Cell Motil. 19: 491-504.
	
Kuhlmann, H. W. (1998). "Photomovements in ciliated protozoa." Naturwissenschaften 85: 143-154.
	
Kuwayama, H. and P. J. M. van Haastert (1998). "cGMP potentiates receptor-stimulated Ca2+ influx in Dictyostelium discoideum." Biochim. Biophys. Acta 1402: 102-108.
	
Kuwayama, H. and P. J. M. van Haastert (1998). "Chemotactic and osmotic signals share a cGMP transduction pathway in Dictyostelium discoideum." FEBS Lett. 424: 248-252.
	
Landolt, J. C., L. M. D. A. Geiser, et al. (1998). Dictyostelid cellualr slime molds from forest epiphyte communities. Inoculum, suppl. to Mycologia.
	
Landolt, J. C. and C. W. Stihler (1998). Dictyostelid cellular slime molds from San Salvador Island, Bahamas. Proc. 7th Symp. Natural History Bahamas (ed. T.K. Wilson).
	
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Laub, M. T. and W. F. Loomis (1998). "A molecular network that produces spontaneous oscillations in excitable cells of Dictyostelium." Mol. Biol. Cell 9: 3521-3532.
	
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Leng, P., D. H. Klatte, et al. (1998). "Skipper, an LTR retrotransposon of Dictyostelium." Nucl. Acids Res. 26: 2008-2015.
	
Levine, H. (1998). "The dynamics of Dictyostelium development." Physica A 249: 53-63.
	
Levitsky, D. I., M. A. Ponomarev, et al. (1998). "Differential scanning calorimetric study of the thermal unfolding of the motor domain fragments of Dictyostelium discoideum myosin II." Eur. J. Biochem. 251: 275-280.
	
Liang, W. C. and J. A. Spudich (1998). "Nucleotide-dependent conformational change near the fulcrum region in Dictyostelium myosin II." Proc. Natl. Acad. Sci. USA 95: 12844-12847.
	
Lindsey, D. F., A. Amerik, et al. (1998). "A deubiquitinating enzyme that disassembles free polyubiquitin chains is required for development but not growth in Dictyostelium." J. Biol. Chem. 273: 29178-29187.
	
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Loomis, W. F. (1998). "Role of PKA in the timing of developmental events in Dictyostelium cells." Microbiol. Mol. Biol. Rev. 62: 684.
	
Loomis, W. F. (1998). The Dictyostelium genome sequencing project. Protist. 149: 209-212.
	
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Moniakis, J. (1998). Molecular cloning, regulation and function of a P-type calcium pump in Dictyostelium discoideum. Toronto, ON (Canada), York University: 139.
	
Moores, S. L. (1998). Regulation of myosin II filament assembly and localization in Dictyostelium. Stanford, CA, Stanford University: 130.
	
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Kimble, M., C. Kuzmiak, et al. (2000). "Microtubule organization and the effects of GFP-tubulin expression in Dictyostelium discoideum." Cell Motil. Cytoskel. 47: 48-62.
	
Kishi, Y., D. Mahadeo, et al. (2000). "Glucose-induced pathways for actin tyrosine dephosphorylation during Dictyostelium spore germination." Exp. Cell Res. 261: 187-198.
	
Kobayashi, M. and H. Inaba (2000). "Photon statistics and correlation analysis of ultraweak light originating from living organisms for extraction of biological information." Appl Opt 39(1): 183-192.
	Ultraweak photon emission phenomena in the visible to near-IR region, originating from biological organisms, are known. This biophoton emission is generated during metabolic processes and constitutes physiological information. We investigated a technique for characterizing the optical radiation field based on photon statistics and correlation analysis to extract information on regulation processes in biochemical reactions and their interactions. We developed the system based on the time-interval measurement of photoelectrons in a photon-counting region and employed data processing with a nonstationary optical field with correction for the correlative properties of the photomultiplier dark current. We analyzed biophoton emission from cellular slime mold (Dictyosterium discoideum) and observed the characteristic variation of this organism's super-Poisson statistics during the developmental process.

Kon, T., H. Adachi, et al. (2000). "amiB, a novel gene required for the growth/differentiation transition in Dictyostelium." Genes to Cells 5: 43-55.
	
Konfortov, B. A., H. M. Cohen, et al. (2000). "A high-resolution HAPPY map of Dictyostelium discoideum chromosome 6." Genome Res. 10: 1737-1742.
	
Koonce, M. P. (2000). "Dictyostelium, a model organism for microtubule-based transport." Protist 151: 17-25.
	
Koonce, M. P. and I. Tikhonenko (2000). "Functional elements within the dynein microtubule-binding domain." Mol. Biol. Cell 11: 523-529.
	
Korn, E. D. (2000). "Coevolution of head, neck, and tail domains of myosin heavy chains." Proc. Natl. Acad. Sci. USA 97: 12559-12564.
	
Kravchenko, V. V., A. B. Medvinskii, et al. (2000). "How the spatial structure of Dictyostelium discoideum population is influenced by its environment." Biofizika 45: 103-111.
	
Kravchenko, V. V., A. B. Medvinskii, et al. (2000). "The structural modification of environment by microorganisms: the formation of Liesegang rings around Dictyostelium discoideum population." Biofizika 45: 93-102.
	
Kuwayama, H., M. Oyama, et al. (2000). "A novel role of differentiation-inducing factor-1 in Dictyostelium development, assessed by the restoration of a developmental defect in a mutant lacking mitogen-activated protein kinase ERK2." Devel. Growth Differ. 42: 531-538.
	
Larochelle, D. A., N. Gerald, et al. (2000). "Molecular analysis of racE function in Dictyostelium." Microsc. Res. Techn. 49: 145-151.
	
Lascu, I., A. Giartosio, et al. (2000). "Quaternary structure of nucleoside diphosphate kinases." J. Bioenerg. Biomembranes 32: 227-236.
	
Laussmann, T., C. Pikzack, et al. (2000). "Diphospho-myo-inositol phosphates during the life cycle of Dictyostelium and Polysphondylium." Eur. J. Biochem. 267: 2447-2451.
	
Lee, S. S., I. Karakesisoglou, et al. (2000). "Dissection of functional domains by expression of point-mutated profilins in Dictyostelium mutants." Eur. J. Cell Biol. 79: 92-103.
	
Levi, S., M. Polyakov, et al. (2000). "Green fluorescent protein and epitope tag fusion vectors for Dictyostelium discoideum." Plasmid 44: 231-238.
	
Li, G. (2000). Genes and pathways mediating the cytotoxicity of the anticancer drug cisplatin in Dictyostelium discoideum. Columbia, MO, University of Missouri: 227.
	
Li, G., H. Alexander, et al. (2000). "Molecular basis for resistance to the anticancer drug cisplatin in Dictyostelium." Microbiology 146: 2219-2227.
	
Liu, X., K. Ito, et al. (2000). "Involvement of tail domains in regulation of Dictyostelium myosin II." Biochem. Biophys. Res. Commun. 271: 75-81.
	
Liu, X., S. Shu, et al. (2000). "Chimeras of Dictyostelium myosin II head and neck domains with Acanthamoeba or chicken smooth muscle myosin II tail domain have greatly increased and unregulated actin-dependent MgATPase activity." Proc. Natl. Acad. Sci. USA 97: 12553-12558.
	
Loughran, G., K. Pinter, et al. (2000). "Identification of STKA-dependent genes in Dictyostelium discoideum." Differentiation 66: 71-80.
	
Ma, S. (2000). Function and regulation of cytoplasmic dynein. Evanston, IL, Northwestern University: 162.
	
Maeda, M. and H. Kuwayama (2000). "A diffusible factor involved in MAP-kinase ERK2-regulated development of Dictyostelium." Devel. Growth Differ. 42: 275-284.
	
Maeda, M., H. Kuwayama, et al. (2000). "Developmental changes in the spatial expression of genes involved in myosin function in Dictyostelium." Dev. Biol. 223: 114-119.
	
Maeda, Y. (2000). Model Organism: the Cellular Slime Mold. Tokyo, IPC.
	
Malnasi-Csizmadia, A., R. J. Woolley, et al. (2000). "Resolution of conformational states of Dictyostelium myosin II motor domain using tryptophan (W501) mutants: implications for the open-closed transition identified by crystallography." Biochemistry 39: 16135-16146.
	
Mangiarotti, G. (2000). "Induction of ribosomal subunits misassembly by antisense RNAs to control cell growth." Exp. Cell Res. 259: 266-273.
	
Mangiarotti, G. and R. Giorda (2000). "Cell type specificity and mechanism of control of a gene may be reverted in different strains of Dictyostelium discoideum." Biochim. Biophys. Acta 1492: 23-30.
	
Maree, A. F. M. (2000). From pattern formation to morphogenesis: multicellular coordination in Dictyostelium discoideum. Utrecht, the Netherlands, Utrecht University: 152.
	
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Matsuura, Y., M. Stewart, et al. (2000). "Structural basis for the higher Ca2+-activation of the regulated actin-activated myosin ATPase observed with Dictyostelium/Tetrahymena actin chimeras." J. Mol. Biol. 296: 579-595.
	
Medvinskii, A. B., A. V. Rusakov, et al. (2000). "The mechanism of formation of Liesegang structures around Dictyostelium discoideum population." Biofizika 45: 525-531.
	
Meili, R., C. Ellsworth, et al. (2000). "A novel Akt/PKB-related kinase is essential for morphogenesis in Dictyostelium." Curr. Biol. 10: 708-717.
	
Merkel, R., R. Simson, et al. (2000). "A micromechanic study of cell polarity and plasma membrane cell body coupling in Dictyostelium." Biophys. J. 79: 707-719.
	
Mimura, M. (2000). Reaction-diffusion systems arising in biological and chemical systems: application of singular limit procedures. Mathematical aspects of evolving interfaces. L. Ambrosio, K. Deckelnick, G. Dziuket al. New York, Springer-Verlag. 1812: 89-121.
	
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Miura, K. and F. Siegert (2000). "Light affects cAMP signaling and cell movement activity in Dictyostelium discoideum." Proc. Natl. Acad. Sci. USA 97: 2111-2116.
	
Miwa, Y., T. Sasaguri, et al. (2000). "Differentiation-inducing factor-1, a morphogen of Dictyostelium, induces G1 arrest and differentiation of vascular smooth muscle cells." Circul. Res. 86: 68-75.
	
Mohrs, M. R., K. P. Janssen, et al. (2000). "Cloning and characterization of beta-COP from Dictyostelium discoideum." Eur. J. Cell Biol. 79: 350-357.
	
Monnat, J., E. M. Neuhaus, et al. (2000). "Identification of a novel saturable endoplasmic reticulum localization mechanism mediated by the C-terminus of a Dictyostelium protein disulfide isomerase." Mol. Biol. Cell 11: 3469-3484.
	
Moreno-Bueno, G., C. Cales, et al. (2000). "Isolation and characterization of casein kinase I from Dictyostelium discoideum." Biochem. J. 349: 527-537.
	
Morita, T., K. Saitoh, et al. (2000). "Involvement of the glucose-regulated protein 94 (Dd-GRP94) in starvation response of Dictyostelium discoideum cells." Biochem. Biophys. Res. Commun. 274: 323-331.
	
Mreyen, M., A. Champion, et al. (2000). "Multiple O-glycoforms on the spore coat protein SP96 in Dictyostelium discoideum - Fuc(alpha1-3)GlcNAc-alpha-1-P-Ser is the major modification." J. Biol. Chem. 275: 12164-12174.
	
Murphy, M. B. (2000). Characterization of protein phosphatase 2A in Dictyostelium. Cleveland, OH, Case Western Reserve University: 144.
	
Nadin, B. M., C. S. Mah, et al. (2000). "The regulative capacity of prespore amoebae as demonstrated by fluorescence-activated cell sorting and green fluorescent protein." Dev. Biol. 217: 173-178.
	
Nagano, S. (2000). "Modeling the model organism Dictyostelium discoideum." Devel. Growth Differ. 42: 541-550.
	
Natarajan, K., C. A. Ashley, et al. (2000). "Related Galpha subunits play opposing roles during Dictyostelium development." Differentiation 66: 136-146.
	
Nelson, M. K., A. Clark, et al. (2000). "An F-Box/WD40 repeat-containing protein important for Dictyostelium cell-type proportioning, slug behaviour, and culmination." Dev. Biol. 224: 42-59.
	
Neuhaus, E. M. and T. Soldati (2000). "A myosin I is involved in membrane recycling from early endosomes." J. Cell Biol. 150: 1013-1026.
	
Nock, S., W. C. Liang, et al. (2000). "Mutational analysis of phosphorylation sites in the Dictyostelium myosin II tail: disruption of myosin function by a single charge change." FEBS Lett. 466: 267-272.
	
Noegel, A. A. and M. Schleicher (2000). "The actin cytoskleleton of Dictyostelium: a story told by mutants." J. Cell Sci. 113: 759-766.
	
O'Halloran, T. J. (2000). "Membrane traffic and cytokinesis." Traffic 1: 921-926.
	
Ogawa, S., R. Yoshino, et al. (2000). "The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization." Mol. Gen. Genet. 263: 514-519.
	
Oishi, N., H. Adachi, et al. (2000). "Novel Dictyostelium unconventional myosin, MyoM, has a putative RhoGEF domain." FEBS Lett. 474: 16-22.
	
Othmer, H. G., B. Lilly, et al. (2000). Pattern formation in a cellular slime mold. The IMA Volumes in Mathematics and its Applications. W. Miller Jr. New York, Springer. 119: 359-383.
	
Ott, A. (2000). cAMP als zentraler Botenstoff der hyperosmotischen Stressantowrt in Dictyostelium discoideum. Munich, Germany, LMU (Ludwig-Maximilians-Universitat Munchen: 143.
	
Ott, A., F. Oehme, et al. (2000). "Osmotic stress response in Dictyostelium is mediated by cAMP." EMBO J. 19: 5782-5792.
	
Pal, C. and B. Papp (2000). Selfish cells threaten multicellular life. Trends Ecol. Evol. 15: 351-352.
	
Palmieri, S. J., T. Nebl, et al. (2000). "Mutant Rac1B expression in Dictyostelium: effects on morphology, growth, endocytosis, development, and the actin cytoskeleton." Cell Motil. Cytoskel. 46: 285-304.
	
Palsson, E. and H. G. Othmer (2000). "A model for individual and collective cell movement in Dictyostelium discoideum." Proc. Natl. Acad. Sci. USA 97: 10448-10453.
	
Panetti, T. S. and D. F. Mosher (2000). "Lysophospholipd-induced cell migration." Annals NYAS 905: 326-329.
	
Papadimou, E., A. Monastirli, et al. (2000). "Additive inhibitory effect of calcipotriol and anthralin on ribonuclease P activity." Biochem. Pharmacol. 60: 91-94.
	
Patel, H., K. D. Guo, et al. (2000). "A temperature-sensitive adenylyl cyclase mutant of Dictyostelium." EMBO J. 19: 2247-2256.
	
Patterson, B. (2000). "Genetic techniques for enhancing biochemical and structural characterization of Dictyostelium myosin II." Methods 22: 299- 306.
	
Pavur, K. S., A. N. Petrov, et al. (2000). "Mapping the functional domains of elongation factor-2 kinase." Biochemistry 39: 12216-12224.
	
Pfeiffer, T., A. Tekos, et al. (2000). "Effects of phosphorothioate modifications on precursor tRNA processing by eukaryotic RNase P enzymes." J. Mol. Biol. 298: 559-565.
	
Ponomarev, M. A., M. Furch, et al. (2000). "Charge changes in loop 2 affect the thermal unfolding of the myosin motor domain bound to F-actin." Biochemistry 39: 4527-4532.
	
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Primpke, G., V. Iassonidou, et al. (2000). "Role of cAMP-dependent protein kinase during growth and early development of Dictyostelium discoideum." Dev. Biol. 221: 101-111.
	
Puius, Y. A., E. V. Fedorov, et al. (2000). "Mapping the functional surface of domain 2 in the gelsolin superfamily." Biochemistry 39: 5322-5331.
	
Pukatzki, S., H. L. Ennis, et al. (2000). "A genetic interaction between a ubiquitin-like protein and ubiquitin-mediated proteolysis in Dictyostelium discoideum." Biochim. Biophys. Acta 1499: 154-163.
	
Ratner, D. I. and R. H. Kessin (2000). "Meeting report: Dictyostelium 2000: a conference on the cell and developmental biology of a social amoeba, Dundee, Scotland, July 30 - August 4, 2000." Protist 151: 291-297.
	
Reeves, W. K., J. B. Jensen, et al. (2000). "New faunal and fungal records from caves in Georgia, USA." J. Cave Karst Studies 62: 169-179.
	
Regan, A. C., N. Sciammetta, et al. (2000). "Synthesis of a phosphinic acid analogue of cyclic AMP." Tetrahedron Lett. 41(43): 8211-8215.
	Synthesis of a cyclic phosphinate ester analogue of cyclic AMP was achieved by using a double Arbuzov-type cyclisation of bis-trimethylsilyl phosphonite onto a sugar dihalide derivative as the key step.

Robinson, D. N. and J. A. Spudich (2000). "Dynacortin, a genetic link between equatorial contractility and global shape control discovered by library complementation of a Dictyostelium discoideum cytokinesis mutant." J. Cell Biol. 150: 823-838.
	
Robinson, D. N. and J. A. Spudich (2000). "Towards a molecular understanding of cytokinesis." Trends Cell Biol. 10: 228-237.
	
Roisin-Bouffay, C., W. Jang, et al. (2000). "A precise group size in Dictyostelium is generated by a cell-counting factor modulating cell-cell adhesion." Mol. Cell 6: 953-959.
	
Rosel, D., F. Puta, et al. (2000). "Molecular characterization of a calmodulin-like Dictyostelium protein CalB." FEBS Lett. 473: 323-327.
	
Rosenfeld, S. S., J. Xing, et al. (2000). "Kinetic and spectroscopic evidence for three actomyosin:ADP states in smooth muscle." J. Biol. Chem. 275: 25418-25426.
	
Saeki, K. and T. Wakabayashi (2000). "A230Y mutation of actin on subdomain 4 is sufficient for higher calcium activation of actin-activated myosin adenosinetriphosphatase in the presence of tropomyosin-troponin." Biochemistry 39: 1324-1329.
	
Saeki, K., T. Yasunaga, et al. (2000). "Role of residues 230 and 236 of actin in myosin-ATPase activation by actin-tropomyosin." Biochem. Biophys. Res. Commun. 275: 428-433.
	
Saito, T., T. Morio, et al. (2000). "A second functional delta5 fatty acid desaturase in the cellular slime mould Dictyostelium discoideum." Eur. J. Biochem. 267: 1813-1818.
	
Salger, K. and B. W. Wetterauer (2000). "Aberrant folate response and premature development in a mutant of Dictyostelium discoideum." Differentiation 66: 197-207.
	
Sameshima, M., Y. Kishi, et al. (2000). "Novel actin cytoskeleton: actin tubules." Cell Struct. Funct. 25: 291-295.
	
Samuilov, V. D., A. V. Oleskin, et al. (2000). "Programmed cell death." Biochem. (Moscow) 65: 873-887.
	
Sasaki, N., R. Ohkura, et al. (2000). "Insertion or deletion of a single residue in the strut sequence of Dictyostelium myosin II abolishes strong binding to actin." J. Biol. Chem. 275: 38705-38709.
	
Sawada, T., M. Aono, et al. (2000). "Structure determination and total synthesis of a novel antibacterial substance, AB0022A, produced by a cellular slime mold." J. Antibiotics 53: 959-966.
	
Sawai, S., Y. Maeda, et al. (2000). "Spontaneous symmetry breaking Turing-type pattern formation in a confined Dictyostelium cell mass." Phys. Rev. Lett. 85: 2212-2215.
	
Schaloske, R., C. Schlatterer, et al. (2000). "A xestospongin C-sensitive Ca2+ store is required for cAMP-induced Ca2+ influx and cAMP oscillations in Dictyostelium." J. Biol. Chem. 275: 8404-8408.
	
Schneider, N., J. M. Schwartz, et al. (2000). "Golvesin-GFP fusions as distinct markers for Golgi and post-Golgi vesicles in Dictyostelium cells." Biol. Cell 92: 495-511.
	
Schwarz, E. C., E. M. Neuhaus, et al. (2000). "Dictyostelium myosin IK is involved in the maintenance of cortical tension and affects motility and phagocytosis." J. Cell Sci. 113: 621-633.
	
Sellers, J. R. (2000). "Myosins: a diverse superfamily." Biochim. Biophys. Acta 1496: 3-22.
	
Senda, S. and M. A. Titus (2000). "A potential mechanism for regulating myosin I binding to membranes in vivo." FEBS Lett. 484: 125-128.
	
Shih, W. M., Z. Gryczynski, et al. (2000). "A FRET-based sensor reveals large ATP hydrolysis-induced conformational changes and three distinct states of the molecular motor myosin." Cell 102: 683-694.
	
Shih, W. M. W. (2000). Probing conformational changes in Dictyostelium myosin II via cysteine engineering. Stanford, CA, Stanford University: 150.
	
Sims, M. D. (2000). Molecular analysis of pimaricin resistance in Dictyostelium discoideum. Stony Brook, NY, State University of New York (SUNY) at Stonybrook: 262.
	
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Solomon, J. M. and R. R. Isberg (2000). "Growth of Legionella pneumophila in Dictyostelium discoideum: a novel system for genetic analysis of host-pathogen interactions." Trends Microbiol. 8: 478-480.
	
Solomon, J. M., A. Rupper, et al. (2000). "Intracellular growth of Legionella pneumophila in Dictyostelium discoideum, a system for genetic analysis of host-pathogen interactions." Inf. Immun. 68: 2939-2947.
	
Srinivasan, S. (2000). Developmentally regulated secretion in Dictyostelium discoideum. Columbia, MO, University of Missouri: 200.
	
Srinivasan, S., H. Alexander, et al. (2000). "Crossing the finish line of development: regulated secretion of Dictyostelium proteins." Trends Cell Biol. 10: 215-219.
	
Srinivasan, S., H. Alexander, et al. (2000). The Dictyostelium fruiting body - A structure of cells and cellulose. Trends Cell Biol. 10: 315.
	
Srinivasan, S., K. R. Griffiths, et al. (2000). "The cellulose-binding activity of the PsB multiprotein complex is required for proper assembly of the spore coat and spore viability in Dictyostelium discoideum." Microbiology 146: 1829-1839.
	
Stathopoulos, C., A. Tsagla, et al. (2000). "Effect of peptidyltransferase inhibitors on ribonuclease P activity from Dictyostelium discoideum - Effect of antibiotics on RNase P." Mol. Biol. Reports 27: 107-111.
	
Steiner, J. R. (2000). Scar, a WASp-like protein, is required for lateral pseudopod formation and chemotaxis in Dictyostelium discoideum. Atlanta, GA, Emory University: 226.
	
Steinmetz, M. O., A. Hoenger, et al. (2000). "Polymerization, three-dimensional structure and mechanical properties of Dictyostelium versus rabbit muscle actin filaments." J. Mol. Biol. 303: 171-184.
	
Stewart, I. (2000). "Spiral slime (mathematical recreations)." Scientific Am. 283 (Nov.): 116-118.
	
Strassmann, J. E., Y. Zhu, et al. (2000). "Altruism and social cheating in the social amoeba Dictyostelium discoideum." Nature 408: 965-967.
	
Strauss, E. (2000). "Simple hosts may help reveal how bacteria infect cells." Science 290: 2245-2247.
	
Sucgang, R., G. Shaulsky, et al. (2000). "Toward the functional analysis of the Dictyostelium discoideum genome." J. Euk. Microbiol. 47: 334-339.
	
Sung, S. (2000). snfA, the Dictyostelium discoideum SNF1/AMPK protein kinase. Logan, UT, Utah State University: 64.
	
Suzuki, Y. (2000). "Detection of the swings of the lever arm of a myosin motor by fluorescence resonance energy transfer of green and blue fluorescent proteins." Methods 22: 355-363.
	
Swigart, P., R. Insall, et al. (2000). "Purification and cloning of phosphatidylinositol transfer proteins from Dictyostelium discoideum: homologues of both mammalian PITPs and Saccharomyces cerevisiae Sec14p are found in the same cell." Biochem. J. 347: 837-843.
	
Takaya, Y., H. Kikuchi, et al. (2000). "Novel acyl alpha-pyronoids, dictyopyrone A, B, and C, from Dictyostelium cellular slime molds." J. Org. Chem. 65: 985-989.
	
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Temesvari, L., L. Y. Zhang, et al. (2000). "Inactivation of lmpA, encoding a LIMPII-related endosomal protein, suppresses the internalization and endosomal trafficking defects in profilin-null mutants." Mol. Biol. Cell 11: 2019-2031.
	
Tessarolo, D. (2000). Cytoskeletal localization and function of calcium-binding protein 1 (CBP1) during Dictyostelium discoideum development. Toronto, ON (Canada), York University: 100.
	
Thomason, P. and R. Kay (2000). "Eukaryotic signal transduction via histidine-aspartate phosphorelay." J. Cell Sci. 113: 3141-3150.
	
Thompson, C. R. L. and R. R. Kay (2000). "Cell-fate choice in Dictyostelium: intrinsic biases modulate sensitivity to DIF signaling." Dev. Biol. 227: 56-64.
	
Thompson, C. R. L. and R. R. Kay (2000). "The role of DIF-1 signaling in Dictyostelium development." Mol. Cell 6: 1509-1514.
	
Titus, M. A. (2000). "The role of unconventional myosins in Dictyostelium endocytosis." J. Euk. Microbiol. 47: 191-196.
	
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Uyeda, T. Q. P., C. Kitayama, et al. (2000). "Myosin II-independent cytokinesis in Dictyostelium: its mechanism and implications." Cell Struct. Funct. 25: 1-10.
	
Uyeda, T. Q. P. and S. Yumura (2000). "Molecular biological approaches to study myosin functions in cytokinesis of Dictyostelium." Microsc. Res. Techn. 49: 136-144.
	
Vadell, E. M. (2000). "Dictyostelids (Eumycetozoa) from soils of Punta Lara, province of Buenos Aires, Argentina." Rev. Argent. Microbiol. 32: 89-96.
	
van Bemmelen, M. X., C. Beghdadi-Rais, et al. (2000). "Expression and one-step purification of Plasmodium proteins in Dictyostelium." Mol. Biochem. Parasitol. 111: 377-390.
	
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Vicker, M. G. (2000). "Reaction-diffusion waves of actin filament polymerization/ depolymerization in Dictyostelium pseudopodium extension and cell locomotion." Biophys. Chem. 84: 87-98.
	
Voit, E. O. (2000). Ch. 9 - Diagnosis and refinement of a model of the tricarboxylic acid cycle in Dictyostelium discoideum. Computational analysis of biochemical systems: a practical guide for biochemists and molecular biologists. E. O. Voit. New York, Cambridge University Press.
	
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Warner, N. and C. L. Rutherford (2000). "Purification and cloning of TF2: A novel protein that binds a regulatory site of the gp2 promoter in Dictyostelium." Arch. Biochem. Biophys 373: 462-470.
	
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Weeks, G. (2000). "Signalling molecules involved in cellular differentiation during Dictyostelium morphogenesis." Curr. Opin. Microbiol. 3: 625-630.
	
Weidenhaupt, M., F. Bruckert, et al. (2000). "Functional and molecular identification of novel members of the ubiquitous membrane fusion proteins alpha- and gamma-SNAP (Soluble N-ethylmaleimide-sensitive factor-attachment proteins) families in Dictyostelium discoideum." Eur. J. Biochem. 267: 2062-2070.
	
Wells, W. (2000). Slimy catenins. A slime mold, like metazoans, has a beta-catenin involved both in signaling and in forming adherens junctions. The Scientist www.the-scientist.com: December 11.
	
Wessels, D., J. Reynolds, et al. (2000). "Clathrin plays a novel role in the regulation of cell polarity, pseudopod formation, uropod stability and motility in Dictyostelium." J. Cell Sci. 113: 21-36.
	
Wessels, D. J., H. Zhang, et al. (2000). "The internal phosphodiesterase RegA is essential for the suppression of lateral pseudopods during Dictyostelium chemotaxis." Mol. Biol. Cell 11: 2803-2820.
	
Wetterauer, B., K. Salger, et al. (2000). "Efficient transformation of Dictyostelium discoideum with a particle inflow gun." Biochim. Biophys. Acta 1499: 139-143.
	
Wetterauer, B. W. (2000). "Protein kinases from Dictyostelium discoideum with similarity to LIM kinases." Biochim. Biophys. Acta 1480: 377-383.
	
Wilkins, A., J. Chubb, et al. (2000). "A novel Dictyostelium RasGEF is required for normal endocytosis, cell motility and multicellular development." Curr. Biol. 10: 1427-1437.
	
Wilkins, A., M. Khosla, et al. (2000). "Dictyostelium RasD is required for normal phototaxis, but not differentiation." Genes Devel. 14: 1407-1413.
	
Williams, J. G. (2000). "STAT signalling in cell proliferation and in development." Curr. Opin. Genet. Devel. 10: 503-507.
	
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Gomer, R. and D. Brazill (2003). The versatile Dictyostelium discoideum - Meeting report: international Dictyostelium conference 2002. Protist. 154: 5-10.
	
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	A breast carcinoma tyrosine phosphoprotein, DDR (Discoidin Domain Receptor), that defines a novel class of receptor tyrosine kinases is presented. The DDR cDNA predicts a polypeptide C-terminal tyrosine kinase domain and an N-terminal domain similar to the Dictyostelium discoideum lectin discoidin I. These domains are connected by an extraordinary hydrophilic proline/glycine-rich domain, which is interrupted by a predicted transmembrane sequence. This extended proline/glycine-rich region suggests an unusual geometry of interaction with ligand or substrates. Discoidin I-type domains may interact with specific cell surface molecules.

Kalavrizioti, D., A. Vourekas, et al. (2003). "Kinetics of inhibition of ribonuclease P activity by peptidyltransferase inhibitors - Effect of antibiotics on RNase P." Mol. Biol. Reports 30: 9-14.
	
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Kollmar, M. and G. Glockner (2003). "Identification and phylogenetic analysis of Dictyostelium discoideum kinesin proteins." BMC Genetics 4:47: 11 pages.
	
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Mukhopadhyay, S. and S. Chatterjee (2003). "Effect of arsenic on cell growth of the cellular slime mould, Dictyostelium discoideum." Indian J. Exp. Biol. 41: 1300-1305.
	
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Nellen, W. and M. Maniak (2003). Dictyostelium: cell culture and molecular tools. Encyclopedia of Life Sciences, Wiley Interscience (John Wiley and Sons).
	Dictyostelium provides an easy-to-grow model system for the study of the cellular functions of a unicellular eukaryote. A variety of conditions initiate a differentiation process resulting in a multicellular structure of low complexity. A plethora of molecular tools allow for easy genetic manipulation.


Nieves-Rivera, A. M. (2003). "Mycological survey of Rio Camuy Caves Park, Puerto Rico." J. Cave Karst Studies 65: 23-28.
	
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Otto, G. (2003). Macroautophagy is required for multicellular development of the social amoeba Dictyostelium discoideum. New York, NY, Columbia University: 143.
	
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Platt, T. G. (2003). Conflict and cooperation in the tropical wasp, Parachartergus colobopterus, and the chimeric multicellular organism, Dictyostelium discoideum. Houston, TX, Rice University: 57.
	
Postma, M. (2003). Spatial and temporal aspects in biological signal transduction. Groningen, the Netherlands, Rijksuniversiteit Groningen: 171.
	
Postma, M., J. Roelofs, et al. (2003). "Uniform cAMP stimulation of Dictyostelium cells induces localized patches of signal transduction and pseudopodia." Mol. Biol. Cell 14: 5019-5027.
	
Prevorovsky, M. and F. Puta (2003). "A/T-rich inverted DNA repeats are destabilized by chaotrope-containing buffer during purification using silica gel membrane technology." BioTechniques 35: 698-702.
	
Queller, D. C., K. R. Foster, et al. (2003). Cooperation and conflict in the social amoeba, Dictyostelium discoideum. Genes, Behaviors and Evolution of Social Insects. T. Kikuchi, N. Azuma and S. Higashi. Sapporo, Japan, Hokkaido Univ. Press: 173-200.
	
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Reymond, C. D. (2003). Use of the regulatory subunit of the cAMP-dependent protein kinase (PKA) from Dictyostelium for cAMP measurements. USA, RMF Dictagene S.A.: 15 pages/13 claims.
	The invention relates to the use of the regulatory subunit (R) of the cAMP dependent protein kinase (PKA) from Dictyostelium discoideum for cAMP detection. It includes constructs for expression of the R-subunit in E. coli and fusion to green fluorescent proteins (GFP). Fluorescence energy transfer is used as a way to monitor cAMP binding, either by using fluorescently labelled cAMP or cGMP, or by using mutant GFPs with modified absorption and emission spectra. FRET changes upon cAMP binding will allow measurement of cAMP level either in vitro or within living cells. 


Rico, M. and T. T. Egelhoff (2003). "Myosin heavy chain kinase B participates in the regulation of myosin assembly into the cytoskeleton." J. Cell. Biochem. 88: 521-532.
	
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Roelofs, J. (2003). Dictyostelium guanylyl cyclases: the development of cGMP signaling. Groningen, Netherlands, Rijksuniversiteit Groningen: 158.
	
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Sakamoto, H., K. Nishio, et al. (2003). "Identification and characterization of novel calcium-binding proteins of Dictyostelium and their spatial expression patterns during development." Devel. Growth Differ. 45: 507-514.
	
Sako, Y. and T. Yanagida (2003). "Single-molecule visualization in cell biology." Nature Rev. Mol. Cell Biol. @pl.): Ss1-Ss5.
	
Sasaki, N., R. Ohkura, et al. (2003). "Dictyostelium myosin II mutations that uncouple the converter swing and ATP hydrolysis cycle." Biochemistry 42: 90-95.
	
Schilde, C. (2003). The role of GSK-3 in the development of the cellular slime mould Dictyostelium discoideum. Dundee, Scotland, University of Dundee.
	
Schlosser, A., B. Klockow, et al. (2003). "Analysis of post-translational modification and characterization of the domain structure of dynamin A from Dictyostelium discoideum." J. Mass Spectrom. 38: 277-U210.
	
Schneider, N., I. Weber, et al. (2003). "A LIM protein involved in the progression of cytokinesis and regulation of the mitotic spindle." Cell Motil. Cytoskel. 56: 130-139.
	
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Schuldt, A. (2003). Leading the pack. Nature Cell Biol. 5: 277.
	
Shu, S., X. Liu, et al. (2003). "Dictylostelium and Acanthamoeba myosin II assembly domains go to the cleavage furrow of Dictyostelium myosin II-null cells." Proc. Natl. Acad. Sci. USA 100: 6499-6504.
	
Soldati, T. (2003). "Unconventional myosins, actin dynamics and endocytosis: a menage a trois?" Traffic 4: 358-366.
	
Soll, D. (2003). Dictyostelium may model diseases involving defects in cellular chemotaxis. ASM News. 69: 246.
	
Soll, D. R., D. Wessels, et al. (2003). "Computer-assisted reconstruction and motion analysis of the three-dimensional cell." TheScientificWorldJOURNAL 3: 827-841.
	
Solomon, J. M., G. S. Leung, et al. (2003). "Intracellular replication of Mycobacterium marinum within Dictyostelium discoideum: efficient replication in the absence of host coronin." Inf. Immun. 71: 3578-3586.
	
Spiegel, F. and S. Stephenson (2003). Slime mold central: eumycetozoan research takes off at the University of Arkansas. Inoculum (Suppl. Mycologia). 54(6): 4-5.
	
Spinney, L. (2003). Slime mould clue to depression. Drug Disc. Today. 8: 817-818.
	
Stasiak, A. (2003). Life cycle of a biologist. EMBO Rep. 4: 457.
	
Steenbergen, J. N. (2003). The evolution of fungal virulence. New York, NY, Yeshiva University: 222.
	
Steenbergen, J. N., J. D. Nosanchuk, et al. (2003). "Cryptococcus neoformans virulence is enhanced after growth in the genetically malleable host Dictyostelium discoideum." Inf. Immun. 71: 4862-4872.
	
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Stephan, M., U. Beshay, et al. (2003). "Influence of medium composition on growth behaviour of Dictyostelium discoideum for cultivation on axenic media." Process Biochem. 39: 333-343.
	
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Sucgang, R., G. K. Chen, et al. (2003). "Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium." Nucl. Acids Res. 31: 2361-2368.
	
Sun, B. G. and R. A. Firtel (2003). "A regulator of G protein signaling-containing kinase is important for chemotaxis and multicellular development in Dictyostelium." Mol. Biol. Cell 14: 1727-1743.
	
Sun, B. G., H. Ma, et al. (2003). "Dictyostelium stress-activated protein kinase alpha, a novel stress-activated mitogen-activated protein kinase kinase kinase-like kinase, is important for the proper regulation of the cytoskeleton." Mol. Biol. Cell 14: 4526-4540.
	
Takahashi-Yanaga, F., Y. Taba, et al. (2003). "Dictyostelium differentiation-inducing factor-3 activates glycogen synthase kinase-3 beta and degrades cyclin D1 in mammalian cells." J. Biol. Chem. 278: 9663-9670.
	
Takeda, K., T. Saito, et al. (2003). "A novel gene trap method using terminator-REMI and 3' rapid amplification of cDNA ends (RACE) in Dictyostelium." Gene 312: 321-333.
	
Tekinay, T., H. L. Ennis, et al. (2003). "Genetic interactions of the E3 ubiquitin ligase component FbxA with cyclic AMP metabolism and a histidine kinase signaling pathway during Dictyostelium discoideum development." Euk. Cell 2: 618-626.
	
Teyssedre, B. (2003). "Chuaria, Tawuia, Longfengshania. Trois classes de fossiles precambriens pour un meme taxon." C.R. Palevol. 2: 503-508.
	
Tsuji, A., Y. Akaza, et al. (2003). "Multinucleation of the sodC-deficient Dictyostelium discoideum." Biol. Pharmaceut. Bull. 26: 1174-1177.
	
Ubeidat, M. and C. L. Rutherford (2003). "Purification and renaturation of Dictyostelium recombinant alkaline phosphatase by continuous elution electrophoresis." Prot. Expr. Purif. 27: 375-383.
	
Uchida, K. S. K., T. Kitanishi-Yumura, et al. (2003). "Myosin II contributes to the posterior contraction and the anterior extension during the retraction phase in migrating Dictyostelium cells." J. Cell Sci. 116: 51-60.
	
Vadell, E. M. (2003). Contribucion a la sistematica y ecologia de los Dictiostelidos del Parque Nacional Iguazu, Misiones, Argentina. Buenos Aires, Universidad de Buenos Aires: 260.
	
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Veltman, D. M., J. S. de Boer, et al. (2003). "Chemoattractant-stimulated calcium influx in Dictyostelium discoideum does not depend on cGMP." Biochim. Biophys. Acta 1623: 129-134.
	
Vischer, H. F., J. C. M. Granneman, et al. (2003). "Both recombinant African catfish LH and FSH are able to activate the African catfish FSH receptor." J. Mol. Endocrinol. 31: 133-140.
	
von Lohneysen, K., N. Pawolleck, et al. (2003). "A Dictyostelium long chain fatty acyl coenzyme A-synthetase mediates fatty acid retrieval from endosomes." Eur. J. Cell Biol. 82: 505-514.
	
Vorobiev, S., B. Strokopytov, et al. (2003). "The structure of nonvertebrate actin: implications for the ATP hydrolytic mechanism." Proc. Natl. Acad. Sci. USA 100: 5760-5765.
	
Wang, F., T. Metcalf, et al. (2003). "Initiation of mucin-type O-glycosylation in Dictyostelium is homologous to the corresponding step in animals and is important for spore coat function." J. Biol. Chem. 278: 51395-51407.
	
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Watanabe, S., K. Sakurai, et al. (2003). "Unexpected roles of a Dictyostelium homologue of eukaryotic EF-2 in growth and differentiation." J. Cell Sci. 116: 2647-2654.
	
Weber, I. (2003). "Reflection interference contrast microscopy." Meth. Enzymol. 361: 34-47.
	
Weeks, G. and G. B. Spiegelman (2003). "Roles played by Ras subfamily proteins in the cell and developmental biology of microorganisms." Cell. Signal. 15: 901-909.
	
Weening, K. E., I. Verkerke-van Wijk, et al. (2003). "Contrasting activities of the aggregative and late pdsA promoters in Dictyostelium development." Dev. Biol. 255: 373-382.
	
Weijer, C. J. (2003). "Visualizing signals moving in cells." Science 300: 96-100.
	
West, C. M. (2003). "Evolutionary and functional implications of the complex glycosylation of Skp1, a cytoplasmic/nuclear glycoprotein associated with polyubiquitination." Cell. Mol. Life Sci. 60: 229-240.
	
West, C. M. (2003). "Comparative analysis of spore coat formation, structure, and function in Dictyostelium." Int. Rev. Cyotol. 222: 237-293.
	
Williams, H. P. and A. J. Harwood (2003). "Cell polarity and Dictyostelium development." Curr. Opin. Microbiol. 6: 621-627.
	
Williams, J. G. (2003). The STAT proteins of Dictyostelium. Signal Transducers and Activators of Transcription (STATs). Activation and Biology. P. B. Sehgal, D. E. Levy and T. Hirano. Boston, Kluwer Academic Publishers: 105-121.
	
Wu, G. and M. Muller (2003). "Glycogen phosphorylase sequences from the amitochondriate protists, Trichomonas vaginalis, Mastigamoeba balamuthi, Entamoeba histolytica and Giardia intestinalis." J. Euk. Microbiol. 50: 366-372.
	
Yamada, Y. and M. Sameshima (2003). "Hypertonic signal promotes stability of Dictyostelium spores via a PKA-independent pathway." FEMS Microbiol. Lett. 229: 159-164.
	
Yasukawa, H., T. Kuroita, et al. (2003). "Identification of a penicillin-sensitive carboxypeptidase in the cellular slime mold Dictyostelium discoideum." Biol. Pharm. Bull. 26: 1018-1020.
	
Yeh, Z. Y. (2003). "Biodiversity inventory of dictyostelid cellular slime molds in Taiwan." Mycotaxon 86 (April/June): 103-110.
	
Yohnaha, H. and Y. Tanaka (2003). "Analysis of genes linked to the branching structure of Polysphondylium pallidum." Tsukuba J. Biol. 2: 79.
	
Yumura, S. and T. Q. P. Uyeda (2003). "Myosins and cell dynamics in cellular slime molds." Int. Rev. Cytol. 224: 173-225.
	
Zhang, H., P. J. Heid, et al. (2003). "Constitutively active protein kinase A disrupts motility and chemotaxis in Dictyostelium discoideum." Euk. Cell 2: 62-75.
	
Zupan, B., I. Bratko, et al. (2003). "GenePath: a system for inference of genetic networks and proposal of genetic experiments." Artif. Intell. Medic. 29: 107-130.
	
Zupan, B., J. Demsar, et al. (2003). "GenePath: a system for automated construction of genetic networks from mutant data." Bioinformatics 19: 383-389.
	
(2004). Amoeba could model chemotaxis in human PMNs. ASM News. 70: 421.
	
(2004). Biologists ID molecular block for social 'cheaters' - Gene's dual role in cooperation, reproduction provides evolutionary protection. Rice University. October 7: 2 pages.
	
Agarwal, M. (2004). Structural and functional characterization of Dictyostelium discoideum RacE in cytokinesis signaling. Worcester, MA, Clark University: 213.
	
Agarwal, M., N. A. Guerin, et al. (2004). "Chimeric analysis of the small GTPase RacE in cytokinesis signaling in Dictyostelium discoideum." Exp. Cell Res. 295: 226-235.
	
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Alexander, H. and S. Alexander (2004). Methods of screening novel agents for use in cancer therapy and prevention. USA, The Curators of The University of Missouri (Columbia, MO) 
	The present invention provides for methods of screening agents for cancer therapeutic and prophylactic activity. In particular embodiments, cells of the cellular slime mold Dictyostelium discoideum are contacted with candidate agents and the expression of genes in the Nucleotide Excision Repair (NER) and Base Excision Repair (BER) pathways are examined. Such genes include the helicases repB and repD, and the apurinic-apyrmidinic endonuclease APE.

Alexander, H. and S. Alexander (2004). Methods for screening novel agents for use in cancer therapy and prevention. USA, The Curators of The University of Missouri: 21 pages/31 claims.
	The present invention provides for methods of screening agents for cancer therapeutic and prophylactic activity. In particular embodiments, cells of the cellular slime mold Dictyostelium discoideum are contacted with candidate agents and the expression of genes in the Nucleotide Excision Repair (NER) and Base Excision Repair (BER) pathways are examined. Such genes include the helicases repB and repD, and the apurinic-apyrmidinic endonuclease APE. 

Asano, Y., T. Mizuno, et al. (2004). "Keratocyte-like locomotion in amiB-null Dictyostelium cells." Cell Motil. Cytoskel. 59: 17-27.
	
Aspegren, A., A. Hinas, et al. (2004). "Novel non-coding RNAs in Dictyostelium discoideum and their expression during development." Nucl. Acids Res. 32: 4646-4656.
	
Baker, D. A. and J. M. Kelly (2004). "Structure, function and evolution of microbial adenylyl and guanylyl cyclases." Mol. Microbiol. 52: 1229-1242.
	
Beck, M., F. Forster, et al. (2004). "Nuclear pore complex structure and dynamics revealed by cryoelectron tomography." Science 306: 1387-1390.
	
Behera, N. and V. Nanjundiah (2004). "Phenotypic plasticity can potentiate rapid evolutionary change." J. Theor. Biol. 226: 177-184.
	
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Kimmel, A. R. (2005). Ch. 9 - The Dictyostelium kinome: protein kinase signalling pathways that regulate growth and development. Dictyostelium Genomics. W. F. Loomis and A. Kuspa. Wymondham, UK, Horizon Bioscience: 211-234.
	
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Kuspa, A. (2005). Ch. 12 - Whole-genome functional analyses in Dictyostelium. Dictyostelium Genomics. W. F. Loomis and A. Kuspa. Wymondham, UK, Horizon Bioscience: 279-296.
	
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Loomis, W. F. (2005). Ch. 1 - Mapping and sequencing the Dictyostelium genome. Dictyostelium Genomics. W. F. Loomis and A. Kuspa. Wymondham, UK, Horizon Bioscience: 1-22.
	
Loomis, W. F. and A. Kuspa (2005). Dictyostelium Genomics. Wymondham, UK, Francis & Taylor (Horizon Bioscience).
	
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Mayanagi, T., A. Amagai, et al. (2005). "DNG1, a Dictyostelium homologue of tumor suppressor ING1 regulates differentiation of Dictyostelium cells." Cell. Mol. Life Sci. 62: 1734- 1743.
	
McDonald, K. (2005). Biologists determine genetic blueprint of social amoeba. UCSD News. May 4: 3 pages.
	
Meima, M. E. (2005). Cyclic nucleotide metabolism and function in Dictyostelium discoideum. Leiden, Netherlands, Universiteit Leiden: 131.
	
Mendoza, M. C. (2005). Dysregulated PP4C/PP4R2/SMEK phosphatase activity mediates the Dictyostelium mek1(-) defects in cell polarization, chemotaxis, and gene expression. San Diego, CA, University of California, San Diego: 117.
	
Mendoza, M. C., F. Du, et al. (2005). "Loss of SMEK, a novel, conserved protein, suppresses mek1 null cell polarity, chemotaxis, and gene expression defects." Mol. Cell. Biol. 25: 7839-7853.
	
Min, J., D. Traynor, et al. (2005). "Sphingosine kinase regulates the sensitivity of Dictyostelium discoideum cells to the anticancer drug cisplatin." Euk. Cell 4: 178-189.
	
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Mishig-Ochiriin, T., C. H. Lee, et al. (2005). "Calcium-induced conformational changes of the recombinant CBP3 protein from Dictyostelium discoideum." Biochim. Biophys. Acta 1748: 157-164.
	
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Olsen, R. M. (2005). Ch. 11 - How many protein encoding genes does Dictyostelium discoideum have? Dictyostelium Genomics. W. F. Loomis and A. Kuspa. Wymondham, UK, Horizon Bioscience: 265-278.
	
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Rivero, F. and L. Eichinger (2005). Ch. 7 - The microfilament system of Dictyostelium discoideum. Dictyostelium Genomics. W. F. Loomis and A. Kuspa. Wymondham, UK, Horizon Bioscience: 125-172.
	
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Seethaler, S. (2005). Social amoeba sheds light on communication in human brain. UCSD News. May 16: 2 pages.
	
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Skupsky, R., W. Losert, et al. (2005). "Distinguishing modes of eukaryotic gradient sensing." Biophys J. 89: 2806-2823.
	
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Benghezal, M., M. O. Fauvarque, et al. (2006). "Specific host genes required for the killing of Klebsiella bacteria by phagocytes." Cell. Microbiol. 8: 139-148.
	
Bennett, M., S. M. N. Onnebo, et al. (2006). "Inositol pyrophosphates: metabolism and signaling." Cell. Mol. Life Sci. 63: 552-564.
	
Boeckeler, K., K. Adley, et al. (2006). "The neuroprotective agent, valproic acid, regulates the mitogen-activated protein kinase pathway through modulation of protein kinase A signalling in Dictyostelium discoideum." Eur. J. Cell Biol. 85: 1047-1057.
	
Boeckeler, K., G. Tischendorf, et al. (2006). "Aberrant stalk development and breakdown of tip dominance in Dictyostelium cell lines with RNAi-silenced expression of calcineurin B." BMC Dev. Biol. 6:12: 11 pages.
	
Bolourani, P., G. B. Spiegelman, et al. (2006). "Delineation of the roles played by RasG and RasC in cAMP-dependent signal transduction during the early development of Dictyostelium discoideum." Mol. Biol. Cell 17: 4543-4550.
	
Bonner, J. T. (2006). "Migration in Dictyostelium polycephalum." Mycologia 98: 260-264.
	
Bosgraaf, L. and P. J. van Haastert (2006). "The regulation of myosin II in Dictyostelium." Eur. J. Cell Biol. 85: 969-979.
	
Bozzaro, S. (2006). "Assaying cell-cell adhesion." Meth. Mol. Biol. 346: 449-467.
	
Brock, D. A., W. N. van Egmond, et al. (2006). "A 60-kilodalton protein component of the counting factor complex regulates group size in Dictyostelium discoideum." Euk. Cell 5: 1532-1538.
	
Brzostowski, J. A. and A. R. Kimmel (2006). "Nonadaptive regulation of ERK2 in Dictyostelium implications for mechanisms of cAMP relay." Mol. Biol. Cell 17: 4220-4227.
	
Cabral, M., C. Anjard, et al. (2006). "Genetic evidence that the acyl coenzyme a binding protein acba and the serine protease/abc transporter tagA function together in Dictyostelium discoideum cell differentiation." Euk. Cell 5: 2024-2032.
	
Caracino, D. (2006). The regulation of Dictyostelium Scar by N-terminal sequences. Atlanta, GA, Emory University: 230.
	
Cerutti, H. and J. A. Casas-Mollano (2006). "On the origin and functions of RNA-mediated silencing: from protists to man." Curr. Genet. 50: 81-99.
	
Charette, S. J., S. Cornillon, et al. (2006). "Identification of low frequency knockout mutants in Dictyostelium discoideum created by single or double homologous recombination." J. Biotechnol. 122: 1-4.
	
Charette, S. J. and P. Cosson (2006). "Exocytosis of late endosomes does not directly contribute membrane to the formation of phagocytic cups or pseudopods in Dictyostelium." FEBS Lett. 580: 4923-4928.
	
Charette, S. J., V. Mercanti, et al. (2006). "A role for adaptor protein-3 complex in the organization of the endocytic pathway in Dictyostelium." Traffic 7: 1528-1538.
	
Chen, F., A. J. Mackey, et al. (2006). "OrthoMCL-DB querying a comprehensive multi-species collection of ortholog groups." Nucl. Acids Res. 34: D363-D368.
	
Chen, L. (2006). Regulation of actin polymerization during chemotaxis in Dictyostelium discoideum. Baltimore, MD, The Johns Hopkins University: 82.
	
Chen, Q., H. Li, et al. (2006). "Contractile ring-independent localization of DdINCENP, a protein important for spindle stability and cytokinesis." Mol. Biol. Cell 17: 779-788.
	
Chen, S. (2006). Identification and characterization of EppA as a potential substrate of DdERK2 in cAMP relay and chemotaxis of Dictyostelium. New York, NY, Yeshiva University: 99.
	
Chen, S. and J. E. Segall (2006). "EppA; a putative substrate of DdERK2; regulates cyclic AMP relay and chemotaxis in Dictyostelium discoideum." Euk. Cell 5: 1136-1146.
	
Cherix, N., R. Froquet, et al. (2006). "A Phg2-Adrm1 pathway participates in the nutrient-controlled developmental response in Dictyostelium." Mol. Biol. Cell 17: 4982-4987.
	
Chisholm, R. L., P. Gaudet, et al. (2006). "dictyBase, the model organism database for Dictyostelium discoideum." Nucl. Acids Res. 34: D423-D427.
	
Choi, C. H., B. J. Kim, et al. (2006). "Reduced glutathione levels affect the culmination and cell fate decision in Dictyostelium discoideum." Dev. Biol. 295: 523-533.
	
Choi, Y. K., J. S. Kong, et al. (2006). "Functional role of sepiapterin reductase in the biosynthesis of tetrahydropteridines in Dictyostelium discoideum Ax2." Biochim. Biophys. Acta 1760: 877-882.
	
Chubb, J. R., G. Bloomfield, et al. (2006). "Developmental timing in Dictyostelium is regulated by the Set1 histone methyltransferase." Dev. Biol. 292: 519-532.
	
Chubb, J. R., T. Trcek, et al. (2006). "Transcriptional pulsing of a developmental gene." Curr. Biol. 16: 1018-1025.
	
Clarke, M. and L. Maddera (2006). "Phagocyte meets prey - Uptake, internalization, and killing of bacteria by Dictyostelium amoebae." Eur. J. Cell Biol. 85: 1001-1010.
	
Clarke, M., A. Muller-Taubenberger, et al. (2006). "Mechanically induced actin-mediated rocketing of phagosomes." Mol. Biol. Cell 17: 4866-4875.
	
Clotworthy, M. and D. Traynor (2006). "On the effects of cycloheximide on cell motility and polarisation in Dictyostelium discoideum." BMC Cell Biol. 7:5: 10 pages.
	
Comer, F. I. and C. A. Parent (2006). "Phosphoinositide 3-kinase activity controls the chemoattractant-mediated activation and adaptation of adenylyl cyclase." Mol. Biol. Cell 17: 357-366.
	
Cornillon, S., L. Gebbie, et al. (2006). "An adhesion molecule in free-living Dictyostelium amoebae with integrin beta features." EMBO Rep. 7: 617-621.
	
Crawley, S. W. (2006). Regulation of class I and class II myosins in Dictyostelium discoideum. Kingston, Ont., Canada, Queen's University: 176.
	
Crawley, S. W., M. A. delaRoche, et al. (2006). "Identification and characterization of an 8-kDa light chain associated with Dictyostelium discoideum MyoB, a class I myosin." J. Biol. Chem. 281: 6307-6315.
	
Dallon, J., W. Jang, et al. (2006). "Mathematically modelling the effects of counting factor in Dictyostelium discoideum." Math. Medicine Biol. 23: 45-62.
	
Dean, S. S. (2006). Regulation of myosin II localization during cytokinesis. Palo Alto, CA, Stanford University: 150.
	
Dondero, F., H. Jonsson, et al. (2006). "Cellular responses to environmental contaminants in amoebic cells of the slime mould Dictyostelium discoideum." Compar. Biochem. Physiol. C 143: 150-157.
	
Dorer, M. S. and R. R. Isberg (2006). "Non-vertebrate hosts in the analysis of host-pathogen interactions." Microbes Infect. 8: 1637-1646.
	
Dormann, D. and C. J. Weijer (2006). "Chemotactic cell movement during Dictyostelium development and gastrulation." Curr. Opin. Genet. Devel. 16: 367-373.
	
Dormann, D. and C. J. Weijer (2006). "Imaging of cell migration." EMBO J. 25: 3480-3493.
	
Dormann, D. and C. J. Weijer (2006). "Visualizing signaling and cell movement during the multicellular stages of Dictyostelium development." Meth. Mol. Biol. 346: 297-309.
	
Durrwang, U., S. Fujita-Becker, et al. (2006). "Dictyostelium myosin-IE is a fast molecular motor involved in phagocytosis." J. Cell Sci. 119: 550-558.
	
Effler, J. C., Y. S. Kee, et al. (2006). "Mitosis-specific mechanosensing and contractile-protein redistribution control cell shape." Curr Biol 16(19): 1962-1967.
	Because cell-division failure is deleterious, promoting tumorigenesis in mammals, cells utilize numerous mechanisms to control their cell-cycle progression. Though cell division is considered a well-ordered sequence of biochemical events, cytokinesis, an inherently mechanical process, must also be mechanically controlled to ensure that two equivalent daughter cells are produced with high fidelity. Given that cells respond to their mechanical environment, we hypothesized that cells utilize mechanosensing and mechanical feedback to sense and correct shape asymmetries during cytokinesis. Because the mitotic spindle and myosin II are vital to cell division, we explored their roles in responding to shape perturbations during cell division. We demonstrate that the contractile proteins myosin II and cortexillin I redistribute in response to intrinsic and externally induced shape asymmetries. In early cytokinesis, mechanical load overrides spindle cues and slows cytokinesis progression while contractile proteins accumulate and correct shape asymmetries. In late cytokinesis, mechanical perturbation also directs contractile proteins but without apparently disrupting cytokinesis. Significantly, this response only occurs during anaphase through cytokinesis, does not require microtubules, and is independent of spindle orientation, but is dependent on myosin II. Our data provide evidence for a mechanosensory system that directs contractile proteins to regulate cell shape during mitosis.

Eichinger, L. and F. Rivero (2006). Dictyostelium discoideum Protocols. Totowa, NJ, Humana Press.
	
Engel, R., P. J. M. van Haastert, et al. (2006). "Spectral characterization of Dictyostelium autofluorescence." Microsc. Res. Techn. 69: 168-174.
	
Ercan, A., M. Panico, et al. (2006). "Molecular characterization of a novel UDP-galactose:fucoside alpha3-galactosyltransferase that modifies Skp1 in the cytoplasm of Dictyostelium." J. Biol. Chem. 281: 12713-12721.
	
Escalante, R. and L. Sastre (2006). "Investigating gene expression: in situ hybridization and reporter genes." Meth. Mol. Biol. 346: 247-260.
	
Etzrodt, M., H. C. Ishikawa, et al. (2006). "Time-resolved responses to chemoattractant, characteristic of the front and tail of Dictyostelium cells." FEBS Lett. 580: 6707-6713.
	
Faix, J. and R. Grosse (2006). "Staying in shape with formins." Dev Cell 10(6): 693-706.
	Formins constitute a diverse protein family present in all eukaryotes examined. They are defined by the presence of a formin homology 2 (FH2) domain, which possesses intrinsic and conserved functions regulating cytoskeletal dynamics. Over the past few years, formins have become recognized as potent nucleators of linear actin filaments that control a large variety of cellular and morphogenetic functions. Here, we review the molecular principles of formin-induced cytoskeletal rearrangements and their consequences for a growing number of biological processes.

Faix, J. and K. Rottner (2006). "The making of filopodia." Curr. Opin. Cell Biol. 18: 18-25.
	
Farbrother, P., C. Wagner, et al. (2006). "Dictyostelium transcriptional host cell response upon infection with Legionella." Cell. Microbiol. 8: 438-456.
	
Fey, P., P. Gaudet, et al. (2006). "dictyBase and the Dicty Stock Center." Meth. Mol. Biol. 346: 51-74.
	
Fischbach, A., S. Adelt, et al. (2006). "Disruption of inositol biosynthesis through targeted mutagenesis in Dictyostelium discoideum: generation and characterization of inositol-auxotrophic mutants." Biochem. J. 397: 509-518.
	
Fischer, M., I. Haase, et al. (2006). "Visualizing cytoskeleton dynamics in mammalian cells using a humanized variant of monomeric red fluorescent protein." FEBS Lett. 580: 2495-2502.
	
Fisher, P. R. and S. J. Annesley (2006). "Slug phototaxis, thermotaxis, and spontaneous turning behavior." Meth. Mol. Biol. 346: 137-170.
	
Fisher, P. R. and Z. Wilczynska (2006). "Contribution of endoplasmic reticulum to Ca2+ signals in Dictyostelium depends on extracellular Ca2+." FEMS Microbiol. Lett. 257: 268-277.
	
Franca-Koh, J., Y. Kamimura, et al. (2006). "Navigating signaling networks: chemotaxis in Dictyostelium discoideum." Curr. Opin. Genet. Devel. 16: 333-338.
	
Fuchs, B. B. and E. Mylonakis (2006). "Using non-mammalian hosts to study fungal virulence and host defense." Curr. Opin. Microbiol. 9: 346-351.
	
Fujita-Becker, S., G. Tsiavaliaris, et al. (2006). "Functional characterization of the N-terminal region of myosin-2." J. Biol. Chem. 281: 36102-36109.
	
Fukuzawa, M., N. V. Zhukovskaya, et al. (2006). "Regulation of Dictyostelium prestalk-specific gene expression by a SHAQKY family MYB transcription factor." Development 133: 1715-1724.
	
Furukawa, R. and M. Fechheimer (2006). "Characterization of cross-linked actin filament gels and bundles using birefringence and polarized light scattering." Meth. Mol. Biol. 346: 407-421.
	
Girard, K. D., S. C. Kuo, et al. (2006). "Dictyostelium myosin II mechanochemistry promotes active behavior of the cortex on long time scales." Proc. Natl. Acad. Sci. USA 103: 2103-2108.
	
Godula, T., H. Sevcikova, et al. (2006). "The emergence of wave emitting centres in an excitable medium." J. Theor. Biol. 240: 136-148.
	
Goldberg, J. M., G. Manning, et al. (2006). "The Dictyostelium kinome - analysis of the protein kinases from a simple model organism." PLoS Genet. 2: e38.
	
Goldberg, J. M., E. S. Wolpin, et al. (2006). "Myosin light chain kinase A is activated by cGMP-dependent and cGMP-independent pathways." FEBS Lett. 580: 2059-2064.
	
Goldbeter, A. (2006). "Oscillations and waves of cyclic AMP in Dicyostelium: a prototype for spatio-temporal organization and pulsatile intercellular communication." Bull. Math. Biol. 68: 1095-1109.
	
Goodwin, T. J., M. I. Butler, et al. (2006). "Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes." BMC Biol. 4:38: 17 pages.
	
Gotthardt, D., V. Blancheteau, et al. (2006). "Proteomic fingerprinting of phagosome maturation and evidence for the role of a Galpha during uptake." Mol. Cell. Proteomics 5.12: 2228-2243.
	
Gotthardt, D., R. Dieckmann, et al. (2006). "Preparation of intact, highly purified phagosomes from Dictyostelium." Meth. Mol. Biol. 346: 439-448.
	
Grimson, M. J. and R. L. Blanton (2006). "Cryofixation methods for ultrastructural studies of Dictyostelium discoideum." Meth. Mol. Biol. 346: 339-365.
	
Guder, C., S. Pinho, et al. (2006). "An ancient Wnt-Dickkopf antagonism in Hydra." Development 133(5): 901-911.
	The dickkopf (dkk) gene family encodes secreted antagonists of Wnt signalling proteins, which have important functions in the control of cell fate, proliferation, and cell polarity during development. Here, we report the isolation, from a regeneration-specific signal peptide screen, of a novel dickkopf gene from the fresh water cnidarian Hydra. Comparative sequence analysis demonstrates that the Wnt antagonistic subfamily Dkk1/Dkk2/Dkk4 and the non-modulating subfamily Dkk3 separated prior to the divergence of cnidarians and bilaterians. In steady-state Hydra, hydkk1/2/4-expression is inversely related to that of hywnt3a. hydkk1/2/4 is an early injury and regeneration responsive gene, and hydkk1/2/4-expressing gland cells are essential for head regeneration in Hydra, although once the head has regenerated they are excluded from it. Activation of Wnt/beta-Catenin signalling leads to the complete downregulation of hydkk1/2/4 transcripts. When overexpressed in Xenopus, HyDkk1/2/4 has similar Wnt-antagonizing activity to the Xenopus gene Dkk1. Based on the corresponding expression patterns of hydkk1/2/4 and neuronal genes, we suggest that the body column of Hydra is a neurogenic environment suppressing Wnt signalling and facilitating neurogenesis.

Ha, S. G., S. Y. Jeong, et al. (2006). "Identification and characterization of a lysosomal membrane protein of Dictyostelium discoideum with monoclonal antibodies." Hybridoma (Larchmt) 25: 336-341.
	
Hadjout, N. (2006). Leukocyte chemotaxis assay development and studies of leukocyte chemotaxis modulation by metallothionein. Storrs, CT, University of Connecticut: 156.
	
Hagedorn, M., E. M. Neuhaus, et al. (2006). "Optimized fixation and immunofluorescence staining methods for Dictyostelium cells." Meth. Mol. Biol. 346: 327-338.
	
Hagiwara, H. (2006). "Taxonomic studies on dictyostelids. 2. Review of the voucher specimens of Dictyostelium brevicaule, D. mucoroides, and D. sphaerocephalum prepared by E. W. Olive and preserved in the Farlow Herbarium (FH)." Bull. Natl. Sci. Mus. Tokyo, Ser. B 32: 47-65.
	
Hagiwara, H. and H. Hosono (2006). "Dictyostelids in Japan. XIV. Dictyostelium rosarium Raper & Cavender and Polysphodylium filamentosum Traub, Hohl & Cavender." Bull. Natl. Sci. Mus. Tokyo, Ser. B 32: 1-8.
	
Hamana, K., H. Hagiwara, et al. (2006). "Analysis of cellular polyamines of slime molds in comparison to the polyamine profiles of phylogenetically related organisms." J. Gen. Appl. Microbiol. 52: 107-112.
	
Han, J. W., L. Leeper, et al. (2006). "Role of RacC for the regulation of wasp and phosphatidylinositol 3-kinase during chemotaxis of Dictyostelium." J. Biol. Chem. 281: 35224-35234.
	
Heinrich, D. and E. Sackmann (2006). "Active mechanical stabilization of the viscoplastic intracellular space of Dictyostelia cells by microtubule-actin crosstalk." Acta Biomater. 2: 619-631.
	
Hennebry, S. C., H. M. Wright, et al. (2006). "Structural and functional evolution of transthyretin and transthyretin-like proteins." Proteins 64: 1024-1045.
	
Heuser, J. (2006). "Editorial: Evidence for recycling of contractile vacuole membrane during osmoregulation in Dictyostelium amoebae - A tribute to Gunther Gerisch." Eur. J. Cell Biol. 85: 859-871.
	
Hinas, A., P. Larsson, et al. (2006). "Identification of the major spliceosomal RNAs in Dictyostelium discoideum reveals developmentally regulated U2 variants and polyadenylated snRNAs." Euk. Cell 5: 924-934.
	
Hiratsuka, T. (2006). "The interaction of Phe472 with a fluorescent inhibitor bound to the complex of myosin subfragment-1 with nucleotide." Biochemistry 45: 1234-1241.
	
Hirose, S., S. H. Payne, et al. (2006). "cis-Acting site controlling bidirectional transcription at the growth-differentiation transition in Dictyostelium discoideum." Euk. Cell 5: 1104-1110.
	
Hsu, D. W., P. Gaudet, et al. (2006). "DNA damage signaling and repair in Dictyostelium discoideum." Cell Cycle 5: 702-708.
	
Huang, E. Y., S. L. Blagg, et al. (2006). "bZlP transcription factor interactions regulate DIF responses in Dictyostelium." Development 133: 449-458.
	
Ibarra, N., S. L. Blagg, et al. (2006). "Nap1 regulates Dictyostelium cell motility and adhesion through SCAR-dependent and -independent pathways." Curr. Biol. 16: 717-722.
	
Iranfar, N., D. Fuller, et al. (2006). "Transcriptional regulation of post-aggregation genes in Dictyostelium by a feed-forward loop involving GBF and LagC." Dev. Biol. 290: 460-469.
	
Jaiswal, J. K., N. Mujumdar, et al. (2006). "Trishanku, a novel regulator of cell-type stability and morphogenesis in Dictyostelium discoideum." Differentiation 74: 596-607.
	
Jang, W. and R. H. Gomer (2006). "A protein in crude cytosol regulates glucose-6-phosphatase activity in crude microsomes to regulate group size in Dictyostelium." J. Biol. Chem. 281: 16377-16383.
	
Jeltsch, A., W. Nellen, et al. (2006). "Two substrates are better than one: dual specificities for Dnmt2 methyltransferases." Trends Biochem Sci 31(6): 306-308.
	Dnmt2 enzymes have been widely conserved during evolution and contain all of the signature motifs of DNA (cytosine-5)-methyltransferases; however, the DNA methyltransferase activity of these proteins is comparatively weak and their biochemical and functional properties remain enigmatic. Recent evidence now shows that Dnmt2 has a novel tRNA methyltransferase activity, raising the possibility that the biological roles of these proteins might be broader than previously thought. This finding has important implications for understanding the evolutionary relationships among these enzymes.

Jennes, I. (2006). "[International Dictyostelium Conference 2005]." Pharm. Unserer Zeit 35: 163.
	
Jeong, S. Y., C. H. Choi, et al. (2006). "Thioredoxin reductase is required for growth and regulates entry into culmination of Dictyostelium discoideum." Mol. Microbiol. 6: 1443-1456.
	
Jin, T. and D. Hereld (2006). "Moving toward understanding eukaryotic chemotaxis." Eur. J. Cell Biol. 85: 905-913.
	
Johnson, B. R. G., R. J. Bushby, et al. (2006). "Self-assembly of actin scaffolds at ponticulin-containing supported phospholipid bilayers." Biophys. J. 90: L21-L23.
	
Joyce, B. R. (2006). Regulation of alkaline phosphatase during development of Dictyostelium. Blacksburg, VA, Virginia Polytechnic Institute and State University: 82.
	
Kafer, J., P. Hogeweg, et al. (2006). "Moving forward moving backwarD directional sorting of chemotactic cells due to size and adhesion differences." PLoS Comput. Biol. 2: e56.
	
Kaller, M., U. Euteneuer, et al. (2006). "Differential effects of heterochromatin protein 1 isoforms on mitotic chromosome distribution and growth in Dictyostelium discoideum." Euk. Cell 5: 530-543.
	
Kaller, M., W. Nellen, et al. (2006). "Epigenetics in Dictyostelium." Meth. Mol. Biol. 346: 491-505.
	
Katoh, M., T. Curk, et al. (2006). "Developmentally regulated DNA methylation in Dictyostelium discoideum." Euk. Cell 5: 18-25.
	
Katz, E. R. (2006). "Kenneth Raper, Elisha Mitchell and Dictyostelium." J. Biosci. 31: 195-200.
	
Kaul, M. and L. Eichinger (2006). "Analysis of gene expression using cDNA microarrays." Meth. Mol. Biol. 346: 75-93.
	
Kaushik, S., B. Katoch, et al. (2006). "Social behaviour in genetically heterogeneous groups of Dictyostelium giganteum." Behavioral Ecol. Sociobiol. 59: 521-530.
	
Kelleher, D. J. and R. Gilmore (2006). "An evolving view of the eukaryotic oligosaccharyltransferase." Glycobiology 16(4): 47R-62R.
	Asparagine-linked glycosylation (ALG) is one of the most common protein modification reactions in eukaryotic cells, as many proteins that are translocated across or integrated into the rough endoplasmic reticulum (RER) carry N-linked oligosaccharides. Although the primary focus of this review will be the structure and function of the eukaryotic oligosaccharyltransferase (OST), key findings provided by the analysis of the archaebacterial and eubacterial OST homologues will be reviewed, particularly those that provide insight into the recognition of donor and acceptor substrates. Selection of the fully assembled donor substrate will be considered in the context of the family of human diseases known as congenital disorders of glycosylation (CDG). The yeast and vertebrate OST are surprisingly complex hetero-oligomeric proteins consisting of seven or eight subunits (Ost1p, Ost2p, Ost3p/Ost6p, Ost4p, Ost5p, Stt3p, Wbp1p, and Swp1p in yeast; ribophorin I, DAD1, N33/IAP, OST4, STT3A/STT3B, Ost48, and ribophorin II in mammals). Recent findings from several laboratories have provided overwhelming evidence that the STT3 subunit is critical for catalytic activity. Here, we will consider the evolution and assembly of the eukaryotic OST in light of recent genomic evidence concerning the subunit composition of the enzyme in diverse eukaryotes.

Kessin, R. H. (2006). "The secret lives of Dictyostelium." Meth. Mol. Biol. 346: 3-14.
	
Khare, A. and G. Shaulsky (2006). "First among equals: competition between genetically identical cells." Nature Rev. Genet. 7: 577-583.
	
Khosla, M., P. Kriebel, et al. (2006). "A secondary disruption of the dmpA gene encoding a large membrane protein allows aggregation defective Dictyostelium rasC- cells to form multicellular structures." Dev. Biol. 292: 68-78.
	
Kikuchi, H., Y. Oshima, et al. (2006). "Anti-leukemic activities of Dictyostelium secondary metabolites: a novel aromatic metabolite, 4-methyl-5-N-pentylbenzene-1,3-diol, isolated from Dictyostelium mucoroides suppresses cell growth in human leukemia K562 and HL-60 cells." Life Sci. 80: 160-165.
	
Kim, J., D. G. Bates, et al. (2006). "Robustness analysis of biochemical network models." Syst. Biol. (Stevenage) 153: 96-104.
	
Kim, L. and A. R. Kimmel (2006). "Gsk3 at the edge: regulation of developmental specification and cell polarization." Curr. Drug Targets 7: 1411-1419.
	
Kimmel, A. R. and J. Faix (2006). "Generation of multiple knockout strains using the Cre-loxP system." Meth. Mol. Biol. 346: 187-199.
	
King, J. and R. Insall (2006). "Parasexual genetics using axenic cells." Meth. Mol. Biol. 346: 125-135.
	
Koch, K. V. (2006). Identification and analysis of Dictyostelium discoideum microtubule associated proteins. Marburg/Lahn, Germany, Philipps-Universitat Marburg: 123.
	
Koch, K. V., Y. Reinders, et al. (2006). "Identification and isolation of Dictyostelium microtubule-associated protein interactors by tandem affinity purification." Eur. J. Cell Biol. 85: 1079-1090.
	
Kollmar, M. (2006). "Thirteen is enough The myosins of Dictyostelium discoideum and their light chains." BMC Genomics 7:183: 15 pages.
	
Kollmar, M. (2006). "Use of the myosin motor domain as large-affinity tag for the expression and purification of proteins in Dictyostelium discoideum." Int. J. Biol. Macromol. 39: 37-44.
	
Koppole, S., J. C. Smith, et al. (2006). "Simulations of the myosin II motor reveal a nucleotide-state sensing element that controls the recovery stroke." J. Mol. Biol. 361: 604-616.
	
Korman, V. L., S. E. B. Anderson, et al. (2006). "Structural dynamics of the actin-myosin interface by site-directed spectroscopy." J. Mol. Biol. 356: 1107-1117.
	
Kortholt, A., H. Rehmann, et al. (2006). "Characterization of the GbpD-activated Rap1 pathway regulating adhesion and cell polarity in Dictyostelium discoideum." J. Biol. Chem. 281: 23367-23376.
	
Kosta, A., C. Laporte, et al. (2006). "How to assess and study cell death in Dictyostelium discoideum." Meth. Mol. Biol. 346: 535-550.
	
Kuhlmann, M., B. Popova, et al. (2006). "RNA interference and antisense-mediated gene silencing in Dictyostelium." Meth. Mol. Biol. 346: 211-226.
	
Kuspa, A. (2006). "Restriction enzyme-mediated integration (REMI) mutagenesis." Meth. Mol. Biol. 346: 201-209.
	
Kuspa, A. and W. F. Loomis (2006). "The genome of Dictyostelium discoideum." Meth. Mol. Biol. 346: 15-30.
	
Kuzdzal, J. J. (2006). Exploiting new terrain: an advantage to sociality in the slime mold Dictyostelium discoideum. Houston, TX, Rice University: 15.
	
Lacayo, C. I. (2006). Significance of cytoarchitecture in modulating actin-based motility and cell morphology. Palo Alto, CA, Stanford University: 142.
	
Laguna, R. K., E. A. Creasey, et al. (2006). "A Legionella pneumophila-translocated substrate that is required for growth within macrophages and protection from host cell death." Proc. Natl. Acad. Sci. USA 103: 18745-18750.
	
Landolt, J. C., S. L. Stephenson, et al. (2006). "Distribution and ecology of dictyostelid cellular slime molds in Great Smoky Mountains National Park." Mycologia 98: 541-549.
	
Landolt, J. C., S. L. Stephenson, et al. (2006). "Dictyostelid cellular slime molds from caves." J. Cave Karst Studies 68: 22-26.
	
Langridge, P. D. and R. R. Kay (2006). "Blebbing of Dictyostelium cells in response to chemoattractant." Exp. Cell Res. 312: 2009-2017.
	
Lecaudey, V. and D. Gilmour (2006). "Organizing moving groups during morphogenesis." Curr. Opin. Cell Biol. 18: 102-107.
	
Leng, X. and H. G. Muller (2006). "Classification using functional data analysis for temporal gene expression data." Bioinformatics 22: 68-76.
	
Levine, H., D. A. Kessler, et al. (2006). "Directional sensing in eukaryotic chemotaxis: A balanced inactivation model." Proc. Natl. Acad. Sci. USA 103: 9761-9766.
	
Li, J. (2006). Studies on the interaction between Dictyostelium PakB and dAbp1. Kingston, Ont., Canada, Queen's University: 80.
	
Lin, Z., S. Sriskanthadevan, et al. (2006). "Solution structures of the adhesion molecule DdCAD-1 reveal new insights into Ca(2+)-dependent cell-cell adhesion." Nature Struct. Mol. Biol. 13: 1016-1022.
	
Litcanu, G. and J. J. L. Velazquez (2006). "Singular perturbation analysis of cAMP signalling in dictyostelium discoideum aggregates." J. Math. Biol. 52: 682-718.
	
Liu, X., S. Shu, et al. (2006). "Phosphorylation of actin Tyr-53 inhibits filament nucleation and elongation and destabilizes filaments." Proc. Natl. Acad. Sci. USA 103: 13694-13699.
	
Lohkamp, B., B. Andersen, et al. (2006). "Purification, crystallization and X-ray diffraction analysis of dihydropyrimidinase from Dictyostelium discoideum." Acta Cryst. Sect F 62: p36-38.
	
Lohkamp, B., B. Andersen, et al. (2006). "The crystal structures of dihydropyrimidinases reaffirm the close relationship between cyclic amidohydrolases and explain their substrate specificity." J. Biol. Chem. 281: 13762-13776.
	
London, R., B. S. Orozco, et al. (2006). "The pursuit of cryptococcal pathogenesis heterologous hosts and the study of cryptococcal host-pathogen interactions." FEMS Yeast Res. 6: 567-573.
	
Loomis, W. F. (2006). "The Dictyostelium genome." Curr. Issues Mol. Biol. 8: 63-73.
	
Loovers, H. M., M. Postma, et al. (2006). "Distinct roles of PI(3,4,5)P-3 during chemoattractant signaling in Dictyostelium: a quantitative in vivo analysis by inhibition of PI3-kinase." Mol. Biol. Cell 17: 1503-1513.
	
MacWilliams, H., K. Doquang, et al. (2006). "A retinoblastoma ortholog controls stalk/spore preference in Dictyostelium." Development 133: 1287-1297.
	
Maeda, M. (2006). "Periodic activation of ERK2 and partial involvement of G protein in ERK2 activation by cAMP in Dictyostelium cells." Meth. Mol. Biol. 346: 468-478.
	
Mahadeo, D. C. and C. A. Parent (2006). "Signal relay during the life cycle of Dictyostelium." Curr. Topics Dev. Biol. 73: 115-140.
	
Malchow, D., D. F. Lusche, et al. (2006). "The contractile vacuole in Ca2+-regulation in Dictyostelium: its essential function for cAMP-induced Ca2+-influx." BMC Dev. Biol. 6:31: 8 pages.
	
Marin, I. (2006). "The Parkinson disease gene lrrk2: evolutionary and structural insights." Mol. Biol. Evol. 23: 2423-2433.
	
Marko, M., Y. Prabhu, et al. (2006). "The annexins of Dictyostelium." Eur. J. Cell Biol. 85: 1011-1022.
	
Marsano, F., E. Ranzato, et al. (2006). A systems biology approach reveals Hg induced stress responses in the social amoeba Dictyostelium discoideum. Marine Environ Res.
	Preliminary work has demonstrated that the social ameba Dictyostelium discoideum is an excellent
bioindicator of water pollution. In this study, cells were exposed to Hg sub-lethal concentrations, a
hazardous contaminant.
Our data demonstrate that nano/micromolar concentrations of Hg (0.5–2 lM) significantly affect
important physiological parameters such as cellular concentration of free calcium, lysosomal
membrane stability and endocytosis rate, without altering cell replication rate or cell survival. To
better understand the molecular mechanisms behind Hg-response, extracts of control and Hg-treated
cells were analysed on two-dimensional electrophoresis (2DE) gels. A reference 2DE map (pI range
3–10) containing some 900 protein spots was obtained. Identification of excised spots was performed
using MALDI TOF peptide mass fingerprinting, and the identities of some 100 proteins were revealed.
Protein identities were grouped as follows: 17% structural proteins, 18% signal-transduction
proteins, 24% metabolic enzymes, 12% stress-related proteins, 5% calcium-binding proteins, and 24% 
miscellaneous proteins. The results further demonstrated that 15 of the identified proteins were
affected by Hg, e.g. glutathione-S-transferase, catalase, thioredoxin 3, GMP synthase, G protein asubunit-
like protein, acidic protein P2, and hypothetical protein gi28828580, all of which show a
dramatic increase up to 4-fold in Hg-treated cells. Preliminary transcriptomic analysis, using
microarrays, revealed an activation of several genes involved in toxicity resistance (e.g., GSHtranferases,
ABC transporters, heavy metal carrier proteins, etc.), metabolic and other redox processes
(e.g., sod, GSH-reductase, thioredoxin, aldo/keto-reductase, etc.), together with a number of
genes not yet characterized. Finally, metabolomic profiles will be integrated in order to obtain a
global overview of the molecular responses to Hg-exposure.

Marx, K. A., Y. Zhou, et al. (2006). "Evidence for long poly(DA).poly(DT) tracts in D. discoideum DNA at high frequencies and their preferential avoidance of nucleosomal DNA core regions." J. Biomol. Struct. Dyn. 23: 429-446.
	
Matsuoka, S., M. Iijima, et al. (2006). "Single-molecule analysis of chemoattractant-stimulated membrane recruitment of a PH-domain-containing protein." J. Cell Sci. 119: 1071-1079.
	
Mattei, S., G. Klein, et al. (2006). "Trafficking and developmental signaling: Alix at the crossroads." Eur. J. Cell Biol. 85: 925-936.
	
Mehdiabadi, N. J., C. N. Jack, et al. (2006). "Kin preference in a social microbe." Nature 442: 881-882.
	
Meier-Schellersheim, M., X. Xu, et al. (2006). "Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method." PLoS Comput. Biol. 2: e82.
	
Mendoza, M. C. and R. A. Firtel (2006). "Assaying chemotaxis of Dictyostelium cells." Meth. Mol. Biol. 346: 393-405.
	
Meng, X., M. Samso, et al. (2006). "A flexible linkage between the dynein motor and its cargo." J. Mol. Biol. 357: 701-706.
	
Mercanti, V., C. Blanc, et al. (2006). "Acidic clusters target transmembrane proteins to the contractile vacuole in Dictyostelium cells." J. Cell Sci. 119: 837-845.
	
Mercanti, V., S. J. Charette, et al. (2006). "Selective membrane exclusion in phagocytic and macropinocytic cups." J. Cell Sci. 119: 4079-4087.
	
Min, J., P. Sridevi, et al. (2006). "Sensitive cell viability assay for use in drug screens and for studying the mechanism of action of drugs in Dictyostelium discoideum." BioTechniques 41: 591-595.
	
Moore, D. and A. Meskauskas (2006). "A comprehensive comparative analysis of the occurrence of developmental sequences in fungal; plant and animal genomes." Mycol. Res. 110: 251-256.
	
Mosig, A., K. Sameith, et al. (2006). "Fragrep an efficient search tool for fragmented patterns in genomic sequences." Genom. Proteom. Bioinf. 4: 56-60.
	
Muller-Taubenberger, A. (2006). "Application of fluorescent protein tags as reporters in live-cell imaging studies." Meth. Mol. Biol. 346: 229-246.
	
Muller-Taubenberger, A. and S. Bozzaro (2006). "Editorial: From cell-cell adhesion and cellular oscillations to spectacular views inside the cell - 50 years of research with Dictyostelium." Eur. J. Cell Biol. 85: 851-858.
	
Muller-Taubenberger, A., M. J. Vos, et al. (2006). "Monomeric red fluorescent protein variants used for imaging studies in different species." Eur. J. Cell Biol. 85: 1119-1129.
	
Muramoto, T. and H. Urushihara (2006). "Small GTPase RacF2 affects sexual cell fusion and asexual development in Dictyostelium discoideum through the regulation of cell adhesion." Devel. Growth Differ. 48: 199-208.
	
Myers, S. A. (2006). Roles of WASP and WIP in actin polymerization and pseudopod formation during chemotaxis. Nashville, TN, Vanderbilt University: 117.
	
Myers, S. A., L. R. Leeper, et al. (2006). "WASP-interacting protein (WIPa) is important for actin filament elongation and prompt pseudopod formation in response to a dynamic chemoattractant gradient." Mol. Biol. Cell 17: 4564-4575.
	
O'Day, D. H. (2006). Calmodulin-mediated signaling in Dictyostelium discoideum: CaMBOT isolation and characterization of the novel poly-domain protein nucleomorphin and other calmodulin-binding proteins. Focus on cellular signalling research. D. T. Leeds, Nova Science Publ.
	
O'Day, D. H., K. Suhre, et al. (2006). "Isolation, characterization, and bioinformatic analysis of calmodulin-binding protein cmbB reveals a novel tandem IP22 repeat common to many Dictyostelium and Mimivirus proteins." Biochem. Biophys. Res. Commun. 346: 879-888.
	
Octtaviani, E., J. C. Effler, et al. (2006). "Enlazin, a natural fusion of two classes of canonical cytoskeletal proteins, contributes to cytokinesis dynamics." Mol. Biol. Cell 17: 5275-5286.
	
Payne, S. H. and W. F. Loomis (2006). "Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences." Euk. Cell 5: 272-276.
	
Peracino, B., C. Wagner, et al. (2006). "Function and mechanism of action of Dictyostelium Nramp1 (Slc11a1) in bacterial infection." Traffic 7: 22-38.
	
Pollitt, A. Y., S. L. Blagg, et al. (2006). "Cell motility and SCAR localisation in axenically growing Dictyostelium cells." Eur. J. Cell Biol. 85: 1091-1098.
	
Popova, B., M. Kuhlmann, et al. (2006). "HeIF, a putative RNA helicase acts as a nuclear suppressor of RNAi but not antisense mediated gene silencing." Nucl. Acids Res. 34: 773-784.
	
Popowicz, G. M., M. Schleicher, et al. (2006). "Filamins: promiscuous organizers of the cytoskeleton." Trends Biochem. Sci. 31: 411-419.
	
Prabhu, Y. and L. Eichinger (2006). "The Dictyostelium repertoire of seven transmembrane domain receptors." Eur. J. Cell Biol. 85: 937-946.
	
Pukatzki, S., A. T. Ma, et al. (2006). "Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system." Proc. Natl. Acad. Sci. USA 103: 1528-1533.
	
Rai, M., Y. Xiong, et al. (2006). "Disruption of the ifkA and ifkB genes results in altered cell adhesion, morphological defects and a propensity to form pre-stalk O cells during development of Dictyostelium." Differentiation 74: 583-595.
	
Reinders, Y., I. Schulz, et al. (2006). "Identification of novel centrosomal proteins in Dictyostelium discoideum by comparative proteomic approaches." J. Proteome Res. 5: 589-598.
	
Rifkin, J. L. and R. R. Goldberg (2006). "Effects of chemoattractant pteridines upon speed of D-discoideum vegetative amoebae." Cell Motil. Cytoskel. 63: 1-5.
	
Ritchie, A. V. (2006). Evolutionary conservation of mechanisms controllong spore and cyst formation in the solitary and social amoeba. Dundee, Scotland, University of Dundee: 143.
	
Rivero, F. and M. Maniak (2006). "Quantitative and microscopic methods for studying the endocytic pathway." Meth. Mol. Biol. 346: 423-438.
	
Romeralo, M. and C. Lado (2006). "Dictyostelids from Mediterranean forests of the south of Europe." Mycol. Progress 5: 231-241.
	
Rosel, D. and A. R. Kimmel (2006). "The COP9 signalosome regulates cell proliferation of Dictyostelium discoideum." Eur. J. Cell Biol. 85: 1023-1034.
	
Rosenblad, M. A., M. D. Lopez, et al. (2006). "Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes." Nucl. Acids Res. 34: 5145-5156.
	
Roth, U., S. Mmuller, et al. (2006). "Proteome analysis of Dictyostelium discoideum." Meth. Mol. Biol. 346: 95-109.
	
Russ, M., D. Croft, et al. (2006). "Myosin heavy-chain kinase A from Dictyostelium possesses a novel actin-binding domain that cross-links actin filaments." Biochem. J. 395: 373-383.
	
Russ, M., R. Martinez, et al. (2006). "Naringenin is a novel inhibitor of Dictyostelium cell proliferation and cell migration." Biochem. Biophys. Res. Commun. 345: 516-522.
	
Ryves, W. J. and A. J. Harwood (2006). "Use of a penetratin-linked peptide in Dictyostelium." Mol. Biotechnol. 33: 123-132.
	
Sa, J. M., M. M. Yamamoto, et al. (2006). "Expression and function of pvcrt-o, a Plasmodium vivax ortholog of pfcrt, in Plasmodium falciparum and Dictyostelium discoideum." Mol. Biochem. Parasitol. 150: 219-228.
	
Saito, T., G. W. Taylor, et al. (2006). "Identification of new differentiation inducing factors from Dictyostelium discoideum." Biochim. Biophys. Acta 1760: 754-761.
	
Samadani, A., J. Mettetal, et al. (2006). "Cellular asymmetry and individuality in directional sensing." Proc. Natl. Acad. Sci. USA 103: 11549-11554.
	
Sasaki, A. T. and R. A. Firtel (2006). "Regulation of chemotaxis by the orchestrated activation of Ras, PI3K, and TOR." Eur. J. Cell Biol. 85: 873-895.
	
Schaap, P., T. Winckler, et al. (2006). "Molecular phylogeny and evolution of morphology in the social amoebas." Science 314: 661-663.
	
Schirenbeck, A., R. Arasada, et al. (2006). "The bundling activity of vasodilator-stimulated phosphoprotein is required for filopodium formation." Proc. Natl. Acad. Sci. USA 103: 7694-7699.
	
Schneider, I. C. and J. M. Haugh (2006). "Mechanisms of gradient sensing and chemotaxis - Conserved pathways, diverse regulation." Cell Cycle 5: 1130-1134.
	
Schulz, I., Y. Reinders, et al. (2006). "An improved method for Dictyostelium centrosome isolation." Meth. Mol. Biol. 346: 479-489.
	
Schwarzl, S. M., J. C. Smith, et al. (2006). "Insights into the chemomechanical coupling of the myosin motor from simulation of its ATP hydrolysis mechanism." Biochemistry 45: 5830-5847.
	
Secko, D. M., C. H. Siu, et al. (2006). "An activated Ras protein alters cell adhesion by dephosphorylating Dictyostelium DdCAD-1." Microbiology SGM 152: 1497-1505.
	
Shanley, L. J., P. Walczysko, et al. (2006). "Influx of extracellular Ca2+ is necessary for electrotaxis in Dictyostelium." J. Cell Sci. 119: 4741-4748.
	
Shigaki, T., I. Rees, et al. (2006). "Identification of three distinct phylogenetic groups of cax cation/proton antiporters." J. Mol. Evol. 63: 815-825.
	
Shu, S., D. C. Mahadeo, et al. (2006). "S-adenosylhomocysteine hydrolase is localized at the front of chemotaxing cells, suggesting a role for transmethylation during migration." Proc. Natl. Acad. Sci. USA 103: 19788-19793.
	
Singleton, C. K., J. H. Kirsten, et al. (2006). "Function of ammonium transporter A in the initiation of culmination of development in Dictyostelium discoideum." Euk. Cell 5: 991-996.
	
Siol, O. (2006). Untersuchungen zum spezifischen Integrations-Mechanismus der TRE5-A retrotransposons in Dictyostelium discoideum. Frankfurt am Main, Germany, Johann Wolfgang Goethe-Universitat: 153.
	
Siol, O., M. Boutliliss, et al. (2006). "Role of RNA polymerase III transcription factors in the selection of integration sites by the Dictyostelium non-long terminal repeat retrotransposon TRE5-A." Mol. Cell. Biol. 26: 8242-8251.
	
Siol, O., T. Dingermann, et al. (2006). "The C-module DNA-binding factor mediates expression of the Dictyostelium aggregation-specific adenylyl cyclase ACA." Euk. Cell 5: 658-664.
	
Somesh, B. P., C. Neffgen, et al. (2006). "Dictyostelium RacH regulates endocytic vesicular trafficking and is required for localization of vacuolin." Traffic 7: 1194-1212.
	
Somesh, B. P., G. Vlahou, et al. (2006). "RacG regulates morphology, phagocytosis and chemotaxis." Euk. Cell 5: 1648-1663.
	
Song, L., S. M. Nadkarni, et al. (2006). "Dictyostelium discoideum chemotaxis: threshold for directed motion." Eur. J. Cell Biol. 85: 981-989.
	
Stavrou, I. (2006). Functional analysis of the clathrin assembly protein, AP180, in Dictyostelium discoideum. Austin, TX, The University of Texas at Austin: 152.
	
Stavrou, I. and T. J. O'Halloran (2006). "The monomeric clathrin assembly protein, AP180, regulates contractile vacuole size in Dictyostelium discoideum." Mol. Biol. Cell 17: 5381-5389.
	
Steffen, A., J. Faix, et al. (2006). "Filopodia formation in the absence of functional WAVE- and Arp2/3-complexes." Mol. Biol. Cell 17: 2581-2591.
	
Strehle, A., M. Schleicher, et al. (2006). "Trix, a novel Rac guanine-nucleotide exchange factor from Dictyostelium discoideum is an actin-binding protein and accumulates at endosomes." Eur. J. Cell Biol. 85: 1035-1045.
	
Taniura, H., N. Sanada, et al. (2006). "A metabotropic glutamate receptor family gene in Dictyostelium discoideum." J. Biol. Chem. 281: 12336-12343.
	
Tekinay, T., M. Y. Wu, et al. (2006). "Function of the Dictyostelium discoideum atg1 kinase during autophagy and development." Euk. Cell 5: 1797-1806.
	
Thomason, P. A., D. T. Brazill, et al. (2006). "A series of Dictyostelium expression vectors for recombination cloning." Plasmid 56: 145-152.
	
Thomason, P. A., S. Sawai, et al. (2006). "The histidine kinase homologue DhkK/Sombrero controls morphogenesis in Dictyostelium." Dev. Biol. 292: 358-370.
	
Todoriki, M. and I. Urabe (2006). "Induced symbiosis: distinctive Escherichia coli-Dictyostelium discoideum transferable co-cultures on agar." Symbiosis 42(3): 135-140.
	Despite the near ubiquity of symbiosis, only a few new symbiotic 
associations have been reported. The establishment of the unique 
amoeba-bacterial symbiosis observed by Jeon and his colleagues has 
been difficult to retrace experimentally mainly because of the failure to 
grow both partners in pure culture. The details of symbiosis origin and 
especially laboratory induction are unknown in all cases. Here, we present 
an experiment in which specific strains of four-year subculture Escherichia 
coli and Dictyostelium discoideum evolved interdependently to produce a 
new morphological entity on agar plates. The cocultured organisms lost 
their pure culture identities under the conditions in which both control 
organisms retained their independent culturability. Between days 32 and 
101 of culturing of E. coli and between days 259 and 645 in D. discoideum 
pure culture identity was lost. Yet through the four years both organisms 
could always be cocultured and stored frozen. We traced the emergence 
of characteristic changes toward a repeatedly inducible symbiotic 
relationship in pure cultures of both cocultured organisms. Since both the 
enteric bacterium and the cellular slime mold are free-living and culturable 
in pure culture, genetically well-characterized. We provide a useful model 
for the laboratory study of symbiotic evolution.

Torija, P., A. Robles, et al. (2006). "Optimization of a large-scale gene disruption protocol in Dictyostelium and analysis of conserved genes of unknown function." BMC Microbiol. 6:75: 7 pages.
	
Torija, P., J. J. Vicente, et al. (2006). "Functional genomics in Dictyostelium: MidA, a new conserved protein, is required for mitochondrial function and development." J. Cell Sci. 119: 1154-1164.
	
Torrents, E., C. Trevisiol, et al. (2006). "Euglena gracilis ribonucleotide reductase the eukaryote class II enzyme and the possible antiquity of eukaryote B12 dependence." J. Biol. Chem. 281: 5604-5611.
	
Uetrecht, A. C. and J. E. Bear (2006). "Coronins: the return of the crown." Trends Cell Biol. 16: 421-426.
	
Unal, C. and M. Steinert (2006). "Dictyostelium discoideum as a model system to study host-pathogen interactions." Meth. Mol. Biol. 346: 507-515.
	
Urushihara, H. (2006). "Cultivation, spore production, and mating." Meth. Mol. Biol. 346: 113-124.
	
Urushihara, H., T. Morio, et al. (2006). "The cDNA sequencing project." Meth. Mol. Biol. 346: 31-49.
	
Urushihara, H. and T. Muramoto (2006). "Genes involved in Dictyostelium discoideum sexual reproduction." Eur. J. Cell Biol. 85: 961-968.
	
van Haastert, P. J. M. (2006). "Analysis of signal transduction: formation of cAMP, cGMP, and Ins(1,4,5)P3 in vivo and in vitro." Meth. Mol. Biol. 346: 369-392.
	
VanRheenen, S. M., Z. Q. Luo, et al. (2006). "Members of a Legionella pneumophila family of proteins with ExoU (phospholipase A) active sites are translocated to target cells." Infect. Immun. 74: 3597-3606.
	
Veltman, D. M. and P. J. van Haastert (2006). "Guanylyl cyclase protein and cGMP product independently control front and back of chemotaxing Dictyostelium cells." Mol. Biol. Cell 17: 3921-3929.
	
Vlahou, G. and F. Rivero (2006). "Rho GTPase signaling in Dictyostelium discoideum: insights from the genome." Eur. J. Cell Biol. 85: 947-959.
	
Wang, J. S., Y. Q. Wang, et al. (2006). "Clathrin light chain: Importance of the conserved carboxy terminal domain to function in living cells." Traffic 7: 824-832.
	
Wang, Y. Q. and T. J. OHalloran (2006). "Abp1 regulates pseudopodium number in chemotaxing Dictyostelium cells." J. Cell Sci. 119: 702-710.
	
Washington Jr, R. W. (2006). The role of the actin-binding domain in the intracellular localization of ABP-120 and alpha-actinin in Dictyostelium discoideum. Storrs, CT, University of Connecticut: 172.
	
Weber, I. (2006). "Is there a pilot in a pseudopod?" Eur. J. Cell Biol. 85: 915-924.
	
Wessels, D., S. Kuhl, et al. (2006). "Application of 2D and 3D DIAS to motion analysis of live cells in transmission and confocal microscopy imaging." Meth. Mol. Biol. 346: 261-279.
	
Wessels, D., T. Srikantha, et al. (2006). "The Shwachman-Bodian-Diamond syndrome gene encodes an RNA-binding protein that localizes to the pseudopod of Dictyostelium amoebae during chemotaxis." J. Cell Sci. 119: 370-379.
	
West, C. M., H. van der Wel, et al. (2006). "Detection of cytoplasmic glycosylation associated with hydroxyproline." Meth. Enzymol. 417: 389-404.
	
West, S. A., A. S. Griffin, et al. (2006). "Social evolution theory for microorganisms." Nature Rev. Microbiol. 4: 597-607.
	
Whitney, N., L. J. Pearson, et al. (2006). "A putative Ariadne-like ubiquitin ligase is required for Dictyostelium discoideum development." Euk. Cell 5: 1820-1825.
	
Wickstead, B. and K. Gull (2006). "A ''holistic'' kinesin phylogeny reveals new kinesin families and predicts protein functions." Mol. Biol. Cell 17: 1734-1743.
	
Wienke, D., A. Drengk, et al. (2006). "Vacuolin, a flotillin/reggie-related protein from Dictyostelium oligomerizes for endosome association." Eur. J. Cell Biol. 85: 991-1000.
	
Wiles, N. S., C. M. Eristi, et al. (2006). "Identification and purification of a DNA-binding protein interacting with the promoter of 5'-nucleotidase in Dictyostelium discoideum." Arch. Biochem. Biophys. 445: 26-35.
	
Willard, S. S. and P. N. Devreotes (2006). "Signaling pathways mediating chemotaxis in the social amoeba, Dictyostelium discoideum." Eur. J. Cell Biol. 85: 897-904.
	
Williams, J. G. (2006). "Transcriptional regulation of Dictyostelium pattern formation." EMBO Rep. 7: 694-698.
	
Williams, R. S., K. Boeckeler, et al. (2006). "Towards a molecular understanding of human diseases using Dictyostelium discoideum." Trends Mol. Med. 12: 415-424.
	
Woznica, D. and D. A. Knecht (2006). "Under-agarose chemotaxis of Dictyostelium discoideum." Meth. Mol. Biol. 346: 311-325.
	
Xu, X., J. A. Brzostowski, et al. (2006). "Using quantitative fluorescence microscopy and FRET imaging to measure spatiotemporal signaling events in single living cells." Meth. Mol. Biol. 346: 281-296.
	
Yang, L. and P. A. Iglesias (2006). "Positive feedback may cause the biphasic response observed in the chemoattractant-induced response of Dictyostelium cells." Syst. Control Lett. 55: 329-337.
	
Yoshida, K. and T. Soldati (2006). "Dissection of amoeboid movement into two mechanically distinct modes." J. Cell Sci. 119: 3833-3844.
	
Yoshida, M., N. Sakuragi, et al. (2006). "Cleavage with phospholipase of the lipid anchor in the cell adhesion molecule, csA, from Dictyostefium discoideum." Compar Biochem. Physiol. B 143: 138-144.
	
Yusof, A. M., E. Jaenicke, et al. (2006). "Mechanism of oligomerisation of cyclase-associated protein from Dictyostelium discoideum in solution." J. Mol. Biol. 362: 1072-1081.
	
Zeng, W., H. E. Seward, et al. (2006). "Resonance energy transfer between green fluorescent protein variants: complexities revealed with myosin fusion proteins." Biochemistry 45: 10482-10491.
	
Zhao, F. and Z. Tao (2006). "[Cellular automata approach to biological pattern formation (I) the aggregation pattern in Dictyostelium discoideum]." Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 23: 304-308.
	
Zhu, Y., V. Stribinskis, et al. (2006). "Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA." Rna 12: 699-706.
	
Zhukovskaya, N. V., M. Fukuzawa, et al. (2006). "The Dictyostelium bZIP transcription factor DimB regulates prestalk-specific gene expression." Development 133: 439-448.
	
(2007). "Social" Dictyostelium shows immune-like behaviors. Microbe. 2: 476.
	
Alvarez Curto, E. (2007). Developmental regulation and evolution of cAMP signalling in Dictyostelium. Leiden, Netherlands, Universiteit Leiden: 117.
	
Alvarez-Curto, E., S. Saran, et al. (2007). "cAMP production by adenylyl cyclase G induces prespore differentiation in Dictyostelium slugs." Development 134: 959-966.
	
Alvarez-Curto, E., K. E. Weening, et al. (2007). "Pharmacological profiling of the Dictyostelium adenylyl cyclases ACA; ACB and ACG." Biochem. J. 401: 309-316.
	
Amagai, A., S. S. Soramoto, et al. (2007). "Ethylene induces zygote formation through an enhanced expression of zyg1 in Dictyostelium mucoroides." Exp. Cell Res. 313: 2493-2503.
	
Andrew, N. and R. H. Insall (2007). "Chemotaxis in shallow gradients is mediated independently of PtdIns 3-kinase by biased choices between random protrusions." Nature Cell Biol. 9: 193-200.
	
Andrews, B. W. and P. A. Iglesias (2007). "An information-theoretic characterization of the optimal gradient sensing response of cells." PLoS Comput. Biol. 3(8):e153: 1489-1497.
	
Andrioli, L. P., G. M. Souza, et al. (2007). "Staurosporine induces tyrosine phosphorylation in Dictyostelium discoideum proteins." Cell Biochem. Funct. 25: 555-561.
	
Annesley, S. J., E. Bandala-Sanchez, et al. (2007). "Filamin repeat segments required for photosensory signalling in Dictyostelium discoideum." BMC Cell Biol. 8:48: 13 pages.
	
Arasada, R., A. Gloss, et al. (2007). "Profilin isoforms in Dictyostelium discoideum." Biochim. Biophys. Acta 1773: 631-641.
	
Bader, S., A. Kortholt, et al. (2007). "Seven Dictyostelium discoideum phosphodiesterases degrade three pools of cAMP and cGMP." Biochem. J. 402: 153-161.
	
Bakthavatsalam, D., D. Brazill, et al. (2007). "A G protein-coupled receptor with a lipid kinase domain is involved in cell-density sensing." Curr. Biol. 17: 892-897.
	
Banerjee, S., P. Vishwanath, et al. (2007). "The evolution of N-glycan-dependent endoplasmic reticulum quality control factors for glycoprotein folding and degradation." Proc Natl Acad Sci U S A 104(28): 11676-11681.
	Asn-linked glycans (N-glycans) play important roles in the quality control (QC) of glycoprotein folding in the endoplasmic reticulum (ER) lumen and in ER-associated degradation (ERAD) of proteins by cytosolic proteasomes. A UDP-Glc:glycoprotein glucosyltransferase glucosylates N-glycans of misfolded proteins, which are then bound and refolded by calreticulin and/or calnexin in association with a protein disulfide isomerase. Alternatively, an alpha-1,2-mannosidase (Mns1) and mannosidase-like proteins (ER degradation-enhancing alpha-mannosidase-like proteins 1, 2, and 3) are part of a process that results in the dislocation of misfolded glycoproteins into the cytosol, where proteins are degraded in the proteasome. Recently we found that numerous protists and fungi contain 0-11 sugars in their N-glycan precursors versus 14 sugars in those of animals, plants, fungi, and Dictyostelium. Our goal here was to determine what effect N-glycan precursor diversity has on N-glycan-dependent QC systems of glycoprotein folding and ERAD. N-glycan-dependent QC of folding (UDP-Glc:glycoprotein glucosyltransferase, calreticulin, and/or calnexin) was present and active in some but not all protists containing at least five mannose residues in their N-glycans and was absent in protists lacking Man. In contrast, N-glycan-dependent ERAD appeared to be absent from the majority of protists. However, Trypanosoma and Trichomonas genomes predicted ER degradation-enhancing alpha-mannosidase-like protein and Mns1 orthologs, respectively, each of which had alpha-mannosidase activity in vitro. Phylogenetic analyses suggested that the diversity of N-glycan-dependent QC of glycoprotein folding (and possibly that of ERAD) was best explained by secondary loss. We conclude that N-glycan precursor length has profound effects on N-glycan-dependent QC of glycoprotein folding and ERAD.

Barth, C., P. Le, et al. (2007). "Mitochondrial biology and disease in Dictyostelium." Int. Rev. Cytol. 263: 207-252.
	
Beck, M., V. Lucic, et al. (2007). "Snapshots of nuclear pore complexes in action captured by cryo-electron tomography." Nature 449: 611-615.
	
Behar, M., N. Hao, et al. (2007). "Mathematical and computational analysis of adaptation via feedback inhibition in signal transduction pathways." Biophys. J. 93: 806-821.
	
Beta, C., D. Wyatt, et al. (2007). "Flow photolysis for spatiotemporal stimulation of single cells." Anal. Chem. 79: 3940-3944.
	
Bigg, A. (2007). Structural and functional characterization of MlcD, a Dictyostelium discoideum myosin I light chain. Kingston, Ont., Canada, Queen's University: 96.
	
Bloomfield, G. and R. R. Kay (2007). "My 2,000 best films: parallel phenotyping of Dictyostelium development." Genome Biol. 8: 220.221-220.223.
	
Boeckeler, K. and R. S. B. Williams (2007). Dictyostelium as a biomedical model. Encyclopedia of Life Sciences, Wiley Interscience (John Wiley and Sons).
	The social amoeba, Dictyostelium discoideum, has been commonly used to investigate cell motility, signal transduction, cell type differentiation and development. With the recent completion of the genome and the increasing number of experimental tools available for the organism, it has now become an attractive model for examining some well-defined biomedical questions.

Bokko, P. B., L. Francione, et al. (2007). "Diverse cytopathologies in mitochondrial disease are caused by amp-activated protein kinase signaling." Mol. Biol. Cell 18: 1874-1886.
	
Bretscher, M. S. and M. Clotworthy (2007). "Using single loxP sites to enhance homologous recombination: ts mutants in Sec1 of Dictyostelium discoideum." PLoS ONE 2(8):e724: 4 pages.
	
Caracino, D., C. Jones, et al. (2007). "The N-terminus of Dictyostelium SCAR interacts with abi and hspc300 and is essential for proper regulation and function." Mol. Biol. Cell 18: 1609-1620.
	
Castoe, T. A., T. Stephens, et al. (2007). "A novel group of type I polyketide synthases (PKS) in animals and the complex phylogenomics of PKSs." Gene 392: 47-58.
	
Charette, S. J. and P. Cosson (2007). "A LYST/beige homolog is involved in biogenesis of Dictyostelium secretory lysosomes." J. Cell Sci. 120: 2338-2343.
	
Chen, G., O. Zhuchenko, et al. (2007). "Immune-like phagocyte activity in the social amoeba." Science 317: 678-681.
	
Chen, J., Y. Lu, et al. (2007). "Efficient expression and primary purification of 6-His tagged human Fas ligand in Dictyostelium discoideum." Biotechnol. Lett. 29: 859-863.
	
Chen, J., M. Reyes, et al. (2007). "Host cell-dependent secretion and translocation of the lepA and lepB effectors of Legionella pneumophila." Cell. Microbiol. 9: 1660-1671.
	
Chen, L., M. Iijima, et al. (2007). "Pla2 and pi3k/pten pathways act in parallel to mediate chemotaxis." Dev. Cell 12: 603-614.
	
Chen, Q., G. S. Lakshmikanth, et al. (2007). "The localization of inner centromeric protein (INCENP) at the cleavage furrow is dependent on Kif12 and involves interactions of the N terminus of INCENP with the actin cytoskeleton." Mol. Biol. Cell 18: 3366-3374.
	
Chen, Y. (2007). PldB, a putative phospholipase D homologue, mediates quorum sensing in Dictyostelium discoideum development. New York, NY, City University of New York: 90.
	
Chen, Y., K. J. McQuade, et al. (2007). "Isoprenylcysteine carboxy methylation is essential for development in Dictyostelium discoideum." Mol. Biol. Cell 18: 4106-4118.
	
Chin, G. and J. Yeston (2007). Editor's choice: Self-puncturing pathogens. Science. 318: 171.
	
Chung, T. (2007). Interaktionsanalysen zur spezifischen Integration des Retrotransposons TRE5-A.1 in Dictyostelium discoideum. Frankfurt am Main, Germany, Johann Wolfgang Goethe Universitat: 129.
	
Chung, T., O. Siol, et al. (2007). "Protein interactions involved in tRNA gene-specific integration of Dictyostelium discoideum non-long terminal repeat retrotransposon TRE5-a." Mol. Cell. Biol. 27: 8492-8501.
	
Czerwinski, E. (2007). Two proteins containing tandem DIII domains, calpain 10 and Dictyostelium Cpl, are involved in cytoskeletal regulation. Toledo, OH, Medical College of Ohio: 154.
	
Da Lage, J. L., E. G. Danchin, et al. (2007). "Where do animal alpha-amylases come from? An interkingdom trip." FEBS Lett. 581: 3927-3935.
	
Damer, C. K., M. Bayeva, et al. (2007). "Copine a is required for cytokinesis, contractile vacuole function, and development in Dictyostelium." Euk. Cell 6: 430-442.
	
Del Alamo, J. C., R. Meili, et al. (2007). "Spatio-temporal analysis of eukaryotic cell motility by improved force cytometry." Proc. Natl. Acad. Sci. USA 104: 13343-13348.
	
Depledge, D. P., R. P. Lower, et al. (2007). "Repseq--a database of amino acid repeats present in lower eukaryotic pathogens." BMC Bioinformatics 8:122: 10 pages.
	
Du, F. (2007). A RabGAP protein and BEACH family proteins regulate contractile vacuole formation and activity and chemotaxis in Dictyostelium. San Diego, CA, Univeristy of California, San Diego: 114.
	
Dutta, S., A. Sardar, et al. (2007). "Molecular and functional characterization of EhPAK3, a p21 activated kinase from Entamoeba histolytica." Gene 402(1-2): 57-67.
	p21-activated kinases (PAKs) are a family of serine/threonine kinases whose activity is regulated by the binding of the small Rho family GTPases as well as by RhoGTPase independent mechanisms. PAKs have wide-ranging functions which include cytoskeletal organisation, cell motility, cell proliferation and survival. We have identified a PAK from Entamoeba histolytica - EhPAK3 that is distributed in the cytoplasm of unstimulated cells and localizes to the caps after induction of capping with Concanavalin A. EhPAK3 contains a GTPase interacting (CRIB) domain, an N-terminal pleckstrin homology (PH) domain and a C-terminal kinase domain. Among the PAKs of E. histolytica studied so far, EhPAK3 bears the maximum similarity to Dictyostelium discoideum PAKC (DdPAKC). Phylogenetic analysis showed that EhPAK3 was closely related to DdPAKC and forms a group with DdPAKA, Dd Myosin I heavy chain kinase (DdMIHCK), and a PAK reported earlier from E. histolytica EhPAK2. Recombinant full-length EhPAK3 undergoes auotophosphorylation and phosphorylates histone H1 in vitro in the absence of any small GTPase. This is the first comprehensive characterization of a PAK protein from E. histolytica, which has constitutive activity and has demonstrated a strong involvement in receptor capping.

Ebisawa, M., M. Ueno, et al. (2007). "Synthesis of dictyomedins using phosphazene base catalyzed diaryl ether formation." Tetrahedron Lett. 48(50): 8918-8921.
	Dictyomedins isolated from dictyostelium cellular slime molds were synthesized by using diaryl ether derivatives as key intermediates for the cyclization to dibenzofuran followed by palladium catalyzed intramolecular biaryl formation.

Erban, R. and H. G. Othmer (2007). "Taxis equations for amoeboid cells." J. Math. Biol. 54: 847-885.
	
Fang, J., J. A. Brzostowski, et al. (2007). "A vesicle surface tyrosine kinase regulates phagosome maturation." J. Cell Biol. 178: 411-423.
	
Feit, I. N., J. Pawlikowski, et al. (2007). "A model for cell type localization in the migrating slug of Dictyostelium discoideum based on differential chemotactic sensitivity to cAMP and differential sensitivity to suppression of chemotaxis by ammonia." J. Biosci. 32: 329-338.
	
Fey, P., A. S. Kowal, et al. (2007). "Protocols for growth and development of Dictyostelium discoideum." Nature Protoc 2: 1307-1316.
	
Fountain, S. J., K. Parkinson, et al. (2007). "An intracellular P2x receptor required for osmoregulation in Dictyostelium discoideum." Nature 448: 200-203.
	
Froquet, R., N. Cherix, et al. (2007). "Alternative host model to evaluate Aeromonas virulence." Appl. Envir. Microbiol. 73: 5657-5659.
	
Gachon, C. M., J. G. Day, et al. (2007). "The Culture Collection of Algae and Protozoa (CCAP): a biological resource for protistan genomics." Gene 406(1-2): 51-57.
	CCAP, the largest European protistan culture collection, is based at the Scottish Association for Marine Science near Oban, Scotland (http://www.ccap.ac.uk). The Collection comprises more than 2700 strains in the public domain, of which 1050 are marine algae, 1300 freshwater algae, and 350 protozoa. The primary mission of CCAP is to maintain and distribute defined cultures and their associated information to its customers. It also has a support and advisory function on all aspects of protistan science. In addition, it is involved in the training of students and researchers in algal identification and culture techniques. In light of the increasing number of fully sequenced protists, the CCAP is striving to provide targeted services and support to workers involved in all aspects of genomic research. At present, the Collection holds several hundred strains of genomic model taxa including: Acanthamoeba, Cafeteria, Cercomonas, Chlamydomonas, Chlorella, Cyanophora, Dictyostelium, Dunaliella, Ectocarpus, Emiliania, Euglena, Micromonas, Naegleria, Nephroselmis, Paramecium, Pavlova, Phaeodactylum, Porphyra, Pseudendoclonium, Pylaiella, Rhodomonas, Scenedesmus, Staurastrum, Tetrahymena, Thalassiosira, Volvox and Zygnema. These strains provide a defined representation of natural variation within model organisms, an increasingly useful resource for post-genomics approaches. Our aim over the next 2-5 years is to add value to the Collection by increasing the number of genome model species, and by offering an integrated, up-to-date, easy-to-use resource that would provide curated information on our strain holdings. In collaboration with other major Biological Resource Centres worldwide, we intend to build a hub providing access to both protistan cultures and their associated bioinformatics data.

Galdeen, S. A. (2007). Levels and dynamics of Dictyostelium myosin 7 and talinA are linked. Twin Cities, MN, University of Minnesota: 84.
	
Galdeen, S. A., S. Stephens, et al. (2007). "Talin influences the dynamics of the myosin VII-membrane interaction." Mol. Biol. Cell 18: 4074-4084.
	
Gao, T., C. Roisin-Bouffay, et al. (2007). "A cell number-counting factor regulates levels of a novel protein, sslA, as part of a group size regulation mechanism in Dictyostelium." Euk. Cell 6: 1538-1551.
	
Gaudet, P., K. E. Pilcher, et al. (2007). "Transformation of Dictyostelium discoideum with plasmid DNA." Nature Protoc 2: 1317-1324.
	
Gerisch, G. and I. Weber (2007). "Toward the structure of dynamic membrane-anchored actin networks: an approach using cryo-electron tomography." Cell Adh Migr 1(3): 145-148.
	In the cortex of a motile cell, membrane-anchored actin filaments assemble into structures of varying shape and function. Filopodia are distinguished by a core of bundled actin filaments within finger-like extensions of the membrane. In a recent paper by Medalia et al(1) cryo-electron tomography has been used to reconstruct, from filopodia of Dictyostelium cells, the 3-dimensional organization of actin filaments in connection with the plasma membrane. A special arrangement of short filaments converging toward the filopod's tip has been called a "terminal cone". In this region force is applied for protrusion of the membrane. Here we discuss actin organization in the filopodia of Dictyostelium in the light of current views on forces that are generated by polymerizing actin filaments, and on the resistance of membranes against deformation that counteracts these forces.

Gilbert, O. M., K. R. Foster, et al. (2007). "High relatedness maintains multicellular cooperation in a social amoeba by controlling cheater mutants." Proc. Natl. Acad. Sci. USA 104: 8913-8917.
	
Gokhale, R. S., R. Sankaranarayanan, et al. (2007). "Versatility of polyketide synthases in generating metabolic diversity." Curr. Opin. Struct. Biol. 17: 736-743.
	
Goldbeter, A. (2007). Biological rhythms as temporal dissipative structures. Adv Chem Phys. S. A. Rice, Wiley Interscience. 135: 253-295.
	
Hachibuko, Y., K. Ito, et al. (2007). "Enzymatic activity and motility of recombinant Arabidopsis myosin XI, MYA1." Plant Cell Physiol. 48: 886-891.
	
Hadwiger, J. A. (2007). "Developmental morphology and chemotactic responses are dependent on Galpha subunit specificity in Dictyostelium." Dev. Biol. 312: 1-12.
	
Hagedorn, M. and T. Soldati (2007). "Flotillin and RacH modulate the intracellular immunity of Dictyostelium to Mycobacterium marinum infection." Cell. Microbiol. 9: 2716-2733.
	
Hagiwara, H. (2007). "Preliminary study of sexual segregation in dictyostelids." Bull. Natl. Sci. Mus. Tokyo, Ser. B 33: 1-8.
	
Haupt, B. J., M. Osbourn, et al. (2007). "Asymmetric elastic properties of Dictyostelium discoideum in relation to chemotaxis." Langmuir 23: 9352-9357.
	
Hilbi, H., S. S. Weber, et al. (2007). "Environmental predators as models for bacterial pathogenesis." Environ Microbiol 9(3): 563-575.
	Environmental bacteria are constantly threatened by bacterivorous predators such as free-living protozoa and nematodes. In the course of their coevolution with environmental predators, some bacteria developed sophisticated defence mechanisms, including the secretion of toxins, or the capacity to avoid lysosomal killing and to replicate intracellularly within protozoa. To analyse the interactions with bacterial pathogens on a molecular, cellular or organismic level, protozoa and other non-mammalian hosts are increasingly used. These include amoebae, as well as genetically tractable hosts, such as the social amoeba Dictyostelium discoideum, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster. Using these hosts, the virulence mechanisms of opportunistic pathogenic bacteria such as Legionella, Mycobacterium, Pseudomonas or Vibrio were found to be not only relevant for the interactions of the bacteria with protozoa, nematodes and insect phagocytes, but also with mammalian hosts including humans. Thus, non-mammalian model hosts provide valuable insight into the pathogenesis of environmental bacteria.

Hilgardt, C., S. C. Muller, et al. (2007). "Reconstruction of cellular variability from spatiotemporal patterns of Dictyostelium discoideum." Nonlinear Biomed. Phys. 1:10: 13 pages.
	
Hinas, A., J. Reimegard, et al. (2007). "The small RNA repertoire of Dictyostelium discoideum and its regulation by components of the RNAi pathway." Nucl. Acids Res. 35: 6714-6726.
	
Hinas, A. and F. Soderbom (2007). "Treasure hunt in an amoeba: non-coding RNAs in Dictyostelium discoideum." Curr. Genet. 51: 141-159.
	
Hoeller, O. and R. R. Kay (2007). "Chemotaxis in the absence of PIP3 gradients." Curr. Biol. 17: 813-817.
	
Imamula, K., T. Kon, et al. (2007). "The coordination of cyclic microtubule association/dissociation and tail swing of cytoplasmic dynein." Proc. Natl. Acad. Sci. USA 104: 16134-16139.
	
Insall, R. and N. Andrew (2007). "Chemotaxis in Dictyostelium: how to walk straight using parallel pathways." Curr. Opin. Microbiol. 10: 578-581.
	
Itoh, G. and S. Yumura (2007). "A novel mitosis-specific dynamic actin structure in Dictyostelium cells." J. Cell Sci. 120: 4302-4309.
	
Iwai, S. and S. Chaen (2007). "Mutation in the sh1 helix reduces the activation energy of the atp-induced conformational transition of myosin." Biochem. Biophys. Res. Commun. 357: 325-329.
	
Jahn, W. (2007). "The association of actin and myosin in the presence of gamma-amido-ATP proceeds mainly via a complex with myosin in the closed conformation." Biochemistry 46: 9654-9664.
	
Jeon, T. J., D. J. Lee, et al. (2007). "Regulation of Rap1 activity by RapGap1 controls cell adhesion at the front of chemotaxing cells." J. Cell Biol. 179: 833-843.
	
Jeon, T. J., D. J. Lee, et al. (2007). "Rap1 controls cell adhesion and cell motility through the regulation of myosin II." J. Cell Biol. 176: 1021-1033.
	
Jockusch, B. M., K. Murk, et al. (2007). "The profile of profilins." Rev. Physiol. Biochem. Pharmacol. 159: 131-149.
	
Joyce, B. R., N. S. Wiles, et al. (2007). "Tf2 binds to the regulatory promoter of alkaline phosphatase in Dicytostelium." Biochim Biophys Acta 1769: 668-677.
	
Jules, M. and C. Buchrieser (2007). "Legionella pneumophila adaptation to intracellular life and the host response: clues from genomics and transcriptomics." FEBS Lett. 581: 2829-2838.
	
Kabacoff, C., Y. Xiong, et al. (2007). "Dynacortin facilitates polarization of chemotaxing cells." BMC Biology 5:53: 53.
	Background: Cell shape changes during cytokinesis and chemotaxis require regulation of the actin cytoskeletal network. Dynacortin, an actin cross-linking protein, localizes to the cell cortex and contributes to cortical resistance, thereby helping to define the cell shape changes of cytokinesis. Dynacortin also becomes highly enriched in cortical protrusions, which are sites of new actin assembly. Results: We studied the effect of dynacortin on cell motility during chemotaxis and on actin dynamics in vivo and in vitro. Dynacortin enriches with the actin, particularly at the leading edge of chemotaxing cells. Cells devoid of dynacortin do not become as polarized as wild-type control cells but move with similar velocities as wild-type cells. In particular, they send out multiple pseudopods that radiate at a broader distribution of angles relative to the chemoattractant gradient. Wild-type cells typically only send out one pseudopod at a time that does not diverge much from 0 degrees on average relative to the gradient. Though dynacortin-deficient cells show normal bulk ( whole-cell) actin assembly upon chemoattractant stimulation, dynacortin can promote actin assembly in vitro. By fluorescence spectroscopy, co-sedimentation and transmission electron microscopy, dynacortin acts as an actin scaffolder in which it assembles actin monomers into polymers with a stoichiometry of I Dyn2:I actin under salt conditions that disfavor polymer assembly. Conclusion: Dynacortin contributes to cell polarization during chemotaxis. By cross-linking and possibly stabilizing actin polymers, dynacortin also contributes to cortical viscoelasticity, which may be critical for establishing cell polarity. Though not essential for directional sensing or motility, dynacortin is required to establish cell polarity, the third core feature of chemotaxis.

Kae, H. (2007). Elucidating the Ras activation pathways in response to cyclic AMP in the aggregation of Dictyostelium discoideum. Vancouver, BC, Canada, The University of British Columbia: 124.
	
Kae, H., A. Kortholt, et al. (2007). "Cyclic AMP signalling in Dictyostelium: G-proteins activate separate ras pathways using specific RasGefs." EMBO Rep. 8: 477-482.
	
Kalavrizioti, D., A. Vourekas, et al. (2007). "DRpp20 and DRpp40: two protein subunits involved in Dictyostelium discoideum ribonuclease P holoenzyme assembly." Gene 400: 52-59.
	
Kaller, M., B. Foldesi, et al. (2007). "Localization and organization of protein factors involved in chromosome inheritance in Dictyostelium discoideum." Biol. Chem. 388: 355-365.
	
Katoh, M., G. Chen, et al. (2007). "Developmental commitment in Dictyostelium discoideum." Euk. Cell 6: 2038-2045.
	
Keizer-Gunnink, I., A. Kortholt, et al. (2007). "Chemoattractants and chemorepellents act by inducing opposite polarity in phospholipase C and PI3-kinase signaling." J. Cell Biol. 177: 579-585.
	
Khaire, N., R. Muller, et al. (2007). "Filamin-regulated F-actin assembly is essential for morphogenesis and controls phototaxis in Dictyostelium." J. Biol. Chem. 282: 1948-1955.
	
Kikuchi, H. (2007). "[novel biologically active compounds isolated from unexploited organisms, cellular sime molds]." Yakugaku Zasshi 127: 1431-1439.
	
Kikuchi, H., K. Nakamura, et al. (2007). "Dihydrodictyopyrones A and C: new members of dictyopyrone family isolated from Dictyostelium cellular slime molds." Tetrahedron Lett. 48(33): 5905-5909.
	We have explored the diversity of secondary metabolites produced by cellular slime molds to evaluate if they are valuable resources for biologically potential substances. From the methanol extract of fruiting bodies of Dicyostelium firmibasis, we obtained new [alpha]-pyranoids, dihydrodictyopyrones A (1) and C (2). Their structures including absolute configurations were determined by spectral means and asymmetric total synthesis. Compounds 1 and 2 are new members of the dictyopyrone family, which are characteristic secondary metabolites of various species of Dictyostelium cellular slime molds.

Kim, H. L., Y. K. Choi, et al. (2007). "Tetrahydropteridine deficiency impairs mitochondrial function in Dictyostelium discoideum AX2." FEBS Lett. 581: 5430-5434.
	
Kim, J., C. Choi, et al. (2007). Glutathione regulates the transition from growth to development in Dictyostelium discoideum. FEBS J.
	Glutathione is a ubiquitous tripeptide, found in most plants,
microorganisms, and all mammalian tissues and most prevalent
reducing thiol-containing compound in eukaryotic cells. Glutathione
serves as cellular thiol redox buffer to maintain a thiol/disulfide
redox potential, and also known to participate in many
cellular processes. Disruption of GCS encoding c-glutamylcysteine
resulted in glutathione auxotrophy and developmental defect in
Dictyostelium discoideum. And GCS-null cells showed different
developmental progress, depending on the level of GSH. To understand
defective development, we investigated the development in
suspension. GCS-null cells depleted GSH did not aggregate and
were still single cells in suspension with addition of cAMP. Interestingly,
the addition of 1mM GSH induced them to aggregate.
However, the defect in aggregation of them was not rescued by
dithiothreitol, N-acetylcysteine and ascorbic acid. GCS-null cells
fail to decrease the expression of the growth-stage gene cprD, and
do not induce the expression of cAR1 (cAMP receptor), acaA (adenylyl
cyclase A) and lagC (aggregation marker) that required for
the earliest stages of development. Dictyostelium cells that enter
the development stage use G protein-coupled receptor signaling to
direct chemotactic migration to a source of cAMP. We overexpressed
cAR1, the most important receptor for cAMP signal cascade,
in GCS-null cells. cAR1 overexpressing GCS-null cells still
fail to aggregate in suspension. These results suggest GCS-null cells
are defective in production of the extracellular cAMP that serves
as the extracellular chemoattractant and in cAMP signal cascade
in D. discoideum development.

Kim, J., P. Heslop-Harrison, et al. (2007). "Stochastic noise and synchronisation during Dictyostelium aggregation make cAMP oscillations robust." PLoS Comput. Biol. 3(11):e218: 2190-2198.
	
Kinseth, M. A. (2007). The physiological role of the GRASP proteins in unconventional secretion and mitotic golgi fragmentation. San Diego, CA, University of California, San Diego: 153.
	
Kinseth, M. A., C. Anjard, et al. (2007). "The golgi-associated protein Grasp is required for unconventional protein secretion during development." Cell 130: 524-534.
	
Kintses, B., M. Gyimesi, et al. (2007). "Reversible movement of switch 1 loop of myosin determines actin interaction." EMBO J. 26: 265-274.
	
Koppole, S., J. C. Smith, et al. (2007). "The structural coupling between atpase activation and recovery stroke in the myosin II motor." Structure 15: 825-837.
	
Kortholt, A., J. S. King, et al. (2007). "Phospholipase C regulation of phosphatidylinositol 3,4,5-trisphosphate-mediated chemotaxis." Mol. Biol. Cell 18: 4772-4779.
	
Krishnan, J. (2007). Modelling gradient perception and polarization in chemotaxing Dictyostelium cells. BMC Systems Biol.
	Poster presentation
Chemotaxis, the directed migration of cells/organisms in response to external chemical gradients, is of great importance in various biological settings such as wound healing, tumour metastasis and development.

This talk deals with modelling efforts aimed at understanding two key sub-processes of eukaryotic chemotaxis: gradient perception, the process by which information about an external concentration field is converted into an internal signal which guides cell motion, and polarization, the persistent localization of various signalling molecules to opposite ends of the cell ("front" and "back"), along with any attendant morphological change.

We first briefly examine models for gradient perception in Dictyostelium. This involves the regulation of phosphoinositide lipids such as PI(3,4,5)P3/PI(3,4)P2, by the receptor, via the enzymes PI3K and PTEN, in a manner consistent with adaptation to homogeneous stimuli. We then discuss a modelling framework developed to link gradient perception with cell polarization. While cell polarization occurs as a result of exposure to an external chemical gradient, there are intrinsic mechanisms which can also lead to cell polarization, which do not require an externally imposed chemical gradient.

Working within our modelling framework, we examine the interaction between external gradient-induced and intrinsic polarization. Model analysis leads to various testable predictions regarding their interaction and is a first step towards elucidating the complexities of the polarization process in this system. This is work done in collaboration with Pablo Iglesias and Peter Devreotes, Johns Hopkins University

Kubohara, Y. (2007). "[Pharmacological activities of the Dictyostelium differentiation-inducing factor-1 (DIF-1): cellular slime molds are fascinating lower eukaryotes!]." Seikagaku 79: 148-151.
	
Kubohara, Y., A. Arai, et al. (2007). "Pharmacological evidence that stalk cell differentiation involves increases in the intracellular Ca(2+) and H(+) concentrations in Dictyostelium discoideum." Dev. Growth Differ. 49: 253-264.
	
Kurz, C. L. and J. J. Ewbank (2007). "Infection in a dish: high-throughput analyses of bacterial pathogenesis." Curr. Opin. Microbiol 10: 10-16.
	
Kuwayama, H. and A. Nagasaki (2007). "Desalted deep sea water increases transformation and homologous recombination efficiencies in Dictyostelium discoideum." J. Mol. Microbiol. Biotechnol. 14: 157-162.
	
Kuzdzal-Fick, J. J., K. R. Foster, et al. (2007). "Exploiting new terrain: an advantage to sociality in the slime mold Dictyostelium discoideum." Behavioral Ecol. 18(2): 433-437.
	Understanding the ecological benefits of social actions is central to explaining the evolution of social behavior. The social amoeba Dictyostelium discoideum has been well studied and is a model for social evolution and development, but surprisingly little is known about its ecology. When starving, thousands of the normally solitary amoebae aggregate to form a differentiated multicellular organism known as a slug. The slug migrates toward the soil surface where it metamorphoses into a fruiting body of hardy spores held up by a dead stalk comprising about one-fifth of the cells. Multicellularity in D. discoideum is thought to have evolved to lift the spores above the hazards of the soil where spores can be picked up for long-distance dispersal. Here, we show that multicellularity has another advantage: local dispersal to new food sources. We find that cells shed by D. discoideum slugs during migration consume and remove bacteria in the path of the slug, although slugs themselves do not breakup. We also show that slugs are adept at local dispersal by comparing migration of slugs with migration of individual cells of the mutant, CAP2, which cannot aggregate and so rely only on cellular movement. In particular, the solitary cells of the aggregation mutant are unable to cross a soil barrier, easily crossed by slugs. We propose that the exploitation of local food patches is an important selective benefit favoring multicellular cooperation in D. discoideum. 


Kypri, E. (2007). Study of LvsB in Dictyostelium discoideum provides insights into the Chediak-Higashi syndrome. United States -- Texas, The University of Texas at Austin.
	The Chediak-Higashi Syndrome is a disorder affecting lysosome biogenesis. At the cellular level, the Chediak-Higashi syndrome is characterized by the presence of grossly enlarged lysosomes in every tissue. Impaired lysosomal function in CHS patients results in many physiological problems, including immunodeficiency, albinism and neurological problems. The Chediak-Higashi syndrome is caused by the loss of a BEACH protein of unknown function named Lyst. In this work, I have studied the function of the Dictyostelium LvsB protein, the ortholog of mammalian Lyst and a protein that is also important for lysosomal function. Using a knock-in approach we tagged LvsB with GFP and expressed it from its single chromosomal locus. GFP-LvsB was observed on endocytic and phagocytic compartments. Specific analysis of the endocytic compartments labeled by LvsB showed that they represented late lysosomes and postlysosomes. The analysis of LvsB-null cells revealed that loss of LvsB resulted in enlarged postlysosomes, in the abnormal localization of proton pumps on postlysosomes and their abnormal acidification. This work demonstrated that the abnormal postlysosomes in LvsB-null cells were produced by the inappropriate fusion of lysosomes with postlysosomal compartments. Furthermore, this work provided the first evidence that LvsB is a functional antagonist of the GTPase Rab14 in vesicle fusion events. In particular, we demonstrated that reduction of Rab14 activity suppressed the LvsB-null phenotype by reducing the enlarged post-lysosomes and the enhanced rate of heterotypic fusion. In contrast, expression of an active form of Rab14 enhanced the LvsB-null phenotype by causing an even more severe enlargement of endosome size. The results provided by this work support the model that LvsB and Lyst proteins act as negative regulators of fusion by limiting the heterotypic fusion of early with late compartments and antagonize Rab GTPases in membrane fusion. The LvsB localization studies and the functional assessment of the LvsB-null phenotype helped make unique contributions to the understanding of the molecular function of Lyst proteins.

Kypri, E., C. Schmauch, et al. (2007). "The BEACH protein lvsB is localized on lysosomes and postlysosomes and limits their fusion with early endosomes." Traffic 8: 774-783.
	
Lam, D., J. P. Levraud, et al. (2007). "Autophagic or necrotic cell death in the absence of caspase and bcl-2 family members." Biochem. Biophys. Res. Commun. 363: 536-541.
	
Langridge, P. D. and R. R. Kay (2007). "Mutants in the Dictyostelium Arp2/3 complex and chemoattractant-induced actin polymerization." Exp. Cell Res. 313: 2563-2574.
	
Laporte, C., A. Kosta, et al. (2007). "A necrotic cell death model in a protist." Cell Death Differ. 14: 266-274.
	
Lee, J. (2007). "The use of gelatin substrates for traction force microscopy in rapidly moving cells." Methods Cell Biol. 83: 297-312.
	
Leslie, M. (2007). A slimy start for immunity. Science. 317: 584.
	
Levi, S. K. and B. S. Glick (2007). "Grasping unconventional secretion." Cell 130: 407-409.
	
Li, H. (2007). From poles to equator: functional analysis of DdAurora during mitosis and cytokinesis in Dictyostelium discoideum. Austin, TX, The University of Texas at Austin: 113.
	
Lieto-Trivedi, A., S. Dash, et al. (2007). "Myosin surface loop 4 modulates inhibition of actomyosin 1B ATPase activity by tropomyosin." Biochemistry 46: 2779-2786.
	
Lippert, U., D. Diao, et al. (2007). "Conserved structural and functional properties of D-domain containing redox-active and -inactive protein disulfide isomerase-related protein chaperones." J. Biol. Chem. 282: 11213-11220.
	
Lobanov, A. V., D. E. Fomenko, et al. (2007). "Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life." Genome Biol. 8: R198.
	
Lombardi, M. L., D. A. Knecht, et al. (2007). "Traction force microscopy in Dictyostelium reveals distinct roles for myosin II motor and actin-crosslinking activity in polarized cell movement." J. Cell Sci. 120: 1624-1634.
	
Loovers, H. M., A. Kortholt, et al. (2007). "Regulation of phagocytosis in dictyostelium by the inositol 5-phosphatase ocrl homolog dd5p4." Traffic 8: 618-628.
	
Mahadeo, D. C., M. Janka-Junttila, et al. (2007). "A chemoattractant-mediated Gi-coupled pathway activates adenylyl cyclase in human neutrophils." Mol. Biol. Cell 18: 512-522.
	
Malchow, D., D. F. Lusche, et al. (2007). "A fast Ca(2+)-induced Ca(2+)-release mechanism in Dictyostelium discoideum." Cell Calcium 43: 521-530.
	
Malnasi-Csizmadia, A., J. Toth, et al. (2007). "Selective perturbation of the myosin recovery stroke by point mutations at the base of the lever arm affects ATP hydrolysis and phosphate release." J. Biol. Chem. 282: 17658-17664.
	
McConnell, R., S. Middlemist, et al. (2007). "An unusually low microsatellite mutation rate in Dictyostelium discoideum, an organism with unusually abundant microsatellites." Genetics 177: 1499-1507.
	
Medalia, O., M. Beck, et al. (2007). "Organization of actin networks in intact filopodia." Curr. Biol. 17: 79-84.
	
Meima, M. E., K. E. Weening, et al. (2007). "Vectors for expression of proteins with single or combinatorial fluorescent protein and tandem affinity purification tags in Dictyostelium." Prot. Expr. Purif. 53: 283-288.
	
Meissner, J. (2007). Effects of myristoylation on the structure and stability of hisactophilin. Canada, University of Waterloo (Canada).
	Hisactophilin is a histidine rich, actin binding protein from Dictyostelium discoideum . The structure of Hisactophilin, an all-beta protein, is typical of the beta-trefoil superfamily of proteins. In addition, hisactophilin is myristoylated, which is a relatively common co-translational modification involving the covalent attachment of a myristic acid group to the N-terminal glycine of a protein. For most modified proteins, a myristoyl group is involved in reversible protein-protein and protein-membrane interactions via a myristoyl switch. The majority of studies on the molecular basis of myristoyl switches have focused on characterizing calcium-myristoyl switches, whereas research has suggested that hisactophilin binds reversibly to membranes by means of a pH dependent myristoyl switch. A number of in vivo studies of the modified protein have been completed to study the function of hisactophilin; however, the structure and stability of the protein have only been characterized using the recombinant non-myristoylated protein. In contrast, this study focuses on the effects of myristoylation on hisactophilin structure and stability. Myristoylated hisactophilin has been prepared by a dual plasmid expression system in E. coli . Optimization of the efficiency of myristoylation was completed for the preparation and purification of myristoylated hisactophilin. Characterization of the structural changes caused by myristoylation were undertaken using multidimensional homo- and heteronuclear NMR experiments. Circular dichroism (CD) was used to obtain low resolution structural data and characterize protein stability as a function of pH using chemical denaturation. The molecular consequences of myristoylation on protein stability and structure, as well as the molecular basis for pH dependent myristoyl switch will be discussed.

Mellgren, R. L. and X. Huang (2007). "Fetuin A stabilizes m-calpain and facilitates plasma membrane repair." J Biol Chem 282(49): 35868-35877.
	Yeast two-hybrid experiments identified alpha(2)-Heremans-Schmid glycoprotein (human fetuin A) as a binding partner for calpain domain III (DIII). The tandem DIIIs of calpain-10 interacted under the most selective culture conditions, but DIIIs of m-calpain, calpain-3, and calpain-5 also interacted under less stringent selection. DIIIs of mu-calpain, calpain-6, and the tandem DIII-like domains of the Dictyostelium Cpl protein did not interact with alpha(2)-Heremans-Schmid glycoprotein in the yeast two-hybrid system. Bovine fetuin A stabilized proteolytic activity of purified m-calpain incubated in the presence of mm calcium chloride and prevented calcium-dependent m-calpain aggregation. Consistent with the yeast two-hybrid studies, fetuin A neither stabilized mu-calpain nor prevented its aggregation. Confocal immunofluorescence microscopy of scratch-damaged L6 myotubes demonstrated accumulation of m-calpain at the wound site in association with the membrane repair protein, dysferlin. m-Calpain also co-localized with fluorescein-labeled fetuin A at the wound site. The effect of fetuin A on calpain-mediated plasma membrane resealing was investigated using fibroblasts from Capns1(-/-) and Capns1(+/+) mouse embryos. Capns1 encodes the small noncatalytic subunit that is required for the proteolytic function of m- and mu-calpains. Thus, Capns1(-/-) fibroblasts do not express these calpains in active form. Fetuin A increased resealing of scrape-damaged wild-type fibroblasts but not Capns1(-/-) fibroblasts. These studies identify fetuin A as a potential extracellular regulator of m-calpain at nascent sites of plasma membrane wounding.

Mendoza, M. C., E. O. Booth, et al. (2007). "MEK1 and protein phosphatase 4 coordinate Dictyostelium development and chemotaxis." Mol. Cell. Biol. 27: 3817-3827.
	
Metcalf, T., H. van der Wel, et al. (2007). "Role of SP65 in assembly of the Dictyostelium discoideum spore coat." Euk. Cell 6: 1137-1149.
	
Mir, H. A., J. Rajawat, et al. (2007). "Signaling molecules involved in the transition of growth to development of Dictyostelium discoideum." Indian J. Exp. Biol. 45: 223-236.
	
Miranda-Saavedra, D. and G. J. Barton (2007). "Classification and functional annotation of eukaryotic protein kinases." Proteins 68: 893-914.
	
Miyanaga, Y., S. Matsuoka, et al. (2007). "Stochastic signal inputs for chemotactic response in Dictyostelium cells revealed by single molecule imaging techniques." Biosystems 88: 251-260.
	
Mizuno, N., A. Narita, et al. (2007). "Three-dimensional structure of cytoplasmic dynein bound to microtubules." Proc. Natl. Acad. Sci. USA 104: 20832-20837.
	
Mogami, T., T. Kon, et al. (2007). "Kinetic characterization of tail swing steps in the ATPase cycle of Dictyostelium cytoplasmic dynein." J. Biol. Chem. 282: 21639-21644.
	
Mondal, S., D. Neelamegan, et al. (2007). "GxcDD, a putative RacGEF, is involved in Dictyostelium development." BMC Cell Biol. 8:23: 14 pages.
	
Muller-Taubenberger, A. and K. I. Anderson (2007). "Recent advances using green and red fluorescent protein variants." Appl Microbiol Biotechnol 77(1): 1-12.
	Fluorescent proteins have proven to be excellent tools for live-cell imaging. In addition to green fluorescent protein (GFP) and its variants, recent progress has led to the development of monomeric red fluorescent proteins (mRFPs) that show improved properties with respect to maturation, brightness, and the monomeric state. This review considers green and red spectral variants, their paired use for live-cell imaging in vivo, in vitro, and in fluorescence resonance energy transfer (FRET) studies, in addition to other recent "two-color" advances including photoswitching and bimolecular fluorescence complementation (BiFC). It will be seen that green and red fluorescent proteins now exist with nearly ideal properties for dual-color microscopy and FRET.

Muramoto, T., H. Kuwayama, et al. (2007). "A stress response kinase, Krsa, controls cAMP relay during the early development of Dictyostelium discoideum." Dev. Biol. 305: 77-89.
	
Mylonakis, E., A. Casadevall, et al. (2007). "Exploiting amoeboid and non-vertebrate animal model systems to study the virulence of human pathogenic fungi." PLoS Pathogens 3(7):e101: 0859-0865.
	
Na, J., B. Tunggal, et al. (2007). "STATc is a key regulator of the transcriptional response to hyperosmotic shock." BMC Genomics 8:123: 14 pages.
	
Nagasaki, A. and T. Q. Uyeda (2007). "Screening of genes involved in cell migration in Dictyostelium." Exp. Cell Res. 314: 1136-1146.
	
Nagesha, D., G. S. Laevsky, et al. (2007). "In vitro imaging of embryonic stem cells using multiphoton luminescence of gold nanoparticles." Int J Nanomedicine 2(4): 813-819.
	Recent advances in nonlinear optical techniques and materials such as quantum wells, nanowires and noble-metal nanoparticles have led to advances in cellular imaging wherein various nanoparticles have been shown to improve both in vitro and in vivo visualization. In this paper, we demonstrate in vitro imaging using multi-photon photoluminescence of gold nanoparticles from two different cell types Dictyostelium discoideum and mouse embryonic stem cells. By observing nanoparticles we show that embryonic stem cells maintained their ability to proliferate for several passages while grown in the presence of gold nanoparticles. The advantages of multi-photon luminescence using gold nanoparticles have important implications for use in stem cell proliferation experiments and in vitro experiments to monitor differentiation.

Narita, A., N. Mizuno, et al. (2007). "Molecular determination by electron microscopy of the dynein-microtubule complex structure." J. Mol. Biol. 372: 1320-1336.
	
Nikravan, N. N. (2007). The study of an autocrine signal transduction pathway that represses cell proliferation in Dictyostelium discoideum. United States -- Texas, Rice University.
	Many secreted factors are believed to inhibit cell proliferation in certain tissues such as tumors; however, the identity and action of most of these factors remains unknown. The recent identification of two autocrine secreted factors, AprA and CfaD, that inhibit cell proliferation in Dictyostelium discoideum , has enabled further study of how these factors regulate cell proliferation in a simple model system. Similar to AprA, the loss of CfaD in Dictyostelium strains increases the rate of cell proliferation in shaking cultures and leads to large fruiting bodies with large spore masses. The overexpression of CfaD causes tall, thin stalks with small spore masses. Analysis of different cell lines suggests that AprA is required for extracellular CfaD to inhibit cell proliferation. In addition, a screen for second-site suppressors of the aprA OE phenotype led to the identification of the Ddcln2 gene that encodes a tripeptidyl peptidase I. Examination of several DdTPPI properties, including an enzymatic activity assay, suggests the possible involvement of DdTPPI in both the AprA and CfaD signal transduction pathways that negatively regulate cell proliferation.

Nizak, C., R. J. Fitzhenry, et al. (2007). "Exploitation of other social amoebae by Dictyostelium caveatum." PLoS ONE 2(2):e212: 9 pages.
	
Noguchi, T. Q., N. Kanzaki, et al. (2007). "A novel system for expressing toxic actin mutants in Dictyostelium and purification and characterization of a dominant lethal yeast actin mutant." J. Biol. Chem. 282: 27721-27727.
	
Omata, W., H. Shibata, et al. (2007). "Dictyostelium differentiation-inducing factor-1 induces glucose transporter 1 translocation and promotes glucose uptake in mammalian cells." Febs J. 274: 3392-3404.
	
Onishi, H. and M. F. Morales (2007). "A closer look at energy transduction in muscle." Proc. Natl. Acad. Sci. USA 104: 12714-12719.
	
Otsuji, M., S. Ishihara, et al. (2007). "A mass conserved reaction-diffusion system captures properties of cell polarity." PLoS Comput. Biol. 3(6):e108: 1040-1054.
	
Pang, T. L., C. J. Wu, et al. (2007). "Dictyostelium gnt15 encodes a protein with similarity to large and plays an essential role in development." Biochem. Biophys. Res. Commun. 360: 83-89.
	
Pilcher, K. E., P. Fey, et al. (2007). "A reliable general purpose method for extracting genomic DNA from Dictyostelium cells." Nature Protoc 2: 1325-1328.
	
Pilcher, K. E., P. Gaudet, et al. (2007). "A general purpose method for extracting RNA from Dictyostelium cells." Nature Protoc 2: 1329-1332.
	
Pockley, P. (2007). Slime mould model of mitochondrial disease earns Australasian Science prize. Australasian Sci. Nov/Dec: 6.
	
Prabhu, Y., S. Mondal, et al. (2007). "A GPCR involved in post aggregation events in Dictyostelium discoideum." Dev. Biol. 312: 29-43.
	
Prabhu, Y., R. Muller, et al. (2007). "GrlJ, a Dictyostelium GABAB-like receptor with roles in post-aggregation development." BMC Dev. Biol. 7:44: 14 pages.
	
Prudden, J., S. Pebernard, et al. (2007). "SUMO-targeted ubiquitin ligases in genome stability." EMBO J 26(18): 4089-4101.
	We identify the SUMO-Targeted Ubiquitin Ligase (STUbL) family of proteins and propose that STUbLs selectively ubiquitinate sumoylated proteins and proteins that contain SUMO-like domains (SLDs). STUbL recruitment to sumoylated/SLD proteins is mediated by tandem SUMO interaction motifs (SIMs) within the STUbLs N-terminus. STUbL-mediated ubiquitination maintains sumoylation pathway homeostasis by promoting target protein desumoylation and/or degradation. Thus, STUbLs establish a novel mode of communication between the sumoylation and ubiquitination pathways. STUbLs are evolutionarily conserved and include: Schizosaccharomyces pombe Slx8-Rfp (founding member), Homo sapiens RNF4, Dictyostelium discoideum MIP1 and Saccharomyces cerevisiae Slx5-Slx8. Cells lacking Slx8-Rfp accumulate sumoylated proteins, display genomic instability, and are hypersensitive to genotoxic stress. These phenotypes are suppressed by deletion of the major SUMO ligase Pli1, demonstrating the specificity of STUbLs as regulators of sumoylated proteins. Notably, human RNF4 expression restores SUMO pathway homeostasis in fission yeast lacking Slx8-Rfp, underscoring the evolutionary functional conservation of STUbLs. The DNA repair factor Rad60 and its human homolog NIP45, which contain SLDs, are candidate STUbL targets. Consistently, Rad60 and Slx8-Rfp mutants have similar DNA repair defects.

Pukatzki, S., A. T. Ma, et al. (2007). "Type VI secretion system translocates a phage tail spike-like protein into target cells where it cross-links actin." Proc. Natl. Acad. Sci. USA 104: 15508-15513.
	
Rajawat, J., I. Vohra, et al. (2007). "Effect of oxidative stress and involvement of poly(ADP-ribose) polymerase (PARP) in Dictyostelium discoideum development." Febs J. 274: 5611-5618.
	
Rall, J. M. (2007). Identification and characterization of distinct classes of cAMP-pulse-induced genes in Dictyostelium discoideum development. Houston, TX, The University of Texas Graduate School of Biomedical Sciences at Houston: 113.
	
Razeto, A., F. Mattiroli, et al. (2007). "Identifying a recombinant alkyldihydroxyacetonephosphate synthase suited for crystallographic studies." Prot. Expr. Purif. 55: 343-351.
	
Razeto, A., F. Mattiroli, et al. (2007). "The crucial step in ether phospholipid biosynthesis: structural basis of a noncanonical reaction associated with a peroxisomal disorder." Structure 15: 683-692.
	
Reiter, L. T., L. H. Do, et al. (2007). "Accentuate the negative: proteome comparisons using the negative proteome database." Fly 1(3): 164-171.
	The availability of complete genome sequence information for diverse organisms including model genetic organisms has ushered in a new era of protein sequence comparisons making it possible to search for commonalities among entire proteomes using the Basic Local Alignment Search Tool (BLAST). Although the identification and analysis of proteins shared by humans and model organisms has proven an invaluable tool to understanding gene function, the sets of proteins unique to a given model organism's proteome have remained largely unexplored. We have constructed a searchable database that allows biologists to identify proteins unique to a given proteome. The Negative Proteome Database (NPD) is populated with pair-wise protein sequence comparisons between each of the following proteomes: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Dictyostelium discoideum, Chlamydomonus reinhardti, Escherichia coli K12, Arabidopsis thaliana and Methanoscarcina acetivorans. Our analysis of negative proteome datasets using the NPD has thus far revealed 107 proteins in humans that may be involved in motile cilia function, 1628 potential pesticide target proteins in flies, 659 proteins shared by flies and humans that are not represented in the less neurologically complex worm proteome, and 180 nuclear encoded human disease associated proteins that are absent from the fly proteome. The NPD is the only online resource where users can quickly perform complex negative and positive comparisons of model organism proteomes. We anticipate that the NPD and the adaptable algorithm which can readily be used to duplicate this analysis on custom sets of proteomes will be an invaluable tool in the investigation of organism specific protein sets.

Repass, S. L. (2007). Study of Hip1r: insights from a Dictyostelium discoideum clathrin adaptor. Austin, TX, The University of Texas at Austin: 126.
	
Repass, S. L., R. J. Brady, et al. (2007). "Dictyostelium Hip1r contributes to spore shape and requires epsin for phosphorylation and localization." J. Cell Sci. 120: 3977-3988.
	
Rivero, F. and F. Cvrkova (2007). Ch. 8: Origins and evolution of the actin cytoskeleton. Eukaryotic membranes and cytoskeleton: origins and evolution. G. Jekely, Landes Bioscience.
	
Rohlfs, M., R. Arasada, et al. (2007). "The Ste20-like kinase SvkA of Dictyostelium discoideum is essential for late stages of cytokinesis." J. Cell Sci. 120: 4345-4354.
	
Romeralo, M., R. Escalante, et al. (2007). "Molecular systematics of dictyostelids: 5.8S ribosomal DNA and internal transcribed spacer region analyses." Euk. Cell 6: 110-116.
	
Romeralo, M., O. Fiz-Palacios, et al. (2007). "A new concept for Dictyostelium sphaerocephalum based on morphology and phylogenetic analysis of nuclear ribosomal internal transcribed spacer region sequences." Can. J. Bot. 85: 104-110.
	
Sacchi, L., C. Larizza, et al. (2007). "Precedence temporal networks to represent temporal relationships in gene expression data." J Biomed. Inform. 40: 761-774.
	
Sandrini, M. P., F. Soderbom, et al. (2007). "Dictyostelium discoideum salvages purine deoxyribonucleosides by highly specific bacterial-like deoxyribonucleoside kinases." J Mol Biol 369: 653-664.
	
Santorelli, L. A. (2007). Mechanisms of cheating behavior in the social amoeba Dictyostelium discoideum. Houston, TX, Rice University: 112.
	
Sasaki, A. T., C. Janetopoulos, et al. (2007). "G protein-independent Ras/PI3K/F-actin circuit regulates basic cell motility." J. Cell Biol. 178: 185-191.
	
Sato, M. J., M. Ueda, et al. (2007). "Input-output relationship in galvanotactic response of Dictyostelium cells." Biosystems 88: 261-272.
	
Satre, M., S. Mattei, et al. (2007). "Mitochondrial carrier family: repertoire and peculiarities of the cellular slime mould Dictyostelium discoideum." Biochimie 89: 1058-1069.
	
Schaap, P. (2007). "Evolution of size and pattern in the social amoebas." Bioessays 29(7): 635-644.
	A fundamental goal of biology is to understand how novel phenotypes evolved through changes in existing genes. The Dictyostelia or social amoebas represent a simple form of multicellularity, where starving cells aggregate to build fruiting structures. This review summarizes efforts to provide a framework for investigating the genetic changes that generated novel morphologies in the Dictyostelia. The foundation is a recently constructed molecular phylogeny of the Dictyostelia, which was used to examine trends in the evolution of novel forms and in the divergence of genes that shape these forms. There is a major trend towards the formation of large unbranched fruiting bodies, which is correlated with the use of cyclic AMP (cAMP) as a secreted signal to coordinate cell aggregation. The role of cAMP in aggregation arose through co-option of a pathway that originally acted to coordinate fruiting body formation. The genotypic changes that caused this innovation and the role of dynamic cAMP signaling in defining fruiting body size and pattern throughout social amoeba evolution are discussed.

Schaloske, R. H., D. Blaesius, et al. (2007). "Arachidonic acid is a chemoattractant for Dictyostelium discoideum cells." J. Biosci. 32: 1281-1289.
	
Schiller, B., J. Voglmeir, et al. (2007). The N-glycosylation potential of Dictyostelium discoideum. FEBS J.
	N-linked glycosylation is a major post-translational modification
of proteins, but details about structures and the enzymes responsible
for their biosynthesis are lacking for many organisms. In the
case of Dictyostelium discoideum, we began by using Western blotting
with an antiserum raised against a plant glycoprotein (horseradish
peroxidase), which recognises core alpha1,3-fucose; these
data indicate that core fucose is expressed by AX3 during starvation
in suspension, at the pseudoplasmodial stage and in fruiting
bodies. As shown by mass spectrometry of wild-type glycans, there
is a developmental shift as soon as the pseudoplasmodial stage is
reached, from larger species such as Hex8HexNAc4Fuc1 and
Hex8HexNAc3 to smaller types like Hex4HexNAc2Fuc1. Linkage
analysis of Hex8HexNAc4Fuc1 revealed the finding of a novel
structure with both inter- and bisecting GlcNAc as well as core fucose.
Such fucosylation is missing from the HL250 mutant strain,
even though, both AX3 and HL250 strains possess a core alpha
1,3-fucosyltransferase activity, as shown by HPLC and linkage
analysis. The fucosylation defect in HL250 is due to a mutation in
GDP-D-Mannose-4,6-Dehydratase (GMD), one of the two
enzymes necessary for enzymatic transformation of GDP-mannose
into GDP-fucose. Expression of recombinant forms showed that
the AX3 GMD is active, whereas the HL250-encoded form is not.
In summary, modern methods verify that Dictyostelium has a
novel N-glycomic potential and that it possess core fucosylation of
the type found in plants and invertebrates.

Schlierf, M., F. Berkemeier, et al. (2007). "Direct observation of active protein folding using lock-in force spectroscopy." Biophys. J. 93: 3989-3998.
	
Schon, E. A. (2007). "Appendix 3. Linearized maps of circular mitochondrial genomes from representative organisms." Meth. Cell Biol. 80: 827-829.
	
Serafimidis, I., G. Bloomfield, et al. (2007). "A new environmentally resistant cell type from Dictyostelium." Microbiology 153: 619-630.
	
Shaulsky, G. and R. H. Kessin (2007). "The cold war of the social amoebae." Curr. Biol. 17: R684-R692.
	
Shimada, N. and T. Kawata (2007). "Evidence that noncoding RNA dutA is a multicopy suppressor of Dictyostelium discoideum STAT protein Dd-STATa." Euk. Cell 6: 1030-1040.
	
Shpakov, A. O. (2007). "[guanylyl cyclases of unicellular eukaryotes: structure, function, and regulatory properties]." Tsitologiia 49: 617-630.
	
Smith, M. G., T. A. Gianoulis, et al. (2007). "New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis." Genes Devel. 21: 601-614.
	
Soon, L. L. (2007). "A discourse on cancer cell chemotaxis: where to from here?" Iubmb Life 59: 60-67.
	
Sousa-Canavez, J. M., D. Beton, et al. (2007). "Identification and domain mapping of Dictyostelium discoideum type-1 protein phosphatase inhibitor-2." Biochimie 89: 692-701.
	
Steinert, M., K. Heuner, et al. (2007). "Legionella pathogenicity: genome structure, regulatory networks and the host cell response." Int. J. Med. Microbiol. 297: 577-587.
	
Strassmann, J. E. and D. C. Queller (2007). Altruism among amoebas. Natural History. Sept.: 24-29.
	
Strmecki, L., G. Bloomfield, et al. (2007). "Proteomic and microarray analyses of the Dictyostelium Zak1-GSK-3 signaling pathway reveal a role in early development." Euk. Cell 6: 245-252.
	
Suwwan de Felipe, K. (2007). Inter-kingdom horizontal gene transfer: a new mechanism for the acquisition of Legionella pneumophila type IV effectors. New York, NY, Columbia University: 219.
	
Takeda, K., A. T. Sasaki, et al. (2007). "Role of phosphatidylinositol 3-kinases in chemotaxis in Dictyostelium." J. Biol. Chem. 282: 11874-11884.
	
Tang, L. (2007). Tsunami is required for directional responses of Dictyostelium in chemotactic gradients during development. Baltimore, MD, The Johns Hopkins University: 96.
	
Tang, S., J. C. Liao, et al. (2007). "Predicting allosteric communication in myosin via a pathway of conserved residues." J. Mol. Biol. 373: 1361-1373.
	
Tannenbaum, E. (2007). "When does division of labor lead to increased system output?" J. Theor. Biol. 247: 413-425.
	
Tiaden, A., T. Spirig, et al. (2007). "The Legionella pneumophila response regulator LqsR promotes host cell interactions as an element of the virulence regulatory network controlled by RpoS and LetA." Cell. Microbiol. 9: 2903-2920.
	
Tiago, T., P. Martel, et al. (2007). "Binding modes of decavanadate to myosin and inhibition of the actomyosin ATPase activity." Biochim. Biophys. Acta 1774: 474-480.
	
Traynor, D. and R. R. Kay (2007). "Possible roles of the endocytic cycle in cell motility." J. Cell Sci. 120: 2318-2327.
	
Tresse, E., A. Kosta, et al. (2007). "From autophagic to necrotic cell death in Dictyostelium." Semin. Cancer Biol. 17: 94-100.
	
Tsujioka, M., N. Zhukovskaya, et al. (2007). "Dictyostelium Myb transcription factors function at culmination as activators of ancillary stalk differentiation." Euk. Cell 6: 568-570.
	
Vadell, E. M. and J. C. Cavender (2007). "Dictyostelids living in the soils of the Atlantic forest, Iguazu region, Misiones, Argentina: description of new species." Mycologia 99: 112-124.
	
Van Driessche, N., H. Alexander, et al. (2007). "Global transcriptional responses to cisplatin in Dictyostelium discoideum identify potential drug targets." Proc. Natl. Acad. Sci. USA 104: 15406-15411.
	
van Haastert, P. J., I. Keizer-Gunnink, et al. (2007). "Essential role of PI3-kinase and phospholipase A2 in Dictyostelium discoideum chemotaxis." J. Cell Biol. 177: 809-816.
	
van Haastert, P. J. and M. Postma (2007). "Biased random walk by stochastic fluctuations of chemoattractant-receptor interactions at the lower limit of detection." Biophys. J. 93: 1787-1796.
	
van Haastert, P. J. and D. M. Veltman (2007). "Chemotaxis: navigating by multiple signaling pathways." Sci. STKE 2007: pe40.
	
van Kuilenburg, A. B., J. Meijer, et al. (2007). "Clinical, biochemical and genetic findings in two siblings with a dihydropyrimidinase deficiency." Mol. Genet. Metab. 91: 157-164.
	
Vats, B. and H. Padh (2007). "Development of soil amoeba Dictyostelium discoideum as an expression system for recombinant human erythropoietin." World J. Microbiol. Biotechnol. 23: 1511-1518.
	
von Philipsborn, A. and M. Bastmeyer (2007). "Mechanisms of gradient detection: a comparison of axon pathfinding with eukaryotic cell migration." Int. Rev. Cytol. 263: 1-62.
	
Vourekas, A., D. Kalavrizioti, et al. (2007). "A 40.7 kDa Rpp30/Rpp1 homologue is a protein subunit of Dictyostelium discoideum RNase P holoenzyme." Biochimie 89: 301-310.
	
Waligorska, A., M. Wianecka-Skoczen, et al. (2007). "Motile activities of Dictyostelium discoideum differ from those in Protista or vertebrate animal cells." Folia Biol (Krakow) 55(3-4): 87-93.
	Cell movement in the amoebae Dictyostelium discoideum has been examined in media differing in monovalent cation concentration (i.e. Na+ and K+). Under isotonic or even slightly hypertonic conditions, the cells move equally well in solutions in which either potassium or sodium ions dominate. However, in strongly hypertonic solutions the amoebae showed motility in a 2% potassium chloride solution, but remained motionless in a hypertonic 2% sodium chloride solution. This inhibition of D. discoideum amoebae movement in a hypertonic sodium chloride solution was fully reversible. Such behaviour corresponds to that of plant, fungi, and some invertebrate animal cells rather than protozoan or vertebrate cells. These observations suggest that studies using D. discoideum as a model for cell motility in vertebrate animal tissue cells should be considered with caution, and would seem to confirm the classification of cellular slime moulds as related rather to Fungi than to Protista. This also shows that the cell membrane models should consider the asymmetry in sodium/potassium ion concentrations found in vertebrate animal cells as one of various possibilities.

Waligorska, A., M. Wianecka-Skoczen, et al. (2007). "Some difficulties in research into cell motile activity under isotropic conditions." Folia Biol. (Krakow) 55: 9-16.
	
Wang, Q., M. A. Deloia, et al. (2007). "The SH3 domain of a M7 interacts with its C-terminal proline-rich region." Prot. Sci. 16: 189-196.
	
Wessels, D., D. F. Lusche, et al. (2007). "PTEN plays a role in the suppression of lateral pseudopod formation during Dictyostelium motility and chemotaxis." J. Cell Sci. 120: 2517-2531.
	
West, C. M., H. van der Wel, et al. (2007). "Prolyl 4-hydroxylase-1 mediates O2 signaling during development of Dictyostelium." Development 134: 3349-3358.
	
Whitney, T. J. (2007). SAGE: A powerful technique used to analyze transcription profiles in lymphangioleiomyomatosis-derived cells and in Dictyostelium amoeba. United States -- Idaho, Idaho State University.
	Serial Analysis of Gene Expression (SAGE) identifies quantitative transcription levels of genes in a particular cell/tissue type, essentially defining the transcriptome. We used SAGE to understand the genes that define Dictyostelium amoeba and to understand the type of cells that cause LAM. The transcriptome of Dictyostelium amoeba contains high levels of transcripts involved in protein translation, cell-maintenance, and metabolism. Ribosomal protein genes were among the most numerous and the most highly transcribed and many cell-signaling genes are expressed. An unexpected result is relatively high levels of many developmental genes including dutA, the most highly represented transcript in our library. Our complete analysis of the amoebae stage SAGE library identifies nearly all of the genes necessary to define amoeba, and provides a reference for comparison with libraries from other stages of development and other amoeba species. LAM is a rare, progressive, lung disease that strikes young women. LAM cells exhibit characteristics that define malignant cells including a progressive nature and the ability to invade adjacent tissues, suggesting that LAM cells are malignant. We constructed a SAGE library from primary LAM-derived cultured cells and compared it to normal lung cells in order to test this hypothesis. Transcription levels of many housekeeping genes, such as is equivalent in both LAM and normal libraries. Genes that are previously reported to be mutated in some forms of LAM, such as TSC1 and TSC2 are not detectable or present at lower levels in LAM cells. Pulmonary-associated transcripts. such as surfactant genes are among the most highly represented in normal lung cells, but are essentially absent in LAM-derived cells, suggesting that LAM cells do not originate from lung cells. Finally, we observed a significant increase in expression of hundreds of transcripts previously reported to be involved in malignant processes such as invasion, metastasis, angiogenesis and tissue remodeling. Examples of these genes include those involved in TGF-² signaling as well as TGF-² responsive genes, several MMPs, and TIMPs 1 and 2. Our findings clearly support the hypothesis that LAM cells have genetically increased metastatic potential, and they appear to metastasize to the lung from another tissue source.

Wilhelm, C., C. Riviere, et al. (2007). "Magnetic control of Dictyostelium aggregation." Phys. Rev. E 75: 041906.
	
Wyatt, D. (2007). Chemotaxis in microfluid channels. Ithaca, NY, Cornell University: 99.
	
Xu, X., M. Meier-Schellersheim, et al. (2007). "Locally controlled inhibitory mechanisms are involved in eukaryotic GPCR-mediated chemosensing." J. Cell Biol. 178: 141-153.
	
Xu, X., A. Muller-Taubenberger, et al. (2007). "Attenuation of phospholipid signaling provides a novel mechanism for the action of valproic acid." Euk. Cell 6: 899-906.
	
Yamada, A., S. I. Matsuyama, et al. (2007). "Phenotypic plasticity of Escherichia coli at initial stage of symbiosis with Dictyostelium discoideum." Biosystems 92: 1-9.
	
Yoshino, R., T. Morio, et al. (2007). "Regulation of ammonia homeostasis by the ammonium transporter AmtA in Dictyostelium discoideum." Euk. Cell 6: 2419-2428.
	
Yoshino, T., Y. Maeda, et al. (2007). "The real factor for polypeptide elongation in Dictyostelium cells is EF-2B, not EF-2A." Biochem. Biophys. Res. Commun. 359: 586-591.
	
Zaki, M., J. King, et al. (2007). "Replacement of the essential Dictyostelium Arp2 gene by its Entamoeba homologue using parasexual genetics." BMC Genet. 8:28: 12 pages.
	
Zhang, H., M. R. Gomez-Garcia, et al. (2007). "Polyphosphate kinase 1, a conserved bacterial enzyme, in a eukaryote, Dictyostelium discoideum, with a role in cytokinesis." Proc. Natl. Acad. Sci. USA 104: 16486-16491.
	
Zhang, M., M. Goswami, et al. (2007). "Regulation of G protein-coupled cAMP receptor activation by a hydrophobic residue in transmembrane helix 3." Mol. Microbiol. 65: 508-520.
	
Zucko, J., N. Skunca, et al. (2007). "Polyketide synthase genes and the natural products potential of Dictyostelium discoideum." Bioinformatics 23: 2543-2549.
	
Agafonov, R. V., Y. E. Nesmelov, et al. (2008). "Muscle and nonmuscle myosins probed by a spin label at equivalent sites in the force-generating domain." Proc Natl Acad Sci U S A 105(36): 13397-13402.
	We have engineered a mutant of Dictyostelium discoideum (Dicty) myosin II that contains the same fast-reacting "SH1" thiol as in muscle myosin, spin-labeled it, and performed electron paramagnetic resonance (EPR) to compare the structure of the force-generating region of the two myosins. Dicty myosin serves as a model system for muscle myosin because of greater ease of mutagenesis, expression, and crystallization. The catalytic domains of these myosins have nearly identical crystal structures in the apo state, but there are significant differences in ATPase kinetics, and there are no crystal structures of skeletal muscle myosin with bound nucleotides, so another structural technique is needed. Previous EPR studies, with a spin label attached to SH1 in muscle myosin, have resolved the key structural states of this region. Therefore, we have performed identical experiments on both myosins spin-labeled at equivalent sites. Spectra were identical for the two myosins in the apo and ADP-bound states. With bound ADP and phosphate analogs, (i) both proteins exhibit two resolved structural states (prepowerstroke, postpowerstroke) in a single biochemical state (defined by the bound nucleotide), and (ii) these structural states are essentially identical in the two myosins but (iii) are occupied to different extents as a function of the biochemical state. We conclude that (i) myosin structural and biochemical states do not have a one-to-one correspondence, and (ii) Dicty myosin can serve as a good analog for structural studies of muscle myosin only if differences in the coupling between biochemical and structural states are taken into account.

Alibaud, L., T. Kohler, et al. (2008). "Pseudomonas aeruginosa virulence genes identified in a Dictyostelium host model." Cell. Microbiol. 10: 729-740.
	
Anjard, C. and W. F. Loomis (2008). "Cytokinins induce sporulation in Dictyostelium." Development 135: 819-827.
	
Aragao, K. S., M. Satre, et al. (2008). "Structure determination of Discoidin II from Dictyostelium discoideum and carbohydrate binding properties of the lectin domain." Proteins 73(1): 43-52.
	The social amoeba Dictyostelium discoideum adopts a cohesive stage upon starvation and then produces Discoidin I and II, two proteins able to bind galactose and N-acetyl-galactosamine. The N-terminal domain or discoidin domain (DS) is widely distributed in eukaryotes where it plays a role in extracellular matrix binding while the C-terminal domain displays sequence similarities to invertebrate lectins. We present the first X-ray structures of the wild-type and recombinant Discoidin II in unliganded state and in complex with monosaccharides. The protein forms a homotrimer which presents two binding surfaces situated on the opposite boundaries of the structure. The binding sites of the N-terminal domain contain PEG molecules that could mimics binding of natural ligand. The C-terminal lectin domain interactions with N-acetyl-D-galactosamine and methyl-beta-galactoside are described. The carbohydrate binding sites are located at the interface between monomers. Specificity for galacto configuration can be rationalized since the axial O4 hydroxyl group is involved in several hydrogen bonds with protein side chains. Titration microcalorimetry allowed characterization of affinity and demonstrated the enthalpy-driven character of the interaction. Those results highlight the structural differentiation of the DS domain involved in many cell-adhesion processes from the lectin activity of Dictyostelium discoidins.

Araki, T., J. Langenick, et al. (2008). "Evidence that DIF-1 and hyper-osmotic stress activate a Dictyostelium STAT by inhibiting a specific protein tyrosine phosphatase." Development 135(7): 1347-1353.
	STATc becomes tyrosine phosphorylated and accumulates in the nucleus when Dictyostelium cells are exposed to the prestalk cell inducer Differentiation inducing factor 1 (DIF-1), or are subjected to hyper-osmotic stress. We show that the protein tyrosine phosphatase PTP3 interacts directly with STATc and that STATc is refractory to activation in PTP3 overexpressing cells. Conversely, overexpression of a dominant inhibitor of PTP3 leads to constitutive tyrosine phosphorylation and ectopic nuclear localisation of STATc. Treatment of cells with DIF-1 or exposure to hyper-osmotic stress induces a decrease in biochemically assayable PTP3 activity and both agents also induce serine-threonine phosphorylation of PTP3. These observations suggest a novel mode of STAT activation, whereby serine-threonine phosphorylation of a cognate protein tyrosine phosphatase results in the inhibition of its activity, shifting the phosphorylation-dephosphorylation equilibrium in favour of phosphorylation.

Arya, R., S. Aslam, et al. (2008). "Production and characterization of pharmacologically active recombinant human phosphodiesterase 4B in Dictyostelium discoideum." Biotechnol J 3(7): 938-947.
	Phosphodiesterase 4B (PDE4B) is an important therapeutic target for asthma and chronic obstructive pulmonary disease. To identify PDE4 subtype-specific compounds using high-throughput assays, full-length recombinant PDE4 proteins are needed in bulk quantity. In the present study, full-length human PDE4B2 was expressed in the cellular slime mould Dictyostelium discoideum (Dd). A cell density of 2 x 10(7) cells/mL was obtained and up to 1 mg/L recombinant PDE4B2 was purified through Ni-NTA affinity chromatography. The expressed protein was soluble and its activity was comparable to PDE4B2 protein expressed in mammalian cells (K(m)=1.7 microM). The functional significance of the Dd expression system is supported by the demonstration that, in concert with proteins expressed in mammalian systems, there are no major changes in the affinity for PDE4B2 inhibitors and substrates. These findings thus provide the first evidence that Dd can be utilized for the expression and purification of functionally active full-length human PDE4B2 in large amounts required for high-throughput screening of pharmacologically active compounds against this therapeutic target.

Arya, R., A. Bhattacharya, et al. (2008). "Dictyostelium discoideum--a promising expression system for the production of eukaryotic proteins." FASEB J 22(12): 4055-4066.
	In general, four different expression systems, namely, bacterial, yeast, baculovirus, and mammalian, are widely used for the overproduction of biochemical enzymes and therapeutic proteins. Clearly, bacterial expression systems offer ease of maneuverability with respect to large-scale production of recombinant proteins, while, a baculovirus expression system ensures proper protein modifications, processing, and refolding of complex proteins. Despite these advantages, mammalian cells remain the preferred host for many eukaryotic proteins of pharmaceutical importance, particularly, those requiring post-translational modifications. Recently, the single-celled slime mold, Dictyostelium discoideum (Dd), has emerged as a promising eukaryotic host for the expression of a variety of heterologous recombinant eukaryotic proteins. This organism possesses the complex cellular machinery required for orchestrating post-translational modifications similar to the one observed in higher eukaryotes. This review summarizes the advantages and disadvantages of Dictyostelium as an alternate system compared to other well-established expression systems. The key lessons learned from the expression of human recombinant proteins in this system are reviewed. Also, the strengths, weaknesses, and challenges associated with industrial-scale production of proteins in Dd expression system are discussed.

Arya, R., S. Gupta, et al. (2008). "Purification of recombinant human phosphodiesterase 7A expressed in Dictyostelium discoideum." Protein Expr Purif 61(2): 149-154.
	Phosphodiesterase plays an important role in regulating inflammatory pathways and T cell function. The development of phosphodiesterase 7 inhibitor may give better efficacy profile over phosphodiesterase 4 inhibitors. However, the recombinant phosphodiesterase 7 is required in large quantity for high-throughput screening of new drugs by in vitro enzymatic assays. In the present study, recombinant human PDE7A1 was expressed in Dictyostelium discoideum under the control of constitutively active actin-15 promoter. The cytosolic localization of the expressed protein was confirmed by immunofluorescence studies. Upto 2 mg of recombinant protein was purified using His-Tag affinity column chromatography followed by ion-exchange Resource Q column purification. The recombinant protein expressed in D. discoideum followed Michaelis-Menten kinetics similar to the protein expressed in mammalian system and showed no major changes in affinity to substrate or inhibitors. Thus, our study clearly demonstrates a robust expression system for successful bulk production of pharmacologically active isoform of human PDE7A1 required for high-throughput assays.

Asano, Y., A. Nagasaki, et al. (2008). "Correlated waves of actin filaments and PIP3 in Dictyostelium cells." Cell Motil Cytoskeleton 65(12): 923-934.
	Chemotaxis-deficient amiB-null mutant Dictyostelium cells show two distinct movements: (1) they extend protrusions randomly without net displacements; (2) they migrate persistently and unidirectionally in a keratocyte-like manner. Here, we monitored the intracellular distribution of phosphatidylinositol (3,4,5)-trisphosphate (PIP(3)) to gain insight into roles PIP(3) plays in those spontaneous motilities. In keratocyte-like cells, PIP(3) showed convex distribution over the basal membrane, with no anterior enrichment. In stalled cells, as well as in wild type cells, PIP(3) repeated wave-like changes, including emergence, expansion and disappearance, on the basal membrane. The waves induced lamellipodia when they approached the cell edge, and the advancing speed of the waves was comparable to the migration speed of the keratocyte-like cells. LY294002, an inhibitor of PI3 kinase, abolished PIP(3) waves in stalled cells and stopped keratocyte-like cells. These results together suggested that keratocyte-like cells are "surfing" on the PIP(3) waves by coupling steady lamellipodial protrusions to the PIP(3) waves. Simultaneous live observation of actin filaments and PIP(3) in wild type or stalled amiB(-) cells indicated that the PIP(3) waves were correlated with wave-like distributions of actin filaments. Most notably, PIP(3) waves often followed actin waves, suggesting that PIP(3) induces local depolymerization of actin filaments. Consistent with this idea, cortical accumulation of PIP(3) was often correlated with local retraction of the periphery. We propose that the waves of PIP(3) and actin filaments are loosely coupled with each other and play important roles in generating spontaneous cell polarity.

Aubert, D. F., R. S. Flannagan, et al. (2008). "A novel sensor kinase-response regulator hybrid controls biofilm formation and type VI secretion system activity in Burkholderia cenocepacia." Infect Immun 76(5): 1979-1991.
	Burkholderia cenocepacia is an important opportunistic pathogen causing serious chronic infections in patients with cystic fibrosis (CF). Adaptation of B. cenocepacia to the CF airways may play an important role in the persistence of the infection. We have identified a sensor kinase-response regulator (BCAM0379) named AtsR in B. cenocepacia K56-2 that shares 19% amino acid identity with RetS from Pseudomonas aeruginosa. atsR inactivation led to increased biofilm production and a hyperadherent phenotype in both abiotic surfaces and lung epithelial cells. Also, the atsR mutant overexpressed and hypersecreted an Hcp-like protein known to be specifically secreted by the type VI secretion system (T6SS) in other gram-negative bacteria. Amoeba plaque assays demonstrated that the atsR mutant was more resistant to Dictyostelium predation than the wild-type strain and that this phenomenon was T6SS dependent. Macrophage infection assays also demonstrated that the atsR mutant induces the formation of actin-mediated protrusions from macrophages that require a functional Hcp-like protein, suggesting that the T6SS is involved in actin rearrangements. Three B. cenocepacia transposon mutants that were found in a previous study to be impaired for survival in chronic lung infection model were mapped to the T6SS gene cluster, indicating that the T6SS is required for infection in vivo. Together, our data show that AtsR is involved in the regulation of genes required for virulence in B. cenocepacia K56-2, including genes encoding a T6SS.

Baek, K., X. Liu, et al. (2008). "Modulation of actin structure and function by phosphorylation of Tyr-53 and profilin binding." Proc Natl Acad Sci U S A 105(33): 11748-11753.
	On starvation, Dictyostelium cells aggregate to form multicellular fruiting bodies containing spores that germinate when transferred to nutrient-rich medium. This developmental cycle correlates with the extent of actin phosphorylation at Tyr-53 (pY53-actin), which is low in vegetative cells but high in viable mature spores. Here we describe high-resolution crystal structures of pY53-actin and unphosphorylated actin in complexes with gelsolin segment 1 and profilin. In the structure of pY53-actin, the phosphate group on Tyr-53 makes hydrogen-bonding interactions with residues of the DNase I-binding loop (D-loop) of actin, resulting in a more stable conformation of the D-loop than in the unphosphorylated structures. A more rigidly folded D-loop may explain some of the previously described properties of pY53-actin, including its increased critical concentration for polymerization, reduced rates of nucleation and pointed end elongation, and weak affinity for DNase I. We show here that phosphorylation of Tyr-53 inhibits subtilisin cleavage of the D-loop and reduces the rate of nucleotide exchange on actin. The structure of profilin-Dictyostelium-actin is strikingly similar to previously determined structures of profilin-beta-actin and profilin-alpha-actin. By comparing this representative set of profilin-actin structures with other structures of actin, we highlight the effects of profilin on the actin conformation. In the profilin-actin complexes, subdomains 1 and 3 of actin close around profilin, producing a 4.7 degrees rotation of the two major domains of actin relative to each other. As a result, the nucleotide cleft becomes moderately more open in the profilin-actin complex, probably explaining the stimulation of nucleotide exchange on actin by profilin.

Bagorda, A. and C. A. Parent (2008). "Eukaryotic chemotaxis at a glance." J Cell Sci 121(16): 2621-2624.
	
Bakthavatsalam, D., D. A. Brock, et al. (2008). "The secreted Dictyostelium protein CfaD is a chalone." J Cell Sci 121(Pt 15): 2473-2480.
	Dictyostelium discoideum cells secrete CfaD, a protein that is similar to cathepsin proteases. Cells that lack cfaD proliferate faster and reach a higher stationary-phase density than wild-type cells, whereas cells that overexpress CfaD proliferate slowly and reach the stationary phase when at a low density. On a per-nucleus basis, CfaD affects proliferation but not growth. The drawback of not having CfaD is a reduced spore viability. Recombinant CfaD has no detectable protease activity but, when added to cells, inhibits the proliferation of wild-type and cfaD(-) cells. The secreted protein AprA also inhibits proliferation. AprA is necessary for the effect of CfaD on proliferation. Molecular-sieve chromatography indicates that in conditioned growth medium, the 60 kDa CfaD is part of a approximately 150 kDa complex, and both chromatography and pull-down assays suggest that CfaD interacts with AprA. These results suggest that two interacting proteins may function together as a chalone signal in a negative feedback loop that slows Dictyostelium cell proliferation.

Barfoot, R. J., K. H. Sheikh, et al. (2008). "Minimal F-actin cytoskeletal system for planar supported phospholipid bilayers." Langmuir 24(13): 6827-6836.
	Preferential binding of F-actin to lipid bilayers containing ponticulin was investigated on both planar supported bilayers and on a cholesterol-based tethering system. The transmembrane protein ponticulin in Dictyostelium discoideum is known to provide a direct link between the actin cytoskeleton and the cell membrane ( Wuestehube, L. J. ; Luna, E. J. J. Cell Biol. 1987, 105, 1741- 1751 ). Purification of ponticulin has allowed an in vitro model of the F-actin cytoskeletal scaffold system to be formed and investigated by AFM, epi-fluorescence microscopy, surface plasmon resonance (SPR), and quartz crystal microbalance with dissipation (QCM-D). Single filament features of F-actin bound to the ponticulin containing lipid bilayer are shown by AFM to have a pitch of 37.3 +/- 1.1 nm and a filament height of 7.0 +/- 1.6 nm. The complementary techniques of QCM-D and SPR were used to obtain dissociation constants for the interaction of F-actin with ponticulin containing bilayers, giving 10.5 +/- 1.7 microM for a physisorbed bilayer and 10.8 +/- 3.6 microM for a tethered bilayer, respectively.

Bennett, N., F. Letourneur, et al. (2008). "Sorting of the v-SNARE VAMP7 in Dictyostelium discoideum: a role for more than one Adaptor Protein (AP) complex." Exp Cell Res 314(15): 2822-2833.
	Soluble N-ethylmaleimide-sensitive-factor Attachment protein Receptors (SNAREs) participate in the specificity of membrane fusions in the cell. The mechanisms of specific SNARE sorting are still however poorly documented. We investigated the possible role of Adaptor Protein (AP) complexes in sorting of the Dictyostelium discoideum v-SNARE VAMP7. In live cells, GFP-VAMP7 is observed in the membrane of endocytic compartments. It is also observed in the plasma membrane of a small proportion of the cells. Mutation of a potential dileucine motif dramatically increases the proportion of cells with GFP-VAMP7 in their plasma membrane, strongly supporting the participation of an AP complex in VAMP7 sorting to the endocytic pathway. A partial increase occurs in knockout cells for the medium subunits of AP-2 and AP-3 complexes, indicating a role for both AP-2 and AP-3. VAMP7, as well as its t-SNAREs partners syntaxin 8 and Vti1, are co-immunoprecipitated with each of the medium subunits of the AP-1, AP-2, AP-3 and AP-4 complexes. This result supports the conclusion that VAMP7 directly interacts with both AP-2 and AP-3. It also raises the hypothesis of an interaction with AP-1 and AP-4. GFP-VAMP7 is retrieved from the endocytic pathway at and/or before the late post-lysosomal stage through an AP-independent mechanism.

Berthold, J., K. Schenkova, et al. (2008). "Rho GTPases of the RhoBTB subfamily and tumorigenesis." Acta Pharmacologica Sinica 29(3): 285-295.
	RhoBTB proteins constitute a subfamily of atypical members within the Rho family of small guanosine triphosphatases (GTPases). Their most salient feature is their domain architecture: a GTPase domain (in most cases, non-functional) is followed by a proline-rich region, a tandem of 2 broad-complex, tramtrack, bric a brac (BTB) domains, and a conserved C-terminal region. In humans, the RhoBTB subfamily consists of 3 isoforms: RhoBTB1, RhoBTB2, and RhoBTB3. Orthologs are present in several other eukaryotes, such as Drosophila and Dictyostelium, but have been lost in plants and fungi. Interest in RhoBTB arose when RHOBTB2 was identified as the gene homozygously deleted in breast cancer samples and was proposed as a candidate tumor suppressor gene, a property that has been extended to RHOBTB1. The functions of RhoBTB proteins have not been defined yet, but may be related to the roles of BTB domains in the recruitment of cullin3, a component of a family of ubiquitin ligases. A model emerges in which RhoBTB proteins are required to maintain constant levels of putative substrates involved in cell cycle regulation or vesicle transport through targeting for degradation in the 26S proteasome. RhoBTB proteins are engrossing the list of Rho GTPases involved in tumorigenesis. Unlike typical Rho GTPases (usually overexpressed or hyperactive), RhoBTB proteins appear to play a part in the carcinogenic process through a mechanism that involves the decreased or abolished expression of the corresponding genes, or more rarely, mutations that result in impaired functioning of the protein, presumably leading to the accumulation of RhoBTB substrates and alterations of the cellular homeostasis.

Beshay, U., K. Friehs, et al. (2008). "Growth of myxamoebae of the cellular slime mold Dictyostelium discoideum in suspension and immobilized form on living bacteria." Process Biochem. 43(11): 1281-1287.
	
Beta, C., G. Amselem, et al. (2008). "A bistable mechanism for directional sensing." New Journal of Physics 10(8): 083015.
	We present a generic mechanism for directional sensing in eukaryotic cells that is based on bistable dynamics. As the key feature of this modeling approach, the velocity of trigger waves in the bistable sensing system changes its sign across cells that are exposed to an external chemoattractant gradient. This is achieved by combining a two-component activator/inhibitor system with a bistable switch that induces an identical symmetry breaking for arbitrary gradient input signals. A simple kinetic example is designed to illustrate the dynamics of a bistable directional sensing mechanism in numerical simulations.

Blacklock, B. J., D. Kelley, et al. (2008). "A fatty acid elongase ELO with novel activity from Dictyostelium discoideum." Biochem Biophys Res Commun 374(2): 226-230.
	Fatty acid elongation was examined in the cellular slime mold, Dictyostelium discoideum. Profiling of the total fatty acid content of D. discoideum indicated that fatty acid elongation is active. Orthologs of the fatty acid elongase ELO family were identified in the D. discoideum genome and the cDNA for one, eloA, was cloned and functionally characterized by expression in yeast. EloA is a highly active ELO with strict substrate specificity for monounsaturated fatty acids, in particular 16:1(Delta9) to produce the unusual 18:1(Delta11) fatty acid. This is the first report on fatty acid elongation in a cellular slime mold.

Bloomfield, G., Y. Tanaka, et al. (2008). "Widespread duplications in the genomes of laboratory stocks of Dictyostelium discoideum." Genome Biol 9(4): R75.
	ABSTRACT: BACKGROUND: Duplications of stretches of the genome are an important source of individual genetic variation, but their unrecognized presence in laboratory organisms would be a confounding variable for genetic analysis. RESULTS: We report here that duplications of 15 kb or more are common in the genome of the social amoeba Dictyostelium discoideum. Most stocks of the axenic 'workhorse' strains Ax2 and Ax3/4 obtained from different laboratories can be expected to carry different duplications. The auxotrophic strains DH1 and JH10 also bear previously unreported duplications. Strain Ax3/4 is known to carry a large duplication on chromosome 2 and this structure shows evidence of continuing instability; we find a further variable duplication on chromosome 5. These duplications are lacking in Ax2, which has instead a small duplication on chromosome 1. Stocks of the type isolate NC4 are similarly variable, though we have identified some approximating the assumed ancestral genotype. More recent wild-type isolates are almost without large duplications, but we can identify small deletions or regions of high divergence, possibly reflecting responses to local selective pressures. Duplications are scattered through most of the genome, and can be stable enough to reconstruct genealogies spanning decades of the history of the NC4 lineage. The expression level of many duplicated genes is increased with dosage, but for others it appears that some form of dosage compensation occurs. CONCLUSION: The genetic variation described here must underlie some of the phenotypic variation observed between strains from different laboratories. We suggest courses of action to alleviate the problem.

Bolourani, P., G. B. Spiegelman, et al. (2008). "Rap1 activation in response to cAMP occurs downstream of ras activation during Dictyostelium aggregation." J. Biol. Chem. 283: 10232-10240.
	
Bornheimer, S. J. (2008). Spatial and temporal regulation of G-protein signaling elucidated by computational modeling and live cell FRET imaging. United States -- California, University of California, San Diego.
	Regulation of G-protein signaling occurs spatially between microdomains of cellular membranes, and temporally due largely to ligand-bound G-protein couple receptors (GPCRs) that speed up G-protein activation and regulator of G-protein signaling (RGS) proteins that speed up deactivation. This dissertation investigates spatial and temporal regulation of G-protein activity primarily through computational modeling and live cell FRET imaging. Computational modeling was used to study how variation in local concentrations of active GPCR, G-protein, and RGS protein affect local G-protein activity and turnover; results predict 16 distinct signaling regimes and numerous intermediate signaling phenomena. Computational methods were also developed to simplify complex biochemical networks; results indicate that a GPCR-G±-RGS complex is required in muscarinic receptor signaling to G±q, and predict that RGS protein can promote biphasic (bell-shaped) dose-response to ligand. To study spatial and temporal regulation of G-protein activity experimentally, two FRET probes of YFP-tagged G±i were developed: GTP-BODIPY TR (for membrane-based high throughput assays) and RGS-CFP (for live-cell imaging). RGS-CFP, unlike previous FRET probes for G-protein activity, is untargeted thereby functioning throughout the cell. RGS-CFP was used to investigate spatial regulation of G-protein activity during cell migration, in which GPCRs and G-proteins are thought, based primarily on chemotaxis of the slime mold Dictyostelium discoideum towards GPCR-ligand, to be distributed roughly homogeneously around the plasma membrane with subtly enhanced G-protein signaling at the front of the cell (a.k.a. leading edge). We studied migration in an alternative system: HeLa cells migrating to close a wound. Here, migration required Gi3 (together with a protein called GIV/Girdin) as did associated processes like actin remodeling and Akt activity; spatially, Gi3-YFP translocated from the Golgi to the leading edge where it accumulated and RGS-CFP, which is primarily cytosolic in resting cells, colocalized with Gi3-YFP at the leading edge where high FRET was observed indicating Gi3-YFP activity. These data demonstrate for the first time specific local regulation of G±i activity at the leading edge of cell migrating to close a wound. Taken together, this dissertation combining computational modeling and live cell FRET imaging sets the stage for quantitative research into G-protein signal transduction at the subcellular level.

Bosgraaf, L., I. Keizer-Gunnink, et al. (2008). "PI3-kinase signaling contributes to orientation in shallow gradients and enhances speed in steep chemoattractant gradients." J Cell Sci 121(Pt 21): 3589-3597.
	Dictyostelium cells that chemotax towards cAMP produce phosphatidylinositol (3,4,5)-trisphosphate [PtdIns(3,4,5)P(3)] at the leading edge, which has been implicated in actin reorganization and pseudopod extension. However, in the absence of PtdIns(3,4,5)P(3) signaling, cells will chemotax via alternative pathways. Here we examined the potential contribution of PtdIns(3,4,5)P(3) to chemotaxis of wild-type cells. The results show that steep cAMP gradients (larger than 10% concentration difference across the cell) induce strong PtdIns(3,4,5)P(3) patches at the leading edge, which has little effect on the orientation but strongly enhances the speed of the cell. Using a new sensitive method for PtdIns(3,4,5)P(3) detection that corrects for the volume of cytosol in pixels at the boundary of the cell, we show that, in shallow cAMP gradient (less than 5% concentration difference across the cell), PtdIns(3,4,5)P(3) is still somewhat enriched at the leading edge. Cells lacking PI3-kinase (PI3K) activity exhibit poor chemotaxis in these shallow gradients. Owing to the reduced speed and diminished orientation of the cells in steep and shallow gradients, respectively, cells lacking PtdIns(3,4,5)P(3) signaling require two- to six-fold longer times to reach a point source of chemoattractant compared with wild-type cells. These results show that, although PI3K signaling is dispensable for chemotaxis, it gives the wild type an advantage over mutant cells.

Bourbon, H. M. (2008). "Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex." Nucl Acids Res 36(12): 3993-4008.
	The multisubunit Mediator (MED) complex bridges DNA-bound transcriptional regulators to the RNA polymerase II (PolII) initiation machinery. In yeast, the 25 MED subunits are distributed within three core subcomplexes and a separable kinase module composed of Med12, Med13 and the Cdk8-CycC pair thought to control the reversible interaction between MED and PolII by phosphorylating repeated heptapeptides within the Rpb1 carboxyl-terminal domain (CTD). Here, MED conservation has been investigated across the eukaryotic kingdom. Saccharomyces cerevisiae Med2, Med3/Pgd1 and Med5/Nut1 subunits are apparent homologs of metazoan Med29/Intersex, Med27/Crsp34 and Med24/Trap100, respectively, and these and other 30 identified human MED subunits have detectable counterparts in the amoeba Dictyostelium discoideum, indicating that none is specific to metazoans. Indeed, animal/fungal subunits are also conserved in plants, green and red algae, entamoebids, oomycetes, diatoms, apicomplexans, ciliates and the 'deep-branching' protists Trichomonas vaginalis and Giardia lamblia. Surprisingly, although lacking CTD heptads, T. vaginalis displays 44 MED subunit homologs, including several CycC, Med12 and Med13 paralogs. Such observations have allowed the identification of a conserved 17-subunit framework around which peripheral subunits may be assembled, and support a very ancient eukaryotic origin for a large, four-module MED. The implications of this comprehensive work for MED structure-function relationships are discussed.

Bozzaro, S., C. Bucci, et al. (2008). "Phagocytosis and host-pathogen interactions in Dictyostelium with a look at macrophages." Int Rev Cell Mol Biol 271: 253-300.
	Research into phagocytosis and host-pathogen interactions in the lower eukaryote Dictyostelium discoideum has flourished in recent years. This chapter presents a glimpse of where this research stands, with emphasis on the cell biology of the phagocytic process and on the wealth of molecular genetic data that have been gathered. The basic mechanistic machinery and most of the underlying genes appear to be evolutionarily conserved, reflecting the fact that phagocytosis arose as an efficient way to ingest food in single protozoan cells devoid of a rigid cell wall. In spite of some differences, the signal transduction pathways regulating phagosome biogenesis are also emerging as ultimately similar between Dictyostelium and macrophages. Both cell types are hosts for many pathogenic invasive bacteria, which exploit phagocytosis to grow intracellularly. We present an overwiew, based on the analysis of mutants, on how Dictyostelium contributes as a genetic model system to decipher the complexity of host-pathogen interactions.

Brady, R. J. (2008). Characterization of the epsin homolog epnA in Dictyostelium discoideum. United States -- Texas, The University of Texas at Austin.
	Clathrin-coated pits on the plasma membrane invaginate into coated vesicles to internalize receptors and membrane. The clathrin adaptor epsin contains an amino-terminal ENTH domain that binds PI(4,5)P2 and a carboxy-terminal domain that binds clathrin, and accessory proteins such as AP2. Here, we assessed how inter- and intramolecular factors affect the contribution of epsin to coated-pit function in living cells. We found Dictyostelium epsin was not required for global clathrin function, but plays an essential role in spore development. We demonstrated that clathrin, but not AP2, was critical for epsin to associate with clathrin-coated pits. We found that the carboxy-terminal region of epsin was essential, but not sufficient, for targeting epsin within clathrin-coated pits on the plasma membrane. In addition to targeting epsin to the membrane, the amino-terminal ENTH domain regulates the interaction between epsin and clathrin, an essential property that cannot be replaced by an alternate PI(4,5)P2 binding domain. Moreover, the ENTH domain facilitates the functional interaction between clathrin and actin during late stages of endocytosis, possibly by regulating the activity of the adaptor Hip1r. Both the ability to bind PI(4,5)P 2 and another function mediated by residue T107 are critical for the activity of the ENTH domain. Our results support a model where the ENTH domain coordinates with the clathrin-binding C-terminal domain to allow a dynamic interaction of epsin with coated pits. Furthermore, we propose that the ENTH domain of epsin facilitates the membrane recruitment and phosphorylation of Hip1r, which in turn mediates the productive interaction of clathrin with the actin cytoskeleton at the plasma membrane.

Brady, R. J., Y. Wen, et al. (2008). "The ENTH and C-terminal domains of Dictyostelium epsin cooperate to regulate the dynamic interaction with clathrin-coated pits." J Cell Sci 121(Pt 20): 3433-3444.
	Epsin contains a phospholipid-binding ENTH domain coupled to C-terminal domain motifs that bind coated pit proteins. We examined how these domains interact to influence epsin function and localization in Dictyostelium. Although not required for global clathrin function, epsin was essential for constructing oval spores during development. Within the epsin protein, we found that features important for essential function were distinct from features targeting epsin to clathrin-coated pits. On its own, the phospholipid-binding ENTH domain could rescue the epsin-null phenotype. Although necessary and sufficient for function, the isolated ENTH domain was not targeted within clathrin-coated pits. The C-terminal domain containing the coated-pit motif was also insufficient, highlighting a requirement for both domains for targeting to coated pits. Replacement of the ENTH domain by an alternative membrane-binding domain resulted in epsin that sequestered clathrin and AP2 and ablated clathrin function, supporting a modulatory role for the ENTH domain. Within the ENTH domain, residues important for PtdIns(4,5)P2 binding were essential for both epsin localization and function, whereas residue T107 was essential for function but not coated pit localization. Our results support a model where the ENTH domain coordinates with the clathrin-binding C-terminal domain to allow a dynamic interaction of epsin with coated pits.

Breitsprecher, D., A. K. Kiesewetter, et al. (2008). "Clustering of VASP actively drives processive, WH2 domain-mediated actin filament elongation." EMBO J 27(22): 2943-2954.
	Vasodilator-stimulated phosphoprotein (VASP) is a key regulator of dynamic actin structures like filopodia and lamellipodia, but its precise function in their formation is controversial. Using in vitro TIRF microscopy, we show for the first time that both human and Dictyostelium VASP are directly involved in accelerating filament elongation by delivering monomeric actin to the growing barbed end. In solution, DdVASP markedly accelerated actin filament elongation in a concentration-dependent manner but was inhibited by low concentrations of capping protein (CP). In striking contrast, VASP clustered on functionalized beads switched to processive filament elongation that became insensitive even to very high concentrations of CP. Supplemented with the in vivo analysis of VASP mutants and an EM structure of the protein, we propose a mechanism by which membrane-associated VASP oligomers use their WH2 domains to effect both the tethering of actin filaments and their processive elongation in sites of active actin assembly.

Bruhn, H. and M. Steinert (2008). Ch. 12: Dictyostelium, a tractable model host organism for Legionella. Legionella: Molecular Microbiology. K. Heuner and M. Swanson, Caister Academic Press.
	
Calvo-Garrido, J., S. Carilla-Latorre, et al. (2008). "Vacuole membrane protein 1, autophagy and much more." Autophagy 4(6): 835-837.
	Vacuole membrane protein 1 (Vmp1) is a putative transmembrane protein that has been associated with different functions including autophagy, cell adhesion, and membrane traffic. Highly similar proteins are present in lower eukaryotes and plants although a homologue is absent in the fungi lineage. We have recently described the first loss-of-function mutation for a Vmp1 homologue in a model system, Dictyostelium discoideum. Our results give a more comprehensive view of the intricate roles played by this new gene. Dictyostelium Vmp1 is an endoplasmic reticulum-resident protein. Cells deficient in Vmp1 display pleiotropic defects in the context of the secretory pathway such as organelle biogenesis, the endocytic pathway, and protein secretion. The biogenesis of the contractile vacuole, an organelle necessary to survive under hypoosmotic conditions, is compromised as well as the structure of the endoplasmic reticulum and the Golgi apparatus. Transmission electron microscopy also shows abnormal accumulation of aberrant double-membrane vesicles, suggesting a defect in autophagosome biogenesis or maturation. The expression of a mammalian Vmp1 in the Dictyostelium mutant complements the phenotype suggesting a functional conservation during evolution. We are taking the first steps in understanding the function of this fascinating protein and recent studies have brought us more questions than answers about its basic function and its role in human pathology.

Calvo-Garrido, J., S. Carilla-Latorre, et al. (2008). "Vacuole membrane protein 1 is an endoplasmic reticulum protein required for organelle biogenesis, protein secretion, and development." Mol Biol Cell 19(8): 3442-3453.
	Vacuole membrane protein 1 (Vmp1) is membrane protein of unknown molecular function that has been associated with pancreatitis and cancer. The social amoeba Dictyostelium discoideum has a vmp1-related gene that we identified previously in a functional genomic study. Loss-of-function of this gene leads to a severe phenotype that compromises Dictyostelium growth and development. The expression of mammalian Vmp1 in a vmp1(-) Dictyostelium mutant complemented the phenotype, suggesting a functional conservation of the protein among evolutionarily distant species and highlights Dictyostelium as a valid experimental system to address the function of this gene. Dictyostelium Vmp1 is an endoplasmic reticulum protein necessary for the integrity of this organelle. Cells deficient in Vmp1 display pleiotropic defects in the secretory pathway and organelle biogenesis. The contractile vacuole, which is necessary to survive under hypoosmotic conditions, is not functional in the mutant. The structure of the Golgi apparatus, the function of the endocytic pathway and conventional protein secretion are also affected in these cells. Transmission electron microscopy of vmp1(-) cells showed the accumulation of autophagic features that suggests a role of Vmp1 in macroautophagy. In addition to these defects observed at the vegetative stage, the onset of multicellular development and early developmental gene expression are also compromised.

Carilla-Latorre, S., J. Calvo-Garrido, et al. (2008). "Dictyostelium transcriptional responses to Pseudomonas aeruginosa: common and specific effects from PAO1 and PA14 strains." BMC Microbiol 8: 109.
	BACKGROUND: Pseudomonas aeruginosa is one of the most relevant human opportunistic bacterial pathogens. Two strains (PAO1 and PA14) have been mainly used as models for studying virulence of P. aeruginosa. The strain PA14 is more virulent than PAO1 in a wide range of hosts including insects, nematodes and plants. Whereas some of the differences might be attributable to concerted action of determinants encoded in pathogenicity islands present in the genome of PA14, a global analysis of the differential host responses to these P. aeruginosa strains has not been addressed. Little is known about the host response to infection with P. aeruginosa and whether or not the global host transcription is being affected as a defense mechanism or altered in the benefit of the pathogen. Since the social amoeba Dictyostelium discoideum is a suitable host to study virulence of P. aeruginosa and other pathogens, we used available genomic tools in this model system to study the transcriptional host response to P. aeruginosa infection. RESULTS: We have compared the virulence of the P. aeruginosa PAO1 and PA14 using D. discoideum and studied the transcriptional response of the amoeba upon infection. Our results showed that PA14 is more virulent in Dictyostelium than PA01using different plating assays. For studying the differential response of the host to infection by these model strains, D. discoideum cells were exposed to either P. aeruginosa PAO1 or P. aeruginosa PA14 (mixed with an excess of the non-pathogenic bacterium Klebsiella aerogenes as food supply) and after 4 hours, cellular RNA extracted. A three-way comparison was made using whole-genome D. discoideum microarrays between RNA samples from cells treated with the two different strains and control cells exposed only to K. aerogenes. The transcriptomic analyses have shown the existence of common and specific responses to infection. The expression of 364 genes changed in a similar way upon infection with one or another strain, whereas 169 genes were differentially regulated depending on whether the infecting strain was either P. aeruginosa PAO1 or PA14. Effects on metabolism, signalling, stress response and cell cycle can be inferred from the genes affected. CONCLUSION: Our results show that pathogenic Pseudomonas strains invoke both a common transcriptional response from Dictyostelium and a strain specific one, indicating that the infective process of bacterial pathogens can be strain-specific and is more complex than previously thought.

Catalano, A. and D. H. O'Day (2008). "Calmodulin-binding proteins in the model organism Dictyostelium: a complete & critical review." Cell. Signal. 20: 277-291.
	
Chamaraux, F., O. Ali, et al. (2008). "Physical model for membrane protrusions during spreading." Phys Biol 5(3): 036009 (036015 pages).
	During cell spreading onto a substrate, the kinetics of the contact area is an observable quantity. This paper is concerned with a physical approach to modeling this process in the case of ameboid motility where the membrane detaches itself from the underlying cytoskeleton at the leading edge. The physical model we propose is based on previous reports which highlight that membrane tension regulates cell spreading. Using a phenomenological feedback loop to mimic stress-dependent biochemistry, we show that the actin polymerization rate can be coupled to the stress which builds up at the margin of the contact area between the cell and the substrate. In the limit of small variation of membrane tension, we show that the actin polymerization rate can be written in a closed form. Our analysis defines characteristic lengths which depend on elastic properties of the membrane-cytoskeleton complex, such as the membrane-cytoskeleton interaction, and on molecular parameters, the rate of actin polymerization. We discuss our model in the case of axi-symmetric and non-axi-symmetric spreading and we compute the characteristic time scales as a function of fundamental elastic constants such as the strength of membrane-cytoskeleton adherence.

Charette, S. J. and P. Cosson (2008). "Altered composition and secretion of lysosome-derived compartments in Dictyostelium AP-3 mutant cells." Traffic 9: 588-596.
	
Chen, C., K. H. Seo, et al. (2008). "Crystallization and preliminary characterization of dihydropteridine reductase from Dictyostelium discoideum." Acta Crystallogr Sect F Struct Biol Cryst Commun 64(Pt 11): 1013-1015.
	Dihydropteridine reductase from Dictyostelium discoideum (dicDHPR) can produce D-threo-BH(4) [6R-(1'R,2'R)-5,6,7,8-tetrahydrobiopterin], a stereoisomer of L-erythro-BH(4), in the last step of tetrahydrobiopterin (BH(4)) recycling. In this reaction, DHPR uses NADH as a cofactor to reduce quinonoid dihydrobiopterin back to BH(4). To date, the enzyme has been purified to homogeneity from many sources. In this report, the dicDHPR-NAD complex has been crystallized using the hanging-drop vapour-diffusion method with PEG 3350 as a precipitant. Rectangular-shaped crystals were obtained. Crystals grew to maximum dimensions of 0.4 x 0.6 x 0.1 mm. The crystal belonged to space group P2(1), with unit-cell parameters a = 49.81, b = 129.90, c = 78.76 A, beta = 100.00 degrees , and contained four molecules in the asymmetric unit, forming two closely interacting dicDHPR-NAD dimers. Diffraction data were collected to 2.16 A resolution using synchrotron radiation. The crystal structure has been determined using the molecular-replacement method.

Chida, J., A. Amagai, et al. (2008). "Establishment of a new method for precisely determining the functions of individual mitochondrial genes, using Dictyostelium cells." BMC Genet 9: 25.
	BACKGROUND: Disruption of mitochondrial genes may become a powerful tool for elucidating precisely the functions of individual mitochondrial genes. However, it is generally difficult to manipulate genetically mitochondrial genes, because 1) a mitochondrion is surrounded by inner and outer membranes, and 2) there are a large number of mtDNA copies in a single cell. This is the reason why we tried to establish a novel method for disrupting a certain mitochondrial gene (rps4), using Dictyostelium cells. RESULTS: Here, we have developed a new method for specifically disrupting a mitochondrial gene (rps4 ; ribosomal protein subunit S4), by a combination of homologous recombination and delivery of an appropriate restriction endonuclease (SfoI) into mitochondria. First, mitochondrially targeted SfoI whose expression is under control of the tetracycline (Tet)-regulated gene expression system was introduced into cells heteroplasmic with respect to the rps4 gene. Then, the heteroplasmic cells were produced by homologous recombination by use of the construct in which the unique SfoI site and the 5'-half of the rps4 coding region were deleted not to be digested by SfoI, and therefore their mitochondria have both the wild-type mtDNA and the mutant mtDNA with the disrupted rps4 gene. In response to removal of Tet from growth medium, SfoI was selectively delivered into mitochondria and digested only the wild-type mtDNA but not the mutated rps4. Thus one can gain rps4-null cells with only the mutated mtDNA, under the Tet-minus condition. CONCLUSION: The mitochondrial gene-disruption method presented here must be widely useful for precisely determining the functions of individual mitochondrial genes. This is the first report to demonstrate complete and specific mitochondrial gene disruption.

Cho, J., J. S. King, et al. (2008). "Dephosphorylation of 2,3-bisphosphoglycerate by MIPP expands the regulatory capacity of the Rapoport-Luebering glycolytic shunt." Proc Natl Acad Sci U S A 105(16): 5998-6003.
	The Rapoport-Luebering glycolytic bypass comprises evolutionarily conserved reactions that generate and dephosphorylate 2,3-bisphosphoglycerate (2,3-BPG). For >30 years, these reactions have been considered the responsibility of a single enzyme, the 2,3-BPG synthase/2-phosphatase (BPGM). Here, we show that Dictyostelium, birds, and mammals contain an additional 2,3-BPG phosphatase that, unlike BPGM, removes the 3-phosphate. This discovery reveals that the glycolytic pathway can bypass the formation of 3-phosphoglycerate, which is a precursor for serine biosynthesis and an activator of AMP-activated protein kinase. Our 2,3-BPG phosphatase activity is encoded by the previously identified gene for multiple inositol polyphosphate phosphatase (MIPP1), which we now show to have dual substrate specificity. By genetically manipulating Mipp1 expression in Dictyostelium, we demonstrated that this enzyme provides physiologically relevant regulation of cellular 2,3-BPG content. Mammalian erythrocytes possess the highest content of 2,3-BPG, which controls oxygen binding to hemoglobin. We determined that total MIPP1 activity in erythrocytes at 37 degrees C is 0.6 mmol 2,3-BPG hydrolyzed per liter of cells per h, matching previously published estimates of the phosphatase activity of BPGM. MIPP1 is active at 4 degrees C, revealing a clinically significant contribution to 2,3-BPG loss during the storage of erythrocytes for transfusion. Hydrolysis of 2,3-BPG by human MIPP1 is sensitive to physiologic alkalosis; activity decreases 50% when pH rises from 7.0 to 7.4. This phenomenon provides a homeostatic mechanism for elevating 2,3-BPG levels, thereby enhancing oxygen release to tissues. Our data indicate greater biological significance of the Rapoport-Luebering shunt than previously considered.

Choe, J. M. (2008). AprA: An autocrine, secreted factor that represses cell proliferation in Dictyostelium discoideum. United States -- Texas, Rice University.
	Dictyostelium cells secrete factors during growth and starvation. AprA (autocrine proliferation repressor), a 60 kDa protein secreted as part of a 150 kDa protein complex, functions as a cell proliferation repressor. In the present study, we expressed recombinant AprA (rAprA) in bacteria. We found that rAprA is bioactive as a proliferation repressor and that rAprA binds to live Dictyostelium cells. rAprA, when added to the growth medium of wild-type and aprA - cells, slows the proliferation of these cells; however, rAprA does not slow the proliferation of crlA - or cfaD - cells. CrlA is a putative receptor, and CfaD is a protein secreted by cells. These findings indicated that rAprA needs CrlA and CfaD to act as a proliferation repressor. However, cells lacking CrlA bound rAprA with high affinity, suggesting that CrlA may not be the receptor for AprA. Thus, AprA binds to cell surface receptors in a signal transduction pathway that involves CrlA and CfaD to negatively regulate cell proliferation.

Choi, C. H., S. J. Park, et al. (2008). "Methylglyoxal accumulation by glutathione depletion leads to cell cycle arrest in Dictyostelium." Mol Microbiol 70(5): 1293-1304.
	Reduced glutathione (GSH) serves as a primary redox buffer and its depletion causes growth inhibition or apoptosis in many organisms. In Dictyostelium discoideum, the null mutant (gcsA(-)) of gcsA encoding gamma-glutamylcysteine synthetase shows growth arrest and developmental defect when GSH is depleted. To investigate the mechanism by which GSH depletion induces growth arrest, a proteomic analysis was performed and aldose reductase (AlrA) was identified as the most prominently induced protein in gcsA(-) cells. Induction of AlrA was dependent on GSH concentration and was repressed by GSH but not effectively by either the reducing agent such as dithiothreitol or overexpression of superoxide dismutase. Methylglyoxal (MG), a toxic alpha-ketoaldehyde, strongly induced alrA expression and AlrA catalysed MG reduction efficiently. The alrA knockdown gcsA(-) cells (gcsA(-)/alrA(as)) exhibited more decreased growth rate than gcsA(-) cells, whereas the gcsA(-) cells overexpressing alrA (gcsA(-)/alrA(oe)) showed the recovery of growth rate. Interestingly, intracellular MG levels were significantly augmented in gcsA(-)/alrA(as) cells compared with gcsA(-) cells following GSH depletion. By contrast, gcsA(-)/alrA(oe) cells showed repression of MG induction. Furthermore, MG treatment inhibited growth of wild-type KAx3 cells, inducing G1 phase arrest. Thus, our findings suggest that MG accumulated by GSH depletion inhibits cell growth in Dictyostelium.

Clemen, C. S., V. Rybakin, et al. (2008). "The coronin family of proteins." Subcell Biochem 48: 1-5.
	The coronins, first described in Dictyostelium discoideum in 1991, have meanwhile been detected in all eukaryotes except plants. They belong to the superfamily of WD40-repeat proteins and represent a large family of proteins, which are often involved in cytoskeletal functions. Phylogenetic studies clearly distinguish 12 subfamilies of which six exclusively occur in vertebrates. In the present book we have made a sincere attempt to provide a comprehensive overview on all aspects of coronin proteins including history, structure, subcellular localization and function in different organisms. In addition, we also included a general overview on the WD40 family of proteins and the structurally related Kelch family. The book should be of interest for scientists outside the field, but is more importantly intended as a fast and competent guide for newcomers as well as doctoral and postdoctoral scientists to coronin research in all its facets.

Colucci, A. M., B. Peracino, et al. (2008). "Dictyostelium discoideum as a model host for meningococcal pathogenesis." Med Sci Monit 14(7): BR134-140.
	BACKGROUND: The aim of the present study was to evaluate the possibility of studying meningococcal virulence in a new model organism, Dictyostelium discoideum, a haploid social soil amoeba that is an established host model for several human pathogens, leading to the discovery of novel virulence mechanisms. MATERIAL/METHODS: A number of virulent and hyper-virulent N. meningitidis strains, including isogenic encapsulated, unencapsulated, and lipooligosaccharide (LOS) outer core-defective derivatives, were used to test the ability of D. discoideum to internalize and grow in the presence of bacteria. Intracellular survival of the internalized bacteria was also monitored. RESULTS: Meningococci were internalized and killed by D. discoideum cells. The presence of a capsule did not affect the internalization, but, as in human cells, it increased the resistance of the internalized bacteria. Although both encapsulated and unencapsulated meningococci supported the growth and development of D. discoideum on an agar surface, in liquid medium the encapsulated strains were toxic to the slime mould cells. Toxicity inversely correlated with meningococcal survival in the assay medium that was not favorable to bacterial replication, suggesting that it may be due to some toxic compound released after bacterial autolysis. Intriguingly, unencapsulated isogenic strains efficiently supported Dictyostelium growth in suspension, opening the possibility that the toxicity may be associated with the capsular polysaccharide. CONCLUSIONS: These results suggest that several meningococcal virulence determinants, such as the capsular polysaccharide, may be remarkably effective also in Dictyostelium cells, stimulating the use of this model host to search for novel meningococcal virulence determinants.

Cornillon, S., R. Froquet, et al. (2008). "Involvement of Sib proteins in the regulation of cellular adhesion in Dictyostelium discoideum." Euk Cell 7(9): 1600-1605.
	Molecular mechanisms ensuring cellular adhesion have been studied in detail in Dictyostelium amoebae, but little is known about the regulation of cellular adhesion in these cells. Here, we show that cellular adhesion is regulated in Dictyostelium, notably by the concentration of a cellular secreted factor accumulating in the medium. This constitutes a quorum-sensing mechanism allowing coordinated regulation of cellular adhesion in a Dictyostelium population. In order to understand the mechanism underlying this regulation, we analyzed the expression of recently identified Dictyostelium adhesion molecules (Sib proteins) that present features also found in mammalian integrins. sibA and sibC are both expressed in vegetative Dictyostelium cells, but the expression of sibC is repressed strongly in conditions where cellular adhesion decreases. Analysis of sibA and sibC mutant cells further suggests that variations in the expression levels of sibC account largely for changes in cellular adhesion in response to environmental cues.

Cosson, P. and T. Soldati (2008). "Eat, kill or die: when amoeba meets bacteria." Curr Opin Microbiol 11(3): 271-276.
	The core function of the innate immune response, phagocytosis, did not evolve first in metazoans but rather in primitive unicellular eukaryotes. Thus, though amoebae separated from the tree leading to metazoan shortly after the divergence of plants, they share many specific functions with mammalian phagocytic cells. Dictyostelium discoideum is by far the most studied amoeba, and it is proving useful to analyze phagocytosis and intracellular killing of bacteria. Since the basic mechanisms involved appear extremely conserved, Dictyostelium provides novel insights into the function of many new gene products. Bacterial pathogenicity was certainly largely developed to resist predatory amoebae in the environment, and this accounts for the fact that a large number of bacterial virulence traits can be studied using Dictyostelium as a host. This provides a particularly powerful system to analyze the complex interactions between pathogenic bacteria and host cells, where both the Dictyostelium host and the bacteria can be manipulated genetically with relative ease.

Crawley, S. W. and G. P. Cote (2008). "Determinants for substrate phosphorylation by Dictyostelium myosin II heavy chain kinases A and B and eukaryotic elongation factor-2 kinase." Biochim Biophys Acta 1784(6): 908-915.
	The alpha kinases are a widespread family of atypical protein kinases characterized by a novel type of catalytic domain. In this paper the peptide substrate recognition motifs for three alpha kinases, Dictyostelium discoideum myosin heavy chain kinase (MHCK) A and MHCK B and mammalian eukaryotic elongation factor-2 kinase (eEF-2K), were characterized by incorporating amino acid substitutions into a previously identified MHCK A peptide substrate (YAYDTRYRR) (Luo X. et al. (2001) J. Biol. Chem. 276, 17836-43). A lysine or arginine in the P+1 position on the C-terminal side of the phosphoacceptor threonine (P site) was found to be critical for peptide substrate recognition by MHCK A, MHCK B and eEF-2K. Phosphorylation by MHCK B was further enhanced 8-fold by a basic residue in the P+2 position whereas phosphorylation by MHCK A was enhanced 2- to 4-fold by basic residues in the P+2, P+3 and P+4 positions. eEF-2K required basic residues in both the P+1 and P+3 positions to recognize peptide substrates. eEF-2K, like MHCK A and MHCK B, exhibited a strong preference for threonine as the phosphoacceptor amino acid. In contrast, the Dictyostelium VwkA and mammalian TRPM7 alpha kinases phosphorylated both threonine and serine residues. The results, together with a phylogenetic analysis of the alpha kinase catalytic domain, support the view that the metazoan eEF-2Ks and the Dictyostelium MHCKs form a distinct subgroup of alpha kinases with conserved properties.

Croce, J. C. and D. R. McClay (2008). "Evolution of the Wnt pathways." Meth Mol Biol 469: 3-18.
	Wnt proteins mediate the transduction of at least three major signaling pathways that play central roles in many early and late developmental decisions. They control diverse cellular behaviors, such as cell fate decisions, proliferation, and migration, and are involved in many important embryological events, including axis specification, gastrulation, and limb, heart, or neural development. The three major Wnt pathways are activated by ligands, the Wnts, which clearly belong to the same gene family. However, their signal is then mediated by three separate sets of extracellular, cytoplasmic, and nuclear components that are pathway-specific and that distinguish each of them. Homologs of the Wnt genes and of the Wnt pathways components have been discovered in many eukaryotic model systems and functional investigations have been carried out for most of them. This review extracts available data on the Wnt pathways, from the protist Dictyostelium discoideum to humans, and provides from an evolutionary prospective the overall molecular and functional conservation of the three Wnt pathways and their activators throughout the eukaryotic superkingdom.

Dalous, J., E. Burghardt, et al. (2008). "Reversal of cell polarity and actin-myosin cytoskeleton reorganization under mechanical and chemical stimulation." Biophys. J. 94: 1063-1074.
	
Davila Lopez, M. and T. Samuelsson (2008). "Early evolution of histone mRNA 3' end processing." Rna 14: 1-10.
	
de Felipe, K. S., R. T. Glover, et al. (2008). "Legionella eukaryotic-like type IV substrates interfere with organelle trafficking." PLoS Pathog 4(8): e1000117.
	Legionella pneumophila, the causative agent of Legionnaires' disease, evades phago-lysosome fusion in mammalian and protozoan hosts to create a suitable niche for intracellular replication. To modulate vesicle trafficking pathways, L. pneumophila translocates effector proteins into eukaryotic cells through a Type IVB macro-molecular transport system called the Icm-Dot system. In this study, we employed a fluorescence-based translocation assay to show that 33 previously identified Legionella eukaryotic-like genes (leg) encode substrates of the Icm-Dot secretion system. To assess which of these proteins may contribute to the disruption of vesicle trafficking, we expressed each gene in yeast and looked for phenotypes related to vacuolar protein sorting. We found that LegC3-GFP and LegC7/YlfA-GFP caused the mis-secretion of CPY-Invertase, a fusion protein normally restricted to the yeast vacuole. We also found that LegC7/YlfA-GFP and its paralog LegC2/YlfB-GFP formed large structures around the yeast vacuole while LegC3-GFP localized to the plasma membrane and a fragmented vacuole. In mammalian cells, LegC2/YlfB-GFP and LegC7/YlfA-GFP were found within large structures that co-localized with anti-KDEL antibodies but excluded the lysosomal marker LAMP-1, similar to what is observed in Legionella-containing vacuoles. LegC3-GFP, in contrast, was observed as smaller structures which had no obvious co-localization with KDEL or LAMP-1. Finally, LegC3-GFP caused the accumulation of many endosome-like structures containing undigested material when expressed in the protozoan host Dictyostelium discoideum. Our results demonstrate that multiple Leg proteins are Icm/Dot-dependent substrates and that LegC3, LegC7/YlfA, and LegC2/YlfB may contribute to the intracellular trafficking of L. pneumophila by interfering with highly conserved pathways that modulate vesicle maturation.

de Keijzer, S., A. Serge, et al. (2008). "A spatially restricted increase in receptor mobility is involved in directional sensing during Dictyostelium discoideum chemotaxis." J Cell Sci 121(Pt 10): 1750-1757.
	The directed cell migration towards a chemotactic source, chemotaxis, involves three complex and interrelated processes: directional sensing, cell polarization and motility. Directional sensing allows migrating eukaryotic cells to chemotax in extremely shallow gradients (<2% across the cell body) of the chemoattractant. Although directional sensing has been observed as spatially restricted responses along the plasma membrane, our understanding of the ;compass' of the cell that controls the gradient-induced translocation of proteins during chemotactic movements is still largely lacking. Until now, the dynamical behaviour and mobility of the chemoattractant-receptor molecule has been neglected in models describing the directional sensing mechanisms. Here, we show by single-molecule microscopy an agonist-induced increase in the mobile fraction of cAMP-receptor at the leading edge of chemotacting Dictyostelium discoideum cells. The onset of receptor mobility was correlated to the uncoupling and activation of the Galpha2-protein. A finite-element simulation showed that the increase in mobile fraction of the activated receptor enabled the amplified generation of activated Gbetagamma-dimers at the leading edge of the cell, faithfully representing a primary linear amplification step in directional sensing. We propose here that modulation of the receptor mobility is directly involved in directional sensing and provides a new mechanistic basis for the primary amplification step in current theoretical models that describe directional sensing.

Delanoe-Ayari, H., S. Iwaya, et al. (2008). "Changes in the magnitude and distribution of forces at different Dictyostelium developmental stages." Cell Motil. Cytoskel. 65: 314-331.
	
Deponte, M. (2008). "Programmed cell death in protists." Biochim Biophys Acta 1783(7): 1396-1405.
	Programmed cell death in protists does not seem to make sense at first sight. However, apoptotic markers in unicellular organisms have been observed in all but one of the six/eight major groups of eukaryotes suggesting an ancient evolutionary origin of this regulated process. This review summarizes the available data on apoptotic markers in non-opisthokonts and elucidates potential functions and evolution of programmed cell death. A newly discovered family of caspase-like proteases, the metacaspases, is considered to exert the function of caspases in unicellular organisms. Important results on metacaspases. however. showed that they cannot be always correlated to the measured proteolytic activity during protist cell death. Thus, a major challenge for apoptosis research in a variety of protists remains the identification of the molecular cell death machinery. (C) 2008 Elsevier B.V. All rights reserved.

Dieckmann, R., N. Gopaldass, et al. (2008). "Monitoring time-dependent maturation changes in purified phagosomes from Dictyostelium discoideum." Meth Mol Biol 445: 327-337.
	The amoeba Dictyostelium discoideum is an established model to study phagocytosis. The sequence of events leading to the internalization and degradation of a particle is conserved in D. discoideum compared to metazoan cells. As its small haploid genome has been sequenced, it is now amenable to genome-wide analysis including organelle proteomics. Therefore, we adapted to Dictyostelium the classical protocol to purify phagosomes formed by ingestion of latex beads particles. The pulse-chase protocol detailed here gives easy access to pure, intact, and synchronized phagosomes from representative stages of the entire process of phagosome maturation. Recently, this protocol was used to generate individual temporal profiles of proteins and lipids during phagosome maturation generating a proteomic fingerprint of six maturation stages (1). In addition, immunolabeling of phagosomes on a coverslip was developed to visualize and quantitate antigen distribution at the level of individual phagosomes.

Du, F., K. Edwards, et al. (2008). "Regulation of contractile vacuole formation and activity in Dictyostelium." EMBO J 27(15): 2064-2076.
	The contractile vacuole (CV) system is the osmoregulatory organelle required for survival for many free-living cells under hypotonic conditions. We identified a new CV regulator, Disgorgin, a TBC-domain-containing protein, which translocates to the CV membrane at the late stage of CV charging and regulates CV-plasma membrane fusion and discharging. disgorgin(-) cells produce large CVs due to impaired CV-plasma membrane fusion. Disgorgin is a specific GAP for Rab8A-GTP, which also localizes to the CV and whose hydrolysis is required for discharging. We demonstrate that Drainin, a previously identified TBC-domain-containing protein, lies upstream from Disgorgin in this pathway. Unlike Disgorgin, Drainin lacks GAP activity but functions as a Rab11A effector. The BEACH family proteins LvsA and LvsD were identified in a suppressor/enhancer screen of the disgorgin(-) large CV phenotype and demonstrated to have distinct functions in regulating CV formation. Our studies help define the pathways controlling CV function.

Duran, M. B. (2008). PaxB, an orthologue of mammalian paxillin, regulates adhesion, differentiation, and morphogenesis in Dictyostelium discoideum. United States -- New York, City University of New York.
	The adhesion of cells to other cells and to the surrounding extracellular matrix is essential for survival, proliferation, differentiation and migration. Focal adhesions, sites where cells are adhered to their substratum, are also important components for tissue formation and wound repair. As in animal cells, such adhesion is critical for the development of the eukaryote Dictyostelium discoideum . In fact, D. discoideum development displays many of the features of animal embryogenesis such as regulated cell-cell adhesion, cell motility and cell morphogenesis. D. discoideum live as individual cells under vegetative conditions, but develop into a multicellular organism under starvation. Cell-cell adhesion is a vital factor for D. disciodeum morphogenesis and is required for multicellular development past the aggregation stage. As in animals, D. discoideum cell adhesion molecules have a mechanical function and may interact with the signal-transduction processes regulating morphogenesis. One regulator protein, PaxB, is an orthologue of mammalian paxillin, a known focal adhesion molecule. Paxillin functions as a docking site on the plasma membrane for signaling and structural proteins, and has been found to play a role in cell-cell cohesion as well as cell-substrate adhesion. To gain a better understanding of the role and regulation of paxillin, we studied the role of D. disciodeum PaxB in differentiation and development. In particular we describe the effects of PaxB overexpression in adhesion and cell-type differentiation. PaxB overexpressing cells (PaxBOE) exhibit increased cell-cell cohesion in non-nutrient buffer, which is lost when Ca 2+ is chelated by EDTA. This suggests adhesion mediated by PaxB is calcium dependent. Interestingly, cells overexpressing paxB are less adhesive to the substratum under equivalent conditions. We show PaxB undergoes serine phosphorylation. In addition, PaxB undergoes adhesion-dependent tyrosine and serine phosphorylation, which is also Ca 2+ dependent. PaxBOE cells can aggregate and form mounds, but subsequent morphogenesis is blocked. This block can be rescued by addition of wild-type cells, indicating a non-cell autonomous role for PaxB. In these chimeras, wild-type cells predominantly localize to the middle section of the spore mass, while PaxBOE cells preferentially are excluded from the spore mass. Taken together, the data suggest calcium dependent cell-substrate adhesion correlates with changes in PaxB tyrosine and serine phosphorylation. The data also imply that proper PaxB protein expression is required for development past the mound stage and for appropriate cell sorting, cell-type differentiation, cell-cell cohesion, and cell-substrate adhesion.

Elias, M. and M. Novotny (2008). "cpRAS: a novel circularly permuted RAS-like GTPase domain with a highly scattered phylogenetic distribution." Biol Direct 3: 21.
	A recent systematic survey suggested that the YRG (or YawG/YlqF) family with the G4-G5-G1-G2-G3 order of the conserved GTPase motifs represents the only possible circularly permuted variation of the canonical GTPase structure. Here we show that a different circularly permuted GTPase domain actually does exist, conforming to the pattern G3-G4-G5-G1-G2. The domain, dubbed cpRAS, is a variant of RAS family GTPases and occurs in two types of larger proteins, either inserted into a region homologous to a bacterial group of proteins classified as COG2373 and potentially related to the alpha-2-macroglobulin family (so far a single protein in Dictyostelium) or in combination with a von Willebrand factor type A (VWA) domain. For the latter protein type, which was found in a few metazoans and several distantly related protists, existence in the common ancestor of opisthokonts, Amoebozoa and excavates followed by at least eight independent losses may be inferred. Our findings thus bring further evidence for the importance of parallel reduction of ancestral complexity in the eukaryotic evolution.

Endres, R. G. and N. S. Wingreen (2008). "Accuracy of direct gradient sensing by single cells." Proc Natl Acad Sci U S A 105(41): 15749-15754.
	Many types of cells are able to accurately sense shallow gradients of chemicals across their diameters, allowing the cells to move toward or away from chemical sources. This chemotactic ability relies on the remarkable capacity of cells to infer gradients from particles randomly arriving at cell-surface receptors by diffusion. Whereas the physical limits of concentration sensing by cells have been explored, there is no theory for the physical limits of gradient sensing. Here, we derive such a theory, using as models a perfectly absorbing sphere and a perfectly monitoring sphere, which, respectively, infer gradients from the absorbed surface particle density or the positions of freely diffusing particles inside a spherical volume. We find that the perfectly absorbing sphere is superior to the perfectly monitoring sphere, both for concentration and gradient sensing, because previously observed particles are never remeasured. The superiority of the absorbing sphere helps explain the presence at the surfaces of cells of signal-degrading enzymes, such as PDE for cAMP in Dictyostelium discoideum (Dicty) and BAR1 for mating factor alpha in Saccharomyces cerevisiae (budding yeast). Quantitatively, our theory compares favorably with recent measurements of Dicty moving up a cAMP gradient, suggesting these cells operate near the physical limits of gradient detection.

Feasley, C. L., C. M. West, et al. (2008). N-Glycosylation of gp130 Implicated in Cell Interactions in Dictyostelium. Glycobiology.
	(145) N-Glycosylation of gp130 Implicated in Cell Interactions in Dictyostelium Christa L. Feasley1; Christopher M. West1; Catherine P. Chia2 1Oklahoma Center for Medical Glycobiology, OUHSC, Oklahoma City, OK; 2University of Nebraska–Lincoln, Lincoln, NE
A 130 kDa plasma membrane glycoprotein (gp130) has been implicated in cell-cell and cell-substratum interactions in the cellular slime mold Dictyostelium discoideum. gp130 is extensively N-glycosylated and probably GPI-anchored. Information about the N-glycans of gp130 may help in the assignment of molecular determinants of the cellular activities. The gp130 sequence predicts an 85 kDa polypeptide with 16 Nglycosylation sequons. SDS-PAGE of PNGase F-digested recombinant gp130 expressed as a soluble glycoprotein in Dictyostelium without its putative GPI anchor suggested a 23 kD shift. Glycosylation site mapping achieved by PNGase F and PNGase A digestion of gp130 tryptic peptides in H2(18)O and analysis by MALDI-TOF-TOF confirmed most of the predicted attachment sites, and most of these were detected in a HILICenriched glycopeptide pool. Monosaccharide compositional analysis demonstrated that gp130 contains only Nacetylglucosamine, mannose and smaller amounts of fucose. Permethylated N-glycans of gp130 were primarily of the N4H8 class, suggesting Man8-type glycans with intersecting and bisecting GlcNAc, as reported in previous biochemical studies and confirmed here using alpha-mannosidase. Low levels of other glycans with the composition N3H8, N2H8, and F1N4H8 were also present. Comparison with overall N-glycans present in vesicular glycoproteins, GPI-anchored glycoproteins, and membrane glycoproteins, showed that these pools have complex yet distinct profiles. gp130 expresses a simple subset of these Nglycans, which correlates with unique properties of gp130 in cell interactions.

Franck, C., W. Ip, et al. (2008). "Contact-mediated cell-assisted cell proliferation in a model eukaryotic single-cell organism: an explanation for the lag phase in shaken cell culture." Phys Rev E Stat Nonlin Soft Matter Phys 77(4 Pt 1): 041905-041901 till 041905-041908.
	In cell culture, when cells are inoculated into fresh media, there can be a period of slow (or lag phase) growth followed by a transition to exponential growth. This period of slow growth is usually attributed to the cells' adaptation to a new environment. However, we argue that, based on observations of shaken suspension culture of Dictyostelium discoideum, a model single-cell eukaryote, this transition is due to a density effect. Attempts to demonstrate the existence of implicit cell signaling via long-range diffusible messengers (i.e., soluble growth factors) through cell-medium separation and microfluidic flow perturbation experiments produced negative results. This, in turn, led to the development of a signaling model based on direct cell-to-cell contacts. Employing a scaling argument for the collision rate due to fluid shear, we reasonably estimate the crossover density for the transition into the exponential phase and fit the observed growth kinetics.

Frasca, G., F. Raynaud, et al. (2008). "Linear patterning of magnetically labeled Dictyostelium cells to display confined development." J. Phys.: Condens. Matter 20: 204149 (204145 pages).
	In severe nutriment conditions, the social amoeba Dictyostelium discoideum enters a particular life cycle where it forms multicellular patterns to achieve aggregation. Extensively observed from an initial dispersed state, its developmental program can usefully be studied from a confined population to implement theoretical developments regarding biological self-organization. The challenge is then to form a cell assembly of well-defined geometrical dimensions without hindering cell behavior. To achieve this goal, we imposed transient constraints by applying temporary external magnetic gradients to trap magnetically labeled cells. Deposits of various numbers of cells were geometrically characterized for different magnetic exposure conditions. We demonstrated that the cell deposit was organized as a three-dimensional (3D) structure by both stacking layers of cells and extending these layers in the substrate plane. This structure evolves during the aggregation phase, forming periodic aggregative centers along the linear initial pattern.

Froquet, R., N. Cherix, et al. (2008). "Control of cellular physiology by tm9 proteins in yeast and Dictyostelium." J. Biol. Chem. 283: 6764-6772.
	
Galardi-Castilla, M., B. Pergolizzi, et al. (2008). "SrfB, a member of the Serum Response Factor family of transcription factors, regulates starvation response and early development in Dictyostelium." Dev Biol 316(2): 260-274.
	The Serum Response Factor (SRF) is an important regulator of cell proliferation and differentiation. Dictyostelium discoideum srfB gene codes for an SRF homologue and is expressed in vegetative cells and during development under the control of three alternative promoters, which show different cell-type specific patterns of expression. The two more proximal promoters directed gene transcription in prestalk AB, stalk and lower-cup cells. The generation of a strain where the srfB gene has been interrupted (srfB(-)) has shown that this gene is required for regulation of actin-cytoskeleton-related functions, such as cytokinesis and macropinocytosis. The mutant failed to develop well in suspension, but could be rescued by cAMP pulsing, suggesting a defect in cAMP signaling. srfB(-) cells showed impaired chemotaxis to cAMP and defective lateral pseudopodium inhibition. Nevertheless, srfB(-) cells aggregated on agar plates and nitrocellulose filters 2 h earlier than wild type cells, and completed development, showing an increased tendency to form slug structures. Analysis of wild type and srfB(-) strains detected significant differences in the regulation of gene expression upon starvation. Genes coding for lysosomal and ribosomal proteins, developmentally-regulated genes, and some genes coding for proteins involved in cytoskeleton regulation were deregulated during the first stages of development.

Garcia, G. L. and C. A. Parent (2008). "Signal relay during chemotaxis." J Microsc 231(3): 529-534.
	The ability of cells to migrate in response to external cues, a process known as chemotaxis, is a fundamental phenomenon in biology. It is exhibited by a wide variety of cell types in the context of embryogenesis, angiogenesis, inflammation, wound healing and many other complex physiological processes. Here, we discuss the signals that control the directed migration of the social amoebae Dictyostelium discoideum both as single cells and in the context of group migration. This multi-cellular organism has served as an excellent model system to decipher amoeboid-like leukocyte migration and has played a key role in establishing signalling paradigms in the chemotaxis field. We envision that Dictyostelium will continue to bring forward basic knowledge as we seek to understand the mechanisms regulating group cell migration.

Gaudet, P., J. G. Williams, et al. (2008). "An anatomy ontology to represent biological knowledge in Dictyostelium discoideum." BMC Genomics 9: 130.
	BACKGROUND: Dictyostelium discoideum is a model system for studying many important physiological processes including chemotaxis, phagocytosis, and signal transduction. The recent sequencing of the genome has revealed the presence of over 12,500 protein-coding genes. The model organism database dictyBase hosts the genome sequence as well as a large amount of manually curated information. RESULTS: We present here an anatomy ontology for Dictyostelium based upon the life cycle of the organism. CONCLUSION: Anatomy ontologies are necessary to annotate species-specific events such as phenotypes, and the Dictyostelium anatomy ontology provides an essential tool for curation of the Dictyostelium genome.

Geberth, D. and M. T. Hutt (2008). "Predicting spiral wave patterns from cell properties in a model of biological self-organization." Phys Rev E Stat Nonlin Soft Matter Phys 78(3 Pt 1): 031917.
	In many biological systems, biological variability (i.e., systematic differences between the system components) can be expected to outrank statistical fluctuations in the shaping of self-organized patterns. In principle, the distribution of single-element properties should thus allow predicting features of such patterns. For a mathematical model of a paradigmatic and well-studied pattern formation process, spiral waves of cAMP signaling in colonies of the slime mold Dictyostelium discoideum, we explore this possibility and observe a pronounced anticorrelation between spiral waves and cell properties (namely, the firing rate) and particularly a clustering of spiral wave tips in regions devoid of spontaneously firing (pacemaker) cells. Furthermore, we observe local inhomogeneities in the distribution of spiral chiralities, again induced by the pacemaker distribution. We show that these findings can be explained by a simple geometrical model of spiral wave generation.

Ghosh, R., A. Chhabra, et al. (2008). "Dissecting the functional role of polyketide synthases in Dictyostelium discoideum: biosynthesis of the differentiation regulating factor 4-methyl-5-pentylbenzene-1,3-diol." J Biol Chem 283(17): 11348-11354.
	Dictyostelium discoideum exhibits the largest repository of polyketide synthase (PKS) proteins of all known genomes. However, the functional relevance of these proteins in the biology of this organism remains largely obscure. On the basis of computational, biochemical, and gene expression studies, we propose that the multifunctional Dictyostelium PKS (DiPKS) protein DiPKS1 could be involved in the biosynthesis of the differentiation regulating factor 4-methyl-5-pentylbenzene-1,3-diol (MPBD). Our cell-free reconstitution studies of a novel acyl carrier protein Type III PKS didomain from DiPKS1 revealed a crucial role of protein-protein interactions in determining the final biosynthetic product. Whereas the Type III PKS domain by itself primarily produces acyl pyrones, the presence of the interacting acyl carrier protein domain modulates the catalytic activity to produce the alkyl resorcinol scaffold of MPBD. Furthermore, we have characterized an O-methyltransferase (OMT12) from Dictyostelium with the capability to modify this resorcinol ring to synthesize a variant of MPBD. We propose that such a modification in vivo could in fact provide subtle variations in biological function and specificity. In addition, we have performed systematic computational analysis of 45 multidomain PKSs, which revealed several unique features in DiPKS proteins. Our studies provide a new perspective in understanding mechanisms by which metabolic diversity could be generated by combining existing functional scaffolds.

Giorgione, J. and M. Clarke (2008). "Heterogeneous modes of uptake for latex beads revealed through live cell imaging of phagocytes expressing a probe for phosphatidylinositol-(3,4,5)-trisphosphate and phosphatidylinositol-(3,4)-bisphosphate." Cell Motil Cytoskeleton 65(9): 721-733.
	Latex beads are the preferred phagocytic substrate in biochemical studies of phagosome composition and maturation. Using living Dictyostelium cells and fluorescent probes, we compared the properties of phagosomes formed to ingest latex beads or digestible prey. Significant differences were found during the initial steps of phagocytosis. During uptake of bacteria or yeast, PHcrac-GFP, a probe that binds to membranes enriched in PI(3,4,5)P(3) and PI(3,4)P(2), always labeled the nascent phagosome and faded shortly after it sealed. However, labeling of bead-containing phagosomes was highly variable. Beads were engulfed by phagosomes either lacking or displaying the PHcrac-GFP label, and that label, if present, often persisted for many minutes, revealing that early trafficking steps for bead-containing phagosomes are quite heterogeneous. Later stages of the endocytic pathway appeared more similar for phagosomes containing prey and latex beads. Both types of phagosomes fused with acidic endosomes while undergoing transport along microtubules, both acquired the V-ATPase and lost it prior to exocytosis, and both bound the late endosome marker vacuolin B, which was transferred to the plasma membrane upon exocytosis. We conclude that caution is needed in extrapolating results from latex bead phagosomes to phagosomes containing physiological substances, especially in early stages of the endocytic pathway.

Giusti, C., A. Kosta, et al. (2008). "Analysis of autophagic and necrotic cell death in Dictyostelium." Meth Enzymol 446: 1-15.
	Non-apoptotic cell death types can be conveniently studied in Dictyostelium discoideum, an exceptionally favorable model not only because of its well-known genetic and experimental advantages, but also because in Dictyostelium there is no apoptosis machinery that could interfere with non-apoptotic cell death. We show here how to conveniently demonstrate, assess, and study these non-apoptotic cell death types. These can be generated by use of modifications of the monolayer technique of Rob Kay et al., and either wild-type HMX44A Dictyostelium cells, leading to autophagic cell death, or the corresponding atg1- autophagy gene mutant cells, leading to necrotic cell death. Methods to follow these non-apoptotic cell death types qualitatively and quantitatively will be reported.

Giusti, C., E. Tresse, et al. (2008). "Autophagic cell death: analysis in Dictyostelium." Biochim Biophys Acta 1793(9): 1422-1431.
	Autophagic cell death (ACD) can be operationally described as cell death with an autophagic component. While most molecular bases of this autophagic component are known, in ACD the mechanism of cell death proper is not well defined, in particular because in animal cells there is poor experimental distinction between what triggers autophagy and what triggers ACD. Perhaps as a consequence, it is often thought that in animal cells a little autophagy is protective while a lot is destructive and leads to ACD, thus that the shift from autophagy to ACD is quantitative. The aim of this article is to review current knowledge on ACD in Dictyostelium, a very favorable model, with emphasis on (1) the qualitative, not quantitative nature of the shift from autophagy to ACD, in contrast to the above, and (2) random or targeted mutations of in particular the following genes: iplA (IP3R), TalB (talinB), DcsA (cellulose synthase), GbfA, ugpB, glcS (glycogen synthase) and atg1. These mutations allowed the genetic dissection of ACD features, dissociating in particular vacuolisation from cell death.

Glockner, G., G. Golderer, et al. (2008). "A first glimpse at the transcriptome of Physarum polycephalum." BMC Genomics 9: 6.
	BACKGROUND: Physarum polycephalum, an acellular plasmodial species belongs to the amoebozoa, a major branch in eukaryote evolution. Its complex life cycle and rich cell biology is reflected in more than 2500 publications on various aspects of its biochemistry, developmental biology, cytoskeleton, and cell motility. It now can be genetically manipulated, opening up the possibility of targeted functional analysis in this organism. METHODS: Here we describe a large fraction of the transcribed genes by sequencing a cDNA library from the plasmodial stage of the developmental cycle. RESULTS: In addition to the genes for the basic metabolism we found an unexpected large number of genes involved in sophisticated signaling networks and identified potential receptors for environmental signals such as light. In accordance with the various developmental options of the plasmodial cell we found that many P. polycephalum genes are alternatively spliced. Using 30 donor and 30 acceptor sites we determined the splicing signatures of this species.Comparisons to various other organisms including Dictyostelium, the closest relative, revealed that roughly half of the transcribed genes have no detectable counterpart, thus potentially defining species specific adaptations. On the other hand, we found highly conserved proteins, which are maintained in the metazoan lineage, but absent in D. discoideum or plants. These genes arose possibly in the last common ancestor of Amoebozoa and Metazoa but were lost in D. discoideum. CONCLUSION: This work provides an analysis of up to half of the protein coding genes of Physarum polycephalum. The definition of splice motifs together with the description of alternatively spliced genes will provide a valuable resource for the ongoing genome project.

Gonzalez-Kristeller, D. C., L. Farage, et al. (2008). "The p450 oxidoreductase, RedA, controls development beyond the mound stage in Dictyostelium discoideum." BMC Dev. Biol. 8:8: 10 pages.
	
Gosset, G., M. Satre, et al. (2008). "Investigation of subcellular acidic compartments using alpha-aminophosphonate 31P nuclear magnetic resonance probes." Anal Biochem 380(2): 184-194.
	The 31P nuclear magnetic resonance (NMR) characteristics, toxicity, and cellular penetration of five linear or cyclic alpha-aminophosphonate highly sensitive pH probes were investigated in Dictyostelium discoideum cells and isolated rat hearts and were compared with three phosphonic acid derivatives. The line width broadening at pH approximately pK(a), which was satisfactorily modelized for all compounds, was significantly limited in biological milieu for the new markers, affording a four- to sixfold better accuracy in pH determination. Cellular uptake or washout of nontoxic concentrations (< 15 mM) of alpha-aminophosphonates occurred by rapid passive permeation, whereas standard probes required a much slower fluid-phase pinocytosis and transport processes that could ultimately lead to trapping. Using mild concentrations (< 4 mM) three alpha-aminophosphonates having 6 < pK(a) < 7 allowed an easy and simultaneous 31P NMR determination of cytosolic, acidic, and extracellular compartments in anoxic-reoxygenated or starving D. discoideum.

Grunt, M., V. Zarsky, et al. (2008). "Roots of angiosperm formins: the evolutionary history of plant FH2 domain-containing proteins." BMC Evol Biol 8: 115.
	BACKGROUND: Shuffling of modular protein domains is an important source of evolutionary innovation. Formins are a family of actin-organizing proteins that share a conserved FH2 domain but their overall domain architecture differs dramatically between opisthokonts (metazoans and fungi) and plants. We performed a phylogenomic analysis of formins in most eukaryotic kingdoms, aiming to reconstruct an evolutionary scenario that may have produced the current diversity of domain combinations with focus on the origin of the angiosperm formin architectures. RESULTS: The Rho GTPase-binding domain (GBD/FH3) reported from opisthokont and Dictyostelium formins was found in all lineages except plants, suggesting its ancestral character. Instead, mosses and vascular plants possess the two formin classes known from angiosperms: membrane-anchored Class I formins and Class II formins carrying a PTEN-like domain. PTEN-related domains were found also in stramenopile formins, where they have been probably acquired independently rather than by horizontal transfer, following a burst of domain rearrangements in the chromalveolate lineage. A novel RhoGAP-related domain was identified in some algal, moss and lycophyte (but not angiosperm) formins that define a specific branch (Class III) of the formin family. CONCLUSION: We propose a scenario where formins underwent multiple domain rearrangements in several eukaryotic lineages, especially plants and chromalveolates. In plants this replaced GBD/FH3 by a probably inactive RhoGAP-like domain, preserving a formin-mediated association between (membrane-anchored) Rho GTPases and the actin cytoskeleton. Subsequent amplification of formin genes, possibly coincident with the expansion of plants to dry land, was followed by acquisition of alternative membrane attachment mechanisms present in extant Class I and Class II formins, allowing later loss of the RhoGAP-like domain-containing formins in angiosperms.

Gruver, J. S., J. P. Wikswo, et al. (2008). "3'-phosphoinositides regulate the coordination of speed and accuracy during chemotaxis." Biophys J 95(8): 4057-4067.
	The PI3K/PTEN pathway, as the regulator of 3'-phosphoinositide (3'-PI) dynamics, has emerged as a key regulator of chemoattractant gradient sensing during chemotaxis in Dictyostelium and other cell types. Previous results have shown 3'-PIs to be important for regulating basal cell motility and sensing the direction and strength of the chemoattractant gradient. We examined the chemotaxis of wild-type cells and cells lacking PTEN or PI3K1 and 2 using analytical methods that allowed us to quantitatively discern differences between the genotype's ability to sense and efficiently respond to changes in gradient steepness during chemotaxis. We found that cells are capable of increasing their chemotactic accuracy and speed as they approach a micropipette in a manner that is dependent on the increasing strength of the concentration gradient and 3'-PI signaling. Further, our data show that 3'-PI signaling affects a cell's ability to coordinate speed and direction to increase chemotactic efficiency. Using to our knowledge a new measurement of chemotactic efficiency that reveals the degree of coordination between speed and accuracy, we found that cells also have the capacity to increase their chemotactic efficiency as they approach the micropipette. Like directional accuracy and speed, the increase in chemotactic efficiency of cells with increased gradient strength is sensitive to 3'-PI dysregulation. Our evidence suggests that receptor-driven 3'-PI signaling regulates the ability of a cell to capitalize on stronger directional inputs and minimize the effects of inaccurate turns to increase chemotactic efficiency.

Gyimesi, M., B. Kintses, et al. (2008). "The mechanism of the reverse recovery-step, phosphate release, and actin activation of Dictyostelium myosin II." J. Biol. Chem. 283: 8153-8163.
	
Gyimesi, M., A. K. Tsaturyan, et al. (2008). "Kinetic characterization of the function of myosin loop 4 in the actin-myosin interaction." Biochemistry 47: 283-291.
	
Harris, M. J. and H. J. Woo (2008). "Energetics of subdomain movements and fluorescence probe solvation environment change in ATP-bound myosin." Eur Biophys J 38(1): 1-12.
	Energetics of conformational changes experienced by an ATP-bound myosin head detached from actin was studied by all-atom explicit water umbrella sampling simulations. The statistics of coupling between large scale domain movements and smaller scale structural features were examined, including the closing of the ATP binding pocket, and a number of key hydrogen bond formations shown to play roles in structural and biochemical studies. The statistics for the ATP binding pocket open/close transition show an evolution of the relative stability from the open state in the early stages of the recovery stroke to the stable closed state after the stroke. The change in solvation environment of the fluorescence probe Trp507 (scallop numbering; 501 in Dictyostelium discoideum) indicates that the probe faithfully reflects the closing of the binding pocket as previously shown in experimental studies, while being directly coupled to roughly the early half of the overall large scale conformational change of the converter domain rotation. The free energy change of this solvation environment change, in particular, is -1.3 kcal/mol, in close agreement with experimental estimates. In addition, our results provide direct molecular level data allowing for interpretations of the fluorescence experiments of myosin conformational change in terms of the de-solvation of Trp side chain.

Harwood, A. J. (2008). "Use of the Dictyostelium stalk cell assay to monitor GSK-3 regulation." Meth Mol Biol 469: 39-43.
	GSK-3 activity mediates cAMP repression of stalk induction of cells in low-density monolayer culture. The lower the GSK-3 activity the greater the percentage of stalk cells formed. This protocol describes a robust and quantitative method utilizing an adapted stalk cell monolayer assay to measure GSK-3 activation.

Harwood, A. J. (2008). "Monitoring patterns of gene expression in Dictyostelium by beta-galacosidase staining." Meth Mol Biol 469: 33-37.
	Monitoring the spatial distribution of prespore and pstB cell types is a sensitive method to monitor GSK-3 and Aar activity during Dictyostelium development. Cell-specific expression of lacZ marker genes can be readily detected using enzymatic cleavage of the substrate X-gal. This protocol describes a simple method for beta-galactosidase staining in developed Dictyostelium structures.

Harwood, A. J. (2008). "Dictyostelium development: a prototypic Wnt pathway?" Meth Mol Biol 469: 21-32.
	Although Wnt signaling is ubiquitous within the animal phylogenetic group, it is unclear how it evolved. Genes related to the components of Wnt pathway are found in other eukaryotes and one of the most studied of these non-metazoan organisms is the social amoeba Dictyostelium discoideum. This organism contains the enzyme GSK-3 and a beta -catenin homolog, Aardvark (Aar). Both are required to regulate pattern formation during multi-cellular stages of Dictyostelium development. Aar is also required for formation of adherens junctions, as seen in animals. Finally, analysis of the completed Dictyostelium genome shows there to be 16 Frizzled (Fz) gene homologs. This chapter discusses Dictyostelium development and the role of these proteins.

He, X. L. and Y. Li (2008). "A new species of Dictyostelium." Mycotaxon 106: 379-383.
	
Heath, R. J. and R. H. Insall (2008). "Dictyostelium MEGAPs: F-BAR domain proteins that regulate motility and membrane tubulation in contractile vacuoles." J Cell Sci 121(Pt 7): 1054-1064.
	PCH family proteins are fundamentally important proteins, linking membrane curvature events with cytoskeletal reorganisation. One group, the MEGAPs (also called srGAPs and WRPs) contain RhoGAP domains in addition to the F-BAR domain. We disrupted MEGAP1 and MEGAP2 in Dictyostelium both singly and in combination. We found a strong cytoskeletal phenotype in MEGAP1(-) cells and a subtle phototaxis defect in MEGAP2(-) slugs. MEGAP1(-)/2(-) cells have an overabundance of filopodia and slug motility and function are affected. The most dramatic changes, however, are on contractile vacuoles. MEGAP1(-)/2(-) cells empty their contractile vacuoles less efficiently than normal and consequently have three times the usual number. GFP-tagged MEGAP1 localises to tubules of the contractile vacuole network and when vacuoles start to empty they recruit cytosolic GFP-MEGAP1. Mutants in the Saccharomyces homologues RGD1 and RGD2 also show abnormal vacuoles, implying that this role is conserved. Thus, MEGAP is an important regulator of the contractile vacuole network, and we propose that tubulation of the contractile vacuole by MEGAP1 represents a novel mechanism for driving vacuole emptying.

Heidel, A. J. and G. Glockner (2008). "Mitochondrial genome evolution in the social amoebae." Mol Biol Evol 25(7): 1440-1450.
	Most mitochondria contain a core set of genes required for mitochondrial function, but beyond this base there are variable genomic features. The mitochondrial genome of the model species Dictyostelium discoideum demonstrated that the social amoebae mitochondrial genomes have a size between those of metazoans and plants, but no comparative study of social amoebae mitochondria has been performed. Here, we present a comparative analysis of social amoebae mitochondrial genomes using D. discoideum, Dictyostelium citrinum, Dictyostelium fasciculatum, and Polysphondylium pallidum. The social amoebae mitochondria have similar sizes, AT content, gene content and have a high level of synteny except for one segmental rearrangement and extensive displacement of tRNAs. From the species that contain the rearrangement, it can be concluded that the event occurred late in the evolution of social amoebae. A phylogeny using 36 mitochondrial genes produced a well-supported tree suggesting that the pairs of D. discoideum/D. citrinum and D. fasciculatum/P. pallidum are sister species although the position of the root is not certain. Group I introns and endonucleases are variable in number and location in the social amoebae. Phylogenies of the introns and endonucleases suggest that there have been multiple recent duplications or extinctions and confirm that endonucleases have the ability to insert into new areas. An analysis of dN/dS ratios in mitochondrial genes revealed that among groups of genes, adenosine triphosphate synthase complex genes have the highest ratio, whereas cytochrome oxidase and nicotinamide adenine dinucleotide (NADH) dehydrogenase genes had the lowest ratio. The genetic codes of D. citrinum, P. pallidum, and D. fasciculatum are the universal code although D. fasciculatum does not use the TGA stop codon. In D. fasciculatum, we demonstrate for the first time that a mitochondrial genome without the TGA stop codon still uses the release factor RF2 that recognizes TGA. Theories of how the genetic code can change and why RF2 may be a constraint against switching codes are discussed.

Heinrich, D., S. Youssef, et al. (2008). "Actin-cytoskeleton dynamics in non-monotonic cell spreading." Cell Adh Migr 2(2): 58-68.
	The spreading of motile cells on a substrate surface is accompanied by reorganization of their actin network. We show that spreading in the highly motile cells of Dictyostelium is non-monotonic, and thus differs from the passage of spreading cells through a regular series of stages. Quantification of the gain and loss of contact area revealed fluctuating forces of protrusion and retraction that dominate the interaction of Dictyostelium cells with a substrate. The molecular basis of these fluctuations is elucidated by dual-fluorescence labeling of filamentous actin together with proteins that highlight specific activities in the actin system. Front-to-tail polarity is established by the sorting out of myosin-II from regions where dense actin assemblies are accumulating. Myosin-IB identifies protruding front regions, and the Arp2/3 complex localizes to lamellipodia protruded from the fronts. Coronin is used as a sensitive indicator of actin disassembly to visualize the delicate balance of polymerization and depolymerization in spreading cells. Short-lived actin patches that co-localize with clathrin suggest that membrane internalization occurs even when the substrate-attached cell surface expands. We conclude that non-monotonic cell spreading is characterized by spatiotemporal patterns formed by motor proteins together with regulatory proteins that either promote or terminate actin polymerization on the scale of seconds.

Helmick, L., A. Antunez de Mayolo, et al. (2008). "Spatiotemporal response of living cell structures in Dictyostelium discoideum with semiconductor quantum dots." Nano Lett 8(5): 1303-1308.
	The ability to monitor the spatial and temporal organization of molecules such as biopolymers within a cell is essential to enable the ability to understand the complexity and dynamics existing in biological processes. However, many limitations currently exist in specifically labeling proteins in living cells. In our study, we incorporate nanometer-sized semiconductor quantum dots (QDs) into living cells for spatiotemporal protein imaging of actin polymers in Dictyostelium discoideum without the necessity of using complicating transmembrane transport approaches. We first demonstrate cytoplasmic distribution of QDs within these living amoebae cells and then show molecular targeting through actin filament labeling. Also, we have developed a microfluidic system to control and visualize the spatiotemporal response of the cellular environment during cell motility, which allows us to demonstrate specific localization control of the QD-protein complexes in living cells. This study provides a valuable tool for the specific targeting and analysis of proteins within Dictyostelium without the encumbrance of transmembrane assisted methods, which has implication in fields including polymer physics, material science, engineering, and biology.

Hickman, M. R. (2008). Ligand-stimulated internalization of a Dictyostelium discoideum G protein-coupled cAMP receptor. United States -- Texas, The University of Texas Graduate School of Biomedical Sciences at Houston.
	The social amoeba, Dictyostelium discoideum , undergoes a remarkable starvation-induced program of development that transforms a population of unicellular amoebae into a fruiting body composed of resistant spores suspended on a stalk. During this development, secreted cAMP drives chemotaxis of the amoebae, leading to their aggregation, and subsequent differentiation and morphogenesis. Four sequentially expressed G protein-coupled receptors (GPCRs) for cAMP play critical roles in this process. The first of these, cAR1, is essential for aggregation as it mediates chemotaxis as well as the propagation of secreted cAMP waves throughout aggregating populations. Ligand-induced internalization has been shown to regulate a variety of GPCRs. However, little was known at the outset of this study about the role of internalization in the regulation of cAR1 function or, for that matter, in developmental systems in general. For this study, cAMP-induced cAR1 internalization was assessed by measuring (1) the reduction of cell surface binding sites for [ 3 H]cAMP and (2) the redistribution of YFP-tagged receptors to the cell's interior, cAMP was found to induce little or no loss of ligand binding (LLB) in vegetative cells. However, the ability to induce LLB increased progressively over the initial 6 hrs of development, reaching <70% in cells undergoing aggregation. Despite these reductions in surface binding, detectable cAR1-YFP redistribution could be induced by cAMP only after the cells reached the mound stage (10 hrs) and was found to occur naturally by the ensuing slug stage (18 hrs). Site-directed substitution of a cluster of 5 serines in the receptor's cytoplasmic tail that was previously shown to be the principal site of cAMP-induced cAR1 phosphorylation impaired both LLB and receptor redistribution and furthermore resulted in mound-stage developmental arrest, suggesting that phosphorylation of cAR1 is a prerequisite for its internalization and that cAR1 internalization is required for post-aggregative development. To assess the involvement of clathrin mediated endocytosis, Dictyostelium cells lacking the clathrin light chain gene ( clc- ) or either of two dynamin genes were examined and found to be defective in LLB and, in the case of clc- cells, also cAR1 redistribution and turnover. Furthermore, cAR1 overexpression in clc- cells (like the serine mutant in wild-type cells) promoted developmental arrest in mounds. The mound-arrest phenotype was also recapitulated in a wild-type background by the specific expression of cAR1 in prestalk cells (but not prespore cells), suggesting that development depends critically on internalization and clearance of cAR1 from these cells. Persistent cAR1 expression following aggregation was found to be associated with aberrant expression of prestalk and prespore genes, which may adversely affect development in the prestalk cell lineage. The PI3 kinase-TORC2 signal transduction pathway, known to be important for Dictyostelium chemotaxis and internalization of yeast pheromone receptors, was examined using chemical inhibitors and null cells and found to be necessary for cAR1 internalization. In conclusion, cAR1 was shown to be similar to other GPCRs in that its internalization depends on phosphorylation of cytoplasmic domain serines, utilizes clathrin and dynamin, and involves the TORC2 complex. In addition, the findings presented here that cAR1 internalization is both developmentally regulated and required for normal development represent a novel regulatory paradigm that might pertain to other GPCRs known to play important roles in the development of humans and other metazoans.

Hilgardt, C., J. Cejkova, et al. (2008). "Streamless aggregation of Dictyostelium in the presence of isopropylidenadenosin." Biophys. Chem. 132: 9-17.
	
Hirata, K., A. Amagai, et al. (2008). "Involvements of a novel protein, Dia2, in cAMP signaling and spore differentiation during Dictyostelium development." Differentiation 76: 310-322.
	
Hooley, P., M. P. Whitehead, et al. (2008). "Eukaryote polyphosphate kinases: is the 'Kornberg' complex ubiquitous?" Trends Biochem Sci 33(12): 577-582.
	Polyphosphate (poly P) is a polymer of up to several hundred phosphate residues and is important to a variety of cell processes. The main poly P synthetic enzyme in many bacteria is poly P kinase 1 (PPK1), which until recently had been detected among eukaryotes in some protists only. There is now evidence for the presence in several other eukaryotes of PPK1 homologues and also a second bacteria-type enzyme, PPK2. The latest genome databases reveal that the 'Kornberg' enzyme complex of three actin-related proteins, termed DdPPK2 in Dictyostelium discoideum, might also be ubiquitous in eukaryotes. Owing to the intimate association of poly P synthesis with the formation of structural fibres, this ubiquity indicates a central role for this molecule in the evolution of eukaryotic cells.

Hounslow, A. M., J. Carran, et al. (2008). "Determination of the microscopic equilibrium dissociation constants for risedronate and its analogues reveals two distinct roles for the nitrogen atom in nitrogen-containing bisphosphonate drugs." J Med Chem 51(14): 4170-4178.
	Microscopic equilibrium dissociation constants, k as, were determined for four nitrogen-containing bisphosphonates (N-BP): risedronate and its analogues 2-(2-aminophenyl)-1-hydroxyethylidene-1,1-bisphosphonate, NE 11807, and NE 97220. The proportion of each and of analogues 2-(3'-( N-ethyl)pyridinium)-ethylidenebisphosphonate and 2-(3-piperinidyl)-1-hydroxyethylidene-1,1-bisphosphonate, having a positively charged nitrogen and three negative charges on the bisphosphonate group ("carbocation analogue") at pH 7.5, was calculated. When set in order of increasing potency at inhibiting farnesyl diphosphate (FDP) synthase (their intracellular target), the N-BPs are also ranked in order of decreasing mole fraction of carbocation analogue. However, only a weak correlation exists between potency for inhibiting FDP synthase and potency for inhibiting Dictyostelium discoideum growth. It is concluded that, although high potency for inhibiting FDP synthase is favored when the nitrogen atom in a N-BP is uncharged, N-BPs having a positively charged nitrogen can still be potent inhibitors of Dictyostelium growth owing to favorable interaction with a second, unidentified target.

Hwang, J. and H. Hagiwara (2008). "Effect of mono- and bicyclic monoterpenoids upon Dictyostelium minutum and Dictyostelium macrocephalum." J. Essential Oil Res. (JEOR) 20: 91-95.
	
Iglesias, P. A. and P. N. Devreotes (2008). "Navigating through models of chemotaxis." Curr Op Cell Biol 20(1): 35-40.
	Chemotaxis in eukaryotic cells involves the coordination of several related but separable processes: motility, polarization, and gradient sensing. Mathematical models that have been proposed to explain chemotaxis typically focus on only one of these processes. We summarize the strengths and weaknesses of the models and point out the need for an integrated model.

Isik, N., J. A. Brzostowski, et al. (2008). "An Elmo-like protein associated with myosin II restricts spurious F-actin events to coordinate phagocytosis and chemotaxis." Dev Cell 15(4): 590-602.
	Elmo proteins positively regulate actin polymerization during cell migration and phagocytosis through activation of the small G protein Rac. We identified an Elmo-like protein, ElmoA, in Dictyostelium discoideum that unexpectedly functions as a negative regulator of actin polymerization. Cells lacking ElmoA display an elevated rate of phagocytosis, increased pseudopod formation, and excessive F-actin localization within pseudopods. ElmoA associates with cortical actin and myosin II. TIRF microscopic observations of functional ElmoA-GFP reveal that a fraction of ElmoA localizes near the presumptive actin/myosin II cortex and the levels of ElmoA and myosin II negatively correlate with that of polymerizing F-actin. F-actin-regulated dynamic dispersions of ElmoA and myosin II are interdependent. Taken together, our data suggest that ElmoA modulates actin/myosin II at the cortex to prevent excessive F-actin polymerization around the cell periphery, thereby maintaining proper cell shape during phagocytosis and chemotaxis.

Iwadate, Y. and S. Yumura (2008). "Molecular dynamics and forces of a motile cell simultaneously visualized by TIRF and force microscopies." Biotechniques 44(6): 739-750.
	Cells must exert traction forces onto the substratum for continuous migration. Molecular dynamics such as actin polymerization at the front of the cell and myosin II accumulation at the rear should play important roles in the exertion of forces required for migration. Therefore, it is important to reveal the relationships between the traction forces and molecular dynamics. Traction forces can be calculated from the deformation of the elastic substratum under a migrating cell. A transparent and colorless elastic substratum with a high refractive index (1.40) and a low Young's modulus (1.0 kPa) were made from a pair of platinum-catalyzed silicones. We used this substratum to develop a new method for simultaneous recording of molecular dynamics and traction forces under a migrating cell in which total internal refractive fluorescence (TIRF) and force microscopies were combined. This new method allows the detection of the spatiotemporal distribution of traction forces produced by individual filopodia in migrating Dictyostelium cells, as well as simultaneous visualization of these traction forces and the dynamics of filamentous myosin II.

Iwadate, Y. and S. Yumura (2008). "Actin-based propulsive forces and myosin-II-based contractile forces in migrating Dictyostelium cells." J Cell Sci 121(Pt 8): 1314-1324.
	It has been suggested that myosin II exerts traction forces at the posterior ends and retracting pseudopodia of migrating cells, but there is no direct evidence. Here, using a combination of total internal reflection fluorescence (TIRF) microscopy and force microscopy with a high spatial resolution of approximately 400 nm, we simultaneously recorded GFP-myosin II dynamics and traction forces under migrating Dictyostelium cells. Accumulation of filamentous myosin II and a subsequent increase in traction forces were detected in pseudopodia just before retraction. In the case of motorless myosin II, traction forces did not increase after accumulation, suggesting that the source of the retraction force is the motor activity of accumulated myosin II. Simultaneous recording of F-actin and traction forces revealed that traction forces were exerted under spot-like regions where F-actin accumulated. Cells migrated in a direction counter to the sum of the force vectors exerted at each spot, suggesting that the stress spots act as scaffolds to transmit the propulsive forces at the leading edge generated by actin polymerization.

Iwai, S. and T. Q. Uyeda (2008). "Visualizing myosin-actin interaction with a genetically-encoded fluorescent strain sensor." Proc Natl Acad Sci U S A 105(44): 16882-16887.
	Many proteins have been shown to undergo conformational changes in response to externally applied force in vitro, but whether the force-induced protein conformational changes occur in vivo remains unclear. To reveal the force-induced conformational changes, or strains, within proteins in living cells, we have developed a genetically encoded fluorescent "strain sensor," by combining the proximity imaging (PRIM) technique, which uses spectral changes of 2 GFP molecules that are in direct contact, and myosin-actin as a model system. The developed PRIM-based strain sensor module (PriSSM) consists of the tandem fusion of a normal and circularly permuted GFP. To apply strain to PriSSM, it was inserted between 2 motor domains of Dictyostelium myosin II. In the absence of strain, the 2 GFP moieties in PriSSM are in contact, whereas when the motor domains are bound to F-actin, PriSSM has a strained conformation, leading to the loss of contact and a concomitant spectral change. Using the sensor system, we found that the position of the lever arm in the rigor state was affected by mutations within the motor domain. Moreover, the sensor was used to visualize the interaction between myosin II and F-actin in Dictyostelium cells. In normal cells, myosin was largely detached from F-actin, whereas ATP depletion or hyperosmotic stress increased the fraction of myosin bound to F-actin. The PRIM-based strain sensor may provide a general approach for studying force-induced protein conformational changes in cells.

Jack, C. N., J. G. Ridgeway, et al. (2008). "Segregate or cooperate- a study of the interaction between two species of Dictyostelium." BMC Evol Biol 8: 293.
	BACKGROUND: A major challenge for evolutionary biology is explaining altruism, particularly when it involves death of one party and occurs across species. Chimeric fruiting bodies of Dictyostelium discoideum and Dictyostelium purpureum develop from formerly independent amoebae, and some die to help others. Here we examine co-aggregation between D. discoideum and D. purpureum, determine its frequency and which party benefits, and the extent of fair play in contribution to the altruistic caste. RESULTS: We mixed cells from both species in equal proportions, and then we analyzed 198 individual fruiting bodies, which always had either a D. discoideum or D. purpureum phenotype (D. discoideum- 98, D. purpureum- 100). Fifty percent of the fruiting bodies that looked like D. discoideum and 22% of the fruiting bodies that looked like D. purpureum were chimeric, though the majority of spores in any given fruiting body belonged to one species (D. discoideum fruiting bodies- 0.85 +/- 0.03, D. purpureum fruiting bodies- 0.94 +/- 0.02). Clearly, there is species level recognition occurring that keeps the cells mostly separate. The number of fruiting bodies produced with the D. discoideum phenotype increased from 225 +/- 32 fruiting bodies when D. discoideum was alone to 486 +/- 61 in the mix treatments. However, the number of D. discoideum spores decreased, although not significantly, from 2.75e7 +/- 1.29e7 spores in the controls to 2.06e7 +/- 8.33e6 spores in the mix treatments. D. purpureum fruiting body and spore production decreased from 719 +/- 111 fruiting bodies and 5.81e7 +/- 1.26e7 spores in the controls to 394 +/- 111 fruiting bodies and 9.75e6 +/- 2.25e6 spores in the mix treatments. CONCLUSION: Both species appear to favor clonality but can cooperate with each other to produce fruiting bodies. Cooperating amoebae are able to make larger fruiting bodies, which are advantageous for migration and dispersal, but both species here suffer a cost in producing fewer spores per fruiting body.

Janetopoulos, C. and R. A. Firtel (2008). "Directional sensing during chemotaxis." FEBS Lett 582(14): 2075-2085.
	Cells have the innate ability to sense and move towards a variety of chemoattractants. We investigate the pathways by which cells sense and respond to chemoattractant gradients. We focus on the model system Dictyostelium and compare our understanding of chemotaxis in this system with recent advances made using neutrophils and other mammalian cell types, which share many molecular components and signaling pathways with Dictyostelium. This review also examines models that have been proposed to explain how cells are able to respond to small differences in ligand concentrations between the anterior leading edge and posterior of the cell. In addition, we highlight the overlapping functions of many signaling components in diverse processes beyond chemotaxis, including random cell motility and cell division.

Jang, W. and R. H. Gomer (2008). "Combining experiments and modelling to understand size regulation in Dictyostelium discoideum." J R Soc Interface 5 Suppl 1: S49-58.
	Little is known about how the sizes of specific organs and tissues are regulated. To try to understand these mechanisms, we have been using a combination of modelling and experiments to study the simple system Dictyostelium discoideum, which forms approximately 20000 cell groups. We found that cells secrete a factor, and as the number of cells increases, the concentration of the factor increases. Diffusion calculations indicated that this lets cells sense the local cell density. Computer simulations predicted, and experiments then showed, that this factor decreases cell-cell adhesion and increases random cell motility. In a group, adhesion forces keep cells together, while random motility forces cause cells to pull apart and separate from each other. As the group size increases above a threshold, the factor concentration goes above a threshold and the cells switch from an adhered state to a separated state. This causes excessively large groups to break apart and/or dissipate, creating an upper limit to group size. In this review, we focus on how computer simulations made testable predictions that led the way to understanding the size regulation mechanism mediated by this factor.

Jeong, S. Y., I. K. Kim, et al. (2008). Structural and biochemical characteristics of thioredoxin reductase from Dictyostelium discoideum. FEBS J.
	Introduction: Thioredoxin reductase (Trr) belongs to a flavoprotein
family of pyridine nucleotide-disulfide oxidoreductase. Trr catalyses the
transfer of the reducing equivalent from NADPH via FAD to the
redox-active disulfide, which then can reduce oxidized thioredoxin. The
reduced thioredoxin serves as an electron donor for the reduction of
disulfide bonds in various proteins.
Methods: Trr and Trr mutants were overexpressed and purified in
Escherichia coli. Biochemical properties of Trr were analyzed by sitedirected
mutagenesis, spectral analysis and X-ray crystallography.
Results: The crystal structure of Trr revealed that the redox-active
disulfide formed between Cys-144 and Cys-147 was juxtaposed to the
isoalloxazine ring of FAD. The mutation at Cys-144 or Cys-147
resulted in complete loss of thioredoxin-reducing activity and changed
spectral properties. Regardless of the presence of NADPH, C144S and
C144A mutant showed the spectral characteristic of the reduced flavin.
In contrast, C147S mutant retained the feature of the oxidized flavin
even with NADPH and showed the strong fluorescence quenching,
indicating that C147S is restricted to the FO conformation.
Conclusions: Our results indicate Dictyostelium discoideum Trr undergoes
the FO/FR conformational change for its catalysis and the point
mutation at each active site cysteine affects the conformational equilibrium.
Also Dictyostelium Trr and its mutants in cysteine are expected
as a model to elucidate the mechanism of the transition between the
FO and FR conformation of thioredoxin reductase.

Jin, T., X. H. Xu, et al. (2008). "Chemotaxis, chemokine receptors and human disease." Cytokine 44(1): 1-8.
	Cell migration is involved in diverse physiological processes including embryogenesis, immunity, and diseases such as cancer and chronic inflammatory disease. The movement of many cell types is directed by extracellular gradients of diffusible chemicals. This phenomenon, referred to as "chemotaxis", was first described in 1888 by Leber who observed the movement of leukocytes toward sites of inflammation. We now know that a large family of small proteins, chemokines, serves as the extracellular signals and a family of G-protein-coupled receptors (GPCRs), chemokine receptors, detects gradients of chemokines and guides cell movement in vivo. Currently, we still know little about the molecular machineries that control chemokine gradient sensing and migration of immune cells. Fortunately, the molecular mechanisms that control these fundamental aspects of chemotaxis appear to be evolutionarily conserved, and studies in lower eukaryotic model systems have allowed us to form concepts, uncover molecular components, develop new techniques, and test models of chemotaxis. These studies have helped our current understanding of this complicated cell behavior. In this review, we wish to mention landmark discoveries in the chemotaxis research field that shaped our current understanding of this fundamental cell behavior and Jay out key questions that remain to be addressed in the future. Published by Elsevier Ltd.

Joseph, J. M., P. Fey, et al. (2008). "The actinome of Dictyostelium discoideum in comparison to actins and actin-related proteins from other organisms." PLoS One 3(7): e2654.
	Actin belongs to the most abundant proteins in eukaryotic cells which harbor usually many conventional actin isoforms as well as actin-related proteins (Arps). To get an overview over the sometimes confusing multitude of actins and Arps, we analyzed the Dictyostelium discoideum actinome in detail and compared it with the genomes from other model organisms. The D. discoideum actinome comprises 41 actins and actin-related proteins. The genome contains 17 actin genes which most likely arose from consecutive gene duplications, are all active, in some cases developmentally regulated and coding for identical proteins (Act8-group). According to published data, the actin fraction in a D. discoideum cell consists of more than 95% of these Act8-type proteins. The other 16 actin isoforms contain a conventional actin motif profile as well but differ in their protein sequences. Seven actin genes are potential pseudogenes. A homology search of the human genome using the most typical D. discoideum actin (Act8) as query sequence finds the major actin isoforms such as cytoplasmic beta-actin as best hit. This suggests that the Act8-group represents a nearly perfect actin throughout evolution. Interestingly, limited data from D. fasciculatum, a more ancient member among the social amoebae, show different relationships between conventional actins. The Act8-type isoform is most conserved throughout evolution. Modeling of the putative structures suggests that the majority of the actin-related proteins is functionally unrelated to canonical actin. The data suggest that the other actin variants are not necessary for the cytoskeleton itself but rather regulators of its dynamical features or subunits in larger protein complexes.

Jurkowski, T. P., M. Meusburger, et al. (2008). "Human DNMT2 methylates tRNA(Asp) molecules using a DNA methyltransferase-like catalytic mechanism." RNA 14(8): 1663-1670.
	Although their amino acid sequences and structure closely resemble DNA methyltransferases, Dnmt2 proteins were recently shown by Goll and colleagues to function as RNA methyltransferases transferring a methyl group to the C5 position of C38 in tRNA(Asp). We observe that human DNMT2 methylates tRNA isolated from Dnmt2 knock-out Drosophila melanogaster and Dictyostelium discoideum. RNA extracted from wild type D. melanogaster was methylated to a lower degree, but in the case of Dictyostelium, there was no difference in the methylation of RNA isolated from wild-type and Dnmt2 knock-out strains. Methylation of in vitro transcribed tRNA(Asp) confirms it to be a target of DNMT2. Using site directed mutagenesis, we show here that the enzyme has a DNA methyltransferase-like mechanism, because similar residues from motifs IV, VI, and VIII are involved in catalysis as identified in DNA methyltransferases. In addition, exchange of C292, which is located in a CFT motif conserved among Dnmt2 proteins, strongly reduced the catalytic activity of DNMT2. Dnmt2 represents the first example of an RNA methyltransferase using a DNA methyltransferase type of mechanism.

Kamimura, Y., Y. Xiong, et al. (2008). "PIP3-independent activation of TorC2 and PKB at the cell's leading edge mediates chemotaxis." Curr Biol 18(14): 1034-1043.
	BACKGROUND: Studies show that high phosphotidylinositol 3,4,5-trisphosphate (PIP(3)) promotes cytoskeletal rearrangements and alters cell motility and chemotaxis, possibly through activation of protein kinase Bs (PKBs). However, chemotaxis can still occur in the absence of PIP(3), and the identities of the PIP(3)-independent pathways remain unknown. RESULTS: Here, we outline a PIP(3)-independent pathway linking temporal and spatial activation of PKBs by Tor complex 2 (TorC2) to the chemotactic response. Within seconds of stimulating Dictyostelium cells with chemoattractant, two PKB homologs, PKBA and PKBR1, mediate transient phosphorylation of at least eight proteins, including Talin, PI4P 5-kinase, two Ras GEFs, and a RhoGap. Surprisingly, all of the substrates are phosphorylated with normal kinetics in cells lacking PI 3-kinase activity. Cells deficient in TorC2 or PKB activity show reduced phosphorylation of the endogenous substrates and are impaired in chemotaxis. The PKBs are activated through phosphorylation of their hydrophobic motifs via TorC2 and subsequent phosphorylation of their activation loops. These chemoattractant-inducible events are restricted to the cell's leading edge even in the absence of PIP(3). Activation of TorC2 depends on heterotrimeric G protein function and intermediate G proteins, including Ras GTPases. CONCLUSIONS: The data lead to a model where cytosolic TorC2, encountering locally activated small G protein(s) at the leading edge of the cell, becomes activated and phosphorylates PKBs. These in turn phosphorylate a series of signaling and cytoskeletal proteins, thereby regulating directed migration.

Kastner, P. M., M. Schleicher, et al. (2008). Cytokinesis in Dictyostelium discoideum is regulated by a SIN-related pathway. ASCB 47th int. meeting, Washington, DC.
	meeting abstract

Katayama, T. and H. Yasukawa (2008). "Analysis of Sir2E in the cellular slime mold Dictyostelium discoideum: cellular localization, spatial expression and overexpression." Dev Growth Differ 50(8): 645-652.
	It has been reported that Dictyostelium discoideum encodes four silent information regulator 2 (Sir2) proteins (Sir2A-D) showing sequence similarity to human homologues of Sir2 (SIRT1-3). Further screening in a database revealed that D. discoideum encodes an additional Sir2 homologue (Sir2E). The amino acid sequence of Sir2E is not similar to those of SIRTs but is similar to those of proteins encoded by Giardia lamblia, Cryptosporidium hominis and Cryptosporidium parvum. Fluorescence of Sir2E-green fluorescent protein fusion protein was detected in the D. discoideum nucleus, indicating that Sir2E is a nuclear localizing protein. Reverse transcription-polymerase chain reaction and whole-mount in situ hybridization analyses showed that D. discoideum expressed sir2E in amoebae in the growth phase and in prestalk cells in the developmental phase. D. discoideum overexpressing sir2E grew faster than the wild type. These results indicate that Sir2E plays important roles both in the growth phase and developmental phase of D. discoideum.

Katayama, T. and H. Yasukawa (2008). "Developmental and spatial expression of sir2 genes in the cellular slime mold Dictyostelium discoideum." Microbes and Environments 23(1): 40-43.
	The cellular slime mold Dictyostelium discoideum grows as unicellular free-living amoebae in the presence of nutrients. Upon starvation, the amoebae aggregate and form multicellular structures that each consist of a stalk and spores. D. discoideum encodes at least four proteins (Sir2A, Sir2B, Sir2C, and Sir2D) homologous to human SIRT. RT-PCR and WISH analyses showed that the genes for Sir2A, Sir2C, and Sir2D were expressed at high levels in growing cells but at decreased levels in developing cells, whereas the gene encoding Sir2B was expressed in the prestalk-cell region in the developmental phase.

Kawakami, S. and H. Hagiwara (2008). "Polysphondylium multicystogenum sp. nov., a new dictyostelid species from Sierra Leone, West Africa." Mycologia 100(2): 347-351.
	Polysphondylium multicystogenum, a new heterothallic species of dictyostelids, is described based on three isolates collected from soils in Sierra Leone, West Africa. This species is characterized by sorophores with a combination of clavate base and ovoid to oblong tip cell, smaller spores and abundant microcyst production under the usual culture conditions for sorocarp formation at 20 C. This is the first report of Polysphondylium producing such abundant microcysts.

Kawakami, S. and H. Hagiwara (2008). "A taxonomic revision of two dictyostelid species, Polysphondylium pallidum and P. album." Mycologia 100(1): 111-121.
	To reevaluate two dictyostelid species, namely, Polysphondylium pallidum and P. album, 92 isolates of the P. pallidum complex from their type localities were examined based on mating relationships and morphological characteristics. In the mating tests three heterothallic mating groups were found among the isolates. They also were different morphologically from each other. These results suggested that they belonged to distinct taxa. By comparison of the three mating groups with the type specimens of P. pallidum and P. album, two of them were identified as P. pallidum and P. album. Based on the examined isolates P. pallidum and P. album were redescribed in detail.

Kay, R. R., P. Langridge, et al. (2008). "Changing directions in the study of chemotaxis." Nature Reviews Molecular Cell Biology 9(6): 455-463.
	Chemotaxis-the guided movement of cells in chemical gradients-probably first emerged in our single-celled ancestors and even today is recognizably similar in neutrophils and amoebae. Chemotaxis enables immune cells to reach sites of infection, allows wounds to heal and is crucial for forming embryonic patterns. Furthermore, the manipulation of chemotaxis may help to alleviate disease states, including the metastasis of cancer cells. This review discusses recent results concerning how cells orientate in chemotactic gradients and the role of phosphatidylinositol-3,4,5-trisphosphate, what produces the force for projecting pseudopodia and a new role for the endocytic cycle in movement.

Keener, M. E. (2008). Studies of the actin binding activity of Dictyostelium discoideum myosin II heavy chain kinase A. United States -- North Carolina, The University of North Carolina at Greensboro.
	Dictyostelium discoideum is a primitive, eukaryotic organism that relies on myosin II and actin contraction for cytokinesis, migration, and other important cellular processes. In order for contraction to occur, myosin II monomers must first assemble into bipolar filaments. In Dictyostelium, bipolar filament assembly is negatively regulated by myosin heavy chain (MHC) phosphorylation. Three kinases have been shown to catalyze MHC phosphorylation (MHCK-A, -B, -C), driving myosin II disassembly. Of the three, MHCK-A is the most extensively studied. Structurally, MHCK-A is comprised of three functional domains: an N-terminal coiled coil region (CC), a catalytic domain, and a WD repeat domain. The CC domain has been shown, in vitro, to bind and bundle actin filaments and inhibit myosin II binding to F-actin. The studies described in this thesis focus on two aims: (1) to understand the role of the CC domain in reorganizing myosin II and actin within the cell and (2) to determine if intramolecular interactions between the CC and WD repeat domains within the MHCK-A molecule are involved in regulating the kinase's activity. To address the first aim, the Triton Cytoskeleton Ghost Isolation Assay was conducted on Ax2, Ax2 + GFP-CC, Ax2 + GFP-C800A, MHK-A null, and MHK-A null + GFP-CC cell lines containing various truncations to determine the analyze the effects of over-expressing the CC domain on myosin II and F-actin organization within the cell. Complementary localization studies were also conducted involving Ax2 wild-type cells and GFP-tagged cells over-expressing the CC domain (GFP-CC) to visually determine myosin II and actin localization within the cell via confocal imaging. Results from the Triton cytoskeleton studies indicate that over-expression of the CC domain in the Ax2 cells leads to an increase in cytoskeletal myosin II. MHK-A null and MHK-A null cells over-expressing the CC domain showed a significant increase in cytoskeletal myosin II in comparison to the Ax2 cells. However, the CC domain had no apparent effect in the absence of endogenous MHCK-A as indicated by the relatively equal amounts of myosin II in both MHK-A null and MHK-null + GFP-CC pellet fractions. Ax2 + GFP-C800A cells exhibit essentially the same level of cytoskeletal myosin II compared to that of the Ax2 cells. Localization studies revealed increased amounts of cytoplasmically-localized myosin II aggregates in the Ax2 + GFP-CC cells in comparison to the Ax2 cells. Also, cells over-expressing the CC domain appear to have more cytoplasmic F-actin than the Ax2 cells. Furthermore, the actin appears to be more aggregated in the CC cells. To address the second aim, purified CC and GST-tagged WD repeat domains were subjected to a GST "pull-down" assay and Western blot to determine if an interaction between the domains exists. Results from these experiments revealed no interaction between the WD repeat and CC domains, evident by the absence of CC in the GST-WD bead-associated fraction. This study shows that the CC domain plays an integral role in reorganizing the actin-myosin cytoskeleton and that the mechanisms regulating the full-length kinase do not appear to be determined by WD repeat and CC domain interactions.

Keller, T. and C. R. Thompson (2008). "Cell type specificity of a diffusible inducer is determined by a GATA family transcription factor." Development 135(9): 1635-1645.
	One poorly understood mechanism of developmental patterning involves the intermingled differentiation of different cell types that then sort out to generate pattern. Examples of this are known in nematodes and vertebrates, and in Dictyostelium it is the major mechanism. However, a general problem with this mechanism is the possibility that different inducers are required for each cell type that arises independently of positional information. Consistent with this idea, in Dictyostelium the signalling molecule DIF acts as a position-independent signal and was thought only to regulate the differentiation of a single cell type (pstO). The results presented here challenge this idea. In a novel genetic selection to isolate genes required for DIF signal transduction, we found a mutant (dimC(-)) that is a hypomorphic allele of a GATA family transcription factor (gtaC). gtaC expression is directly regulated by DIF, and GtaC rapidly translocates to the nucleus in response to DIF. gtaC(-) null cells showed some hallmark DIF signalling defects. Surprisingly, other aspects of the mutant were distinct from those of other DIF signalling mutants, suggesting that gtaC regulates a subset of DIF responses. For example, pstO cell differentiation appeared normal. However, we found that pstB cells were mislocalised and the pstB-derived basal disc was much reduced or missing. These defects are due to a failure to respond to DIF as they are phenocopied in other DIF signalling mutants. These findings therefore identify a novel small-molecule-activated GATA factor that is required to regulate the cell type-specific effects of DIF. They also reveal that a non-positional signal can regulate the differentiation of multiple cell types through differential interpretation in receiving cells.

Kikuchi, H., S. Ishiko, et al. (2008). "Biological activities of novel derivatives of DIF-1 isolated from Dictyostelium." Biochem Biophys Res Commun 377(3): 1012-1017.
	The differentiation-inducing factor-1 (DIF-1) is a lipophilic signal molecule (chlorinated alkylphenone) that induces stalk cell differentiation in the cellular slime mold Dictyostelium discoideum. In addition, DIF-1 and its derivatives have been shown to possess anti-leukemic activity and glucose consumption-promoting activity in vitro in mammalian cells. In this study, to assess the chemical structure-effect relationship of DIF-1, we synthesized eight derivatives of DIF-1 and investigated their stalk cell-inducing activity in Dictyostelium cells and pharmacological activities in mammalian cells. Of the derivatives, two amide derivatives of DIF-1, whose hydrophobic indexes are close to that of DIF-1, induced stalk cell differentiation as strongly as DIF-1 in Dictyostelium cells. It was also found that some derivatives suppressed cell growth in human K562 leukemia cells and promoted glucose consumption in mouse 3T3-L1 cells. These results give us valuable information as to the chemical structure-effect relationship of DIF-1.

Kim, J., D. G. Bates, et al. (2008). "Evaluation of stochastic effects on biomolecular networks using the generalized Nyquist stability criterion." Ieee Transactions on Automatic Control 53(8): 1937-1941.
	Stochastic differential equations. are now commonly used to model biomolecular networks in systems biology, and much recent research has been devoted to the development of methods to analyse their stability properties. Stability analysis of such systems may be performed using the Laplace transform, which requires the calculation of the exponential matrix involving time symbolically. However, the calculation of the symbolic exponential matrix is not feasible for problems of even moderate size, as the required computation time increases exponentially with the matrix order. To address this issue, we present a novel method for approximating the Laplace transform which does not require the exponential matrix to be calculated explicitly. The calculation time associated with the proposed method does not increase exponentially with the size of the system, and the approximation error is shown to be of the same order as existing methods. Using this approximation method, we show how a straightforward application of the generalized Nyquist stability criterion provides necessary and sufficient conditions for the stability of stochastic biomolecular networks. The usefulness and computational efficiency of the proposed method is illustrated through its application to the problem of analysing a model for limit-cycle oscillations in cAMP during aggregation of Dictyostelium cells.

Kim, J., D. G. Bates, et al. (2008). "Linear time-varying models can reveal non-linear interactions of biomolecular regulatory networks using multiple time-series data." Bioinformatics 24(10): 1286-1292.
	MOTIVATION: Inherent non-linearities in biomolecular interactions make the identification of network interactions difficult. One of the principal problems is that all methods based on the use of linear time-invariant models will have fundamental limitations in their capability to infer certain non-linear network interactions. Another difficulty is the multiplicity of possible solutions, since, for a given dataset, there may be many different possible networks which generate the same time-series expression profiles. RESULTS: A novel algorithm for the inference of biomolecular interaction networks from temporal expression data is presented. Linear time-varying models, which can represent a much wider class of time-series data than linear time-invariant models, are employed in the algorithm. From time-series expression profiles, the model parameters are identified by solving a non-linear optimization problem. In order to systematically reduce the set of possible solutions for the optimization problem, a filtering process is performed using a phase-portrait analysis with random numerical perturbations. The proposed approach has the advantages of not requiring the system to be in a stable steady state, of using time-series profiles which have been generated by a single experiment, and of allowing non-linear network interactions to be identified. The ability of the proposed algorithm to correctly infer network interactions is illustrated by its application to three examples: a non-linear model for cAMP oscillations in Dictyostelium discoideum, the cell-cycle data for Saccharomyces cerevisiae and a large-scale non-linear model of a group of synchronized Dictyostelium cells. AVAILABILITY: The software used in this article is available from http://sbie.kaist.ac.kr/software

King, J. S. and R. H. Insall (2008). "Chemotaxis: TorC before you Akt." Curr Biol 18(18): R864-866.
	Chemotaxis uses intertwined signalling pathways, each individually dispensable. Recent work shows that Dictyostelium PKB/Akt can be spatially regulated independently of phosphatidylinositol (3,4,5)-trisphosphate via phosphorylation by TOR complex 2, placing this complex at the hub of chemotaxis.

Kintses, B., Z. Yang, et al. (2008). "Experimental investigation of the seesaw mechanism of the relay region that moves the myosin lever arm." J Biol Chem 283(49): 34121-34128.
	A seesaw-like movement of the relay region upon the recovery step of myosin was recently simulated in silico. In this model the relay helix tilts around its pivoting point formed by a phenylalanine cluster (Phe(481), Phe(482), and Phe(652)), which moves the lever arm of myosin. To study the effect of the elimination of the proposed pivoting point, these phenylalanines were mutated to alanines in two Dictyostelium myosin II motor domain constructs (M(F481A, F482A) and M(F652A)). The relay movement was followed by the fluorescence change of Trp(501) located in the relay region. The steady-state and transient kinetic fluorescence experiments showed that the lack of the phenylalanine fulcrum perturbs the formation of the "up" lever arm state, and only moderate effects were found in the nucleotide binding, the formation of the "down" lever arm position, and the ATP hydrolysis steps. We conclude that the lack of the fulcrum decouples the distal part of the relay from the nucleotide binding site upon the recovery step. Our molecular dynamics simulations also showed that the conformation of the motor is not perturbed by the mutation in the down lever arm state, however, the lack of the pivoting point rearranges the dynamic pattern of the kink region of the relay helix.

Kirsten, J. H., Y. Xiong, et al. (2008). "Subcellular localization of ammonium transporters in Dictyostelium discoideum." BMC Cell Biol 9: 71.
	BACKGROUND: With the exception of vertebrates, most organisms have plasma membrane associated ammonium transporters which primarily serve to import a source of nitrogen for nutritional purposes. Dictyostelium discoideum has three ammonium transporters, Amts A, B and C. Our present work used fluorescent fusion proteins to determine the cellular localization of the Amts and tested the hypothesis that the transporters mediate removal of ammonia generated endogenously from the elevated protein catabolism common to many protists. RESULTS: Using RFP and YFP fusion constructs driven by the actin 15 promoter, we found that the three ammonium transporters were localized on the plasma membrane and on the membranes of subcellular organelles. AmtA and AmtB were localized on the membranes of endolysosomes and phagosomes, with AmtB further localized on the membranes of contractile vacuoles. AmtC also was localized on subcellular organelles when it was stabilized by coexpression with either the AmtA or AmtB fusion transporter. The three ammonium transporters exported ammonia linearly with regard to time during the first 18 hours of the developmental program as revealed by reduced export in the null strains. The fluorescently tagged transporters rescued export when expressed in the null strains, and thus they were functional transporters. CONCLUSION: Unlike ammonium transporters in most organisms, which import NH3/NH4+ as a nitrogen source, those of Dictyostelium export ammonia/ammonium as a waste product from extensive catabolism of exogenously derived and endogenous proteins. Localization on proteolytic organelles and on the neutral contractile vacuole suggests that Dictyostelium ammonium transporters may have unique subcellular functions and play a role in the maintenance of intracellular ammonium distribution. A lack of correlation between the null strain phenotypes and ammonia excretion properties of the ammonium transporters suggests that it is not the excretion function that is important for coupling ammonia levels to the slug versus culmination choice, but rather a sensor and/or signaling function of these proteins that is important.

Klein, J. C. (2008). Molecular dynamics of myosin II by site-directed spin-labeling and EPR. United States -- Minnesota, University of Minnesota.
	The actin-binding cleft is a deep, solvent-filled cavity that extends from the actin-binding interface to the nucleotide-binding pocket of skeletal myosin. The cleft has been predicted to close partially upon ATP hydrolysis and to close fully with strong actin binding, as is predicted by existing myosin crystal structures. Paradoxically, none of these crystal structures contains actin. We present a structurally dynamic model for nucleotide- and actin-induced closure of the actin-binding cleft, based on site-directed spin labeling and electron paramagnetic resonance (EPR) in Dictyostelium myosin II. To test the validity of crystal structures, we compared experimental EPR measureables to those extracted from trajectories of computational simulations of spin-labeled crystal structures. Single-cysteine labeling sites were engineered to probe mobility and accessibility within the cleft. For these sites, addition of ADP and vanadate, trapping the post-hydrolysis biochemical state, influenced probe mobility and accessibility slightly, while actin binding caused more dramatic changes in accessibility, consistent with cleft closure. Explicit incorporation of the spin label side chain in computational simulations of structural models yielded results in closer agreement with experiment. We engineered five pairs of cysteine labeling sites to straddle the cleft, each pair having one label on the upper 50 kDa domain and one on the lower 50 kDa domain. Distances between spin-labeled sites were determined from the resulting spin-spin interactions, as measured by CW-EPR for distances 0.7-2 nm or DEER for distances 1.7-6 nm. Due to the high distance resolution of EPR, at least two distinct structural states of the cleft were resolved. Each of the biochemical states tested (pre-hydrolysis, post-hydrolysis, and rigor), reflects a mixture of at least two of these structural states, indicating that the coupling between biochemical and structural states is not rigid. The resulting picture is much more dynamic than previously envisioned, with both "open" and "closed" conformations of the cleft interconverting, even in the rigor actomyosin complex.

Klein, J. C., A. R. Burr, et al. (2008). "Actin-binding cleft closure in myosin II probed by site-directed spin labeling and pulsed EPR." Proc Natl Acad Sci U S A 105(35): 12867-12872.
	We present a structurally dynamic model for nucleotide- and actin-induced closure of the actin-binding cleft of myosin, based on site-directed spin labeling and electron paramagnetic resonance (EPR) in Dictyostelium myosin II. The actin-binding cleft is a solvent-filled cavity that extends to the nucleotide-binding pocket and has been predicted to close upon strong actin binding. Single-cysteine labeling sites were engineered to probe mobility and accessibility within the cleft. Addition of ADP and vanadate, which traps the posthydrolysis biochemical state, influenced probe mobility and accessibility slightly, whereas actin binding caused more dramatic changes in accessibility, consistent with cleft closure. We engineered five pairs of cysteine labeling sites to straddle the cleft, each pair having one label on the upper 50-kDa domain and one on the lower 50-kDa domain. Distances between spin-labeled sites were determined from the resulting spin-spin interactions, as measured by continuous wave EPR for distances of 0.7-2 nm or pulsed EPR (double electron-electron resonance) for distances of 1.7-6 nm. Because of the high distance resolution of EPR, at least two distinct structural states of the cleft were resolved. Each of the biochemical states tested (prehydrolysis, posthydrolysis, and rigor), reflects a mixture of these structural states, indicating that the coupling between biochemical and structural states is not rigid. The resulting model is much more dynamic than previously envisioned, with both open and closed conformations of the cleft interconverting, even in the rigor actomyosin complex.

Kolsch, V., P. G. Charest, et al. (2008). "The regulation of cell motility and chemotaxis by phospholipid signaling." J Cell Sci 121(Pt 5): 551-559.
	Phosphoinositide 3-kinase (PI3K), PTEN and localized phosphatidylinositol (3,4,5)-trisphosphate [PtdIns(3,4,5)P3] play key roles in chemotaxis, regulating cell motility by controlling the actin cytoskeleton in Dictyostelium and mammalian cells. PtdIns(3,4,5)P3, produced by PI3K, acts via diverse downstream signaling components, including the GTPase Rac, Arf-GTPases and the kinase Akt (PKB). It has become increasingly apparent, however, that chemotaxis results from an interplay between the PI3K-PTEN pathway and other parallel pathways in Dictyostelium and mammalian cells. In Dictyostelium, the phospholipase PLA2 acts in concert with PI3K to regulate chemotaxis, whereas phospholipase C (PLC) plays a supporting role in modulating PI3K activity. In adenocarcinoma cells, PLC and the actin regulator cofilin seem to provide the direction-sensing machinery, whereas PI3K might regulate motility.

Kornberg, A. (2008). "Abundant microbial inorganic polyphosphate, poly P kinase are underappreciated." Microbe 3: 119-123.
	
Kortholt, A. and P. J. van Haastert (2008). "Highlighting the role of Ras and Rap during Dictyostelium chemotaxis." Cell Signal 20(8): 1415-1422.
	Chemotaxis, the directional movement towards a chemical compound, is an essential property of many cells and has been linked to the development and progression of many diseases. Eukaryotic chemotaxis is a complex process involving gradient sensing, cell polarity, remodelling of the cytoskeleton and signal relay. Recent studies in the model organism Dictyostelium discoideum have shown that chemotaxis does not depend on a single molecular mechanism, but rather depends on several interconnecting pathways. Surprisingly, small G-proteins appear to play essential roles in all these pathways. This review will summarize the role of small G-proteins in Dictyostelium, particularly highlighting the function of the Ras subfamily in chemotaxis.

Kosta, A., M. F. Luciani, et al. (2008). "Marked mitochondrial alterations upon starvation without cell death, caspases or Bcl-2 family members." Biochim Biophys Acta 1783(10): 2013-2019.
	Dictyostelium HMX44A cells can withstand starvation under monolayer conditions for a few days without dying. They die only when the differentiation factor DIF-1 is exogenously added. Still, when HMX44A were subjected to starvation without addition of DIF-1 they showed, by electron microscopy and electron tomography, gross mitochondrial lesions including marked cristae alterations with frequent "holes" probably originating from dilated cristae. Since these cells did not die as shown for instance by FACS analysis, these results showed unexpected resilience of cells bearing markedly altered mitochondria, and thus showed that apparently destructive mitochondrial alterations may not lead to cell death. Also, these marked mitochondrial lesions could not be caused by caspases or bcl-2 family members, which these cells do not encode.

Kriebel, P. W., V. A. Barr, et al. (2008). "Collective cell migration requires vesicular trafficking for chemoattractant delivery at the trailing edge." J Cell Biol 183(5): 949-961.
	Chemoattractant signaling induces the polarization and directed movement of cells secondary to the activation of multiple effector pathways. In addition, chemotactic signals can be amplified and relayed to proximal cells via the synthesis and secretion of additional chemoattractant. The mechanisms underlying such remarkable features remain ill defined. We show that the asymmetrical distribution of adenylyl cyclase (ACA) at the back of Dictyostelium discoideum cells, an essential determinant of their ability to migrate in a head-to-tail fashion, requires vesicular trafficking. This trafficking results in a local accumulation of ACA-containing intracellular vesicles and involves intact actin, microtubule networks, and de novo protein synthesis. We also show that migrating cells leave behind ACA-containing vesicles, likely secreted as multivesicular bodies and presumably involved in the formation of head-to-tail arrays of migrating cells. We propose that similar compartmentalization and shedding mechanisms exist in mammalian cells during embryogenesis, wound healing, neuron growth, and metastasis.

Krishnan, J. and P. A. Iglesias (2008). "Systems analysis of regulatory processes underlying eukaryotic gradient perception." IEEE Transactions on Circuits and Systems I-Regular Papers: 126-138.
	This paper analyzes regulatory processes involved in the biological process of directed cell locomotion-known as chemotaxis. We focus on the nature of regulation involved in a subprocess of chemotaxis called gradient perception. We examine two different models from a dynamics/control perspective to gain insight into the working mechanisms of these models. One model is a minimal model which reconciles gradient perception to the property of adaptation. The second model is a biochemical model of a lipid network and its regulation by enzymes. In both cases, we focus on the extent of regulation of the modules/networks by inputs, and examine various limiting cases. Both the models and the resulting insights have broader applicability than the context in which they were developed.

Kubohara, Y., H. Kikuchi, et al. (2008). "Exploitation of the derivatives of Dictyostelium differentiation-inducing factor-1, which promote glucose consumption in mammalian cells." Life Sci 83(17-18): 608-612.
	AIMS: The differentiation-inducing factor-1 (DIF-1) is a signal molecule that induces stalk cell formation in the cellular slime mold Dictyostelium discoideum. DIF-1 has also been shown to possess pharmacological activities, such as the suppression of tumor cell growth and the promotion of glucose uptake in non-transformed mammalian cells. In this study, we tried to develop compounds that possess weaker anti-tumor activity and stronger glucose uptake-promoting activity than DIF-1. MAIN METHODS: We investigated the in vitro effects of 12 derivatives of DIF-1 on glucose consumption in mouse 3T3-L1 cells and on cell growth in K562 human leukemia cells. We also examined the effect of a good compound on the blood glucose concentration in KK-Ay diabetic mice. KEY FINDINGS: We found that some derivatives at 20 microM promoted glucose consumption more than twice as fast as the control. Of the derivatives, a compound named DIF-1(3M), which has a weaker anti-leukemic effect than DIF-1, promoted glucose consumption as strongly as DIF-1 in confluent 3T3-L1 cells. While DIF-1 at 20 microM was inhibitory to the cell growth of 3T3-L1, DIF-1(3M) at 20 microM exhibited no inhibitory effect on the growing cells. We also found that DIF-1(3M) injected (10-12.5 mg/kg body weight) intraperitoneally in mice tended to lower the blood glucose concentration. SIGNIFICANCE: The present results open the possibility for the development of new agents that possess strong glucose-uptake-promoting activity but little anti-tumor activity and may have therapeutic potential for the treatment of diabetes and/or obesity.

Kuwayama, H., T. Yanagida, et al. (2008). "DNA oligonucleotide-assisted genetic manipulation increases transformation and homologous recombination efficiencies: evidence from gene targeting of Dictyostelium discoideum." J. Biotechnol. 133: 418-423.
	
Lam, D. and P. Golstein (2008). "A specific pathway inducing autophagic cell death is marked by an ip3r mutation." Autophagy 4: 349-350.
	
Lam, D., A. Kosta, et al. (2008). "The inositol 1,4,5-trisphosphate receptor is required to signal autophagic cell death." Mol. Biol. Cell 19: 691-700.
	
Landolt, J. C., J. C. Cavender, et al. (2008). "New species of dictyostelid cellular slime moulds from Australia." Australian System. Bot. 28: 50-66.
	
Langenick, J., T. Araki, et al. (2008). "A Dictyostelium homologue of the metazoan Cbl proteins regulates STAT signalling." J Cell Sci 121(Pt 21): 3524-3530.
	Cbl proteins downregulate metazoan signalling pathways by ubiquitylating receptor tyrosine kinases, thereby targeting them for degradation. They contain a phosphotyrosine-binding region, comprising an EF-hand and an SH2 domain, linked to an E3 ubiquitin-ligase domain. CblA, a Dictyostelium homologue of the Cbl proteins, contains all three conserved domains. In a cblA(-) strain early development occurs normally but migrating cblA(-) slugs frequently fragment and the basal disc of the culminants that are formed are absent or much reduced. These are characteristic features of mutants in signalling by DIF-1, the low-molecular-mass prestalk and stalk cell inducer. Tyrosine phosphorylation of STATc is induced by DIF-1 but in the cblA(-) strain this response is attenuated relative to parental cells. We present evidence that CblA fulfils this function, as a positive regulator of STATc tyrosine phosphorylation, by downregulating PTP3, the protein tyrosine phosphatase responsible for dephosphorylating STATc. Thus Cbl proteins have an ancient origin but, whereas metazoan Cbl proteins regulate tyrosine kinases, the Dictyostelium Cbl regulates via a tyrosine phosphatase.

Larsson, P., A. Hinas, et al. (2008). "De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring." Genome Res 18(6): 888-899.
	Genome data are increasingly important in the computational identification of novel regulatory non-coding RNAs (ncRNAs). However, most ncRNA gene-finders are either specialized to well-characterized ncRNA gene families or require comparisons of closely related genomes. We developed a method for de novo screening for ncRNA genes with a nucleotide composition that stands out against the background genome based on a partial sum process. We compared the performance when assuming independent and first-order Markov-dependent nucleotides, respectively, and used Karlin-Altschul and Karlin-Dembo statistics to evaluate the significance of hits. We hypothesized that a first-order Markov-dependent process might have better power to detect ncRNA genes since nearest-neighbor models have been shown to be successful in predicting RNA structures. A model based on a first-order partial sum process (analyzing overlapping dinucleotides) had better sensitivity and specificity than a zeroth-order model when applied to the AT-rich genome of the amoeba Dictyostelium discoideum. In this genome, we detected 94% of previously known ncRNA genes (at this sensitivity, the false positive rate was estimated to be 25% in a simulated background). The predictions were further refined by clustering candidate genes according to sequence similarity and/or searching for an ncRNA-associated upstream element. We experimentally verified six out of 10 tested ncRNA gene predictions. We conclude that higher-order models, in combination with other information, are useful for identification of novel ncRNA gene families in single-genome analysis of D. discoideum. Our generalizable approach extends the range of genomic data that can be searched for novel ncRNA genes using well-grounded statistical methods.

Lee, N. S., M. Rodriguez, et al. (2008). "Dictyostelium kinase DPYK3 negatively regulates STATc signaling in cell fate decision." Dev Growth Differ 50(7): 607-613.
	DPYK3, a member of the Dictyostelium TKL (tyrosine kinase like) kinase family, was ablated by homologous recombination. dpyk3- cells displayed aberrant pattern formation during development. The prestalk O zone was not properly formed and, instead, the prespore zone was expanded in dpyk3- slugs. During development, the transcription factor STATc (signal transducers and activators of transcription c) was persistently phosphorylated and ecmAO expression level was kept low in dpyk3- cells. Furthermore, in response to differentiation inducing factor-1 (DIF-1) in suspension culture, dpyk3- cells displayed persistent STATc phosphorylation and reintroduction of DPYK3 in dpyk3- cells restored transient STATc phosphorylation similarly to wild type cells. In contrast to the positive STAT regulation by Janus Kinase in metazoans, Dictyostelium DPYK3 negatively regulates STATc during development in response to DIF-1 signaling.

Lee, N. S., S. Veeranki, et al. (2008). "The function of PP2A/B56 in non-metazoan multicellular development." Differentiation 76(10): 1104-1110.
	DB56, the Dictyostelium B56 homolog, displayed high sequence homology to other eukaryotic B56 subunits of the PP2A and a specific association with the PP2A catalytic subunit. Cells lacking DB56, psrA(-), displayed higher PP2A phosphatase activity compared with the wild type, approximately 10 hr of delayed expression of ecmA and ecmB prestalk markers, and inefficient culmination. The prespore marker cotB declined as wild-type cells culminate, but no such decline was observed from psrA(-) cells. Interestingly, psrA(-) cells exhibited higher GSK3 kinase activity. Furthermore, the expression of the dominant negative GSK3 mutant (K84/85M) in psrA(-) cells improved both prestalk and prespore expression patterns similarly to wild-type cells. However, culmination was not restored in psrA(-) cells expressing dominant negative GSK3, which suggests that PP2A/DB56 has an extra target during terminal differentiation. This report shows that PP2A/DB56 controls not only metazoan development, but also non-metazoan cell fate decision processes.

Letcher, A. J., M. J. Schell, et al. (2008). "Do mammals make all their own inositol hexakisphosphate?" Biochem J 416(2): 263-270.
	A highly specific and sensitive mass assay for inositol hexakisphosphate (InsP6) was characterized. This centres around phosphorylating InsP6 with [32P]ATP using a recombinant InsP6 kinase from Giardia lambia, followed by HPLC of the 32P-labelled products with an internal [3H]InsP7 standard. This assay was used to quantify InsP6 levels in a variety of biological samples.Concentrations of InsP6 in rat tissues varied from 10-20 microM (assuming 64% of wet weight of tissue is cytosol water), whereas using the same assumption axenic Dictyostelium discoideum cells contained 352 +/- 11 microM InsP6. HeLa cells were seeded at low density and grown to confluence, at which point they contained InsP6 levels per mg of protein similar to rat tissues. This amounted to 1.952 +/- 0.117 nmol InsP6 per culture dish, despite the cells being grown in serum shown to contain no detectable(less than 20 pmol per dish) InsP6. These results demonstrate that mammalian cells synthesize all their own InsP6. Human blood was analysed, and although the white cell fraction contained InsP6 at a concentration comparable with other tissues, in serum and platelet-free plasma no InsP6 was detected (<1 nM InsP6). Human urine was also examined, and also contained no detectable (<5 nM) InsP6. These results suggest that dietary studies purporting to measure InsP6 at micromolar concentrations in human plasma or urine may not have been quantifying this inositol phosphate. Therefore claims that administrating InsP6 in the diet or applying it topically can produce health benefits by increasing extracellular InsP6 levels may require reassessment.

Li, H., Q. Chen, et al. (2008). "Dictyostelium Aurora kinase has properties of both Aurora A and Aurora B kinases." Euk Cell 7(5): 894-905.
	Aurora kinases are highly conserved proteins with important roles in mitosis. Metazoans contain two kinases, Aurora A and B, which contribute distinct functions at the spindle poles and the equatorial region respectively. It is not currently known whether the specialized functions of the two kinases arose after their duplication in animal cells or were already present in their ancestral kinase. We show that Dictyostelium discoideum contains a single Aurora kinase, DdAurora, that displays characteristics of both Aurora A and B. Like Aurora A, DdAurora has an extended N-terminal domain with an A-box sequence and localizes at the spindle poles during early mitosis. Like Aurora B, DdAurora binds to its partner DdINCENP and localizes on centromeres at metaphase, the central spindle during anaphase, and the cleavage furrow at the end of cytokinesis. DdAurora also has several unusual properties. DdAurora remains associated with centromeres in anaphase, and this association does not require an interaction with DdINCENP. DdAurora then localizes at the cleavage furrow, but only at the end of cytokinesis. This localization is dependent on DdINCENP and the motor proteins Kif12 and myosin II. Thus, DdAurora may represent the ancestral kinase that gave rise to the different Aurora kinases in animals and also those in other organisms.

Li, L., M. Driscoll, et al. (2008). "Binary and gray-scale patterning of chemical functionality on polymer films." J Am Chem Soc 130(41): 13512-13513.
	We present a facile technique for the gray-scale chemical functionalization of polymer surfaces with high dynamic range. We demonstrate the use of this technique to create amine-functionalized substrates that are used for the patterned binding of fluorophores and the patterned synthesis of peptides. Studies of the behavior of the model organism Dictyostelium discoideum indicate the biocompatibility of the functionalized substrates.

Li, L., S. F. Norrelykke, et al. (2008). "Persistent cell motion in the absence of external signals: a search strategy for eukaryotic cells." PLoS One 3(5): e2093.
	BACKGROUND: Eukaryotic cells are large enough to detect signals and then orient to them by differentiating the signal strength across the length and breadth of the cell. Amoebae, fibroblasts, neutrophils and growth cones all behave in this way. Little is known however about cell motion and searching behavior in the absence of a signal. Is individual cell motion best characterized as a random walk? Do individual cells have a search strategy when they are beyond the range of the signal they would otherwise move toward? Here we ask if single, isolated, Dictyostelium and Polysphondylium amoebae bias their motion in the absence of external cues. METHODOLOGY: We placed single well-isolated Dictyostelium and Polysphondylium cells on a nutrient-free agar surface and followed them at 10 sec intervals for approximately 10 hr, then analyzed their motion with respect to velocity, turning angle, persistence length, and persistence time, comparing the results to the expectation for a variety of different types of random motion. CONCLUSIONS: We find that amoeboid behavior is well described by a special kind of random motion: Amoebae show a long persistence time ( approximately 10 min) beyond which they start to lose their direction; they move forward in a zig-zag manner; and they make turns every 1-2 min on average. They bias their motion by remembering the last turn and turning away from it. Interpreting the motion as consisting of runs and turns, the duration of a run and the amplitude of a turn are both found to be exponentially distributed. We show that this behavior greatly improves their chances of finding a target relative to performing a random walk. We believe that other eukaryotic cells may employ a strategy similar to Dictyostelium when seeking conditions or signal sources not yet within range of their detection system.

Li, M. S., A. M. Gabovich, et al. (2008). "New method for deciphering free energy landscape of three-state proteins." J Chem Phys 129(10): 105102.
	We have developed a new simulation method to estimate the distance between the native state and the first transition state and the distance between the intermediate state and the second transition state of a protein which mechanically unfolds via intermediates. Assuming that the end-to-end extension DeltaR is a good reaction coordinate to describe the free energy landscape of proteins subjected to an external force, we define the midpoint extension DeltaR(*) between two transition states from either constant force or constant loading rate pulling simulations. In the former case, DeltaR(*) is defined as a middle point between two plateaus in the time-dependent curve of DeltaR, while, in the latter one, it is a middle point between two peaks in the force-extension curve. Having determined DeltaR(*), one can compute times needed to cross two transition state barriers starting from the native state. With the help of the Bell and microscopic kinetic theory, force dependencies of these unfolding times can be used to locate the intermediate state and to extract unfolding barriers. We have applied our method to the titin domain I27 and the fourth domain of Dictyostelium discoideum filamin (DDFLN4) and obtained reasonable agreement with experiments, using the C(alpha)-Go model.

Liao, X. H., A. Majithia, et al. (2008). "Growth control via TOR kinase signaling, an intracellular sensor of amino acid and energy availability, with crosstalk potential to proline metabolism." Amino Acids 35(4): 761-770.
	The TOR (Target of Rapamycin) protein kinase pathway plays a central role in sensing and responding to nutrients, stress, and intracellular energy state. TOR complex 1 (TORC1) is comprised of TOR, Raptor, and Lst8 and its activity is sensitive to inhibition by the macrolide antibiotic rapamycin. TORC1 regulates protein synthesis, ribosome biogenesis, autophagy, and ultimately cell growth through the phosphorylation of S6 K, 4E-BP, and other substrates. As TORC1 activity is positively or negatively modulated in response to upstream regulators, cellular growth rate is, respectively, enhanced or suppressed. A separate multiprotein TOR complex, TORC2, is insensitive to direct inhibition by rapamycin and does not regulate growth patterns directly; TORC2 can, however, impact certain aspects of TORC1 signaling and cell survival. TOR signaling is an ancient pathway, conserved among the yeasts, Dictyostelium, C. elegans, Drosophila, mammals, and Arabidopsis. This review will focus on the regulation of TORC1 in mammalian cells in the context of amino acid sensing/regulation and intracellular ATP homeostasis, but will also include comparisons among other organisms.

Liu, M., G. M. Conover, et al. (2008). "Legionella pneumophila EnhC is required for efficient replication in tumour necrosis factor alpha-stimulated macrophages." Cell Microbiol 10(9): 1906-1923.
	Legionella pneumophila enhC(-) mutants were originally identified as being defective for uptake into host cells. In this work, we found that the absence of EnhC resulted in defective intracellular growth when dissemination of intracellular bacteria to neighbouring cells was expected to occur. No such defect was observed during growth within the amoeba Dictyostelium discoideum. Culture supernatants containing the secreted products of infected macrophages added to host cells restricted the growth of the DeltaenhC strain, while tumour necrosis factor alpha (TNF-alpha), at concentrations similar to those found in macrophage culture supernatants, could reproduce the growth restriction exerted by culture supernatants on L. pneumophilaDeltaenhC. The absence of EnhC also caused defective trafficking of the Legionella-containing vacuole in TNF-alpha-treated macrophages. EnhC was shown to be an envelope-associated protein largely localized to the periplasm, with its expression induced in post-exponential phase, as is true for many virulence-associated proteins. Furthermore, the absence of EnhC appeared to affect survival under stress conditions, as the DeltaenhC mutant was more susceptible to H(2)O(2) treatment than the wild-type strain. EnhC therefore is a unique virulence factor that is required for growth specifically when macrophages have heightened potential to restrict microbial replication.

Liu, R., E. V. Linardopoulou, et al. (2008). "Formins in development: Orchestrating body plan origami." Biochim Biophys Acta.
	Formins, proteins defined by the presence of an FH2 domain and their ability to nucleate linear F-actin de novo, play a key role in the regulation of the cytoskeleton. Initially thought to primarily regulate actin, recent studies have highlighted a role for formins in the regulation of microtubule dynamics, and most recently have uncovered the ability of some formins to coordinate the organization of both the microtubule and actin cytoskeletons. While biochemical analyses of this family of proteins have yielded many insights into how formins regulate diverse cytoskeletal reorganizations, we are only beginning to appreciate how and when these functional properties are relevant to biological processes in a developmental or organismal context. Developmental genetic studies in fungi, Dictyostelium, vertebrates, plants and other model organisms have revealed conserved roles for formins in cell polarity, actin cable assembly and cytokinesis. However, roles have also been discovered for formins that are specific to particular organisms. Thus, formins perform both global and specific functions, with some of these roles concurring with previous biochemical data and others exposing new properties of formins. While not all family members have been examined across all organisms, the analyses to date highlight the significance of the flexibility within the formin family to regulate a broad spectrum of diverse cytoskeletal processes during development.

Lombardi, M. L. (2008). Biomechanics and molecular mechanisms of amoeboid cell movement. United States -- Connecticut, University of Connecticut.
	Cell movement is a multistep cycle that is essential for many biological events and involves the integration of biochemical and biophysical signals. This process requires the coordination of protrusion and adhesion formation at the cell front with retraction and detachment of adhesions at the rear edge. Many systems, such as fish epithelial keratocytes, leukocytes, fibroblasts and Dictyostelium , have been used with fluorescence microscopy, molecular biology, and biochemistry to provide information about the major proteins and molecular mechanisms underlying these processes. However, our knowledge of the biomechanics of cell migration, i.e. whether these proteins and mechanisms are able to generate the necessary forces for movement, is still limited. Here we have used a gelatin-based traction force assay to detect the traction forces produced by wild-type (NC4A2), myosin II essential light chain mutant ( mlcE - ), and myosin II heavy chain mutant ( mhcA - ) Dictyostelium cells, and GFP-myosin II expressing Dictyostelium . We found that for each cell type, the most rapid movement occurred when an asymmetric distribution of traction stress exists, in which forces at the rear are significantly greater than at the front, irrespective of the absolute value of traction stress magnitude. We propose that cell speed for each cell type is determined by the rate and extent to which traction stress asymmetry develops, and can be related to the distinct roles of myosin II motor and actin cross-linking activity. We also gathered evidence that rapid movement in Dictyostelium cells can be regulated by mechano-chemical signaling. By performing high resolution Ca 2+ imaging, we found that these cells display transient increases in Ca 2+ that are dependent on both intracellular and extracellular calcium and can be inhibited by gadolinium (Gd 3+ ). The data provide evidence for the role of stretch activated calcium channels (SACs) in stimulating these Ca 2+ transients initiating calcium-dependent retraction. Taken together, these results emphasize the importance of the integration of the biomechanics and cellular pathways in the regulation of rapid movement in Dictyostelium cells. These studies can be applied with other cell types, such as leukocytes, to understand cell motility in healthy and abnormal diseased states and for the development of novel drug treatments.

Lombardi, M. L., D. A. Knecht, et al. (2008). "Mechano-chemical signaling maintains the rapid movement of Dictyostelium cells." Exp Cell Res 314(8): 1850-1859.
	The survival of Dictyostelium cells depends on their ability to efficiently chemotax, either towards food or to form multicellular aggregates. Although the involvement of Ca2+ signaling during chemotaxis is well known, it is not clear how this regulates cell movement. Previously, fish epithelial keratocytes have been shown to display transient increases in intracellular calcium ([Ca2+]i) that are mediated by stretch-activated calcium channels (SACs), which play a role in retraction of the cell body [J. Lee, A. Ishihara, G. Oxford, B. Johnson, and K. Jacobson, Regulation of cell movement is mediated by stretch-activated calcium channels. Nature, 1999. 400(6742): p. 382-6.]. To investigate the involvement of SACs in Dictyostelium movement we performed high resolution calcium imaging in wild-type (NC4A2) Dictyostelium cells to detect changes in [Ca2+]i. We observed small, brief, Ca2+ transients in randomly moving wild-type cells that were dependent on both intracellular and extracellular sources of calcium. Treatment of cells with the SAC blocker gadolinium (Gd3+) inhibited transients and decreased cell speed, consistent with the involvement of SACs in regulating Dictyostelium motility. Additional support for SAC activity was given by the increase in frequency of Ca2+ transients when Dictyostelium cells were moving on a more adhesive substratum or when they were mechanically stretched. We conclude that mechano-chemical signaling via SACs plays a major role in maintaining the rapid movement of Dictyostelium cells.

Loomis, W. F. (2008). "cAMP oscillations during aggregation of Dictyostelium." Adv Exp Med Biol 641: 39-48.
	For many years it has been known that developing cells of Dictyostelium discoideum show periodic surges as they aggregate. When it was discovered that the cells were responding chemotactically to cAMP gradients produced within the populations, experiments were carried out that demonstrated similar periodic changes in the concentration of extracellular cAMP. Moreover, homogenous populations of developed cells held in suspension could be shown to respond to cAMP by changes in cell shape. Such suspensions showed spontaneous oscillations in light scattering as well as cAMP levels as the result of entrainment of the cells. The molecular components necessary for the pulsatile release of cAMP were uncovered by analyzing the behavior of a large number of strains with defined mutations isolated from saturation mutagenic screens. Subsequent genetic and biochemical studies established the connections between a dozen proteins essential for spontaneous oscillations. Computer simulations of a molecular circuit based on these results showed that it is able to account for the temporal and quantitative aspects of the oscillatory system. The circuit also appears to be coupled to the construction and dismantling of the actin/myosin cortical layer that ensures that pseudopods are restricted to the anterior of cells during chemotaxis and that the cells do not back-track when the natural wave is behind them. Since the same molecular clock controls both signal production and signal response, these behaviors are always kept strictly in phase.

Lopez, M. D. and T. Samuelsson (2008). "Early evolution of histone mRNA 39 end processing." RNA 14(1): 1-10.
	The replication-dependent histone mRNAs in metazoa are not polyadenylated, in contrast to the bulk of mRNA. Instead, they contain an RNA stem-loop (SL) structure close to the 39 end of the mature RNA, and this 39 end is generated by cleavage using a machinery involving the U7 snRNP and protein factors such as the stem-loop binding protein ( SLBP). This machinery of 39 end processing is related to that of polyadenylation as protein components are shared between the systems. It is commonly believed that histone 39 end processing is restricted to metazoa and green algae. In contrast, polyadenylation is ubiquitous in Eukarya. However, using computational approaches, we have now identified components of histone 39 end processing in a number of protozoa. Thus, the histone mRNA stem-loop structure as well as the SLBP protein are present in many different protozoa, including Dictyostelium, alveolates, Trypanosoma, and Trichomonas. These results show that the histone 39 end processing machinery is more ancient than previously anticipated and can be traced to the root of the eukaryotic phylogenetic tree. We also identified histone mRNAs from both metazoa and protozoa that are polyadenylated but also contain the signals characteristic of histone 39 end processing. These results provide further evidence that some histone genes are regulated at the level of 39 end processing to produce either polyadenylated RNAs or RNAs with the 39 end characteristic of replication-dependent histone mRNAs.

Lorenz, T. and J. Reinstein (2008). "The influence of proline isomerization and off-pathway intermediates on the folding mechanism of eukaryotic UMP/CMP Kinase." J Mol Biol 381(2): 443-455.
	The globular 22-kDa protein UMP/CMP from Dictyostelium discoideum (UmpK) belongs to the family of nucleoside monophosphate (NMP) kinases. These enzymes not only show high sequence and structure similarities but also share the alpha/beta-fold, a very common protein topology. We investigated the protein folding mechanism of UmpK as a representative for this ubiquitous enzyme class. Equilibrium stability towards urea and the unfolding and refolding kinetics were studied by means of fluorescence and far-UV CD spectroscopy. Although the unfolding can be described by a two-state process, folding kinetics are rather complex with four refolding phases that can be resolved and an additional burst phase. Moreover, two of these phases exhibit a pronounced rollover in the refolding limb that cannot be explained by aggregation. Whilst secondary structure formation is not observed in the burst phase reaction, folding to the native structure is strongly influenced by the slowest phase, since 30% of the alpha-helical CD signal is restored therein. This process can be assigned to proline isomerization and is strongly accelerated by the Escherichia coli peptidyl-prolyl isomerase trigger factor. The analysis of our single-mixing and double-mixing experiments suggests the occurrence of an off-pathway intermediate and an unproductive collapsed structure, which appear to be rate limiting for the folding of UmpK.

Lu, Y. H., Y. Wang, et al. (2008). "Influence of medium components on growth kinetics of Dictyostelium discoideum." World J. Microbiol. Bbiotechnol. 24: 491-499.
	
Lucas-Lopez, C., J. S. Allingham, et al. (2008). "The small molecule tool (S)-(-)-blebbistatin: novel insights of relevance to myosin inhibitor design." Org Biomol Chem 6(12): 2076-2084.
	The small molecule blebbistatin is now a front line tool in the study of myosin function. Chemical modification of the tricyclic core of blebbistatin could deliver the next generation of myosin inhibitors and to help address this we report here on the impact of structural changes in the methyl-substituted aromatic ring of blebbistatin on its biological activity. Chemical methods for the preparation of isomeric methyl-containing analogues are reported and a series of co-crystal structures are used to rationalise the observed variations in their biological activity. These studies further support the view that the previously identified binding mode of blebbistatin to Dictyostelium discoideum myosin II is of relevance to its mode of action. A discussion of the role that these observations have on planning the synthesis of focused libraries of blebbistatin analogues is also provided including an assessment of possibilities by computational methods. These studies are ultimately directed at the development of novel myosin inhibitors with improved affinity and different selectivity profiles from blebbistatin itself.

Ludlow, M., D. Traynor, et al. (2008). "Extracellular ATP and ADP mediate Ca2+ influx in Dictyostelium discoideum." Purinergic Signalling 4: S5-S6.
	
Ludlow, M. J., L. Durai, et al. (2008). "Functional characterisation of intracellular Dictyostelium discoideum P2X receptors." J Biol Chem.
	Indicative of cell surface P2X ion channel activation, extracellular ATP evokes a rapid and transient calcium influx in the model eukaryote Dictyostelium discoideum. Five P2X-like proteins (dP2XA-E) are present in this organism. However, their roles in purinergic signalling are unclear since dP2XA proved to have an intracellular localisation on the contractile vacuole where it is thought to be required for osmoregulation. To determine functional properties of the remaining four dP2X-like proteins and to assess their cellular roles, we recorded membrane currents from expressed cloned receptors and generated a quintuple knockout Dictyostelium strain devoid of dP2X receptors. ATP evoked inward currents at dP2XB and dP2XE receptors but not at dP2XC or dP2XD. beta,gamma-imido-ATP was more potent than ATP at dP2XB but a weak partial agonist at dP2XE. Currents in dP2XB and dP2XE were strongly inhibited by Na(+) but insensitive to copper and the P2 receptor antagonists PPADS and suramin. Unusual for P2X channels, dP2XA and dP2XB were also Cl(-) permeable. The extracellular purinergic response to ATP persisted in p2xA/B/C/D/E quintuple knockout Dictyostelium demonstrating that dP2X channels are not responsible. dP2XB,C,D, and E were found to be intracellular localised to the contractile vacuole with the ligand binding domain facing the lumen. However, quintuple p2xA/B/C/D/E null cells were still capable of regulating cell volume in water demonstrating that, contrary to previous findings, dP2X receptors are not required for osmoregulation. Responses to the calmodulin antagonist calmidazolium however were reduced in p2xA/B/C/D/E null cells suggesting that dP2X receptors play a role in intracellular calcium signalling.

Ludlow, M. J., D. Traynor, et al. (2008). "Purinergic-mediated Ca2+ influx in Dictyostelium discoideum." Cell Calcium 44(6): 567-579.
	The presence of five P2X-like genes (p2xA-E) in Dictyostelium suggests that nucleotides other than cAMP may act as extracellular signalling molecules in this model eukaryote. However, p2xA was found to have an exclusively intracellular localisation making it unclear whether Dictyostelium utilise P2 receptors in a manner analogous to vertebrates. Using an apoaequorin expressing strain we show here that Dictyostelium do possess cell surface P2 receptors that facilitate Ca(2+) influx in response to extracellular ATP and ADP (EC(50)=7.5microM and 6.1microM, respectively). Indicative of P2X receptor activation, responses were rapid reaching peak within 2.91+/-0.04s, required extracellular Ca(2+), were inhibited by Gd(3+), modified by extracellular pH and were not affected by deletion of either the single Gbeta or iplA genes. Responses also remained unaffected by disruption of p2xA or p2xE showing that these genes are not involved. Cu(2+) and Zn(2+) inhibited purine-evoked Ca(2+) influx with IC(50) values of 0.9 and 6.3microM, respectively. 300microM Zn(2+) completely abolished the initial large rapid rise in intracellular Ca(2+) revealing the presence of an additional smaller, slower P2Y-like response. The existence of P2 receptors in Dictyostelium makes this organism a valuable model to explore fundamental aspects of purinergic signalling.

Maeda, Y. T., J. Inose, et al. (2008). "Ordered patterns of cell shape and orientational correlation during spontaneous cell migration." PLoS One 3(11): e3734.
	BACKGROUND: In the absence of stimuli, most motile eukaryotic cells move by spontaneously coordinating cell deformation with cell movement in the absence of stimuli. Yet little is known about how cells change their own shape and how cells coordinate the deformation and movement. Here, we investigated the mechanism of spontaneous cell migration by using computational analyses. METHODOLOGY: We observed spontaneously migrating Dictyostelium cells in both a vegetative state (round cell shape and slow motion) and starved one (elongated cell shape and fast motion). We then extracted regular patterns of morphological dynamics and the pattern-dependent systematic coordination with filamentous actin (F-actin) and cell movement by statistical dynamic analyses. CONCLUSIONS/SIGNIFICANCE: We found that Dictyostelium cells in both vegetative and starved states commonly organize their own shape into three ordered patterns, elongation, rotation, and oscillation, in the absence of external stimuli. Further, cells inactivated for PI3-kinase (PI3K) and/or PTEN did not show ordered patterns due to the lack of spatial control in pseudopodial formation in both the vegetative and starved states. We also found that spontaneous polarization was achieved in starved cells by asymmetric localization of PTEN and F-actin. This breaking of the symmetry of protein localization maintained the leading edge and considerably enhanced the persistence of directed migration, and overall random exploration was ensured by switching among the different ordered patterns. Our findings suggest that Dictyostelium cells spontaneously create the ordered patterns of cell shape mediated by PI3K/PTEN/F-actin and control the direction of cell movement by coordination with these patterns even in the absence of external stimuli.

Major, B., F. Bruckert, et al. (2008). "Coatings on tin and Ti(C,N) basis for biomedical application to blood contact and tin/CrN multilayered tribological systems produced by pulsed laser deposition." Archives of Metallurgy and Materials 53(1): 39-48.
	Research activity on surface engineering performed at the IMIM PAS in last years has been presented. Experiments were focused on TiN and Ti(C,N) thin coatings produced on titanium and biologically applied polyurethane substrates by application of pulsed laser deposition (PLD), magnetron sputtering (MS), and hybrid PLD/MS, at room temperature. Bio-physical tests of the kinetics of shear flow-induced cell detachment have been carried out. Model eucariotic cells easy to manipulate using technics of molecular biology have been used in experiments. Fluorescence patterns obtained after the performed test at kinetics condition tests have been used to establish kinetics curves. A microstructure examination by application of XRD and transmission electron microscopy have been performed. On the basis of the real cell detachment experiment, a finite element simulation was done. The highest shear stress was estimated for the region of the radius of the whole pierced in the center of the upper disc. There are an increasing number of applications in tribology where the properties of a single material are not sufficient. One way to surmount this problem is to use a multilayer coating. Application of metallic interlayers improves adhesion of nitride hard layer in multilayer systems. Tribological coatings consisted of 4, 8 and 32 layers of Cr/CrN and Ti/TiN types were fabricated with the PLD technique. It is found in transmission electron examinations on thin foils prepared from cross-section that both nitride-based multilayer structures studied are characterized by small columnar crystallite sizes and high defect density, what might raise their hardness but compromise coating adhesion. The intermediate metallic layers contained larger sized and less defective columnar structure compared to the nitride layers located at close to the substrate which should improve the coatings toughness. Switching from single layer to multi-layer metal/nitride composition improved resistance to delamination.

Major, R., F. Bruckert, et al. (2008). "Kinetics of eukaryote cells adhesion under shear flow detachment on the PLD deposited surfaces." Bulletin of the Polish Academy of Sciences-Technical Sciences 56(3): 223-228.
	Hybryd PLD method was used for deposition high quality thin Ti, TiN, Ti(C,N) and DLC coatings. The kinetic energy of the evaporated particles was controlled by application of variation of different reactive and non reactive atmospheres during deposition. The purpose was to improve adhesion by building, a bridge between the real ceramic coating and the substrate. A new layer composition layout was proposed by application of a buffer. starting layer. Advanced HRTEM investigation based oil high resolution transmission electron microscopy was used to reveal structure dependence Oil specific atmosphere in the reactive chamber. New experimental technique to examine the crystallographic orientation based oil X-ray texture tomography was applied to estimate contribution of the atmosphere to crystall orientation. Using Dictyostelium discoideum cells as a model organism for specific and nonspecific adhesion, kinetics of shear flow-induced cell detachment was studied. For a given cell, detachment occurs for critical Stress Values caused by the applied hydrodynamic pressure above a threshold. Cells are then removed from the Substrate with an apparent first-order rate reaction that strongly depends oil the stress. The threshold stress depends oil cell size and physicochemical properties of the substrate, but it is not affected by depolymerization of the actin and tubulin cytoskeleton.

Malchow, D., D. F. Lusche, et al. (2008). "A fast Ca2+-induced Ca2+-release mechanism in Dictyostelium discoideum." Cell Calcium 43(6): 521-530.
	In vertebrate cells calcium-induced calcium release (CICR) is thought to be responsible for rapid cytosolic Ca(2+) elevations despite the occurrence of strong Ca(2+) buffering within the cytosol. In Dictyostelium, a CICR mechanism has not been reported. While analyzing Ca(2+) regulation in a vesicular fraction of Dictyostelium rich in Ca(2+)-flux activity, containing contractile vacuoles (CV) as the main component of acidic Ca(2+) stores and ER, we detected a rapid Ca(2+) change upon addition of Ca(2+) (CIC). CIC was three times larger in active stores accumulating Ca(2+) than before Ca(2+) uptake and in inactivated stores. Ca(2+) release was demonstrated with the calmodulin antagonist W7 that inhibits the V-type H(+)ATPase activity and Ca(2+) uptake of acidic Ca(2+) stores. W7 caused a rapid and large increase of extravesicular Ca(2+) ([Ca(2+)](e)), much faster and larger than thapsigargin (Tg), a Ca(2+)-uptake inhibitor of the ER. W7 treatment blocked CIC indicating that a large part of CIC is due to Ca(2+) release. The height of CIC depended on the filling state of the Ca(2+) stores. CIC was virtually unchanged in the iplA(-) strain that lacks a putative IP(3) or ryanodine receptor thought to be located at the endoplasmic reticulum. By contrast, CIC was reduced in two mutants, HGR8 and lvsA(-), that are impaired in acidic Ca(2+)-store function. Purified Ca(2+) stores enriched in CV still displayed CIC, indicating that CV are a source of Ca(2+)-induced Ca(2+) release. CIC-defective mutants were altered in their oscillatory properties. The irregularity of the HGR8 oscillation suggests that the principal oscillator is affected in this mutant.

Mallick, B. C., J. S. Kim, et al. (2008). Conformational stability and folding of calcium-binding protein from Dictyostelium discoideum. FEBS J.
	Introduction: The protein calfumirin-1 containing the EF-hand motifs
from Dictyostelium discoideum bind Ca2+-ions with high affinity and
regulate cell differentiations and proliferation. The mechanism of
Ca2+-binding and the conformational changes is important and need
to be address. We investigated the conformational changes and the
structural stability induced upon Ca2+-binding to the protein at studied
conditions.
Methods: The coding region of CAF-1 was amplified by PCR, cloned
to pET-15b-expression vector and expressed in E. coli as His-fusion
protein. The protein conformational changes and thermal stability were
monitored by using fluorescence and circular dichroism. The binding
isotherms of Ca2+-CAF-1 were monitored by Isothermal Titration
Calorimeter (ITC).
Results: The stochiometric titration of [Ca2+]/[CAF-1] binding
showed 50% of the signal changes at a ratio equivalent to the binding
sites in the protein. The thermal denaturation of apo- and holo-CAF-1
monitored by circular dichroism and the thermodynamics parameters
obtained have good correlation to explain the protein stability. The
stability against chemical denaturation was found to be Ca2+-ion
dependant. The comparative binding of hydrophobic probe (ANS) to
apo-and holo-CAF-1 indicates the conformational changes. The
stability of the protein-Ca2+-binding interaction parameters were
obtained by ITC experiments.
Conclusions: The Ca2+-dependence conformational changes and stability
of CAF-1 under physiological conditions helps to understand the
mechanisms that required Ca2+-ions during the life cycle of D. discoideum.

Marin, I., W. N. van Egmond, et al. (2008). "The Roco protein family: a functional perspective." FASEB J 22(9): 3103-3110.
	In this review, we discuss the evolutionary, biochemical, and functional data available for members of the Roco protein family. They are characterized by having a conserved supradomain that contains a Ras-like GTPase domain, called Roc, and a characteristic COR (C-terminal of Roc) domain. A kinase domain and diverse regulatory and protein-protein interaction domains are also often found in Roco proteins. First detected in the slime mold Dictyostelium discoideum, they have a broad phylogenetic range, being present in both prokaryotes and eukaryotes. The functions of these proteins are diverse. The best understood are Dictyostelium Rocos, which are involved in cell division, chemotaxis, and development. However, this family has received extensive attention because mutations in one of the human Roco genes (LRRK2) cause familial Parkinson disease. Other human Rocos are involved in epilepsy and cancer. Biochemical data suggest that Roc domains are capable of activating kinase domains intramolecularly. Interestingly, some of the dominant, disease-causing mutations in both the GTPase and kinase domains of LRRK2 increase kinase activity. Thus, Roco proteins may act as stand-alone transduction units, performing roles that were thought so far to require multiple proteins, as occur in the Ras transduction pathway.

Marsano, F., L. Boatti, et al. (2008). Proteomic effects of different Hg concentration in Dictyostelium discoideum amoebae. Comp Biochem Physiol A- Mol Integr. Physiol.
	We used bidimensional electrophoresis with immunological and
mass spectrometry (MALDI and nanoLC-ESI-Q-TOF) techniques to
identify proteomic changes evoked in Dictyostelium amoebae by
different Hg concentrations. Indeed, it was used a lower dose-2 μMdetermining
physiological changes(e.g., lysosomal membrane stability),
and an higher concentration-10 μM-eliciting also effects on
mortality (few%) and cell replication. High-resolution 2DE proteomic
maps of soluble proteins unveiled two distinct signatures. Peptide
identification showed a response to oxidative stress at low Hg dose:13
proteins were up-regulated and among these GST-catalase and
thioredoxin were involved. Such molecular fingerprinting disappeared
at higher concentration, where12 proteins were downregulated
and only 2 were overexpressed. A battery of antibodies was
used to get clues on protein responses. Westernblot with anti-GST
antibodies revealed the overexpression in both conditions, but
immunofluorescence staining showed a compartimentalization at
the higher concentration, which is consistent with 2DE results. Antiubiquitin
staining revealed augmented protein ubiquitination at high
molecular weights and also an increase of ubiquitin availability only at
the high dose. Data were supported by DNA-microarrays indicating a
dose dependent overexpression of the proteasome complex genes,
which – together with dramatic lysosomal destabilization – suggests
the occurrence of non-physiological catabolic processes. Protein
carbonylation was assayed by spectrophotometric and 2DE westernblot
analyses. Results demonstrated an increase in protein oxidation
after the treatment with the higher Hg dose (14 spots). Severe oxidative
stress injuries were also confirmed by the lysosomal accumulation
of lipofuscin. In conclusion, the observed proteomic changes
may be related to two different physiological status of Hg exposed
amoebae: (i) a stress syndrome during which cells adapt, propagate
and survive; (ii) a toxic syndrome affecting several cellular, physiological
functions and finally cell survival.

Martinac, B., Y. Saimi, et al. (2008). "Ion channels in microbes." Physiol Rev 88(4): 1449-1490.
	Studies of ion channels have for long been dominated by the animalcentric, if not anthropocentric, view of physiology. The structures and activities of ion channels had, however, evolved long before the appearance of complex multicellular organisms on earth. The diversity of ion channels existing in cellular membranes of prokaryotes is a good example. Although at first it may appear as a paradox that most of what we know about the structure of eukaryotic ion channels is based on the structure of bacterial channels, this should not be surprising given the evolutionary relatedness of all living organisms and suitability of microbial cells for structural studies of biological macromolecules in a laboratory environment. Genome sequences of the human as well as various microbial, plant, and animal organisms unambiguously established the evolutionary links, whereas crystal-lographic studies of the structures of major types of ion channels published over the last decade clearly demonstrated the advantage of using microbes as experimental organisms. The purpose of this review is not only to provide an account of acquired knowledge on microbial ion channels but also to show that the study of microbes and their ion channels may also hold a key to solving unresolved molecular mysteries in the future.

McMahon, P. M., D. R. Hostetter, et al. (2008). "Temperature dependence of myosin-II tail fragment assembly." J Muscle Res Cell Motil 29(2-5): 109-118.
	Dictyostelium myosin-II bipolar thick filament (BTF) assembly is heavily dependent on ionic strength and temperature and is reversible by the phosphorylation of just three threonines. Truncated tail fragments of Dictyostelium myosin-II are commonly used as models for BTF assembly, as they self-assemble into regular paracrystals that recapitulate the ionic strength and phosphorylation dependence of full-length Dictyostelium myosin-II BTF assembly. Here we show that Dictyostelium myosin-II tail fragment assembly is highly temperature dependent, similar to full-length Dictyostelium myosin-II. Assembly of paracrystals was far more robust at 4 degrees C than at higher temperatures. Pre-assembled paracrystals disassembled completely when shifted to 37 degrees C, indicating that assembly does not greatly improve the thermostability of these tail fragments. The melting temperatures of individual Dictyostelium myosin-II tail coiled-coils under both low and high ionic strength conditions that prohibit paracrystal assembly are extremely low, 21 degrees C and 28 degrees C, respectively. These data are consistent with reversible thermal denaturation of the coiled-coil as the most likely explanation for assembly incompetence under either very low ionic strength or high temperature conditions. Assembled paracrystals of a structurally similar fragment of nonmuscle myosin-IIA were far more thermodynamically stable than their Dictyostelium counterparts at the temperatures examined here.

McMains, V. C., X. H. Liao, et al. (2008). "Oscillatory signaling and network responses during the development of Dictyostelium discoideum." Ageing Res Rev 7(3): 234-248.
	Periodic biological variations reflect interactions among molecules and cells, or even organisms. The Dictyostelium cAMP oscillatory circuit is a highly robust example. cAMP oscillations in Dictyostelium arise intracellularly by a complex interplay of activating and inhibiting pathways, are transmitted extracellularly, and synchronize an entire local population. Once established, cAMP signal-relay persists stably for hours. On a two-dimensional surface, >100,000 cells may form a single coordinated territory. In suspension culture, >10(10) cells can oscillate in harmony. This review focuses on molecular mechanisms that cyclically activate and attenuate signal propagation and on chemotactic responses to oscillatory wave progression.

Meinhardt, H. (2008). "Models of biological pattern formation: From elementary steps to the organization of embryonic axes." Curr Top Dev Biol 81: 1-63.
	An inroad into an understanding of the complex molecular interactions on which development is based can be achieved by uncovering the minimum requirements that describe elementary steps and their linkage. Organizing regions and other signaling centers can be generated by reactions that involve local self-enhancement coupled to antagonistic reactions of longer range. More complex patterns result from a chaining of such reactions in which one pattern generates the prerequisites for the next. Patterning along the single axis of radial symmetric animals including the small freshwater polyp hydra can be explained in this way. The body pattern of such ancestral organisms evolved into the brain of higher organisms, while trunk and midline formation are later evolutionary additions. The equivalent of the hydra organizer is the blastopore, for instance, the marginal zone in amphibians. It organizes the anteroposterior axis. The Spemann organizer, located on this primary organizer, initiates and elongates the midline, which is responsible for the dorsoventral pattern. In contrast, midline formation in insects is achieved by an inhibitory signal from a dorsal organizer that restricts the midline to the ventral side. Thus, different modes of midline formation are proposed to be the points of no return in the separation of phyla. The conversion of the transient patterns of morphogenetic signaling into patterns of stable gene activation can be achieved by genes whose gene products have a positive feedback on the activity of their own gene. If several such autoregulatory genes mutually exclude each other, a cell has to make an unequivocal decision to take a particular pathway. Under the influence of a gradient, sharply confined regions with particular determinations can emerge. Borders between regions of different gene activities, and the areas of intersection of two such borders, become the new signaling centers that initiate secondary embryonic fields. As required for leg and wing formation, these new fields emerge in pairs at defined positions, with defined orientation and left-right handedness. Recent molecular-genetic results provide strong support for theoretically predicted interactions. By computer simulations it is shown that the regulatory properties of these models correspond closely to experimental observations (animated simulations are available at www.eb.tuebingen.mpg.de/meinhardt). (c) 2008, Elsevier Inc.

Menotta, M., A. Amicucci, et al. (2008). "Molecular and functional characterization of a Rho GDP dissociation inhibitor in the filamentous fungus Tuber borchii." BMC Microbiol 8: 57.
	BACKGROUND: Small GTPases of the Rho family function as tightly regulated molecular switches that govern important cellular functions in eukaryotes. Several families of regulatory proteins control their activation cycle and subcellular localization. Members of the guanine nucleotide dissociation inhibitor (GDI) family sequester Rho GTPases from the plasma membrane and keep them in an inactive form. RESULTS: We report on the characterization the RhoGDI homolog of Tuber borchii Vittad., an ascomycetous ectomycorrhizal fungus. The Tbgdi gene is present in two copies in the T. borchii genome. The predicted amino acid sequence shows high similarity to other known RhoGDIs. Real time PCR analyses revealed an increased expression of Tbgdi during the phase preparative to the symbiosis instauration, in particular after stimulation with root exudates extracts, that correlates with expression of Tbcdc42. In a translocation assay TbRhoGDI was able to solubilize TbCdc42 from membranes. Surprisingly, TbRhoGDI appeared not to interact with S. cerevisiae Cdc42, precluding the use of yeast as a surrogate model for functional studies. To study the role of TbRhoGDI we performed complementation experiments using a RhoGDI null strain of Dictyostelium discoideum, a model organism where the roles of Rho signaling pathways are well established. For comparison, complementation with mammalian RhoGDI1 and LyGDI was also studied in the null strain. Although interacting with Rac1 isoforms, TbRhoGDI was not able to revert the defects of the D. discoideum RhoGDI null strain, but displayed an additional negative effect on the cAMP-stimulated actin polymerization response. CONCLUSION: T. borchii expresses a functional RhoGDI homolog that appears as an important modulator of cytoskeleton reorganization during polarized apical growth that antecedes symbiosis instauration. The specificity of TbRhoGDI actions was underscored by its inability to elicit a growth defect in S. cerevisiae or to compensate the loss of a D. discoideum RhoGDI. Knowledge of the cell signaling at the basis of cytoskeleton reorganization of ectomycorrhizal fungi is essential for improvements in the production of mycorrhized plant seedlings used in timberland extension programs and fruit body production.

Mettetal II, J. T. (2008). Signal processing and decision making in single cells. United States -- Massachusetts, Massachusetts Institute of Technology.
	Cells are not simple passive observers oblivious to their environment, but sense and adapt to environmental changes in order to thrive. In addition to sensing the presence of signals in the environment, cells can extract information relating to the dynamics and spatial location of these signals and implement a response to these extracellular perturbations. This work examines a variety of signal-processing and decision-making processes across several different organisms. To explore the connection between biological network topology and temporal signal processing, we study how periodic signals are propagated in the Hog1 osmotic-response pathway of the budding yeast Saccharomyces cerevisiae . Utilizing systems identification tools from control engineering, we study how the cells rapidly and robustly maintain osmotic homeostasis. By measuring the expression level of key proteins we begin to understand how fluctuating environments regulate gene expression. The lac operon in Escherichia coli has the ability to display a bistable, "all-or-nothing" response to sugar. To understand how noise drives transitions between these two stable states, we measure switching dynamics in a population of cells. A simple model is constructed that can make predictions about system behavior unavailable from a deterministic model. Further, by measuring individual switching events in a similar bistable system implemented in the Galactose utilization pathway of Saccharomyces cerevisiae , we find that correlations in switching times of related individuals can be explained in terms of correlations in levels of key regulatory proteins. Many single celled organisms, such as the slime mold Dictyostelium discoideum , can sense and respond to concentration gradients of extracellular signaling molecules. We find that the cells' ability to detect an extracellular signal is influenced by an asymmetric intracellular signal, which varies in direction and magnitude from cell-to-cell. Further, a model that accounts for both signals predicts the observed population response to directed stimuli. Finally, we explore a "bet-hedging" strategy for fluctuating environments with an engineered population of Saccharomyces cerevisiae cells that randomly switch between two phenotypes. Each phenotype is fit to one of two alternating environments. We find that to optimize fitness, cells must tune the phenotypic transition rates in accordance with the rate of environmental transitions. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)

Miyagishima, S. Y., H. Kuwayama, et al. (2008). "Evolutionary linkage between eukaryotic cytokinesis and chloroplast division by dynamin proteins." Proc Natl Acad Sci U S A 105(39): 15202-15207.
	Chloroplasts have evolved from a cyanobacterial endosymbiont and been retained for more than 1 billion years by coordinated chloroplast division in multiplying eukaryotic cells. Chloroplast division is performed by ring structures at the division site, encompassing both the inside and the outside of the two envelopes. A part of the division machinery is derived from the cyanobacterial cytokinetic activity based on the FtsZ protein. In contrast, other parts of the division machinery involve proteins specific to eukaryotes, including a member of the dynamin family. Each member of the dynamin family is involved in the division or fusion of a distinct eukaryotic membrane system. To gain insight into the kind of ancestral dynamin protein and eukaryotic membrane activity that evolved to regulate chloroplast division, we investigated the functions of the dynamin proteins that are most closely related to chloroplast division proteins. These proteins in the amoeba Dictyostelium discoideum and Arabidopsis thaliana localize at the sites of cell division, where they are involved in cytokinesis. Our results suggest that the dynamin for chloroplast division is derived from that involved in eukaryotic cytokinesis. Therefore, the chloroplast division machinery is a mixture of bacterial and eukaryotic cytokinesis components, with the latter a key factor in the synchronization of endosymbiotic cell division with host cell division, thus helping to establish the permanent endosymbiotic relationship.

Mondal, S., D. Bakthavatsalam, et al. (2008). "Linking Ras to myosin function: RasGEF Q, a Dictyostelium exchange factor for RasB, affects myosin II functions." J Cell Biol 181(5): 747-760.
	Ras guanine nucleotide exchange factor (GEF) Q, a nucleotide exchange factor from Dictyostelium discoideum, is a 143-kD protein containing RasGEF domains and a DEP domain. We show that RasGEF Q can bind to F-actin, has the potential to form complexes with myosin heavy chain kinase (MHCK) A that contain active RasB, and is the predominant exchange factor for RasB. Overexpression of the RasGEF Q GEF domain activates RasB, causes enhanced recruitment of MHCK A to the cortex, and leads to cytokinesis defects in suspension, phenocopying cells expressing constitutively active RasB, and myosin-null mutants. RasGEF Q(-) mutants have defects in cell sorting and slug migration during later stages of development, in addition to cell polarity defects. Furthermore, RasGEF Q(-) mutants have increased levels of unphosphorylated myosin II, resulting in myosin II overassembly. Collectively, our results suggest that starvation signals through RasGEF Q to activate RasB, which then regulates processes requiring myosin II.

Mortimer, D., T. Fothergill, et al. (2008). "Growth cone chemotaxis." Trends Neurosci 31(2): 90-98.
	Wiring up the nervous system depends on the precise guidance of axonal growth cones to their targets. A key mechanism underlying this guidance is chemotaxis, whereby growth cones detect and follow molecular gradients. Although recent work has uncovered many of the molecules involved in this process, the mechanisms underlying chemotactic axon guidance are still unclear. Here we compare growth cones with neutrophils and Dictyostelium discoideum, systems for which a clear conceptual framework for chemotaxis has recently emerged. This analogy suggests particular ways in which the three key steps of directional sensing, polarisation and motility might be implemented in chemotaxing growth cones.

Muramoto, T. and J. R. Chubb (2008). "Live imaging of the Dictyostelium cell cycle reveals widespread S phase during development, a G2 bias in spore differentiation and a premitotic checkpoint." Development 135(9): 1647-1657.
	The regulation of the Dictyostelium cell cycle has remained ambiguous owing to difficulties in long-term imaging of motile cells and a lack of markers for defining cell cycle phases. There is controversy over whether cells replicate their DNA during development, and whether spores are in G1 or G2 of the cell cycle. We have introduced a live-cell S-phase marker into Dictyostelium cells that allows us to precisely define cycle phase. We show that during multicellular development, a large proportion of cells undergo nuclear DNA synthesis. Germinating spores enter S phase only after their first mitosis, indicating that spores are in G2. In addition, we demonstrate that Dictyostelium heterochromatin is copied late in S phase and replicates via accumulation of replication factors, rather than recruitment of DNA to pre-existing factories. Analysis of variability in cycle times indicates that regulation of the cycle manifests at a single random transition in G2, and we present the first identified checkpoint in Dictyostelium, which operates at the G2-M transition in response to DNA damage.

Nag, D. K., I. Tikhonenko, et al. (2008). "Disruption of four kinesin genes in Dictyostelium." BMC Cell Biol 9: 21.
	BACKGROUND: Kinesin and dynein are the two families of microtubule-based motors that drive much of the intracellular movements in eukaryotic cells. Using a gene knockout strategy, we address here the individual function(s) of four of the 13 kinesin proteins in Dictyostelium. The goal of our ongoing project is to establish a minimal motility proteome for this basal eukaryote, enabling us to contrast motor functions here with the often far more elaborate motor families in the metazoans. RESULTS: We performed individual disruptions of the kinesin genes, kif4, kif8, kif10, and kif11. None of the motors encoded by these genes are essential for development or viability of Dictyostelium. Removal of Kif4 (kinesin-7; CENP-E family) significantly impairs the rate of cell growth and, when combined with a previously characterized dynein inhibition, results in dramatic defects in mitotic spindle assembly. Kif8 (kinesin-4; chromokinesin family) and Kif10 (kinesin-8; Kip3 family) appear to cooperate with dynein to organize the interphase radial microtubule array. CONCLUSION: The results reported here extend the number of kinesin gene disruptions in Dictyostelium, to now total 10, among the 13 isoforms. None of these motors, individually, are required for short-term viability. In contrast, homologs of at least six of the 10 kinesins are considered essential in humans. Our work underscores the functional redundancy of motor isoforms in basal organisms while highlighting motor specificity in more complex metazoans. Since motor disruption in Dictyostelium can readily be combined with other motility insults and stresses, this organism offers an excellent system to investigate functional interactions among the kinesin motor family.

Nagasaki, A. and T. Q. Uyeda (2008). "Chemotaxis-mediated scission contributes to efficient cytokinesis in Dictyostelium." Cell Motil Cytoskeleton 65(11): 896-903.
	Interphase amoeba of Entamoeba invadens are attracted to the furrowing region of a neighboring dividing cell to assist with the division. A seemingly similar behavior has been observed in Dictyostelium discoideum, but in this case, it has not been shown whether the movements were truly directed toward the furrowing region or whether they have any relevance. We thus used myosin II-null cells, which spend more time than wild type cells in cytokinesis, and successfully demonstrated that nearly half of the division events involve the attraction of a neighbor cell to the furrowing region. Cells lacking the beta subunit of the trimeric G protein (Gbeta), which are incapable of chemotaxis, did not show such midwifery. Culturing wild type cells flattened under agarose sheets also slowed the cytokinesis process, and this allowed us to demonstrate that phosphatidylinositol trisphosphate was enriched in the anterior region of midwifing cells, consistent with the view that midwifery in D. discoideum is also chemotaxis. On substrates, while only 3.6% of wild type cells were multinucleate, 8.1% of Gbeta-null cells were multinucleate, and this was reduced to 3.4% when they were surrounded by wild type cells. Conversely, multinucleated wild type cells increased to 6.8% when they were surrounded by Gbeta-null cells. Thus, Gbeta-null cells frequently fail to divide because they cannot assist each other's division and midwifery ensures successful cytokinesis in Dictyostelium discoideum.

Nagayama, K., S. Itono, et al. (2008). "Antisense RNA inhibition of the beta subunit of the Dictyostelium discoideum mitochondrial processing peptidase induces the expression of mitochondrial proteins." Biosci Biotechnol Biochem 72(7): 1836-1846.
	We cloned and characterized a cDNA encoding the Dictyostelium discoideum beta subunit of mitochondrial processing peptidase (Ddbeta-MPP). Western blot analysis of the mitochondrial subfractions revealed that Ddbeta-MPP is located in the mitochondrial matrix and membrane, whereas Dd(alpha)-MPP, another subunit of DdMPP, is located only in the matrix. Although expression of Ddbeta-MPP mRNA is down-regulated during early development, the level of the Ddbeta-MPP protein is constant throughout the Dictyostelium life cycle. In a transformant expressing the antisense RNA of the beta-MPP gene, unexpectedly, the beta-MPP protein increased about 1.8-fold relative to the wild type, and its mRNA increased 4.5-fold. Expression of other mitochondrial proteins, alpha-MPP and Cox IV, was also induced. These results suggest that antisense RNA inhibition of the beta-MPP gene induces gene expression of mitochondrial proteins, presumably in a retrograde signaling manner. This is the pathway of the transfer of information from the mitochondria to the nucleus.

Nakagawa, S., Y. Niimura, et al. (2008). "Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes." Nucl Acids Res 36(3): 861-871.
	Understanding regulatory mechanisms of protein synthesis in eukaryotes is essential for the accurate annotation of genome sequences. Kozak reported that the nucleotide sequence GCCGCC (A/G)CCAUGG (AUG is the initiation codon) was frequently observed in vertebrate genes and that this 'consensus' sequence enhanced translation initiation. However, later studies using invertebrate, fungal and plant genes reported different 'consensus' sequences. In this study, we conducted extensive comparative analyses of nucleotide sequences around the initiation codon by using genomic data from 47 eukaryote species including animals, fungi, plants and protists. The analyses revealed that preferred nucleotide sequences are quite diverse among different species, but differences between patterns of nucleotide bias roughly reflect the evolutionary relationships of the species. We also found strong biases of A/G at position 23, A/C at position 22 and C at position +5 that were commonly observed in all species examined. Genes with higher expression levels showed stronger signals, suggesting that these nucleotides are responsible for the regulation of translation initiation. The diversity of preferred nucleotide sequences around the initiation codon might be explained by differences in relative contributions from two distinct patterns, GCCGCCAUG and AAAAAAAUG, which implies the presence of multiple molecular mechanisms for controlling translation initiation.

Nakajima, A. and K. Kaneko (2008). "Regulative differentiation as bifurcation of interacting cell population." J Theor Biol 253(4): 779-787.
	In multicellular organisms, several cell states coexist. For determining each cell type, cell-cell interactions are often essential, in addition to intracellular gene expression dynamics. Based on dynamical systems theory, we propose a mechanism for cell differentiation with regulation of populations of each cell type by taking simple cell models with gene expression dynamics. By incorporating several interaction kinetics, we found that the cell models with a single intracellular positive-feedback loop exhibit a cell fate switching, with a change in the total number of cells. The number of a given cell type or the population ratio of each cell type is preserved against the change in the total number of cells, depending on the form of cell-cell interaction. The differentiation is a result of bifurcation of cell states via the intercellular interactions, while the population regulation is explained by self-consistent determination of the bifurcation parameter through cell-cell interactions. The relevance of this mechanism to development and differentiation in several multicellular systems is discussed. (C) 2008 Elsevier Ltd. All rights reserved.

Naorem, A. and P. P. Sadhale (2008). "Identification and characterization of DdRPB4, a subunit of Dictyostelium discoideum RNA polymerase II." Biochem Biophys Res Commun 377(4): 1141-1146.
	Rpb4, the fourth largest subunit of the eukaryotic RNA polymerase II (RNAPII), is required for growth at extreme temperatures and for an appropriate response to nutrient starvation in yeast. Sequence homologs of Rpb4 are found in most sequenced genomes from yeast to humans. To elucidate the role of this subunit in nutrient starvation, we chose Dictyostelium discoideum, a soil amoeba, which responds to nutrient deprivation by undergoing a complex developmental program. Here we report the identification of homolog of Saccharomyces cerevisiae RPB4 in D. discoideum. Localization and complementation studies suggest that Rpb4 is functionally conserved. DdRPB4 transcript and protein levels are developmentally regulated. Although DdRPB4 could not be deleted, overexpression revealed that the Rpb4 protein is essential for cell survival and is regulated stringently at the post-transcriptional level in D. discoideum. Thus maintaining a critical level of Rpb4 is important for this organism.

Newman, T. J. (2008). "Grid-free models of multicellular systems, with an application to large-scale vortices accompanying primitive streak formation." Curr. Top. Dev. Biol. 81: 157-182.
	
Nunez-Corcuera, B., I. Serafimidis, et al. (2008). "A new protein carrying an NmrA-like domain is required for cell differentiation and development in Dictyostelium discoideum." Dev Biol 321(2): 331-342.
	We have isolated a Dictyostelium mutant unable to induce expression of the prestalk-specific marker ecmB in monolayer assays. The disrupted gene, padA, leads to a range of phenotypic defects in growth and development. We show that padA is essential for growth, and we have generated a thermosensitive mutant allele, padA(-). At the permissive temperature, mutant cells grow poorly; they remain longer at the slug stage during development and are defective in terminal differentiation. At the restrictive temperature, growth is completely blocked, while development is permanently arrested prior to culmination. padA(-) slugs are deficient in prestalk A cell differentiation and present an abnormal ecmB expression pattern. Sequence comparisons and predicted three-dimensional structure analyses show that PadA carries an NmrA-like domain. NmrA is a negative transcriptional regulator involved in nitrogen metabolite repression in Aspergillus nidulans. PadA predicted structure shows a NAD(P)(+)-binding domain, which we demonstrate that is essential for function. We show that padA(-) development is more sensitive to ammonia than wild-type cells and two ammonium transporters, amtA and amtC, appear derepressed during padA(-) development. Our data suggest that PadA belongs to a new family of NAD(P)(+)-binding proteins that link metabolic changes to gene expression and is required for growth and normal development.

Ostrowski, E. A., M. Katoh, et al. (2008). "Kin discrimination increases with genetic distance in a social amoeba." PLoS Biol 6(11): e287.
	In the social amoeba Dictyostelium discoideum, thousands of cells aggregate upon starvation to form a multicellular fruiting body, and approximately 20% of them die to form a stalk that benefits the others. The aggregative nature of multicellular development makes the cells vulnerable to exploitation by cheaters, and the potential for cheating is indeed high. Cells might avoid being victimized if they can discriminate among individuals and avoid those that are genetically different. We tested how widely social amoebae cooperate by mixing isolates from different localities that cover most of their natural range. We show here that different isolates partially exclude one another during aggregation, and there is a positive relationship between the extent of this exclusion and the genetic distance between strains. Our findings demonstrate that D. discoideum cells co-aggregate more with genetically similar than dissimilar individuals, suggesting the existence of a mechanism that discerns the degree of genetic similarity between individuals in this social microorganism.

Palsson, E. (2008). "A 3-D model used to explore how cell adhesion and stiffness affect cell sorting and movement in multicellular systems." J Theor Biol 254(1): 1-13.
	A three-dimensional mathematical model is used to determine the effects of adhesion and cell signalling on cell movements during the aggregation and slug stages of Dictyostelium discoideum (Dd) and to visualize cell sorting. The building blocks of the model are individual deformable ellipsoidal cells, where movement depends on internal parameter state (cell size and stiffness) and on external cues from the neighboring cells, extracellular matrix, and chemical signals. Cell movement and deformation are calculated from equations of motion using the total force acting on each cell, ensuring that forces are balanced. The simulations show that the sorting patterns of prestalk and prespore cells, emerging during the slug stage, depend critically on the type of cell adhesion and not just on chemotactic differences between cells. This occurs because cell size and stiffness can prevent the otherwise faster cells from passing the slower cells. The patterns are distinctively different when the prestalk cells are more or less adhesive than the prespore cells. These simulations suggest that sorting is not solely due to differential chemotaxis, and that differences in both adhesion strength and type between different cell types play a very significant role, both in Dictyostelium and other systems.

Patel, H., I. Konig, et al. (2008). "The multi-FERM-domain-containing protein FrmA is required for turnover of paxillin-adhesion sites during cell migration of Dictyostelium." J Cell Sci 121(Pt 8): 1159-1164.
	FERM domain proteins, including talins, ERMs, FAK and certain myosins, regulate connections between the plasma membrane, cytoskeleton and extracellular matrix. Here we show that FrmA, a Dictyostelium discoideum protein containing two talin-like FERM domains, plays a major role in normal cell shape, cell-substrate adhesion and actin cytoskeleton organisation. Using total internal reflection fluorescence (TIRF) microscopy we show that FrmA-null cells are more adherent to substrate than wild-type cells because of an increased number, persistence and mislocalisation of paxillin-rich cell-substrate adhesions, which is associated with decreased motility. We show for the first time that talinA colocalises with paxillin at the distal ends of filopodia to form cell-substrate adhesions and indeed arrives prior to paxillin. After a period of colocalisation, talin leaves the adhesion site followed by paxillin. Whereas talinA-rich spots turnover prior to the arrival of the main body of the cell, paxillin-rich spots turn over as the main body of the cell passes over it. In FrmA-null cells talinA initially localises to cell-substrate adhesion sites at the distal ends of filopodia but paxillin is instead localised to stabilised adhesion sites at the periphery of the main cell body. This suggests a model for cell-substrate adhesion in Dictyostelium whereby the talin-like FERM domains of FrmA regulate the temporal and spatial control of talinA and paxillin at cell-substrate adhesion sites, which in turn controls adhesion and motility.

Pieters, J. (2008). "Coronin 1 in innate immunity." Subcell Biochem 48: 116-123.
	The WD repeat containing family of coronin proteins is generally referred to as F-actin-interacting proteins. While in lower eukaryotes such as Dictyostelium discoideum, the single short coronin protein regulates several F-actin dependent processes such as motility, phagocytosis and macropinocytosis, the function of any of the seven coronin isoforms in mammals is far less understood. This chapter describes the current knowledge on mammalian coronin 1 (coronin 1A), the closest homologue to Dictyostelium short coronin that is exclusively expressed in leukocytes. Recent work based on biochemical, molecular biological and genetic analysis suggest that coronin 1 has evolved a function that is quite different from the F-actin regulatory function of Dictyostelium short coronin. Rather, mammalian coronin 1 is involved in the regulation of leukocyte specific signaling events.

Pollitt, A. Y. and R. H. Insall (2008). "Abi mutants in Dictyostelium reveal specific roles for the SCAR/WAVE complex in cytokinesis." Curr Biol 18(3): 203-210.
	Actin polymerization drives multiple cell processes involving movement and shape change. SCAR/WAVE proteins connect signaling to actin polymerization through the activation of the Arp2/3 complex. SCAR/WAVE is normally found in a complex with four other proteins: PIR121, Nap1, Abi2,and HSPC300 (Figure S1A available online) [1-3]. However,there is no consensus as to whether the complex functions as an unchanging unit or if it alters its composition in response to stimulation, as originally proposed by Edenet al. [1]. It also is unclear whether complex members exclusively regulate SCAR/WAVEs or if they have additional targets [4-6]. Here, we analyze the roles of the unique Dictyostelium Abi. We find that abiA null mutants show less severe defects in motility than do scar null cells, indicating--unexpectedly--that SCAR retains partial activity in the absence of Abi. Furthermore, abiA null mutants have a serious defect in cytokinesis, which is not seen in other SCAR complex mutants and is seen only when SCAR itself is present. Detailed examination reveals that normal cytokinesis requires SCAR activity, apparently regulated through multiple pathways.

Ragaz, C., H. Pietsch, et al. (2008). "The Legionella pneumophila phosphatidylinositol-4 phosphate-binding type IV substrate SidC recruits endoplasmic reticulum vesicles to a replication-permissive vacuole." Cell Microbiol 10(12): 2416-2433.
	Legionella pneumophila, the causative agent of Legionnaires' disease, uses the intracellular multiplication/defective organelle trafficking (Icm/Dot) type IV secretion system to establish within amoebae and macrophages an endoplasmic reticulum (ER)-derived replication-permissive compartment, the Legionella-containing vacuole (LCV). The Icm/Dot substrate SidC and its paralogue SdcA anchor to LCVs via phosphatidylinositol-4 phosphate [PtdIns(4)P]. Here we identify the unique 20 kDa PtdIns(4)P-binding domain of SidC, which upon heterologous expression in Dictyostelium binds to LCVs and thus is useful as a PtdIns(4)P-specific probe. LCVs harbouring L. pneumophilaDeltasidC-sdcA mutant bacteria recruit ER and ER-derived vesicles less efficiently and carry endosomal but not lysosomal markers. The phenotypes are complemented by supplying sidC on a plasmid. L. pneumophilaDeltasidC-sdcA grows at wild-type rate in calnexin-negative LCVs, suggesting that communication with the ER is dispensable for establishing a replicative compartment. The amount of SidC and calnexin is directly proportional on isolated LCVs, and in a cell-free system, the recruitment of calnexin-positive vesicles to LCVs harbouring DeltasidC-sdcA mutant bacteria is impaired. Beads coated with purified SidC or its 70 kDa N-terminal fragment recruit ER vesicles in Dictyostelium and macrophage lysates. Our results establish SidC as an L. pneumophila effector protein, which anchors to PtdIns(4)P on LCVs and recruits ER vesicles to a replication-permissive vacuole.

Rappel, W. J. and H. Levine (2008). "Receptor noise limitations on chemotactic sensing." Proc Natl Acad Sci U S A 105(49): 19270-19275.
	Chemotactic eukaryotic cells are able to detect chemoattractant gradients that are both shallow and have a low background concentration. Under these conditions, the noise in the number of bound receptors can be significant and needs to be taken into account in determining the directional sensing process. Here, we quantify numerically the number of bound receptors on the membrane of a disk-shaped cell by using a numerical Monte Carlo tool. The obtained time traces of the receptor occupancy can be used as inputs for any directional sensing model. We investigate the response of the local excitation global inhibition model and a recently developed balanced inactivation model. We determine a measure for the motility of the cell for each model, based on the relevant output variable, as a function of experimental parameters, resulting in several experimentally testable predictions. Furthermore, we show that these two models behave in a qualitatively different fashion when the background concentration is varied. Thus, to properly characterize the sensitivity of cells to receptor occupancy, it is not sufficient to examine the input signal. Rather, one needs to take into account the response of the second messenger pathway.

Rapuru, S. K. (2008). Chemical composition and anti-proliferative activity of several medicinal plants. United States -- North Carolina, The University of North Carolina at Greensboro.
	Plants are valuable sources of medicinal compounds and their use for healing is well known from ancient times. Natural drugs obtained from plants represent about 25% of the prescription drug market in the United States. Plants have a long history of use in the treatment of various cancer types. Currently, 60% of the anticancer agents available in the market are derived from natural sources. Since phytoconstituents play a vital role in the discovery of various anticancer drugs, they have been chosen as the area of focus for our research. In this proposed study, four medicinal plants with reported anticancer activity were selected ( Hydrastis canadensis, Curcuma longa, Zingiber officinalis , and Alpinia officinarum ). All these plants were extracted by percolation and tested for anti-proliferative activity against Dictyostelium cells. C. longa, Z. officinalis and A. officinarum organic extracts all showed significant anti-proliferative activity in this preliminary bioassay. Of the three active extracts, the turmeric extract was chosen for further investigation because of its great historical significance and the promising results of recent phase I clinical trials. Using flash chromatography, a total of nine fractions were obtained from the complex C. longa organic extract. Curcumin in these fractions was identified and quantified using high performance liquid chromatography - electrospray ionization mass spectrometry (HPLC-ESI-MS). Other active components (demethoxycurcumin, bisdemethoxycurcumin and ar-tumerone) were also characterized using the same system. All these fractions were then tested for in vitro anti-proliferative activity against MCF-7 cells using the XTT assay to determine whether activity correlates with the presence of curcumin in the fractions, or whether other (perhaps unidentified) compounds are involved. The results indicated that the major component curcumin was responsible for the majority of the anti-proliferative activity of the complex turmeric extract. Although no synergistic activity was seen for the various constituents present in the complex extract in this case, a novel approach for probing potential synergistic or additive effects was demonstrated. This approach could be applied to future investigations of synergistic or additive activity of medicinal plants.

Reichl, E. M. (2008). Cytokinesis contraction through the remodeling of a disordered actin network. United States -- Maryland, The Johns Hopkins University.
	Contractile networks are fundamental to many cellular functions, particularly cytokinesis and cell motility. Here, we analyze a contractile network that drives furrow ingression during Dictyostelium cytokinesis. The ultimate goal of all signaling pathways in cytokinesis is to control the mechanical separation of the mother cell into two daughter cells. Because of the intrinsic mechanical nature of cytokinesis, it is essential to fully understand how cell shapes and material properties of the cell are generated, how these shapes and material properties create force and how motor proteins, such as myosin-II, modify the system to achieve successful cytokinesis. Contrary to the assumptions of the contractile ring hypothesis, these equatorial actin and myosin-II networks are highly disordered, similar to observations in mammalian cells. Myosin-II generates regional mechanics by increasing cleavage furrow cortical viscoelasticity and slows furrow ingression during late cytokinesis as compared to myoII mutant cleavage furrows. Crosslinking proteins similarly contribute to cell mechanics and have spatially distinct kinetics with the slower crosslinkers found in the cleavage furrow cytoskeleton. The total F-actin concentration must also be regulated by proteins such as the actin-severing protein cofilin. Thereby, myosin-II and actin crosslinkers increase equatorial cortical tension and generate a more elastic network, allowing for contractility in the absence of a circumferential, highly ordered cytoskeletal array.

Reichl, E. M., Y. Ren, et al. (2008). "Interactions between myosin and actin crosslinkers control cytokinesis contractility dynamics and mechanics." Curr Biol 18(7): 471-480.
	INTRODUCTION: Contractile networks are fundamental to many cellular functions, particularly cytokinesis and cell motility. Contractile networks depend on myosin-II mechanochemistry to generate sliding force on the actin polymers. However, to be contractile, the networks must also be crosslinked by crosslinking proteins, and to change the shape of the cell, the network must be linked to the plasma membrane. Discerning how this integrated network operates is essential for understanding cytokinesis contractility and shape control. Here, we analyzed the cytoskeletal network that drives furrow ingression in Dictyostelium. RESULTS: We establish that the actin polymers are assembled into a meshwork and that myosin-II does not assemble into a discrete ring in the Dictyostelium cleavage furrow of adherent cells. We show that myosin-II generates regional mechanics by increasing cleavage furrow stiffness and slows furrow ingression during late cytokinesis as compared to myoII nulls. Actin crosslinkers dynacortin and fimbrin similarly slow furrow ingression and contribute to cell mechanics in a myosin-II-dependent manner. By using FRAP, we show that the actin crosslinkers have slower kinetics in the cleavage furrow cortex than in the pole, that their kinetics differ between wild-type and myoII null cells, and that the protein dynamics of each crosslinker correlate with its impact on cortical mechanics. CONCLUSIONS: These observations suggest that myosin-II along with actin crosslinkers establish local cortical tension and elasticity, allowing for contractility independent of a circumferential cytoskeletal array. Furthermore, myosin-II and actin crosslinkers may influence each other as they modulate the dynamics and mechanics of cell-shape change.

Rericha, E. C. and C. A. Parent (2008). "Steering in quadruplet: the complex signaling pathways directing chemotaxis." Sci Signal 1(22): pe26.
	Studies in the social amoeba Dictyostelium discoideum reveal that signaling cascades coordinating chemotactic directional sensing and migration are complex, with redundant pathways emerging as cells differentiate. Lack of accumulation of the leading-edge marker phosphatidylinositol-3,4,5-trisphosphate can be compensated by a pathway containing phospholipase A2 (PLA2) in early developed cells and guanylyl cyclase (GC) in later developed, polarized cells. Because numerous signaling networks operational during Dictyostelium chemotaxis are conserved in mammalian cells, PLA2 and GC pathways may also be effective in higher eukaryotes, providing avenues for future research.

Ritchie, A. V., S. van Es, et al. (2008). "From drought sensing to developmental control: evolution of cyclic AMP signaling in social amoebas." Mol Biol Evol 25(10): 2109-2118.
	Amoebas and other protists commonly encyst when faced with environmental stress. Although little is known of the signaling pathways that mediate encystation, the analogous process of spore formation in dictyostelid social amoebas is better understood. In Dictyostelium discoideum, secreted cyclic AMP (cAMP) mediates the aggregation of starving amoebas and induces the differentiation of prespore cells. Intracellular cAMP acting on cAMP-dependent protein kinase (PKA) triggers the maturation of spores and prevents their germination under the prevalent conditions of high osmolality in the spore head. The osmolyte-activated adenylate cyclase, ACG, produces cAMP for prespore differentiation and inhibition of spore germination. To retrace the origin of ACG function, we investigated ACG gene conservation and function in species that span the dictyostelid phylogeny. ACG genes, osmolyte-activated ACG activity, and osmoregulation of spore germination were detected in species that represent the 4 major groups of Dictyostelia. Unlike the derived species D. discoideum, many basal Dictyostelia have retained the ancestral mechanism of encystation from solitary amoebas. In these species and in solitary amoebas, encystation is independently triggered by starvation or by high osmolality. Osmolyte-induced encystation was accompanied by an increase in cAMP and prevented by inhibition of PKA, indicating that ACG and PKA activation mediate this response. We propose that high osmolality signals drought in soil amoebas and that developmental cAMP signaling in the Dictyostelia has evolved from this stress response.

Rivero, F. (2008). "Endocytosis and the actin cytoskeleton in Dictyostelium discoideum." Int Rev Cell Mol Biol 267: 343-397.
	Endocytosis, an essential process of all eukaryotic cells, requires the actin cytoskeleton for proper functioning. The soil amoeba Dictyostelium discoideum is well known for its contribution to the actin cytoskeleton field. The genetic tractability and the availability of appropriate tools have made of Dictyostelium an attractive model for studies of endocytosis and vesicle trafficking as well. These tools include a large palette of fluorescent protein fusions and the combination of improved fractionation methods with high throughput techniques along with the recently propagated use of the amoeba a host for microbial pathogens. In this review I discuss in a comprehensive manner the evidence accumulated in the literature towards a participation of components of the microfilament system of D. discoideum in endocytic trafficking and conclude with a model that describes the sequence of events and the components involved during the well-investigated uptake phase of the endocytic process in the soil amoeba.

Rodriguez, M., B. Kim, et al. (2008). "MPL1, a novel phosphatase with leucine-rich repeats, is essential for proper ERK2 phosphorylation and cell motility." Euk Cell 7(6): 958-966.
	The novel Dictyostelium phosphatase MPL1 contains six leucine-rich repeats at the amino-terminal end and a phosphatase domain at the carboxyl end. Similarly architectured phosphatases exist among other protozoa, such as Entamoeba histolytica, Leishmania major, and Trypanosoma cruzi. MPL1 was strongly induced after 5 h of development; ablation by homologous recombination led to defective streaming and aggregation during development. In addition, cyclic AMP (cAMP)-pulsed mpl1(-) cells showed reduced random and directional motility. At the molecular level, mpl1(-) cells displayed higher prestimulus and persistent poststimulus ERK2 phosphorylation in response to cAMP stimulation. Consistent with their phenotype of persistent ERK2 phosphorylation, mpl1(-) cells also displayed an aberrant pattern of cAMP production, resembling that of the regA(-) cells. Reintroduction of a full-length MPL1 into mpl1(-) cells restored aggregation, ERK2 regulation, random and directional motility, and cAMP production similar to wild-type cells. We propose that MPL1 is a novel phosphatase essential for proper regulation of ERK2 phosphorylation and optimal motility during development.

Rohlk, C., M. Rohlfs, et al. (2008). "Properties of the Kinesin-1 motor DdKif3 from Dictyostelium discoideum." Eur. J. Cell Biol. 87: 234-249.
	
Rollins, A. W. (2008). Biogeography, microhabitat associations and structure of the myxomycete and dictyostelid communities associated with North American grasslands. United States -- Arkansas, University of Arkansas.
	The distribution and ecology of two groups of eumycetozoans, the dictyostelids and the myxomycetes, were, studied in nine study areas that spanned both longitudinal and latitudinal gradients across the grasslands of North America. Several ecological patterns were observed for both groups. Overall, the two groups were found to be common components of the biota of grassland ecosystem. Dictyostelid species richness, diversity, and abundance decreased from the tall grasslands to short grasslands, presumably in response to the gradient of decreasing precipitation. The assemblages of species associated with open grasslands and forests displayed appreciable differences. Parameters associated with soil chemistry and disturbance regimes were found to affect the dictyostelid assemblages. Myxomycete assemblages were found to become more dissimilar westward along the precipitation gradient. Furthermore, there was a surprising difference in the frequency of myxomycete recovery between grass and forb microhabitats. In addition, the myxomycete assemblages associated with open grasslands and gallery forests were quite different. The results of the present study support the importance of the microhabitats in determining the assemblages of species present at a particular locality.

Romeralo, M. and C. Lado (2008). "The biodiversity of dictyostelids in a Spanish Biosphere Reserve." Nova Hedwigia 87(1-2): 247-259.
	The results of a biodiversity survey of the dictyostelid cellular slime moulds from Somiedo Natural Park and Biosphere Reserve (Asturias, Spain) are presented. Surface soil samples were collected during 2005 from different forests and were plated out for cellular slime moulds. During this study 12 species of dictyostelids were isolated, belonging to two of the three recognized genera of the group, Dictyostelium and Polysphondylium. Comments on their taxonomic characters, diversity and distribution, and micrographs of relevant morphological details are included. Dictyostelium macrocephalum is reported for the first time from Europe and Polysphondylium violaceum is a new record for the Mediterranean area.

Russell, T. R. (2008). Cloning & cellular characterization of myosin II heavy chain kinase D from Dictyostelium discoideum. United States -- North Carolina, The University of North Carolina at Greensboro.
	The thesis research presented here focused on studies of a novel myosin II heavy chain kinase D (MHCK D) expressed in Dictyostelium discoideum cells. MHCK D is made up of four distinct domains: a short coiled-coil region (Coil), a region rich in serine, asparagine, proline, & glutamine residues (SNPQ), a kinase catalytic domain (Cat), and a WD-repeat segment (WD). A major component of this project was to amplify the Catalytic and WD repeat domains (Cat-WD) from genomic DNA. The Cat-WD truncation of MHCK D was cloned into pTX-GFP & pTX-Flag plasmids for expression in Dictyostelium cells. The recombinant plasmids were electroporated into Dictyostelium cells to over-express the fusion protein (GFP, or flag-tagged). To determine if MHCK D does phosphorylate the Myosin heavy chain, which in turn drives bi-polar filament disassembly, the phenotype of cells over-expressing the Cat-WD domain were compared to the phenotype of Myosin II-null cells and non-recombinant wild type cells. Cells over-expressing the Cat-WD domain from MHCK D, showed a phenotype similar to Myosin II-null cells, indicating that the Cat-WD domain plays a role in Myosin II bi-polar filament disassembly resulting from phosphorylation of the myosin heavy chain. Another aim of the thesis research focused on expression of the mhkd gene during the multi-cellular development cycle of Dictyostelium, using Reverse Transcriptase-PCR (RT-PCR). The results indicate that mhkd is expressed throughout the multi-cellular development cycle, as well as during the vegetative growth phase of Dictyostelium. In summary, the results reveal that the Cat-WD domain of MHCK D drives Myosin II bi-polar filament disassembly leading to defects in cytokinesis, and is expressed in both vegetative cells as well as cells undergoing the multi-cellular development cycle. These studies provide a basis for future research focused on activation, localization, and substrate targeting of MHCK D.

Saito, T., A. Kato, et al. (2008). "DIF-1 induces the basal disc of the Dictyostelium fruiting body." Dev Biol 317(2): 444-453.
	The polyketide DIF-1 induces Dictyostelium amoebae to form stalk cells in culture. To better define its role in normal development, we examined the phenotype of a mutant blocking the first step of DIF-1 synthesis, which lacks both DIF-1 and its biosynthetic intermediate, dM-DIF-1 (des-methyl-DIF-1). Slugs of this polyketide synthase mutant (stlB(-)) are long and thin and rapidly break up, leaving an immotile prespore mass. They have approximately 30% fewer prestalk cells than their wild-type parent and lack a subset of anterior-like cells, which later form the outer basal disc. This structure is missing from the fruiting body, which perhaps in consequence initiates culmination along the substratum. The lower cup is rudimentary at best and the spore mass, lacking support, slips down the stalk. The dmtA(-) methyltransferase mutant, blocked in the last step of DIF-1 synthesis, resembles the stlB(-) mutant but has delayed tip formation and fewer prestalk-O cells. This difference may be due to accumulation of dM-DIF-1 in the dmtA(-) mutant, since dM-DIF-1 inhibits prestalk-O differentiation. Thus, DIF-1 is required for slug migration and specifies the anterior-like cells forming the basal disc and much of the lower cup; significantly the DIF-1 biosynthetic pathway may supply a second signal - dM-DIF-1.

Santorelli, L. A., C. R. L. Thompson, et al. (2008). "Facultative cheater mutants reveal the genetic complexity of cooperation in social amoebae." Nature 451: 1107-1110.
	
Sasaki, K., S. C. Chae, et al. (2008). "An immediate-early gene, srsA: its involvement in the starvation response that initiates differentiation of Dictyostelium cells." Differentiation 76(10): 1093-1103.
	When nutrients are depleted, Dictyostelium cells undergo cell cycle arrest and initiate a differentiation program for survival. We have found a novel gene, srsA, which is rapidly expressed in the first 5 min following the removal of nutrients and is turned off within an hour. This gene encodes a small protein with no significant similarity to previously characterized proteins. Disruption of srsA results in delayed expression of the early genes acaA and carA that encode adenylyl cyclase and the cAMP receptor necessary for chemotactic aggregation, respectively. Streaming is delayed several hours and the aggregates are larger than normal in the mutant strains. These phenotypes are cell-autonomous. Overexpression of srsA also results in delayed aggregation. Some of the slugs of the srsA(OE) strains showed stalked migration reminiscent of the slugs of the related species Dictyostelium mucoroides. The terminal structures formed by srsA(OE) cells were grossly abnormal and contained very few viable spores. When cells overexpressing srsA were developed together with an excess of wild-type cells, the fruiting bodies were still abnormal, indicating that the mutant cells have a dominant effect on late development. These findings suggest that srsA may be involved in both the starvation response and late differentiation.

Satulovsky, J., R. Lui, et al. (2008). "Exploring the control circuit of cell migration by mathematical modeling." Biophys. J. 94: 3671-3683.
	
Sawai, S., X. J. Guan, et al. (2008). "High-throughput analysis of spatio-temporal dynamics in Dictyostelium." Genome Biol. 8: R144 (115 pages).
	
Sawarkar, R., N. Roy, et al. (2008). "Heat shock protein 90 regulates development in Dictyostelium discoideum." J Mol Biol 383(1): 24-35.
	Cytosolic heat shock protein 90 (Hsp90) has been implicated in diverse biological processes such as protein folding, cell cycle control, signal transduction, development, and morphological evolution. Model systems available for studying Hsp90 function either allow ease of manipulation for biochemical studies or facilitate a phenomenological study of its role in influencing phenotype. In this work, we have explored the use of the cellular slime mold Dictyostelium discoideum to examine cellular functions of Hsp90 in relation to its multicellular development. In addition to cloning, purification, biochemical characterization, and examination of its crystal structure, our studies, using a pharmacological inhibitor of Hsp90, demonstrate a role for the cytoplasmic isoform (HspD) in D. discoideum development. Inhibition of HspD function using geldanamycin (GA) resulted in delayed aggregation and arrest of D. discoideum development at the 'mound' stage. Crystal structure of the amino-terminal domain of HspD showed a binding pocket similar to that described for yeast Hsp90. Fluorescence spectroscopy, as well as GA-coupled beads affinity pulldown, confirmed a specific interaction between HspD and GA. The results presented here provide an important insight into the function of HspD in D. discoideum development and emphasize the potential of the cellular slime mold to serve as an effective model for studying the many roles of Hsp90 at cellular and organismal levels.

Schiller, B., J. Voglmeir, et al. (2008). Developmental Changes in N-Glycan Fucosylation in Dictyostelium. Glycobiology.
	Developmental and cohesion defects in Dictyostelium discoideum
have been associated with alterations in the glycosylation pattern.
Therefore the protein-bound N-glycans have been subject to
studies for more than 20 years, so far exact structures have not
been determined. It has been suggested that core α 1,3 fucose
epitopes decrease during development, while addition of
“peripheral fucose” increases. N-glycan preparations as well as
crude lysates were hence prepared of amoeba during growth and
development. Results from Western blotting using an antibody
specific for α 1,3-fucose indicated the presence of this epitope
throughout development, even suggesting an increase. This data
though was contradicted by RP-HPLC, NP-HPLC and massspectrometry
analysis. We thus postulate that the amount of core α
1,3-fucosylated glycans does not increase during development, and
believe the lower binding of antibody to lysates from midlogphase
cells to be due to the highly unusual structure of the major
glycan assembled during growth. This novel glycan contains both
inter- and bisecting N-acetylglucosamine residues as well as core α
1,3-fucose. The amount of this large oligomannosidic glycan
decreases as the cells differentiate while smaller fucosylated
glycans appear, some of them also carrying inter- and bisecting Nacetylglucosamines.
It is well known that especially fucosylated
structures are associated with numerous human diseases. Studying
the alteration of glycans carrying fucose epitopes during the
development of single Dictyostelium discoideum cells to
multicellular fruiting bodies with distinct cell types has the
capability to help to shed light on mechanisms such as cellrecognition
and adhesion.

Schmauch, C. and M. Maniak (2008). "Competition between targeting signals in hybrid proteins provides information on their relative in vivo affinities for subcellular compartments." Eur. J. Cell Biol. 87: 57-68.
	
Schnittler, M. and J. Tesmer (2008). "A habitat colonisation model for spore-dispersed organisms - Does it work with eumycetozoans?" Mycol Res 112: 697-707.
	Spore productivities and establishment probabilities of eumycetozoans were estimated and compared with quantitative data obtained from field surveys, using series of cultures of a given substrate. Spore numbers per spore case were found to increase from one to four in protostelids to up to 10(5)-10(6) in myxomycetes, whereas average spore size decreased slightly from 14.8 mu m for protostelids to 10.3 mu m in myxomycetes. Spore numbers of fructifications calculated from dimensions of spores and fruit bodies were in good agreement with direct counts carried out for six species of myxomycetes. A colonisation model is presented that estimates frequencies (as a percent of successfully colonized habitat islands), which is independent of a given density of spore rain and the sexual system of the species being considered. Whereas asexual species need a minimum spore rain of ca 0.7 spores per habitat island to reach a frequency of 50 %, this figure is at least 2.4-fold higher for sexual species, depending from the incompatibility system assumed. Data from cultures indicate that the maximum potential spore rain is usually three orders of magnitude higher than the minimum figure required to create the observed frequencies. Eumycetozoans seem to follow the evolutionary trends predicted by the model. Species with sexual reproductive systems produce often more spores than asexual ones; many morphospecies haven sexual and asexual strains; and back-conversion from sexual to asexual reproduction occurs occasionally. (C) 2008 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Seale, K. T., R. S. Reiserer, et al. (2008). "Mirrored pyramidal wells for simultaneous multiple vantage point microscopy." J Microsc 232(1): 1-6.
	We report a novel method for obtaining simultaneous images from multiple vantage points of a microscopic specimen using size-matched microscopic mirrors created from anisotropically etched silicon. The resulting pyramidal wells enable bright-field and fluorescent side-view images, and when combined with z-sectioning, provide additional information for 3D reconstructions of the specimen. We have demonstrated the 3D localization and tracking over time of the centrosome of a live Dictyostelium discoideum. The simultaneous acquisition of images from multiple perspectives also provides a five-fold increase in the theoretical collection efficiency of emitted photons, a property which may be useful for low-light imaging modalities such as bioluminescence, or low abundance surface-marker labelling.

Seo, J. H., J. S. Kim, et al. (2008). Glutathione is essential to initiate development in Dictyostelium discoideum. FEBS J.
	Introduction: Glutathione is the most abundant non-protein thiolcontaining
compound and known as a major source of reducing
equivalents in eukaryotes. In Dictyostelium discoideum glutathione is
required for growth and development. Disruption of gcsA encoding cglutamylcysteine
synthetase (GCS), an essential enzyme in glutathione
biosynthesis, resulted in glutathione auxotrophy and failed to develop.
Methods: Cellular reactive oxygen species (ROS) level was measured
by using 2,7-dichlorofluorescin diacetate (DCFH-DA) and detected by
a fluorescence spectrophotometer. And concentration of intracellular
methylglyoxal was analyzed by quantification of quinoxaline, the derivative
of methylglyoxal, with high performance liquid chromatography
(HPLC).
Results: The transcriptional expression of gcsA was induced as aggregation
progressed. To investigate roles of glutathione in development
of D. discoideum, Cellular ROS level was measured. In KAx3 cells, cellular
ROS level was increased as soon as the nutrition exhausted but in
a short time the level was decreased. The cellular ROS level of GCSnull
mutants was higher and sustained longer than KAx3 cells. And
interestingly as D. discoideum started to develop, the concentration of
intracellular methylglyoxal was decreased in both KAx3 and GCS-null
cells. While the level of methylglyoxal in KAx3 cells decreased gradually,
the level of methylglyoxal in GCS-null mutants increased.
Conclusions: According to the above results we hypothesized that
there might be correlations between intracellular ROS, methylglyoxal
and glutathione during early development of D. discoideum. The study
of ROS and methylglyoxal in GCS-null mutants could help to understand
the transition from growth to development in D. discoideum.

Seo, M. C., S. Kim, et al. (2008). "Discoidin domain receptor 1 mediates collagen-induced inflammatory activation of microglia in culture." J Neurosci Res 86(5): 1087-1095.
	Discoidin domain receptor 1 (DDR1) is a nonintegrin collagen receptor tyrosine kinase with an extracellular domain homologous to discoidin 1 of a soil-living amoeba Dictyostelium discoideum. We have previously demonstrated that DDR1 mediates collagen-induced nitric oxide production in J774A.1 murine macrophages. Because collagen is one of the main components of extracellular matrix in the central nervous system, we hypothesized that collagen also induces inflammatory activation of brain microglia, and DDR1 may mediate collagen-induced microglial activation. Using BV-2 mouse microglial cells and mouse primary microglial cultures, we have demonstrated that (1) collagen induces inflammatory activation of microglia as evidenced by production of nitric oxide, expression of inducible nitric oxide synthase, COX-2, CD40, and matrix metalloproteinase-9; (2) DDR1 is expressed in microglia and is phosphorylated by collagen treatment; and (3) collagen-induced microglial activation is abrogated by DDR1 blockade but not by integrin neutralization. We have further shown that p38 MAPK, c-Jun N-terminal kinase, and nuclear factor-kappa B are involved in the collagen-DDR1-induced microglial activation. Our results suggest that collagen can induce inflammatory activation of brain microglia and that DDR1 mediates this effect of collagen in an integrin-independent manner.

Sforzini, S., A. Dagnino, et al. (2008). "Use of highly sensitive sublethal stress responses in the social amoeba Dictyostelium discoideum for an assessment of freshwater quality." Sci Total Environ 395(2-3): 101-108.
	In this work, the sensitivity of a battery of tests on the social amoeba Dictyostelium discoideum has been assessed within a freshwater toxicity study. The results obtained from the evaluation of survival and replication rate of D. discoideum were compared to those derived with a series of widely used tests for freshwater toxicity assessment, i. e. bioassays using Vibrio fischeri, Daphnia magna and Pseudokirchneriella subcapitata. The effects on sublethal endpoints, i.e. lysosomal membrane stability (LMS) and endocytotic rate, were analysed in conjunction with high-level endpoints to verify the potential to make a typical bioassay more sensitive. The field ecotoxicological investigation employing D. discoideum is part of a monitoring study assessing environmental quality of the Bormida River (Italy), subjected until recently to a chronic industrial pollution. The survey was carried out at several stations (upstream and downstream of a chemical factory outlet) in two different periods. In 2002, the results of chemical analyses performed on river water indicated no contamination. The ecotoxicological data obtained in this period showed that no evidence of biological effects was observed using V. fischeri and D. magna bioassays. In spite of the previous classical acute toxicity tests, significant differences in cell viability of D. discoideum were found. By analysing the effects measured on LMS and endocytotic rate, more relevant changes were observed for these sublethal stress biomarkers compared to survival. The chronic toxicity data showed significant changes in cell growth both of P. subcapitata and D. discoideum. Nevertheless, more sensitive and rapid responses were obtained when assessing the effects of exposure on D. discoideum. The chemical and ecotoxicological data obtained in 2006 indicated a full recovery of the quality of the river water (neither contamination nor toxicity found). Altogether, the results reported in this study underline that the use of a battery of biomarkers in conjunction with high-level endpoints may help follow the pollutant-induced stress syndrome in the organisms from early sublethal effects to starting mortality.

Shanina, N. A., E. M. Lazareva, et al. (2008). "[High molecular weight protein detected in higher plant cells by antibodies against dynein is associated with vesicular organelles including Golgi apparatus]." Ontogenez 39(1): 28-38.
	The cytoplasmic dynein is a multisubunit complex driving organelles along microtubules to their minus-end. We used antibodies against two functional domains (motor and microtubule-binding) of one of principal components of the complex--dynein heavy chain of slime mould Dictyostelium discoideum--to test root meristem cells of wheat Triticum aestivum. The antibodies reacted with a high molecular weight protein (> 500 kDa) in the total cell extract and the band recognized by the antibodies in plant extracts had a lower electrophoretic mobility than the high molecular weight band of mammalian dynein. Antibodies coupled to protein A-Sepharose precipitated the high molecular weight protein from the purified cell extracts. Immunocytochemical analysis demonstrated that the antigen recognized by antibodies against dynein heavy chains is associated with the vesicles whose localization depends on the cell cycle stage. The antigen-positive vesicles were localized to the perinuclear region in interphase and early prophase, to the spindle periphery and to spindle pole region during mitosis, and to the interzonal region in the period of fragmoplast and cell plate formation. Some antigen-positive vesicles also reacted with antibodies against Golgi protein markers. The obtained data indicate that higher plant cells contain a high molecular weight protein interacting with antibodies against the motor and microtubules-binding domains of Dictyostelium dynein heavy chain. The revealed antigen was associated with the vesicular structures in the cytoplasm including the Golgi apparatus.

Shaulsky, G. (2008). "The cheatin' amoeba." Scientist 22(7): 30-36.
	
Shibata, T. and M. Ueda (2008). "Noise generation, amplification and propagation in chemotactic signaling systems of living cells." Biosystems 93(1-2): 126-132.
	Theoretical considerations of stochastic signal transduction in living cells have revealed the gain-fluctuation relation, which provides a theoretical framework to describe quantitatively how noise is generated, amplified and propagated along a signaling cascade in living cells. We chose the chemotactic signaling of bacteria and eukaryotic cells as a typical example of noisy signal transduction and applied the gain-fluctuation relation to these signaling systems in order to analyze the effects of noise on signal transduction. Comparing our theoretical analysis with the experimental results of chemotaxis in bacteria Escherichia coli and eukaryote Dictyostelium discoideum revealed that noise in signal transduction systems limits the cells' chemotactic ability and contributes to their behavioral variability. Based on the kinetic properties of signaling molecules in living cells, the gain-fluctuation relation can quantitatively explain stochastic cellular behaviors.

Shimada, N., N. Kanno-Tanabe, et al. (2008). "GBF-dependent family genes morphologically suppress the partially active Dictyostelium STATa strain." Devel. Genes Evol. 218: 55-68.
	
Shina, M. C. and A. A. Noegel (2008). "Invertebrate coronins." Subcell Biochem 48: 88-97.
	Coronins are highly conserved among species, but their function is far from being understood in detail. Here we will introduce members of the family of coronin like proteins from Drosophila melanogaster, Caenorhabditis elegans and the social amoeba Dictyostelium discoideum. Genetic data from D. discoideum and D. melanogaster revealed that coronins in general are important regulators of many actin-dependent processes.

Shpak, M., J. R. Kugelman, et al. (2008). "The phylogeny and evolution of deoxyribonuclease II: an enzyme essential for lysosomal DNA degradation." Mol. Phylogenet. Evol. 47: 841-854.
	
Shpakov, A. O. and M. N. Pertseva (2008). "Signaling systems of lower eukaryotes and their evolution." Int Rev Cell Mol Biol 269: 151-282.
	Making progress in the study of hormone-sensitive signaling systems in vertebrates and human requires a better understanding of how chemosignaling systems in lower eukaryotes originated and how molecular mechanisms of signal transduction via these systems function. This review is devoted to the structural-functional organization of chemosignaling systems and their components in unicellular organisms such as Dictyostelium discoideum, yeasts and related fungi, flagellates, and ciliates. The attention is focused on receptors of the serpentine type, heterotrimeric GTP-binding proteins and adenylyl and guanylyl cyclases, generators of cAMP and cGMP, present in various forms in a majority of eukaryotic signaling systems coupled with G proteins. Signaling systems involving the receptor component not coupled with G proteins, the receptor forms of adenylyl and guanylyl cyclases of Trypanosoma and ciliates, in particular, are also analyzed. A comparison of signal transduction systems of lower and higher eukaryotes revealed a number of peculiarities and similarities between them. The problem of evolution of chemosignaling systems in lower eukaryotes is viewed through the authors' hypothesis about the prokaryotic genesis of the systems.

Sillo, A., G. Bloomfield, et al. (2008). "Genome-wide transcriptional changes induced by phagocytosis or growth on bacteria in Dictyostelium." BMC Genomics 9: 291.
	BACKGROUND: Phagocytosis plays a major role in the defense of higher organisms against microbial infection and provides also the basis for antigen processing in the immune response. Cells of the model organism Dictyostelium are professional phagocytes that exploit phagocytosis of bacteria as the preferred way to ingest food, besides killing pathogens. We have investigated Dictyostelium differential gene expression during phagocytosis of non-pathogenic bacteria, using DNA microarrays, in order to identify molecular functions and novel genes involved in phagocytosis. RESULTS: The gene expression profiles of cells incubated for a brief time with bacteria were compared with cells either incubated in axenic medium or growing on bacteria. Transcriptional changes during exponential growth in axenic medium or on bacteria were also compared. We recognized 443 and 59 genes that are differentially regulated by phagocytosis or by the different growth conditions (growth on bacteria vs. axenic medium), respectively, and 102 genes regulated by both processes. Roughly one third of the genes are up-regulated compared to macropinocytosis and axenic growth. Functional annotation of differentially regulated genes with different tools revealed that phagocytosis induces profound changes in carbohydrate, amino acid and lipid metabolism, and in cytoskeletal components. Genes regulating translation and mitochondrial biogenesis are mostly up-regulated. Genes involved in sterol biosynthesis are selectively up-regulated, suggesting a shift in membrane lipid composition linked to phagocytosis. Very few changes were detected in genes required for vesicle fission/fusion, indicating that the intracellular traffic machinery is mostly in common between phagocytosis and macropinocytosis. A few putative receptors, including GPCR family 3 proteins, scaffolding and adhesion proteins, components of signal transduction and transcription factors have been identified, which could be part of a signalling complex regulating phagocytosis and adaptational downstream responses. CONCLUSION: The results highlight differences between phagocytosis and macropinocytosis, and provide the basis for targeted functional analysis of new candidate genes and for comparison studies with transcriptomes during infection with pathogenic bacteria.

Siltberg-Liberles, J., I. H. Steen, et al. (2008). "The phylogeny of the aromatic amino acid hydroxylases revisited by characterizing phenylalanine hydroxylase from Dictyostelium discoideum." Gene 427(1-2): 86-92.
	The social amoeba Dictyostelium discoideum contains only one aromatic amino acid hydroxylase (AAAH) gene compared to at least three in metazoans. As shown in this work this gene codes for a phenylalanine hydroxylase (DictyoPAH) and phylogenetic analysis places this enzyme close to the precursor AAAHs, aiding to define the evolutionary history of the AAAH family. DictyoPAH shows significant similarities to other eukaryote PAH, but it exhibits higher activity with tetrahydrodictyopterin (DH4) than with tetrahydrobiopterin (BH4) as cofactor. DH4 is an abundant tetrahydropterin in D. discoideum while BH4 is the natural cofactor of the AAAHs in mammals. Moreover, DictyoPAH is devoid of the characteristic regulatory mechanisms of mammalian PAH such as positive cooperativity for L-Phe and activation by preincubation with the substrate. Analysis of the few active site substitutions between DictyoPAH and mammalian PAH, including mutant expression analysis, reveals potential structural determinants for allosteric regulation.

Stephens, L., L. Milne, et al. (2008). "Moving towards a better understanding of chemotaxis." Curr Biol 18(11): R485-R494.
	Eukaryotic cells are thought to move across supporting surfaces through a combination of coordinated processes: polarisation; extension of dynamic protrusions from a leading edge; adhesion-associated stabilisation of some protrusions; centripetal pulling against those leading adhesions; and de-adhesion at the rear. Gradients of extracellular ligands can be detected by cells and then used to guide them either towards the source (in the case of a chemoattractant) or away from the source (in the case of a chemorepellent) - such migration is termed chemotaxis. Recent work suggests that chemotaxis probably emerges from the ability of cells to spatially encode extracellular gradients of ligands, a process for which phosphoinositide 3'-kinase (PI3K) signals alone are insufficient, and to use that vectorial information to bias movement by enhancing the survival, and not the formation, of the protrusions that experience the greatest stimulation.

Stewman, S. F. (2008). Stochastic models of growth and guidance in biology: A physical chemist's adventures with pollen tubes and filopodial bundles. United States -- Illinois, The University of Chicago.
	Motile cells display a myriad of complex and interconnected behaviors that span multiple time and distance scales. Mathematical modeling is a useful tool to help understand the systems involved in chemotropic cell motility. This dissertation develops minimal, stochastic models for features of motility at both the sub-cellular and supercellular level. At the sub-cellular level, we develop a model to study how cytoskeletal bundles arise in animal cells. At the supercellular level, we study the how pollen tubes, the motile carrier of plant sperm, change their growth in response to ovules present on the media. A fundamental question in subcellular motility is how proteins self-organize into structures capable of generating or responding to the forces. Motility is largely the result of the cytoskeleton, a network of stiff, dynamic filaments composed of the protein actin and many proteins that bind to it (Pollard et al., 2000). Many of these actin-binding proteins are involved in cross-linking the network of filaments, and variations in their local concentrations are known to cause changes in the network topology (Pollard & Cooper, 1986; Svitkina et al., 2003; Mejillano et al., 2004). Chapter 2 focuses on a series of related in vitro experiments (Vignjevic et al., 2003; Haviv et al., 2006) that show how the protein fascin affects a transition between a low-density, highly-branched network and a high-density tightly bundled network. We present a novel lattice model of these in vitro experiments. At each site on this lattice, the mean filament direction is represented as a finite set of directions, using a Potts-like spin variable (Potts, 1952). The processes of polymerization and branching are introduced with facilitation rules, which control which sites are able to change state flipping spins, and bundling is introduced as an energetic coupling between adjacent sites of the same spin. We use this model to investigate whether bundle formation can result from collisions of growing filaments alone, or whether relaxation of pre-existing filaments is needed for sizable bundles to form. To this end, we present an analysis of how these bundles are nucleated on the lattice, and how the size of the bead in the experiment will affect the number of bundles present. Currently, it is too computationally expensive for a simulation to study both kinetic and thermal bundle formation, and in Chapter 3, we present an algorithm to study filament-filament collisions that shows promise in overcoming computational limitations. At the supercellular level, one fundamental question for cell motility is how cells are guided in processes that range from stem-cell wound response to slime-mold feeding. In Chapter 4, we focus on guidance in the plant reproductive system, where plant biologists have long speculated about the mechanisms that guide pollen tubes to ovules. By combining microscopy, quantitative analysis, and modeling we have extended recent semi-in vitro work to quantitatively analyze how pollen tubes growing on an artificial medium respond to dissected ovules placed on the medium, and probe the mechanisms responsible for the response. Our analysis indicates that pollen tubes are more attracted to ovules incubated on an artificial medium for longer times. To understand this attraction, we defined a metric than measures how pollen tubes turn in response to an ovule. Analysis of this metric demonstrate that the turns pollen tubes make are consistent with following a gradient, and that pollen tubes show a significant turning response at distances of 100-150 ¼m, which are longer than previously reported. Our data also show that pollen tubes slow their rate of growth near micropyles of functional ovules and that the distance where slowing begins increases with the incubation time of the ovule. To probe the mechanisms suggested by this data, we developed a stochastic model for pollen tube growth in which pollen tubes turn in response to a difference in the fraction of theoretical receptors bound by a ligand across the two side of a tube tip. The attractant was modeled by assuming that it was continuously released by the ovules, and that it diffused isotropically on the media. Simulations showed that this model recapitulates many of the features seen in vitro, and gave an estimate of the diffusion constant of the attractant. Further, they show how slower rates of growth near the micropyle affected guidance: slower rates greatly increase the ability of pollen tubes to target ovules successfully. References Haviv, L., Brill-Karniely, Y., Mahaffy, R., Backouche, F., Ben-Shaul, A., Pollard, T. D. & Bernheim-Groswasser, A. (2006). Proc. Nat. Acad. Sci. USA 103, 4906-4911. Mejillano, M. R., ichiro Kojima, S., Applewhite, D. A., Gertler, F. B., Svitkina, T. M. & Borisy, G. G. (2004). Cell 118, 363-73. Pollard, T. D., Blanchoin, L. & Mullins, R. D. (2000). Annual Review of Biophysical Biomolecular Structure 29, 545-576. Pollard, T. D. & Cooper, J. A. (1986). Annu Rev Biochem 55, 987-1035. Potts, R. B. (1952). Proc. Cambridge Philos. Soc. 48, 106-109. Svitkina, T. M., Bulanova, E. A., Chaga, O. Y., Vignjevic, D. M., Kojima, S., Vasiliev, J. M. & Borisy, G. G. (2003). J. Cell Biol. 160, 409-421. Vignjevic, D., Yarar, D., Welch, M. D., Peloquin, J., Svitkina, T. & Borisy, G. G. (2003). J. Cell Biol. 160, 951-962.

Sunaga, N., M. Monna, et al. (2008). "Expression of zinc transporter family genes in Dictyostelium." Int J Dev Biol 52(4): 377-381.
	Regulation of the zinc ion concentration is physiologically important to control the activities of a variety of cellular molecules. A BLAST search against a conserved domain of known zinc transporters identified twelve putative zinc transporter family genes in the Dictyostelium genome. Phylogenetic analysis revealed the presence of three zinc transporter subfamilies in Dictyostelium. One subfamily of proteins, consisting of the ZntA-D proteins, has weak homology to the STAT3-inducible LIV-1 protein. In addition, in situ hybridization revealed that the zntA-D genes are expressed in the pstAB cells, this expression being absent in the Dd-STATa null mutant. Thus, Dd-STATa may control stalk cell differentiation through some members of the zinc transporter family genes during Dictyostelium development.

Sunderland, M. E. (2008). Studying development: The value of diversity, theory, and synthesis. United States -- Arizona, Arizona State University.
	Today there is a set of assumptions about how best to study developmental biology. This is reflected in the way that science is funded. The National Institutes of Health in the United States, the Wellcome Trust in the United Kingdom, and the Canadian Institutes of Health Research reward research that focuses on understanding a select few defined model organisms, especially at the genomic and proteomic ('omics') level. Research programs are increasingly centered on one model organism, and on generating mass amounts of 'omics' data for potential analysis. This dissertation makes the case that there is a historically consistent alternative to this approach, which is supported by the works of successful, mainstream biologists. This alternative approach emphasizes the importance of including theoretical grounding as well as data, knowledge of the diversity of organisms, and a synthetic orientation to biology. This dissertation presents three case studies to demonstrate this alternative. An in depth examination of Thomas Hunt Morgan's Regeneration , John Tyler Bonner's Morphogenesis: An Essay on Development and Alejandro Sánchez Alvarado's contemporary research program offers three examples of synthetic approaches to development that relied strongly on studying a diversity of organisms and emphasized the fundamental importance of theory. Although at first glance these examples might seem like exemplars of the status quo, since Morgan, Bonner, and Sánchez Alvarado are each renowned for their pioneering work on a single model organism (the fruit fly Drosophila melanogaster , the cellular slime mold Dictyostelium discoideum and the freshwater planarian Schmidtea mediterranea , respectively), this dissertation shows that each articulated a fundamentally different alternative approach before later narrowing his focus. Spanning from 1901 to the present day, these examples present a historically consistent alternative to studying development, which raises questions about the assumptions that substantiate the status quo approach.

Taft, M. H., F. K. Hartmann, et al. (2008). "Dictyostelium myosin-5b is a conditional processive motor." J Biol Chem 283(40): 26902-26910.
	Dictyostelium myosin-5b is the gene product of myoJ and one of two closely related myosin-5 isoenzymes produced in Dictyostelium discoideum. Here we report a detailed investigation of the kinetic and functional properties of the protein. In standard assay buffer conditions, Dictyostelium myosin-5b displays high actin affinity in the presence of ADP, fast ATP hydrolysis, and a high steady-state ATPase activity in the presence of actin that is rate limited by ADP release. These properties are typical for a processive motor that can move over long distances along actin filaments without dissociating. Our results show that a physiological decrease in the concentration of free Mg(2+)-ions leads to an increased rate of ADP release and shortening of the fraction of time the motor spends in the strong actin binding states. Consistently, the ability of the motor to efficiently translocate actin filaments at very low surface densities decreases with decreasing concentrations of free Mg(2+)-ions. In addition, we provide evidence that the observed changes in Dd myosin-5b motor activity are of physiological relevance and propose a mechanism by which this molecular motor can switch between processive and non-processive movement.

Takagi, H., M. J. Sato, et al. (2008). "Functional analysis of spontaneous cell movement under different physiological conditions." PLoS One 3(7): e2648.
	Cells can show not only spontaneous movement but also tactic responses to environmental signals. Since the former can be regarded as the basis to realize the latter, playing essential roles in various cellular functions, it is important to investigate spontaneous movement quantitatively at different physiological conditions in relation to a cell's physiological functions. For that purpose, we observed a series of spontaneous movements by Dictyostelium cells at different developmental periods by using a single cell tracking system. Using statistical analysis of these traced data, we found that cells showed complex dynamics with anomalous diffusion and that their velocity distribution had power-law tails in all conditions. Furthermore, as development proceeded, average velocity and persistency of the movement increased and as too did the exponential behavior in the velocity distribution. Based on these results, we succeeded in applying a generalized Langevin model to the experimental data. With this model, we discuss the relation of spontaneous cell movement to cellular physiological function and its relevance to behavioral strategies for cell survival.

Tang, L., J. Franca-Koh, et al. (2008). "tsunami, the Dictyostelium homolog of the Fused kinase, is required for polarization and chemotaxis." Genes Dev 22(16): 2278-2290.
	In a forward genetic screen for chemotaxis mutants in Dictyostelium discoideum, we identified a loss-of-function mutation, designated tsunami, encoding a homolog of the Fused kinase. Cells lacking tsuA function could not effectively perform chemotaxis and were unable to become polarized or correctly orient pseudopods in chemotactic gradients. While tsuA(-) cells were able to couple receptor occupancy to phosphatidylinositol (3,4,5) trisphosphate (PIP3) production and actin polymerization, the PIP3 response was prolonged and basal F-actin levels were increased. Interestingly, TsuA localizes to the microtubule network and puncta mainly found at the cell periphery. Analysis of the gene uncovered a novel C-terminal domain that we designated the Tsunami Homology (TH) domain. Both the kinase domain and the TH domain are required to rescue the phenotypic defects of tsuA(-) cells. While kinase activity is not required for localization to microtubules, the TH domain is essential. Thus, localization of kinase activity to microtubules is critical for TsuA function. We propose that functions in association with the microtubule network may underlie the divergent roles of Fused kinase proteins in different organisms.

Tang, Y. (2008). Characterization of CnrN-mediated size regulation in Dictyostelium. United States -- Texas, Rice University.
	An interesting but largely unanswered question in biology is how eukaryotic organisms precisely regulate the size of multicellular tissues or groups of cells. Developing Dictyostelium cells aggregate in dendritic streams using relayed pulses of adenosine 3'5'-cyclic monophosphate (cAMP) as a chemoattractant to form <20,000-cell fruiting bodies. Counting factor (CF), a secreted protein complex, regulates group size by increasing cell motility and decreasing cell-cell adhesion to induce the breakup of excessively large aggregation streams. We used a second-site suppressor screen by conducting random insertional mutagenesis in smlA - cells which over-secrete CF to search for CF signal transduction components, and found that an insertion in the cnrN gene affects group size. Cells lacking CnrN ( cnrN - cells) form small aggregation territories with few streams, which then form small fruiting bodies. Expressing CnrN in cnrN - cells rescues the abnormal phenotype. Computer simulations suggested that in the absence of stream formation, CF should be unable to affect group size. As predicted, cnrN - group size is insensitive to the addition or depletion of CF, even though CF regulates the motility of cnrN - cells. cnrN - cells have excessively large cAMP-stimulated cAMP pulses, and the small territory phenotype can be rescued by developing cells in the presence of the cAMP-hydrolyzing enzyme cAMP phosphodiesterase or simply by starving cells at low densities. The predicted amino acid sequence of CnrN has similarity to phosphatase and tensin homologs (PTENs). PTENs play a key role in inhibiting phosphatidylinositol 3' kinase (PI3K) dependent pathways. In Dictyostelium , cAMP pulses activate PI3Ks, and activated PI3Ks in turn stimulate adenylyl cyclase to produce cAMP. As indicated by the sequence similarity of CnrN to PTEN, in response to cAMP stimulation, cnrN - cells show elevated and extended activation of PI3K-dependent pathways, including PIP 3 accumulation, Akt activation, actin polymerization, and adenylyl cyclase-catalysed cAMP production. Our results suggest that CnrN has functional similarity to PTEN and regulates the cAMP pulse size by negatively regulating PI3K-dependent pathways, and that CnrN-mediated regulation on territory and stream formation may use a CF-independent mechanism.

Tang, Y. and R. H. Gomer (2008). "A protein with similarity to PTEN regulates aggregation territory size by decreasing cyclic AMP pulse size during Dictyostelium discoideum development." Euk Cell 7(10): 1758-1770.
	An interesting but largely unanswered biological question is how eukaryotic organisms regulate the size of multicellular tissues. During development, a lawn of Dictyostelium cells breaks up into territories, and within the territories the cells aggregate in dendritic streams to form groups of approximately 20,000 cells. Using random insertional mutagenesis to search for genes involved in group size regulation, we found that an insertion in the cnrN gene affects group size. Cells lacking CnrN (cnrN(-)) form abnormally small groups, which can be rescued by the expression of exogenous CnrN. Relayed pulses of extracellular cyclic AMP (cAMP) direct cells to aggregate by chemotaxis to form aggregation territories and streams. cnrN(-) cells overaccumulate cAMP during development and form small territories. Decreasing the cAMP pulse size by treating cnrN(-) cells with cAMP phosphodiesterase or starving cnrN(-) cells at a low density rescues the small-territory phenotype. The predicted CnrN sequence has similarity to phosphatase and tensin homolog (PTEN), which in Dictyostelium inhibits cAMP-stimulated phosphatidylinositol 3-kinase signaling pathways. CnrN inhibits cAMP-stimulated phosphatidylinositol 3,4,5-trisphosphate accumulation, Akt activation, actin polymerization, and cAMP production. Our results suggest that CnrN is a protein with some similarities to PTEN and that it regulates cAMP signal transduction to regulate territory size.

Tang, Y. and R. H. Gomer (2008). "CnrN regulates Dictyostelium group size using a counting factor-independent mechanism." Commun Integr Biol 1(2): 185-187.
	One of the simplest examples of a complex behavior is the aggregation of solitary Dictyostelium discoideum amoebae to form a 20,000-cell fruiting body. A field of starving amoebae first breaks up into territories. In each territory, the cells form a spider-like pattern of streams of cells. As part of a negative feedback loop, counting factor (CF), a secreted protein complex whose concentration increases with the size of the stream, prevents over-sized fruiting bodies from being formed by increasing cell motility and decreasing cell-cell adhesion, which causes the breakup of excessively large streams. Cells lacking the phosphatase CnrN (cnrN(-) cells) form small aggregation territories and few streams.1 In this report, we present computer simulations that suggest that in the absence of stream formation, CF should be unable to affect group size. As predicted, cnrN(-) group size is insensitive to the addition or depletion of CF. Together, the data indicate that CnrN regulates group size by regulating both the break-up of a field of cells into aggregation territories and stream formation during development, and that CnrN-mediated and CF-mediated group size regulation use different mechanisms.

Tatischeff, I., F. Lavialle, et al. (2008). "Dictyostelium extracellular vesicles containing Hoechst 33342 transfer the dye into the nuclei of living cells: a fluorescence study." J. Fluoresc. 18: 319-328.
	
Taylor, N. M. (2008). Characterization of a putative novel Ras effector in Dictyostelium discoideum. United States -- California, University of California, San Diego.
	A putative novel Ras effector, TJ1, was identified through reverse genetics and characterized through chemotaxis, developmental and biochemical assays to determine its role in Dictyostelium discoideum. Additionally, the Ras association (RA) domains within TJ1 were deleted and subsequent cell lines were characterized to determine their function in TJ1. TJ1 is required for proper chemotaxis. Compared to wild-type cells, tj1-null cells were not polarized, did not chemotax, and as a result displayed a delay in initial stages of development. Additionally, findings indicate that a fully functional TJ1 protein requires at least one of the two RA domains therein. Disruption of either of the two individual RA domains in TJ1 does not result in strong defects in chemotaxis, development or localization, whereas the deletion of both RA domains leads to a reduced ability to chemotax and therefore a subsequent delay in the stages of early development. Initial experiments suggest that there is no interaction between TJ1 and Ras proteins, however more experiments need to be conducted to further explore the role of TJ1 as a novel Ras effector in Dictyostelium. Presently, the complete mechanisms of the Ras signaling pathway is largely unknown. Characterizing TJ1 and the RA domains therein should shed light on how TJ1 is involved in Ras signaling in Dictyostelium discoideum and presumably how Ras signaling operates in other organisms based on the conservation of pathways across species.

Thapa, P. (2008). Methodology for the directional growth of conducting nanowires and their attachment to live cells. United States -- Oklahoma, Oklahoma State University.
	Scope and Method of Study . The purpose of this study was to develop a technique as an alternative approach for establishing cell-to-wire contact by the use of nanowire grown from Directed Electrochemical Nanowire Assembly (DENA) technique with weak perturbation to living cells. Findings and Conclusions . Methodology for the long-range growth of metallic and polymeric nanowires between on-chip electrodes has been established. Theoretical modelling reveals that there is a strong, long-range component of the applied potential that extends entirely across the gap between a user-chosen pair of electrodes. This component defines a vector of maximum ion-flux in the laboratory reference frame. For the metallic nanowires, this voltage-component tends to bring the crystallographic axis of growth into coincidence with the flux vector. For the polymeric nanowires, this channel of maximum ion flux restricts polymerization to the channel-region. Hence, amorphous materials may be grown with wire-like geometries, and the growth-path of the wires may be controlled. These wire-laden chips are useful substrates for cell physiological studies. To this end, the electrotactical behavior of Dictyostelium discoideum cells has been exploited to induce the formation of strong mechanical contacts between individual pseudopodia and the tips of biased polymeric wires in a manner that is only weakly perturbative to the cells. This capability is expected to facilitate electro-mechanical probing of cellular processes.

Tian, R., C. Unal, et al. (2008). The Dictyostelium response to infection with Legionella. Eur. J Cell Biol.
	The professional phagocyte, Dictyostelium discoideum, is a useful model for the study of the medically relevant infection of host cells by pathogenic microorganisms. The analysis of infected D. discoideum revealed that L. pneumophila triggers a stress response, interferes with intracellular vesicle fusion and profoundly influences and exploits the metabolism of its host. Comparative studies with pathogenic and non-pathogenic L. pneumophila 24 hours post-infection identified 240 differentially expressed genes that appear to be involved in the pathogenic response (Farbrother et al., Cell Microbiol 3:438-456, 2006). More than 50 of these genes have orthologues in human. The upregulated autophagy 9 (ATG9) gene was selected for further studies. Autophagy contributes to many physiological and pathological processes, including morphogenesis, cancer, neurodegenerative disorders and infectious diseases. ATG9- cells display severe developmental defects, consistent with a role of autophagy during development. In addition, the mutant has a strong phagocytosis defect, pointing to a role of ATG9 in phagocytosis and infection. Expression profiling revealed a large number of differentially regulated genes and a clear enrichment of lysozyme activity and protein degradation among these genes. Further studies are aimed to illuminate the function of ATG9 during phagocytosis and infection.

Tikhonenko, I., D. K. Nag, et al. (2008). "Kinesin-5 is not essential for mitotic spindle elongation in Dictyostelium." Cell Motil Cytoskeleton 65(11): 853-862.
	The proper assembly and operation of the mitotic spindle is essential to ensure the accurate segregation of chromosomes and to position the cytokinetic furrow during cell division in eukaryotes. Not only are dynamic microtubules required but also the concerted actions of multiple motor proteins are necessary to effect spindle pole separation, chromosome alignment, chromatid segregation, and spindle elongation. Although a number of motor proteins are known to play a role in mitosis, there remains a limited understanding of their full range of functions and the details by which they interact with other spindle components. The kinesin-5 (BimC/Eg5) family of motors is largely considered essential to drive spindle pole separation during the initial and latter stages of mitosis. We have deleted the gene encoding the kinesin-5 member in Dictyostelium, (kif13), and find that, in sharp contrast with results found in vertebrate, fly, and yeast organisms, kif13(-) cells continue to grow at rates indistinguishable from wild type. Phenotype analysis reveals a slight increase in spindle elongation rates in the absence of Kif13. More importantly, there is a dramatic, premature separation of spindle halves in kif13(-) cells, suggesting a novel role of this motor in maintaining spindle integrity at the terminal stages of division.

Tresse, E., C. Giusti, et al. (2008). "Autophagy and autophagic cell death in Dictyostelium." Meth Enzymol 451: 343-358.
	Autophagic cell death can be conveniently studied in Dictyostelium discoideum, an exceptionally favorable model not only because of its well-known genetic and experimental advantages but also because in Dictyostelium there is no apoptosis machinery that could interfere with nonapoptotic cell death. Moreover, autophagic cell death in Dictyostelium can be dissociated into a starvation-induced sensitization stage, during which autophagy is induced, and a death induction stage. We show here how to demonstrate, assess and analyze this autophagic cell death. This can be studied in vivo during the development of Dictyostelium, and in vitro, using modifications of the monolayer technique of Rob Kay et al. Methods to follow this autophagic cell death qualitatively and quantitatively are reported.

Tresse, E., A. Kosta, et al. (2008). "A UDP-glucose derivative is required for vacuolar autophagic cell death." Autophagy 4(5): 680-691.
	Autophagic cell death in Dictyostelium can be dissociated into a starvation-induced sensitization stage and a death induction stage. A UDP-glucose pyrophosphorylase (ugpB) mutant and a glycogen synthase (glcS) mutant shared the same abnormal phenotype. In vitro, upon starvation alone mutant cells showed altered contorted morphology, indicating that the mutations affected the pre-death sensitization stage. Upon induction of cell death, most of these mutant cells underwent death without vacuolization, distinct from either autophagic or necrotic cell death. Autophagy itself was not grossly altered as shown by conventional and electron microscopy. Exogenous glycogen or maltose could complement both ugpB(-) and glcS(-) mutations, leading back to autophagic cell death. The glcS(-) mutation could also be complemented by 2-deoxyglucose that cannot undergo glycolysis. In agreement with the in vitro data, upon development glcS(-) stalk cells died but most were not vacuolated. We conclude that a UDP-glucose derivative (such as glycogen or maltose) plays an essential energy-independent role in autophagic cell death.

Tsiavaliaris, G., S. Fujita-Becker, et al. (2008). "Mechanism, regulation, and functional properties of Dictyostelium myosin-1B." J. Biol. Chem. 283: 4520-4527.
	
Tsujioka, M., K. Yoshida, et al. (2008). "Overlapping functions of the two talin homologues in Dictyostelium." Euk Cell 7(5): 906-916.
	Talin is a cytoskeletal protein involved in constructing and regulating focal adhesions in animal cells. The cellular slime mold Dictyostelium discoideum has two talin homologues, talA and talB, and earlier studies have characterized the single knockout mutants. talA(-) cells show reduced adhesion to the substrates and slightly impaired cytokinesis leading to a high proportion of multinucleated cells in the vegetative stage, while the development is normal. In contrast, talB(-) cells are characterized by reduced motility in the developmental stage, and they are arrested at the tight-mound stage. Here, we created and analyzed a double mutant with a disruption of both talA and talB. Defects in adhesion to the substrates, cytokinesis, and development were more severe in cells with a disruption of both talA and talB. The talA(-) talB(-) cells failed to attach to the substrates in the vegetative stage, exhibited a higher proportion of multinucleated cells than talA(-) cells, and showed more-reduced motility during the development and an earlier developmental arrest than talB(-) cells at the loose-mound stage. Moreover, overexpression of either talA or talB compensated for the loss of the other talin, respectively. The analysis of talA(-) talB(-) cells also revealed that talin was required for the formation of paxillin-rich adhesion sites and that there was another adhesion mechanism which is independent of talin in the developmental stage. This is the first study demonstrating overlapping functions of two talin homologues, and our data further indicate the importance of talin.

Urushihara, H. (2008). "Developmental biology of the social amoeba: history, current knowledge and prospects." Dev Growth Differ 50 Suppl 1: S277-281.
	The cellular slime molds are known as the social amoebae because they conditionally construct multicellular forms in which cell differentiation takes place. Among them, Dictyostelium discoideum has many advantages as an experimental system and is widely used as a model organism. This review aims to reconsider how it has contributed to the understanding of developmental mechanisms and what should be done in the future. Chemotaxis, cell differentiation, genome and transcriptome, and the ecological and evolutionary implications of development are discussed.

van der Wel, H., I. J. Blader, et al. (2008). Conservation of the Skp1 Modification Pathway of Dictyostelium in Toxoplasma gondii. Glycobiology.
	
van Egmond, W. N., A. Kortholt, et al. (2008). "Intramolecular activation mechanism of the Dictyostelium LRRK2 homolog Roco protein GbpC." J Biol Chem 283(44): 30412-30420.
	GbpC is a large multidomain protein involved in cGMP-mediated chemotaxis in the cellular slime mold Dictyostelium discoideum. GbpC belongs to the Roco family of proteins that often share a central core region, consisting of leucine-rich repeats, a Ras domain (Roc), a Cor domain, and a MAPKKKinase domain. In addition to this core, GbpC contains a RasGEF domain and two cGMP-binding domains. Here, we report on an intramolecular signaling cascade of GbpC. In vitro, the RasGEF domain of GbpC specifically accelerates the GDP/GTP exchange of the Roc domain. Moreover, cGMP binding to GbpC strongly stimulates the binding of GbpC to GTP-agarose, suggesting cGMP-stimulated GDP/GTP exchange at the Roc domain. The function of the protein in vivo was investigated by rescue analysis of the chemotactic defect of gbpC null cells. Mutants that lack a functional guanine exchange factor (GEF), Roc, or kinase domain are inactive in vivo. Together, the results suggest a four-step intramolecular activation mechanism of the Roco protein GbpC: cGMP binding to the cyclic nucleotide-binding domains, activation of the GEF domain, GDP/GTP exchange of Roc, and activation of the MAPKKK domain.

Veeranki, S., B. Kim, et al. (2008). "The GPI-anchored superoxide dismutase SodC is essential for regulating basal Ras activity and for chemotaxis of Dictyostelium discoideum." J Cell Sci 121(Pt 18): 3099-3108.
	A genetic screen for Dictyostelium mutant displaying high level of constitutive phosphatidylinositol (3,4,5)-trisphosphate led to the finding that the glycosylphosphatidylinositol (GPI)-anchored superoxide dismutase SodC regulates small GTPase Ras. Cells that lack SodC exhibited constitutively high levels of active Ras, more membrane localization of GFP-PHcrac, and defects in chemoattractant sensing, cell polarization and motility. These defects of SodC-lacking cells were partially restored by expression of wild-type SodC but not by the catalytically inactive mutant SodC (H245R, H247Q). Furthermore, an inhibition of PI3K activity in SodC-deficient cells by LY294002 only partially restored chemoattractant sensing and cell polarization, consistent with the fact that SodC-deficient cells have aberrantly high level of active Ras, which functions upstream of PI3K. A higher level of active GFP-RasG was observed in SodC-deficient cells, which significantly decreased upon incubation of SodC-deficient cells with the superoxide scavenger XTT. Having constitutively high levels of active Ras proteins and more membrane localization of GFP-PHcrac, SodC-deficient cells exhibited severe defects in chemoattractant sensing, cell polarization and motility.

Veltman, D. M., I. Keizer-Gunnik, et al. (2008). "Four key signaling pathways mediating chemotaxis in Dictyostelium discoideum." J Cell Biol 180(4): 747-753.
	Chemotaxis is the ability of cells to move in the direction of an external gradient of signaling molecules. Cells are guided by actin-filled protrusions in the front, whereas myosin filaments retract the rear of the cell. Previous work demonstrated that chemotaxis of unpolarized amoeboid Dictyostelium discoideum cells is mediated by two parallel pathways, phosphoinositide-3-kinase (PI3K) and phospholipase A2 (PLA2). Here, we show that polarized cells exhibit very good chemotaxis with inhibited PI3K and PLA2 activity. Using genetic screens, we demonstrate that this activity is mediated by a soluble guanylyl cyclase, providing two signals. The protein localizes to the leading edge where it interacts with actin filaments, whereas the cyclic guanosine monophosphate product induces myosin filaments in the rear of the cell. We conclude that chemotaxis is mediated by multiple signaling pathways regulating protrusions at the front and rear of the cell. Cells that express only rear activity are polarized but do not exhibit chemotaxis, whereas cells with only front signaling are unpolarized but undergo chemotaxis.

Veltman, D. M. and P. J. van Haastert (2008). "The role of cGMP and the rear of the cell in Dictyostelium chemotaxis and cell streaming." J. Cell Sci. 121: 120-127.
	
Vicente, J. J., M. Galardi-Castilla, et al. (2008). "Structural and functional studies of a family of Dictyostelium discoideum developmentally regulated, prestalk genes coding for small proteins." BMC Microbiol. 8:1: 16 pages.
	
Vicker, M. G. and J. F. Grutsch (2008). "Dual chemotaxis signalling regulates Dictyostelium development: intercellular cyclic AMP pulses and intracellular F-actin disassembly waves induce each other." Eur J Cell Biol 87(10): 845-861.
	Aggregating Dictyostelium discoideum amoebae periodically emit and relay cAMP, which regulates their chemotaxis and morphogenesis into a multicellular, differentiated organism. Cyclic AMP also stimulates F-actin assembly and chemotactic pseudopodium extension. We used actin-GFP expression to visualise for the first time intracellular F-actin assembly as a spatio-temporal indicator of cell reactions to cAMP, and thus the kinematics of cell communication, in aggregating streams. Every natural cAMP signal pulse induces an autowave of F-actin disassembly, which propagates from each cell's leading end to its trailing end at a linear rate, much slower than the calculated and measured velocities of cAMP diffusion in aggregating Dictyostelium. A sequence of transient reactions follows behind the wave, including anterior F-actin assembly, chemotactic pseudopodium extension and cell advance at the cell front and, at the back, F-actin assembly, extension of a small retrograde pseudopodium (forcing a brief cell retreat) and chemotactic stimulation of the following cell, yielding a 20s cAMP relay delay. These dynamics indicate that stream cell behaviour is mediated by a dual signalling system: a short-range cAMP pulse directed from one cell tail to an immediately following cell front and a slower, long-range wave of intracellular F-actin disassembly, each inducing the other.

Vourekas, A., V. Stamatopoulou, et al. (2008). The RNA component of ribonuclease P from Dictyostelium discoideum. FEBS J.
	
Waligorska, A., M. Wianecka-Skoczen, et al. (2008). "Reversible inhibition of movement in the amoebae Dictyostelium discoideum and its effect on chemoattractant recognition." Folia Biol (Krakow) 56(3-4): 123-131.
	The cell fixatives formaldehyde and KMnO4 at low concentrations reversibly inhibit the movement of D. discoideum amoebae without directly interfering with cell viability. This inhibition of cell movement is accompanied by the decreased attachment of cells to substratum. When the tenacity and attachment of immobilized cells are artificially increased by compressing cells between two glass surfaces, the amoebae begin to move even in the presence of the fixatives. Amoebae starved for 24 hours, subjected to fixatives and a mineral salt solution in which they remained motionless, maintained chemotactic responses to folic acid and only after a few hours of active locomotion became reactive to cAMP, in contrast to amoebae that reacted to cAMP after starvation in the absence of fixatives.

Washington, R. W. and D. A. Knecht (2008). "Actin binding domains direct actin-binding proteins to different cytoskeletal locations." BMC Cell Biol 9: 10.
	Background: Filamin (FLN) and non-muscle alpha-actinin are members of a family of F-actin cross-linking proteins that utilize Calponin Homology domains ( CH-domain) for actin binding. Although these two proteins have been extensively characterized, little is known about what regulates their binding to F-actin filaments in the cell. Results: We have constructed fusion proteins consisting of green fluorescent protein (GFP) with either the entire cross-linking protein or its actin-binding domain ( ABD) and examined the localization of these fluorescent proteins in living cells under a variety of conditions. The full-length fusion proteins, but not the ABD's complemented the defects of cells lacking both endogenous proteins indicating that they are functional. The localization patterns of filamin ( GFP-FLN) and alpha-actinin ( GFP-alpha A) were overlapping but distinct. GFP-FLN localized to the peripheral cell cortex as well as to new pseudopods of unpolarized cells, but was observed to localize to the rear of polarized cells during cAMP and folate chemotaxis. GFP-alpha A was enriched in new pseudopods and at the front of polarized cells, but in all cases was absent from the peripheral cortex. Although both proteins appear to be involved in macropinocytosis, the association time of the GFP-probes with the internalized macropinosome differed. Surprisingly, the localization of the GFP-actin-binding domain fusion proteins precisely reflected that of their respective full length constructs, indicating that the localization of the protein was determined by the actin-binding domain alone. When expressed in a cell line lacking both filamin and alpha-actinin, the probes maintain their distinct localization patterns suggesting that they are not functionally redundant. Conclusion: These observations strongly suggest that the regulation of the binding of these proteins to actin filaments is built into the actin-binding domains. We suggest that different actin binding domains have different affinities for F-actin filaments in functionally distinct regions of the cytoskeleton.

Wilhelm, C. (2008). "Out-of-equilibrium microrheology inside living cells." Phys Rev Lett 101(2): 028101.
	Both forced and spontaneous motions of magnetic microbeads engulfed by Dictyostelium cells have served as experimental probes of intracellular dynamics. The complex shear modulus G*(omega), determined from active oscillatory measurements, has a power-law dynamics and increases with the probe size, reflecting intracellular structural complexity. The combined use of passive microrheology allows one to derive the power spectrum of active forces acting on intracellular phagosomes and to test the validity of the fluctuation-dissipation theorem inside living cells.

Wilhelm, C., F. Lavialle, et al. (2008). "Intracellular trafficking of magnetic nanoparticles to design multifunctional biovesicles." Small 4(5): 577-582.
	
Xiong, H., F. Rivero, et al. (2008). "Dictyostelium Sun-1 connects the centrosome to chromatin and ensures genome stability." Traffic 9(5): 708-724.
	The centrosome-nucleus attachment is a prerequisite for faithful chromosome segregation during mitosis. We addressed the function of the nuclear envelope (NE) protein Sun-1 in centrosome-nucleus connection and the maintenance of genome stability in Dictyostelium discoideum. We provide evidence that Sun-1 requires direct chromatin binding for its inner nuclear membrane targeting. Truncation of the cryptic N-terminal chromatin-binding domain of Sun-1 induces dramatic separation of the inner from the outer nuclear membrane and deformations in nuclear morphology, which are also observed using a Sun-1 RNAi construct. Thus, chromatin binding of Sun-1 defines the integrity of the nuclear architecture. In addition to its role as a NE scaffold, we find that abrogation of the chromatin binding of Sun-1 dissociates the centrosome-nucleus connection, demonstrating that Sun-1 provides an essential link between the chromatin and the centrosome. Moreover, loss of the centrosome-nucleus connection causes severe centrosome hyperamplification and defective spindle formation, which enhances aneuploidy and cell death significantly. We highlight an important new aspect for Sun-1 in coupling the centrosome and nuclear division during mitosis to ensure faithful chromosome segregation.

Yamada, A., S. Matsuyama, et al. (2008). "Phenotypic plasticity of Escherichia coli at initial stage of symbiosis with Dictyostelium discoideum." Biosystems 92(1): 1-9.
	We observed the change in the physiological state of Escherichia coli cells at the initial stage for establishing a new symbiotic relationship with Dictyostelium discoideum cells. For the physiological state, we monitored green fluorescence intensity due to a green fluorescent protein (GFP) gene integrated into the chromosome by flow cytometry (FCM). On co-cultivation of the two species, a new population of E. coli cells with increased GFP concentration appeared, and when the formation of mucoidal colonies housing the coexisting two species began, most E. coli cells were from the new population. Further experiments suggest that the physiological change is induced by interaction with D. discoideum cells and is reversible, although the processes of the changes in both directions seem to proceed gradually. The observed phenotypic plasticity, together with natural selection under a co-cultivation environment, may be important for leading to the evolution of a new symbiotic system.

Yamada, Y., H. Y. Wang, et al. (2008). "A new family of transcription factors." Development 135(18): 3093-3101.
	CudA, a nuclear protein required for Dictyostelium prespore-specific gene expression, binds in vivo to the promoter of the cotC prespore gene. A 14 nucleotide region of the cotC promoter binds CudA in vitro and ECudA, an Entamoeba CudA homologue, also binds to this site. The CudA and ECudA DNA-binding sites contain a dyad and, consistent with a symmetrical binding site, CudA forms a homodimer in the yeast two-hybrid system. Mutation of CudA binding sites within the cotC promoter reduces expression from cotC in prespore cells. The CudA and ECudA proteins share a 120 amino acid core of homology, and clustered point mutations introduced into two highly conserved motifs within the ECudA core region decrease its specific DNA binding in vitro. This region, the presumptive DNA-binding domain, is similar in sequence to domains in two Arabidopsis proteins and one Oryza protein. Significantly, these are the only proteins in the two plant species that contain an SH2 domain. Such a structure, with a DNA-binding domain located upstream of an SH2 domain, suggests that the plant proteins are orthologous to metazoan STATs. Consistent with this notion, the DNA sequence of the CudA half site, GAA, is identical to metazoan STAT half sites, although the relative positions of the two halves of the dyad are reversed. These results define a hitherto unrecognised class of transcription factors and suggest a model for the evolution of STATs and their DNA-binding sites.

Yang, L. (2008). Mathematical modeling of Dictyostelium discoideum chemotaxis: Gradient sensing and motility. United States -- Maryland, The Johns Hopkins University.
	Chemotaxis is a process in which cells respond to chemical stimuli in their environment and move towards or away from the chemical cue. Chemotaxis is a crucial function of many cell types and plays critical roles in all stages of development. In eukaryotic chemotaxis, a cell must sense the extracellular gradient, choose a direction of motion, polarize and finally deform the cell body to produce motility. Cells achieve this by localizing key signaling as well as force generating molecules to the correct location within the cell. Failure of this process can mean extermination in single cellular organisms, as well as diseases in multicellular bodies. In this dissertation, we apply a multidisciplinary approach, combining cell biology, mathematical modeling, as well as control systems analysis to study Dictyostelium chemotaxis. We start by introducing a basic mathematical model, which accounts for some of the behaviors seen in chemotaxing cells. One weakness of the biochemical model emerges as the lack of power in signal amplification. Next, we use the basic model as a motif, based on biological evidence, to build a detailed biochemical model based on key molecular players in the Dictyostelium gradient sensing pathway. This model is able to consolidate previous experimental results, as well as propose several null hypotheses. It also exhibits increased amplification of the input signal, matching that of drug treated cells. However, the level of amplification exhibited by this model is still lacking compared to that of untreated cells. To search for means of further signal amplification in the Dictyostelium system, we target a critical signaling protein PTEN, and observe its activation patterns in the living cell. As a result, we uncover a possible biochemical feedback pathway regulating the binding dynamics of PTEN. When added to the computational model, this feedback pathway is able to improve the signal amplification performance of the model. We then perform theoretical control systems analysis to study the effect of feedback on the underlying reduced model. We show that the addition of feedback can account for certain nonlinear features seen in chemotaxing cells. While many simulation and analysis tools are available to study biological organisms as stationary objects, there are few practical methods to study cell motion and deformation. Another aspect of this thesis involve developing a computational framework to simulate large deformations of the cell body, such as cell motion during chemotaxis. We develop a viscoelastic model of the mechanical cell based on micropipette aspiration assays. This mechanical model is then coupled with level set methods to provide the moving cell framework. Finally, we are able to combine the stationary biochemical model of gradient sensing with the moving cell framework to achieve true cell morphology and motion in simulation. Our simulation framework is used to explore the relations between cell shape and force generation.

Yang, L., J. C. Effler, et al. (2008). "Modeling cellular deformations using the level set formalism." BMC Syst Biol 2: 68.
	BACKGROUND: Many cellular processes involve substantial shape changes. Traditional simulations of these cell shape changes require that grids and boundaries be moved as the cell's shape evolves. Here we demonstrate that accurate cell shape changes can be recreated using level set methods (LSM), in which the cellular shape is defined implicitly, thereby eschewing the need for updating boundaries. RESULTS: We obtain a viscoelastic model of Dictyostelium cells using micropipette aspiration and show how this viscoelastic model can be incorporated into LSM simulations to recreate the observed protrusion of cells into the micropipette faithfully. We also demonstrate the use of our techniques by simulating the cell shape changes elicited by the chemotactic response to an external chemoattractant gradient. CONCLUSION: Our results provide a simple but effective means of incorporating cellular deformations into mathematical simulations of cell signaling. Such methods will be useful for simulating important cellular events such as chemotaxis and cytokinesis.

Yang, Y., H. Yu, et al. (2008). "Extensive conformational transitions are required to turn on ATP hydrolysis in myosin." J Mol Biol 381(5): 1407-1420.
	Conventional myosin is representative of biomolecular motors in which the hydrolysis of adenosine triphosphate (ATP) is coupled to large-scale structural transitions both in and remote from the active site. The mechanism that underlies such "mechanochemical coupling," especially the causal relationship between hydrolysis and allosteric structural changes, has remained elusive despite extensive experimental and computational analyses. In this study, using combined quantum mechanical and molecular mechanical simulations and different conformations of the myosin motor domain, we provide evidence to support that regulation of ATP hydrolysis activity is not limited to residues in the immediate environment of the phosphate. Specifically, we illustrate that efficient hydrolysis of ATP depends not only on the proper orientation of the lytic water but also on the structural stability of several nearby residues, especially the Arg238-Glu459 salt bridge (the numbering of residues follows myosin II in Dictyostelium discoideum) and the water molecule that spans this salt bridge and the lytic water. More importantly, by comparing the hydrolysis activities in two motor conformations with very similar active-site (i.e., Switches I and II) configurations, which distinguished this work from our previous study, the results clearly indicate that the ability of these residues to perform crucial electrostatic stabilization relies on the configuration of residues in the nearby N-terminus of the relay helix and the "wedge loop." Without the structural support from those motifs, residues in a closed active site in the post-rigor motor domain undergo subtle structural variations that lead to consistently higher calculated ATP hydrolysis barriers than in the pre-powerstroke state. In other words, starting from the post-rigor state, turning on the ATPase activity requires not only displacement of Switch II to close the active site but also structural transitions in the N-terminus of the relay helix and the "wedge loop," which have been proposed previously to be ultimately coupled to the rotation of the converter subdomain 40 A away.

Yew, Z. T., S. Krivov, et al. (2008). "Free-energy landscapes of proteins in the presence and absence of force." J Phys Chem B 112(51): 16902-16907.
	The equilibrium properties of the fourth immunoglobulin domain of filamin from Dictyostelium discoideum (ddFLN4) in the absence and presence of a small force (0-6 pN) pulling the termini apart is characterized through atomistic numerical simulation. The equilibrium free-energy landscape of ddFLN4 is found to change in a complex fashion that cannot be described in terms of one-dimensional projections as usually done in the interpretation of mechanical (un)folding experiments. Nonequilibrium unfolding simulations reveal that the major unfolding intermediate corresponds to a marginally populated state at equilibrium that only appears when a force larger than 4 pN is applied. Finally, we show that if the free-energy difference between states is taken to be linear in the applied force, the proportionality coefficient is not the difference in the end-to-end distance between pair of states as generally assumed even though the data can be reasonably fitted. The present results suggest that mechanical unfolding experiments may reveal states that are not accessible in the absence of force. Thus, special care should be taken when trying to interpret both equilibrium and nonequilibrium mechanical (un)folding experiments in light of the (un)folding properties in the absence of a force.

Yumura, S., M. Ueda, et al. (2008). "Multiple mechanisms for accumulation of myosin II filaments at the equator during cytokinesis." Traffic 9(12): 2089-2099.
	Total internal reflection fluorescence microscopy revealed how individual bipolar myosin II filaments accumulate at the equatorial region in dividing Dictyostelium cells. Direct observation of individual filaments in live cells provided us with much convincing information. Myosin II filaments accumulated at the equatorial region by at least two independent mechanisms: (i) cortical flow, which is driven by myosin II motor activities and (ii) de novo association to the equatorial cortex. These two mechanisms were mutually redundant. At the same time, myosin II filaments underwent rapid turnover, repeating their association and dissociation with the actin cortex. Examination of the lifetime of mutant myosin filaments in the cortex revealed that the turnover mainly depended on heavy chain phosphorylation and that myosin motor activity accelerated the turnover. Double mutant myosin II deficient in both motor and phosphorylation still accumulated at the equatorial region, although they displayed no cortical flow and considerably slow turnover. Under this condition, the filaments stayed for a significantly longer time at the equatorial region than at the polar regions, indicating that there are still other mechanisms for myosin II accumulation such as binding partners or stabilizing activity of filaments in the equatorial cortex.

Zhang, S. (2008). Dictyostelium NF1-mediated Ras signaling is essential for directional sensing, polarization and cell motility. United States -- California, University of California, San Diego.
	In response to a chemoattractant signal, amoeboid cells such as neutrophils, macrophages, and Dictyostelium cells are able to polarize and move towards the chemoattractant source. During Dictyostelium chemotaxis, it is known that cells amplify and differentially localize specific signaling responses at the future anterior and posterior of the cell leading to outwardly directed F-actin polymerization and myosin II-mediated contractility at the front and back, respectively. However, how cells initially detect and orient themselves in chemoattractant gradients remains largely unknown. Ras activation is the earliest polarized response to chemoattractant gradients downstream from heterotrimeric G proteins in Dictyostelium and inhibition of Ras signaling results in directional migration defects. Activated Ras is enriched at the leading edge, promoting the localized activation of key chemotactic effectors, such as PI3K and TORC2. To investigate the role of Ras in directional sensing, I studied the effect of its misregulation using cells with disrupted RasGAP activity. I identified an orthologue of mammalian NF1, DdNF1, as a major regulator of Ras activity in Dictyostelium . nfaA - cells fail to spatially and temporally regulate Ras activity, which leads to misregulated downstream PI3K activity and F-actin polymerization. As a result, severe cytokinesis and chemotaxis defects in nfaA - cells are observed. Through both genetic and biochemical approaches, I identified RasG as the major target of DdNF1 GAP activity in chemotaxis. Using unpolarized, latrunculin-treated cells, I showed that tight regulation of Ras is required for directional sensing. It is speculated that the uniformly distributed DdNF1 functions as a global inactivator of Ras activity, coupled to putative local activators (e.g. RasGEFs), unidentified global inhibitors as well as positive feedback signaling, leads to persistence and amplification of the Ras signal at the front and promotes leading edge formation. Consequently, cells migrate up the gradients. Together, it is suggested that Ras is part of the cell's compass, and that the RasGAP-mediated regulation of Ras activity affects directional sensing. Further, growing nfaA - cells exhibit elevated Ras activity and display enhanced random cellular movement, consistent with the model that a G protein-independent Ras/PI3K/F-actin circuit regulates basic cell motility.

Zhang, S., P. G. Charest, et al. (2008). "Spatiotemporal regulation of Ras activity provides directional sensing." Curr Biol 18(20): 1587-1593.
	Cells' ability to detect and orient themselves in chemoattractant gradients has been the subject of numerous studies, but the underlying molecular mechanisms remain largely unknown [1]. Ras activation is the earliest polarized response to chemoattractant gradients downstream from heterotrimeric G proteins in Dictyostelium, and inhibition of Ras signaling results in directional migration defects [2]. Activated Ras is enriched at the leading edge, promoting the localized activation of key chemotactic effectors, such as PI3K and TORC2 [2-5]. To investigate the role of Ras in directional sensing, we studied the effect of its misregulation by using cells with disrupted RasGAP activity. We identified an ortholog of mammalian NF1, DdNF1, as a major regulator of Ras activity in Dictyostelium. We show that disruption of nfaA leads to spatially and temporally unregulated Ras activity, causing cytokinesis and chemotaxis defects. By using unpolarized, latrunculin-treated cells, we show that tight regulation of Ras is important for gradient sensing. Together, our findings suggest that Ras is part of the cell's compass and that the RasGAP-mediated regulation of Ras activity affects directional sensing.

Allan, C. Y. and P. R. Fisher (2009). "In Vivo Measurements of Cytosolic Calcium in Dictyostelium discoideum." Methods Mol Biol 571: 291-308.
	The involvement of calcium signalling during chemotaxis in Dictyostelium discoideum is well documented. Spatiotemporal increases of intracellular calcium ([Ca(2+)](i)) have been observed within seconds of stimulation with the chemoattractants folic acid and cAMP. This rise in [Ca(2+)](i) localises to the rear cortex of the cell (J. Cell Sci. 109:2673-2678, 1996) and has been found to be not essential for chemotaxis, but likely to be involved in fine tuning of chemotactic responses (EMBO J. 19:4846-4854, 2000). Measurements of cytosolic Ca(2+) ([Ca(2+)](c)) responses have involved the use of different Ca(2+) probes including ectopically expressed aequorin (a Ca(2+)-sensitive photoprotein), the fluorescent dye fura-2-dextran and the radioisotope (45)Ca(2+). The aequorin method (J. Cell Sci. 110:2845-2853, 1997) offers nonperturbing, real-time measurement of cytosolic free Ca(2+) in suspensions of cells, but the low levels of light emission preclude measurements on individual cells. Fura-2 imaging (Cell Calcium 22:65-74, 1997; Eur. J. Cell Biol. 58:172-181, 1992; Biochem. J. 332:541-548, 1998; BMC Cell Biol. 6:13, 2005) has the advantage of allowing Ca(2+) responses to be observed in individual cells so that the subcellular localisation of the response and differences amongst individual cells can be observed. However data collection is more labour intensive, much smaller numbers of cells are sampled, the cells are unavoidably damaged physically during loading and the time resolution (s) is much less than that provided by the aequorin method (ms). (45)Ca(2+) uptake assays (Cell Biol. Int. Rep. 2:71-79, 1978; J. Cell Biol. 112:103-110, 1991) allow measurement of Ca(2+) influx from the medium by cell suspensions with a time resolution of the order of seconds. Radioactive Ca(2+) uptake measurements are unsullied by but equally do not provide information about Ca(2+) efflux, intracellular Ca(2+) release or sequestration or changes in cytosolic free Ca(2+) levels.

Alonso-Latorre, B., R. Meili, et al. (2009). "Distribution of traction forces associated with shape changes during amoeboid cell migration." Conf Proc IEEE Eng Med Biol Soc 2009: 3346-3349.
	Amoeboid motility results from the cyclic repetition of shape changes leading to periodic oscillations of the cell length (motility cycle). We analyze the dominant modes of shape change and their association to the traction forces exerted on the substrate using Principal Component Analysis (PCA) of time-lapse measurements of cell shape and traction forces in migrating Dictyostelium cells. Using wild-type cells (wt) as reference, we investigated Myosin II activity by studying Myosin II heavy chain null cells (mhcA-) and Myosin II essential light chain null cells (mlcE-). We found that wt, mlcE-and mhcA- cells utilize similar modes of shape changes during their motility cycle, although these shape changes are implemented at a slower pace in Myosin II null mutants. The number of dominant modes of shape changes is surprisingly few with only four modes accounting for 75% of the variance in all cases. The three principal shape modes are dilation/elongation, bending, and bulging of the front/back. The second mode, resulting from sideways protrusion/retraction, is associated to lateral asymmetries in the cell traction forces, and is significantly less important in mhcA- cells. These results indicate that the mechanical cycle of traction stresses and cell shape changes remains remarkably similar for all cell lines but is slowed down when myosin function is lost, probably due to a reduced control on the spatial organization of the traction stresses.

Amagai, A. (2009). "A novel function of ethylene." Gene Regul Syst Bio 3: 21-30.
	The cellular slime mold, Dictyostelium mucoroides-7 (Dm7) exhibits clear dimorphism; macrocyst formation as a sexual process and sorocap formation as an asexual process. These two life cycles are regulated by two regulators, ethylene and cyclic AMP (cAMP). This is the first report demonstrating a novel function of ethylene at the cellular level. That is, ethylene induces a zygote formed by cell fusion and subsequent nuclear fusion. Recently, the function of ethylene at the molecular level has been clarified as it induces zygote formation through an enhanced expression of a novel gene, zyg1. The signaling pathway for induction or inhibition of zygote formation is now trying to be clarified focusing on the ZYG1 protein.

Anjard, C., Y. Su, et al. (2009). "Steroids initiate a signaling cascade that triggers rapid sporulation in Dictyostelium." Development 136(5): 803-812.
	Encapsulation of prespore cells of Dictyostelium discoideum is controlled by several intercellular signals to ensure appropriate timing during fruiting body formation. Acyl-CoA-binding protein, AcbA, is secreted by prespore cells and processed by the prestalk protease TagC to form the 34 amino acid peptide SDF-2 that triggers rapid encapsulation. AcbA is secreted when gamma-aminobutyric acid (GABA) is released from prespore cells and binds to GrlE, a G protein-coupled receptor (GPCR). Analysis of SDF-2 production in mutant strains lacking Galpha subunits and GPCRs, either as pure populations or when mixed with other mutant strains, uncovered the non-cell-autonomous roles of GrlA, Galpha4 and Galpha7. We found that Galpha7 is essential for the response to GABA and is likely to be coupled to GrlE. GrlA-null and Galpha4-null cells respond normally to GABA but fail to secrete it. We found that they are necessary for the response to a small hydrophobic molecule, SDF-3, which is released late in culmination. Pharmacological inhibition of steroidogenesis during development blocked the production of SDF-3. Moreover, the response to SDF-3 could be blocked by the steroid antagonist mifepristone, whereas hydrocortisone and other steroids mimicked the effects of SDF-3 when added in the nanomolar range. It appears that SDF-3 is a steroid that elicits rapid release of GABA by acting through the GPCR GrlA, coupled to G protein containing the Galpha4 subunit. SDF-3 is at the head of the cascade that amplifies the signal for encapsulation to ensure the rapid, synchronous formation of spores.

Annesley, S. J. and P. R. Fisher (2009). "Dictyostelium discoideum-a model for many reasons." Mol Cell Biochem 329(1-2): 73-91.
	The social amoeba or cellular slime mould Dictyostelium discoideum is a "professional" phagocyte that has long been recognized for its value as a biomedical model organism, particularly in studying the actomyosin cytoskeleton and chemotactic motility in non-muscle cells. The complete genome sequence of D. discoideum is known, it is genetically tractable, readily grown clonally as a eukaryotic microorganism and is highly accessible for biochemical, cell biological and physiological studies. These are the properties it shares with other microbial model organisms. However, Dictyostelium combines these with a unique life style, with motile unicellular and multicellular stages, and multiple cell types that offer for study an unparalleled variety of phenotypes and associated signalling pathways. These advantages have led to its recent emergence as a valuable model organism for studying the molecular pathogenesis and treatment of human disease, including a variety of infectious diseases caused by bacterial and fungal pathogens. Perhaps surprisingly, this organism, without neurons or brain, has begun to yield novel insights into the cytopathology of mitochondrial diseases as well as other genetic and idiopathic disorders affecting the central nervous system. Dictyostelium has also contributed significantly to our understanding of NDP kinase, as it was the Dictyostelium enzyme whose structure was first determined and related to enzymatic activity. The phenotypic richness and tractability of Dictyostelium should provide a fertile arena for future exploration of NDPK's cellular roles.

Annesley, S. J. and P. R. Fisher (2009). "Dictyostelium slug phototaxis." Meth Mol Biol 571: 67-76.
	Dictyostelium slugs are able to respond to environmental stimuli in an extremely sensitive and efficient way. This enables a slug to migrate to more favourable locations for formation of fruiting bodies and dispersal of spores. Phototaxis is a readily assayed phenotype and reflects the interactions of environmental stimuli with morphogenetic signalling systems controlling the movement of the slug. The methods for assaying phototaxis are described here. Qualitative phototaxis tests are described and can be used for rapid screening of potential mutants or effects of pharmacological agents. These tests are simple to conduct yet care must be taken in order to avoid the effects of high cell density which can be misleading when interpreting results. Quantitative phototaxis tests can be performed with known cell densities of amoebae which ensures that any effects seen are caused by the mutation or pharmacological agent and not simply due to differences in cell densities.

Annesley, S. J. and P. R. Fisher (2009). Scaffolding proteins that regulate the actin cytoskeleton in cell movement. Cell Movement: New Research Trends. T. Abrue and G. Silva, Nova Science Publishers, Inc.: 1-50.
	Actin is the main component of the microfilament system in all eukaryotic 
cells and is essential for most intra- and inter-cellular movement including 
muscle contraction, cell movement, cytokinesis, cytoplasmic organisation and 
intracellular transport. The polymerisation and depolymerisation of actin 
filaments in nonmuscle cells is highly regulated and the reorganisation of 
the actin cytoskeleton can occur within seconds after chemotactic stimulation.  
There are many proteins which are involved in the regulation of the actin 
cytoskeleton. These include receptors which receive chemotactic stimuli, 
G proteins, second messengers, signalling molecules, kinases, phosphatases 
and transcription factors. These proteins are varied and numerous and are 
involved in multiple pathways. Despite the large number of proteins, there 
are not enough to coordinate the various responses of the cytoskeleton. An
 additional level of regulation is conferred by scaffolding proteins. Due to 
the presence of numerous protein interaction domains, scaffolding proteins
 can tether various proteins to a certain location within the cell to 
facilitate the rapid transfer of signals from one protein to the next. 
This colocalisation of the components of a particular pathway also helps 
to prevent unwanted crosstalk with components of other pathways. Tethering 
receptors, kinases, phosphatases and cytoskeletal components to a particular 
location within a cell helps ensure efficient relaying and feedback inhibition 
of signals to enable rapid activation and inactivation of responses.  
Scaffolding proteins are also thought to stabilise the otherwise weak 
interactions between particular proteins in a cascade and to catalyse the 
activation of the pathway components.  There are numerous scaffolding 
proteins involved in the regulation of the cytoskeleton and this chapter 
has focussed on examples from several groups of scaffolding proteins 
including the MAPK scaffolds, the AKAPs, scaffolds of the post synaptic 
density and actin binding scaffolding proteins.

Aubry, L., D. Guetta, et al. (2009). "The arrestin fold: variations on a theme." Curr Genomics 10(2): 133-142.
	Endocytosis of ligand-activated plasma membrane receptors has been shown to contribute to the regulation of their downstream signaling. beta-arrestins interact with the phosphorylated tail of activated receptors and act as scaffolds for the recruitment of adaptor proteins and clathrin, that constitute the machinery used for receptor endocytosis. Visual- and beta-arrestins have a two-lobe, immunoglobulin-like, beta-strand sandwich structure. The recent resolution of the crystal structure of VPS26, one of the retromer subunits, unexpectedly evidences an arrestin fold in this protein, which is otherwise unrelated to arrestins. From a functional point of view, VPS26 is involved in the retrograde transport of the mannose 6-P receptor from the endosomes to the trans-Golgi network. In addition to the group of genuine arrestins and Vps26, mammalian cells harbor a vast repertoire of proteins that are related to arrestins on the basis of their PFAM Nter and Cter arrestin- domains, which are named Arrestin Domain- Containing proteins (ADCs). The biological role of ADC proteins is still poorly understood. The three subfamilies have been merged into an arrestin-related protein clan.This paper provides an overall analysis of arrestin clan proteins. The structures and functions of members of the subfamilies are reviewed in mammals and model organisms such as Drosophila, Caenorhabditis, Saccharomyces and Dictyostelium.

Baboolal, T. G., T. Sakamoto, et al. (2009). "The SAH domain extends the functional length of the myosin lever." Proc Natl Acad Sci U S A 106(52): 22193-22198.
	Stable, single alpha-helix (SAH) domains are widely distributed in the proteome, including in myosins, but their functions are unknown. To test whether SAH domains can act as levers, we replaced four of the six calmodulin-binding IQ motifs in the levers of mouse myosin 5a (Myo5) with the putative SAH domain of Dictyostelium myosin MyoM of similar length. The SAH domain was inserted between the IQ motifs and the coiled coil in a Myo5 HMM construct in which the levers were truncated from six to two IQ motifs (Myo5-2IQ). Electron microscopy of this chimera (Myo5-2IQ-SAH) showed the SAH domain was straight and 17 nm long as predicted, restoring the truncated lever to the length of wild-type (Myo5-6IQ). The powerstroke (of 21.5 nm) measured in the optical trap was slightly less than that for Myo5-6IQ but much greater than for Myo5-2IQ. Myo5-2IQ-SAH moved processively along actin at physiological ATP concentrations with similar stride and run lengths to Myo5-6IQ in in-vitro single molecule assays. In comparison, Myo5-2IQ is not processive under these conditions. Solution biochemical experiments indicated that the rear head did not mechanically gate the rate of ADP release from the lead head, unlike Myo5-6IQ. These data show that the SAH domain can form part of a functional lever in myosins, although its mechanical stiffness might be lower. More generally, we conclude that SAH domains can act as stiff structural extensions in aqueous solution and this structural role may be important in other proteins.

Bagorda, A., S. Das, et al. (2009). "Real-time measurements of cAMP production in live Dictyostelium cells." J Cell Sci.
	Cyclic AMP has a crucial role during the entire developmental program of the social amoebae Dictyostelium, acting both as an intracellular second messenger and, when secreted, as a directional cue that is relayed to neighboring cells during chemotaxis. Although significant knowledge about cAMP production in chemotaxing cells has been derived from studies performed on cell populations, cAMP dynamics at the single cell level have not been investigated. To examine this, we used a FRET-based cAMP sensor that possesses high cAMP sensitivity and great temporal resolution. We show the transient profile of cAMP accumulation in live Dictyostelium cells and establish that chemoattractants control intracellular cAMP dynamics by regulating synthesis via the adenylyl cyclase ACA. aca(-) cells show no significant change in FRET response following chemoattractant addition. Furthermore, cells lacking ACB, the other adenylyl cyclase expressed in chemotaxing cells, behave similarly to wild-type cells. We also establish that the RegA is the major phosphodiesterase that degrades intracellular cAMP in chemotaxis-competent cells. Interestingly, we failed to measure intracellular cAMP compartmentalization in actively chemotaxing cells. We conclude that cytosolic cAMP, which is destined to activate PKA, is regulated by ACA and RegA and does not compartmentalize during chemotaxis.

Bakthavatsalam, D., J. M. Choe, et al. (2009). "A Dictyostelium chalone uses G proteins to regulate proliferation." BMC Biol 7: 44.
	BACKGROUND: Several studies have shown that organ size, and the proliferation of tumor metastases, may be regulated by negative feedback loops in which autocrine secreted factors called chalones inhibit proliferation. However, very little is known about chalones, and how cells sense them. We previously identified two secreted proteins, AprA and CfaD, which act as chalones in Dictyostelium. Cells lacking AprA or CfaD proliferate faster than wild-type cells, and adding recombinant AprA or CfaD to cells slows their proliferation. RESULTS: We show here that cells lacking the G protein components Galpha8, Galpha9, and Gbeta proliferate faster than wild-type cells despite secreting normal or high levels of AprA and CfaD. Compared with wild-type cells, the proliferation of galpha8-, galpha9- and gbeta- cells are only weakly inhibited by recombinant AprA (rAprA). Like AprA and CfaD, Galpha8 and Gbeta inhibit cell proliferation but not cell growth (the rate of increase in mass and protein per nucleus), whereas Galpha9 inhibits both proliferation and growth. galpha8- cells show normal cell-surface binding of rAprA, whereas galpha9- and gbeta- cells have fewer cell-surface rAprA binding sites, suggesting that Galpha9 and Gbeta regulate the synthesis or processing of the AprA receptor. Like other ligands that activate G proteins, rAprA induces the binding of [3H]GTP to membranes, and GTPgammaS inhibits the binding of rAprA to membranes. Both AprA-induced [3H]GTP binding and the GTPgammaS inhibition of rAprA binding require Galpha8 and Gbeta but not Galpha9. Like aprA- cells, galpha8- cells have reduced spore viability. CONCLUSION: This study shows that Galpha8 and Gbeta are part of the signal transduction pathway used by AprA to inhibit proliferation but not growth in Dictyostelium, whereas Galpha9 is part of a differealnt pathway that regulates both proliferation and growth, and that a chalone signal transduction pathway uses G proteins.

Balbo, A. and S. Bozzaro (2009). "A novel bioassay for evaluating soil bio-hazards using Dictyostelium as biosensor: validation and application to the Bio-Bio project." Fresenius Environ. Bull. 17(8b): 1137-1143.
	An easy and cheap biosensor has been developed for assessing soil biohazards. The toxicity assay is based on inhibition of Dictyostelium development, a soil amoeba undergoing multicellular development and cell differentia-tion under starving conditions. The sensitivity of the assay was assessed in soil samples with increasing concentra-tions of heavy metals and by comparison with standard bio-assays on a battery of soils collected from contaminated industrial sites. Dictyostelium appears to be highly sensi-tive to polycyclic aromatic hydrocarbons, mineral oil and, to a lesser extent, to heavy metals. The assay has been applied in a concerted action with other bioassays within the frame of the BIO-BIO project. 

Banerjee, S., P. W. Robbins, et al. (2009). "Molecular characterization of nucleocytosolic O-GlcNAc transferases of Giardia lamblia and Cryptosporidium parvum." Glycobiology 19(4): 331-336.
	O-Linked N-acetylglucosaminyltransferase (OGT) catalyzes the transfer of a single GlcNAc to the Ser or Thr of nucleocytoplasmic proteins. OGT activity, which may compete with that of kinases, is involved in signaling in animals and plants, and abnormalities in OGT activities have been associated with type 2 diabetes. Here, we show that ogt genes that predict enzymes with characteristic tetratricopeptide repeats and a spindly domain are present in some protists (Giardia, Cryptosporidium, Toxoplasma, and Dictyostelium) but are absent from the majority of protists examined (e.g., Plasmodium, Trypanosoma, Entamoeba, and Trichomonas). Similarly, ogt genes are present in some fungi but are absent from numerous other fungi, suggesting that secondary loss is an important contributor to the evolution of ogt genes. Nucleocytosolic extracts of Giardia and Cryptosporidium show OGT activity, and recombinant Giardia and Cryptosporidium OGTs are active in yeast and bacteria, respectively. These results suggest the possibility that O-GlcNAc modification of nucleocytosolic proteins also has function(s) in simple eukaryotes.

Baviskar, S. (2009). Molecular genetic approach to the functional analysis of a regulatory protein in Dictyostelium discoideum & research on assessments and constructivism in science education. United States -- Idaho, Idaho State University: 239.
	This dissertation includes two sections. Section I consists of the molecular biological research project "Functional analysis of the Dd-grp94 ( Dictyostelium discoideum glucose regulated protein 94 kilodalton) gene in D. discoideum. " To elucidate the biological roles of the Dd-grp94 gene, two molecular genetic approaches were adopted. Using a gene replacement technique Dd-grp94 insertion mutants could not be obtained despite successful incorporation of altered gene sequences. This indicated that Dd-grp94 might be an essential gene in D. discoideum. Using an RNA interference (RNAi) approach, it was concluded that Dd-grp94 plays a crucial and specific role in determining normal cell structure, growth and differentiation. Section II, "Science Education and Pedagogy" includes the education research project, statement of teaching philosophy, supervised teaching internship reports and reflections and publications in the field of science education. The goals of the education research project: "A survey of graduate teaching assistants of Idaho State University to know their attitudes toward teaching and education", were to discover teaching assistants' (TA) attitudes toward teaching before and after TA experience at ISU, the types of TA training and support services that were available to them and the TA training methods that they thought might help in improving their performance. Overall, the results of the study show that the TAs attitudes toward teaching and education were favorable. They also reported lack of proper training when they became a TA for the first time. The respondents also indicated the training methods/policies that should be made part of the TA training for the benefit of undergraduate education in general and teaching assistants in particular. While writing my statement of teaching philosophy, I cogitated on my understanding about how students learn and how teaching could facilitate the process of learning. It also made me conscious about the problems faced by the teachers and students in college science classrooms and the teaching and assessment methods that need to be reviewed to ameliorate the problems. The objective of supervised teaching internships was to gain experiences in teaching large classes using traditional and non-traditional teaching methods. The internships gave me the opportunity to test formative and summative assessment techniques. It also made me aware of my weaknesses and strengths as a teacher. The Doctor of Arts coursework encouraged me to review and compare journal articles on science education and education research. This led to the recognition that a gap exists between theoretical and practical aspects of science education. In collaboration with my colleagues and teachers, I co-authored two articles on constructivist teaching methods titled "Essential Criteria to Characterize Constructivist Teaching: Derived from a review of the literature and applied to five constructivist-teaching method articles" and "A Field Guide to Constructivism in the College Science Classroom: Four Essential Criteria and a Guide to their Usage". The third article "Moving Students from Information Recitation to Information Understanding: Exploiting Bloom's Taxonomy in Creating Science Questions" addresses how assessments could be used to know the level of students' understanding.

Benabentos, R., S. Hirose, et al. (2009). "Polymorphic members of the lag gene family mediate kin discrimination in Dictyostelium." Curr Biol 19(7): 567-572.
	Self and kin discrimination are observed in most kingdoms of life and are mediated by highly polymorphic plasma membrane proteins. Sequence polymorphism, which is essential for effective recognition, is maintained by balancing selection. Dictyostelium discoideum are social amoebas that propagate as unicellular organisms but aggregate upon starvation and form fruiting bodies with viable spores and dead stalk cells. Aggregative development exposes Dictyostelium to the perils of chimerism, including cheating, which raises questions about how the victims survive in nature and how social cooperation persists. Dictyostelids can minimize the cost of chimerism by preferential cooperation with kin, but the mechanisms of kin discrimination are largely unknown. Dictyostelium lag genes encode transmembrane proteins with multiple immunoglobulin (Ig) repeats that participate in cell adhesion and signaling. Here, we describe their role in kin discrimination. We show that lagB1 and lagC1 are highly polymorphic in natural populations and that their sequence dissimilarity correlates well with wild-strain segregation. Deleting lagB1 and lagC1 results in strain segregation in chimeras with wild-type cells, whereas elimination of the nearly invariant homolog lagD1 has no such consequences. These findings reveal an early evolutionary origin of kin discrimination and provide insight into the mechanism of social recognition and immunity.

Beta, C. (2009). "Spatiotemporal stimulation of single cells using flow photolysis." Meth Mol Biol 571: 321-332.
	Quantitative studies of chemotactic signaling require experimental techniques that can expose single cells to chemical stimuli with high resolution in both space and time. Recently, we have introduced the method of flow photolysis (Anal. Chem. 79:3940-3944, 2007), which combines microfluidic techniques with the photochemical release of caged compounds. This method allows us to tailor chemical stimuli on the length scale of individual cells with subsecond temporal resolution. In this chapter, we provide a detailed protocol for the setup of flow photolysis experiments and exemplify this versatile approach by initiating membrane translocation of fluorescent fusion proteins in chemotactic Dictyostelium discoideum cells.

Betapudi, V. and T. T. Egelhoff (2009). "Roles of an Unconventional Protein Kinase and Myosin II in Amoeba Osmotic Shock Responses." Traffic.
	Abstract The contractile vacuole (CV) is a dynamic organelle that enables Dictyostelium amoeba and other protist to maintain osmotic homeostasis by expelling excess water. In the present study, we have uncovered a mechanism that coordinates the mechanics of the CV with myosin II, regulated by VwkA, an unconventional protein kinase that is conserved in an array of protozoa. Green fluorescent protein (GFP)-VwkA fusion proteins localize persistently to the CV during both filling and expulsion phases of water. In vwkA null cells, the established CV marker dajumin still localizes to the CV, but these structures are large, spherical and severely impaired for discharge. Furthermore, myosin II cortical localization and assembly are abnormal in vwkA null cells. Parallel analysis of wild-type cells treated with myosin II inhibitors or of myosin II null cells also results in enlarged CVs with impaired dynamics. We suggest that the myosin II cortical cytoskeleton, regulated by VwkA, serves a critical conserved role in the periodic contractions of the CV, as part of the osmotic protective mechanism of protozoa.

Blanc, C., S. J. Charette, et al. (2009). "Dictyostelium Tom1 participates to an ancestral ESCRT-0 complex." Traffic 10(2): 161-171.
	Sorting of ubiquitinated proteins to multivesicular bodies (MVBs) in mammalian cells relies on proteins with a Vps27/Hrs/STAM (VHS) domain. Here, we show that the amoeba Dictyostelium presents only one protein with a VHS domain: DdTom1. We demonstrate that the VHS domain of DdTom1 is followed by a Golgi-localized, gamma-ear-containing, ADP-ribosylation-factor-binding and Tom1 (GAT) domain that binds ubiquitin, and by a non-conserved C-terminal domain that can recruit clathrin, EGFr pathway substrate 15 and tumor susceptibility gene 101, a component of the MVB biogenesis machinery [endosomal complexes required for transport (ESCRT) complexes]. Both VHS and GAT domains interact with phospholipids and therefore could ensure the recruitment of DdTom1 to endosomal membranes. We propose that DdTom1 participates in an ancestral ESCRT-0 complex implicated in the sorting of ubiquitinated proteins into MVBs.

Blau-Wasser, R., U. Euteneuer, et al. (2009). "CP250, a Novel Acidic Coiled Coil Protein of the Dictyostelium centrosome, Affects Growth, Chemotaxis, and the Nuclear Envelope." Mol Biol Cell 20(20): 4348-4361.
	The Dictyostelium centrosome is a nucleus associated body consisting of a box-shaped core surrounded by the corona, an amorphous matrix functionally equivalent to the pericentriolar material of animal centrosomes which is responsible for the nucleation and anchoring of microtubules. Here we describe CP250 a component of the corona, an acidic coiled coil protein that is present at the centrosome throughout interphase while disappearing during prophase and reappearing at the end of late telophase. Amino acids 756-1148 of the 2110 amino acids are sufficient for centrosomal targeting and cell cycle-dependent centrosome association. Mutant cells lacking CP250 are smaller in size, growth on bacteria is delayed, chemotaxis is altered, and development is affected, which, in general, are defects observed in cytoskeletal mutants. Furthermore, loss of CP250 affected the nuclear envelope and led to reduced amounts and altered distribution of Sun-1, a conserved nuclear envelope protein that connects the centrosome to chromatin.

Boatti, L., F. Marsano, et al. (2009). "Environmental proteomics in the social amoeba Dictyostelium discoideum." Compar Biochem Physiol - Part A: Mol Integr Physiol 154(1 (Suppl. 1)): S13-S14.
	Bidimensional electrophoresis and protein identification by tandem
mass spectrometry (nanoLC-ESI-Q-TOF) were used to evaluate
quantitative changes of protein expression determined by sub-lethal
amounts of some widespread pollutants. Our results pointed out that
different Hg doses (NOEC and LOEC for the replication rate) provided
distinct protein expressed signatures (PESs). In fact, protein identification
showed an adaptive response to oxidative stress at low dose – 13
up-regulated proteins – involving increased expression among others
of GST, SOD, catalase and thioredoxin. Such molecular fingerprint
disappeared at the higher concentration in which 12 spots out of 14
were downregulated. Moreover, differences emerged also in terms of post-translational modification (protein carbonylation) and such PESs
were correlated with the metabolic and physiological status of the cell.
Furthermore, Dictyostelium amoebae challenged with different classes
of chemicals, at the same equitoxic levels for lysosomal membrane
stability, showed distinct signatures for both dissimilar and similar
acting pollutants such as the heavy metal Ni, the organophosphate
Chlorpyrifos, and two nicotyl-receptor agonist biocides: Imidacloprid
and Thiacloprid. In the case of Ni (15 changing proteins), we observed
features involved in different processes such as nitrogen compounds
metabolism and protein folding, while Chlorpyrifos interested, in
particular, the energetic metabolism with 5 out of 13 changing
proteins. Imidacloprid and its congener Thiacloprid rendered 3 and
14 changing polypeptides. Both treatments determined the downexpression
of a different ATP synthetase, but apart from this analogy,
two completely different PESs were found. In conclusion, these results
validated the use of PES identification for ecotoxicological surveys.

Bosgraaf, L. and P. J. Van Haastert (2009). "The ordered extension of pseudopodia by amoeboid cells in the absence of external cues." PLoS One 4(4): e5253.
	Eukaryotic cells extend pseudopodia for movement. In the absence of external cues, cells move in random directions, but with a strong element of persistence that keeps them moving in the same direction Persistence allows cells to disperse over larger areas and is instrumental to enter new environments where spatial cues can lead the cell. Here we explore cell movement by analyzing the direction, size and timing of approximately 2000 pseudopodia that are extended by Dictyostelium cells. The results show that pseudpopod are extended perpendicular to the surface curvature at the place where they emerge. The location of new pseudopods is not random but highly ordered. Two types of pseudopodia may be formed: frequent splitting of an existing pseudopod, or the occasional extension of a de novo pseudopod at regions devoid of recent pseudopod activity. Split-pseudopodia are extended at approximately 60 degrees relative to the previous pseudopod, mostly as alternating Right/Left/Right steps leading to relatively straight zigzag runs. De novo pseudopodia are extended in nearly random directions thereby interrupting the zigzag runs. Persistence of cell movement is based on the ratio of split versus de novo pseudopodia. We identify PLA2 and cGMP signaling pathways that modulate this ratio of splitting and de novo pseudopodia, and thereby regulate the dispersal of cells. The observed ordered extension of pseudopodia in the absence of external cues provides a fundamental insight into the coordinated movement of cells, and might form the basis for movement that is directed by internal or external cues.

Bosgraaf, L. and P. J. Van Haastert (2009). "Navigation of chemotactic cells by parallel signaling to pseudopod persistence and orientation." PLoS One 4(8): e6842.
	The mechanism of chemotaxis is one of the most interesting issues in modern cell biology. Recent work shows that shallow chemoattractant gradients do not induce the generation of pseudopods, as has been predicted in many models. This poses the question of how else cells can steer towards chemoattractants. Here we use a new computational algorithm to analyze the extension of pseudopods by Dictyostelium cells. We show that a shallow gradient of cAMP induces a small bias in the direction of pseudopod extension, without significantly affecting parameters such as pseudopod frequency or size. Persistent movement, caused by alternating left/right splitting of existing pseudopodia, amplifies the effects of this bias by up to 5-fold. Known players in chemotactic pathways play contrasting parts in this mechanism; PLA2 and cGMP signal to the cytoskeleton to regulate the splitting process, while PI 3-kinase and soluble guanylyl cyclase mediate the directional bias. The coordinated regulation of pseudopod generation, orientation and persistence by multiple signaling pathways allows eukaryotic cells to detect extremely shallow gradients.

Bosgraaf, L., P. J. M. van Haastert, et al. (2009). "Analysis of Cell Movement by Simultaneous Quantification of Local Membrane Displacement and Fluorescent Intensities Using Quimp2." Cell Motil Cytoskel 66(3): 156-165.
	The use of fluorescent markers in living cells has increased dramatically in the recent years. The quantitative analysis of the images requires specific analysis software. Previously, the program Quimp was launched for quantitating fluorescent intensities at the membrane or the cortex of the cell. However, Quimp is not well suited to quantitate local membrane displacement. Here we present Quimp2 that is capable of tracking membrane subregions in time, which enables the simultaneous quantification of fluorescent intensities and membrane movement. Quimp2 has two new tools, (i) conversion filters to analyze movies obtained with fluorescent, DIC and phase contrast different microscopes, and (ii) a macro that calculates the local membrane displacement and provides various options to display the results. Quimp2 is used here to investigate the molecular mechanism of cell movement by correlating the dynamics of local membrane movement with the local concentration of myosin and F-actin. Cell Motil. Cytoskeleton 66: 156-165,2009. (C) 2009 Wiley-Liss, Inc.

Breitsprecher, D., A. K. Kiesewetter, et al. (2009). "Analysis of Actin Assembly by In Vitro TIRF Microscopy." Meth Mol Biol 571: 401-415.
	Since directed movement toward an extracellular chemoattractant requires rapid and continuous reorgani-zation of the actin cytoskeleton to form complex structures such as a protruding lamellipodium, it is of great interest to analyze and understand the individual contribution of proteins specifically involved in this process. Over the last decade, enormous progress has been made toward understanding the versatile molecular mechanisms underlying actin-based cell motility and the regulation of site-specific F-actin assembly and disassembly. In spite of this wealth of knowledge and due to the constant discovery of novel regulatory factors, many questions remain to be answered. In this chapter, we describe a powerful method that allows to study the effects of actin-binding proteins on the assembly of single filaments by in vitro total internal reflection fluorescence (TIRF) microscopy using purified proteins and fluorescently labeled actin.

Bretschneider, T., K. Anderson, et al. (2009). "The three-dimensional dynamics of actin waves, a model of cytoskeletal self-organization." Biophys J 96(7): 2888-2900.
	Actin polymerization is typically initiated at specific sites in a cell by membrane-bound protein complexes, and the resulting structures are involved in specialized cellular functions, such as migration, particle uptake, or mitotic division. Here we analyze the potential of the actin system to self-organize into waves that propagate on the planar, substrate-attached membrane of a cell. We show that self-assembly involves the ordered recruitment of proteins from the cytoplasmic pool and relate the organization of actin waves to their capacity for applying force. Three proteins are shown to form distinct three-dimensional patterns in the actin waves. Myosin-IB is enriched at the wave front and close to the plasma membrane, the Arp2/3 complex is distributed throughout the waves, and coronin forms a sloping layer on top of them. CARMIL, a protein that links myosin-IB to the Arp2/3 complex, is also recruited to the waves. Wave formation does not depend on signals transmitted by heterotrimeric G-proteins, nor does their propagation require SCAR, a regulator upstream of the Arp2/3 complex. Propagation of the waves is based on an actin treadmilling mechanism, indicating a program that couples actin assembly to disassembly in a three-dimensional pattern. When waves impinge on the cell perimeter, they push the edge forward; when they reverse direction, the cell border is paralyzed. These data show that force-generating, highly organized supramolecular networks are autonomously formed in live cells from molecular motors and proteins controlling actin polymerization and depolymerization.

Brown, M. W., F. W. Spiegel, et al. (2009). "Phylogeny of the "forgotten" cellular slime mold, Fonticula alba, reveals a key evolutionary branch within Opisthokonta." Mol Biol Evol.
	The shared ancestry between Fungi and animals has been unequivocally demonstrated by abundant molecular and morphological data for well over a decade. Along with the animals and Fungi, multiple protists have been placed in the supergroup Opisthokonta making it exceptionally diverse. In an effort to place the cellular slime mold Fonticula alba, an amoeboid protist with aggregative, multicellular fruiting, we sequenced five nuclear encoded genes; small subunit ribosomal RNA, actin, beta-tubulin, elongation factor 1-alpha, and the cytosolic isoform of heat shock protein 70 for phylogenetic analyses. Molecular trees demonstrate that Fonticula is an opisthokont that branches sister to filose amoebae in the genus Nuclearia. Fonticula plus Nuclearia are sister to Fungi. We propose a new name for this well-supported clade, Nucletmycea, incorporating Nuclearia, Fonticula, and Fungi. Fonticula represents the first example of a cellular slime mold morphology within Opisthokonta. Thus, there are four types of multicellularity in the supergroup - animal, fungal, colonial, and now aggregative. Our data indicate that multicellularity in Fonticula evolved independent of that found in the fungal and animal radiations. With the rapidly expanding sequence and genomic data becoming available from many opisthokont lineages, Fonticula may be fundamental to understanding opisthokont evolution as well as any possible commonalities involved with the evolution of multicellularity.

Bruce, T. (2009). Functional interaction of RacF2 and the WASp family protein, scar, in the Rab8 signaling pathway of the social amoeba, Dictyostelium discoideum. United States -- South Carolina, Clemson University: 171.
	The small GTPase, Rab8, has been shown to play a role in cell-cell adhesion and restructuring of the actin cytoskeleton in both mammalian cells and the lower eukaryote, Dictyostelium discoideum . In D. discoideum , cells expressing constitutively activated Rab8 (Rab8CA) display reduced cell-cell adhesion and increased actin-rich protrusions as well as delayed aggregation. Rab8 has been implicated in the restructuring of the actin cytoskeleton, but no specific pathway for this action has been identified. In other systems, actin-rich membrane extension formation is regulated by WASp family proteins, including SCAR. Here we provide evidence of a functional relationship between the WASp family protein, SCAR, and Rab8. This provides the first genetic evidence in any cell system of a functional interaction between Rab8 and a WASp family protein. SCAR is known to be directly activated by Rac. Our results indicate that Rab8 interacts directly with RacF2 to rescue aggregation in cells expressing Rab8CA. While we were unable to demonstrate that RacF2 interacts directly with SCAR, we have demonstrated that RacF2 likely interacts directly with Rab8 to control cell-cell adhesion. Additionally, we have begun to conduct similar experiments in mammalian cells. To this end, we have developed and expressed EGFP (enhanced green fluorescent protein) chimeras of wildtype as well as constitutively active and dominant negative mutant forms of Rab8 in mammalian cells. In addition, we have designed a Rab8 activation assay based on its interaction with GCK, a germinal center kinase, which interacts directly with the active, GTP-bound form of Rab8. We have also investigated the effect of expression of mutant versions of Rab8 on GCK intracellular levels.

Brzostowski, J. A., P. Fey, et al. (2009). "The Elmo family forms an ancient group of actin-regulating proteins." Commun Integr Biol 2(4): 337-340.
	The Elmo protein family members are important mediators of small G protein activity, regulating actin-mediated processes such as chemotaxis and engulfment. Until recently,1 Elmo function has not been explored in professional phagocytes such as Dictyostelium discoideum. We discuss the significance of this family with respect to pathways that regulate Rac signaling, we present a comparison of Elmo proteins between representative taxa, and discuss our findings on ElmoA, one of six Elmo proteins found in D. discoideum.

Burnstock, G. and A. Verkhratsky (2009). "Evolutionary origins of the purinergic signalling system." Acta Physiol (Oxf) 195(4): 415-447.
	Purines appear to be the most primitive and widespread chemical messengers in the animal and plant kingdoms. The evidence for purinergic signalling in plants, invertebrates and lower vertebrates is reviewed. Much is based on pharmacological studies, but important recent studies have utilized the techniques of molecular biology and receptors have been cloned and characterized in primitive invertebrates, including the social amoeba Dictyostelium and the platyhelminth Schistosoma, as well as the green algae Ostreococcus, which resemble P2X receptors identified in mammals. This suggests that contrary to earlier speculations, P2X ion channel receptors appeared early in evolution, while G protein-coupled P1 and P2Y receptors were introduced either at the same time or perhaps even later. The absence of gene coding for P2X receptors in some animal groups [e.g. in some insects, roundworms (Caenorhabditis elegans) and the plant Arabidopsis] in contrast to the potent pharmacological actions of nucleotides in the same species, suggests that novel receptors are still to be discovered.

Buttery, N. J., D. E. Rozen, et al. (2009). "Quantification of social behavior in D. discoideum reveals complex fixed and facultative strategies." Curr Biol 19(16): 1373-1377.
	Understanding the maintenance of cooperation requires an understanding of the nature of cheaters and the strategies used to mitigate their effects. However, it is often difficult to determine how cheating or differential social success has arisen. For example, cheaters may employ different strategies (e.g., fixed and facultative), whereas other causes of unequal fitness in social situations can result in winners and losers without cheating. To address these problems, we quantified the social success of naturally occurring genotypes of Dictyostelium discoideum during the formation of chimeric fruiting bodies, consisting of dead stalk cells and viable spores. We demonstrate that an apparent competitive dominance hierarchy of spore formation in chimera is partly due to a fixed strategy where genotypes exhibit dramatically different spore allocations. However, we also find complex, variable facultative strategies, where genotypes change their allocation in chimera. By determining the magnitude and direction of these changes, we partition facultative cheating into two forms: (1) promotion of individual fitness through selfish behaviour ("self-promotion") and (2) coercion of other genotypes to act cooperatively. Our results demonstrate and define social interactions between D. discoideum isolates, thus providing a conceptual framework for the study of the genetic mechanisms that underpin social evolution.

Chen, J., H. Chen, et al. (2009). "Long-term production of soluble human Fas ligand through immobilization of Dictyostelium discoideum in a fibrous bed bioreactor." Appl Microbiol Biotechnol 82(2): 241-248.
	The production of recombinant glycoproteins in Dictyostelium discoideum by conventional cell culture methods was limited by low cell density as well as low growth rate. In this work, cotton towel with a good adsorption capability for D. discoideum cells was used as the immobilization matrix in an external fibrous bed bioreactor (FBB) system. With batch cultures in the FBB, the concentration of immobilized cells in the cotton fiber carrier increased to 1.37 x 10(8) cells per milliliter after 110-h cultivation, which was about tenfold higher than the maximal cell density in the conventional free-cell culture. Correspondingly, a high concentration of soluble human Fas ligand (hFasL; 173.7 microg l(-1)) was achieved with a high productivity (23 microg l(-1) h(-1)). The FBB system also maintained a high density of viable cells for hFasL production during repeated-batch cultures, achieving a productivity of 9 approximately 10 microg l(-1) h(-1) in all three batches studied during 15 days. The repeated-batch culture using immobilized cells of D. discoideum in the FBB system thus provides a good method for long-term and high-level production of hFasL.

Choe, J. M., D. Bakthavatsalam, et al. (2009). "Dictyostelium cells bind a secreted autocrine factor that represses cell proliferation." BMC Biochem 10: 4.
	BACKGROUND: Dictyostelium cells secrete the proteins AprA and CfaD. Cells lacking either AprA or CfaD proliferate faster than wild type, while AprA or CfaD overexpressor cells proliferate slowly, indicating that AprA and CfaD are autocrine factors that repress proliferation. CfaD interacts with AprA and requires the presence of AprA to slow proliferation. To determine if CfaD is necessary for the ability of AprA to slow proliferation, whether AprA binds to cells, and if so whether the binding requires the presence of CfaD, we examined the binding and effect on proliferation of recombinant AprA. RESULTS: We find that the extracellular accumulation of AprA increases with cell density and reaches a concentration of 0.3 microg/ml near a stationary cell density. When added to wild-type or aprA- cells, recombinant AprA (rAprA) significantly slows proliferation at 0.1 microg/ml and higher concentrations. From 4 to 64 microg/ml, the effect of rAprA is at a plateau, slowing but not stopping proliferation. The proliferation-inhibiting activity of rAprA is roughly the same as that of native AprA in conditioned growth medium. Proliferating aprA- cells show saturable binding of rAprA to 92,000 +/- 11,000 cell-surface receptors with a KD of 0.03 +/- 0.02 microg/ml. There appears to be one class of binding site, and no apparent cooperativity. Native AprA inhibits the binding of rAprA to aprA- cells with a Ki of 0.03 mug/ml, suggesting that the binding kinetics of rAprA are similar to those of native AprA. The proliferation of cells lacking CrlA, a cAMP receptor-like protein, or cells lacking CfaD are not affected by rAprA. Surprisingly, both cell types still bind rAprA. CONCLUSION: Together, the data suggest that AprA functions as an autocrine proliferation-inhibiting factor by binding to cell surface receptors. Although AprA requires CfaD for activity, it does not require CfaD to bind to cells, suggesting the possibility that cells have an AprA receptor and a CfaD receptor, and activation of both receptors is required to slow proliferation. We previously found that crlA- cells are sensitive to CfaD. Combined with the results presented here, this suggests that CrlA is not the AprA or CfaD receptor, and may be the receptor for an unknown third factor that is required for AprA and CfaD activity.

Chuai, M., D. Dormann, et al. (2009). "Imaging cell signalling and movement in development." Semin Cell Dev Biol.
	Imaging is a method of choice to investigate the complex spatio-temporal cellular dynamics and the signalling pathways that control them during development. The ability to tag many proteins in vivo makes it possible to analyse the detailed dynamics of these interactions ranging over several orders of magnitude; from the study of single molecule events on the millisecond and nanometre scale up to the complex three-dimensional behaviour of cells in tissues on the millimetre scale over time periods of hours to days. Great advances are being made in the detailed study of molecular processes using high resolution imaging techniques in transparent samples close to the surface of cells or tissues, where light scattering is minimal. The major challenge is to translate some of these methods to the study of cells and tissues in their native 3D environment. These imaging methods require novel and innovative analysis methods to fully exploit the information available in these data. We will illustrate some of these points in the investigation of the development of the cellular slime mould Dictyostelium discoideum and the study of cell behaviours during gastrulation in the chick embryo.

Cornelis, P. (2009). "Shielding, a new pathogen defence mechanism against PMNs." Microbiology 155(Pt 11): 3474-3475.
	
Driscoll, M., R. Kopace, et al. (2009). "The adventures of Dicty, the Dictyostelium cell." Chaos 19(4): 041110.
	
Duran, M. B., A. Rahman, et al. (2009). "Dictyostelium discoideum Paxillin Regulates Actin-Based Processes." Protist 160(2): 221-232.
	Paxillin is a key player in integrating the actin cytoskeleton with adhesion, and thus is essential to numerous cellular processes, including proliferation, differentiation, and migration in animal cells. PaxB, the Dictyostelium discoideum orthologue of paxillin, has been shown to be important for adhesion and development, much like its mammalian counterpart. Here, we use the overproduction of PaxB to gain better insight into its role in regulating the actin cytoskeleton and adhesion. We find that PaxB-overexpressing (PaxBOE) cells can aggregate and form mounds normally, but are blocked in subsequent development. This arrest can be rescued by addition of wild-type cells, indicating a non-cell autonomous role for PaxB. PaxBOE cells also have alterations in several actin-based processes, including adhesion, endocytosis, motility, and chemotaxis. PaxBOE cells exhibit an EDTA-sensitive increase in cell-cell cohesion, suggesting that PaxB-mediated adhesion is Ca(2+) or Mg(2+) dependent. Interestingly, cells overexpressing paxB are less adhesive to the substratum. In addition, PaxBOE cells display decreased motility under starved conditions, decreased endocytosis, and are unable to efficiently chemotax up a folate gradient. Taken together, the data suggest that proper expression of PaxB is vital for the regulation of development and actin-dependent processes.

Elzie, C. A., J. Colby, et al. (2009). "Dynamic localization of G proteins in Dictyostelium discoideum." J Cell Sci 122(15): 2597-2603.
	Extracellular stimuli exert their effects on eukaryotic cells via serpentine G-protein-coupled receptors and mediate a vast number of physiological responses. Activated receptors stimulate heterotrimeric G-proteins, consisting of three subunits, ?, ? and ?. In Dictyostelium discoideum, cAMP binds to the cAMP receptor cAR1, which is coupled to the heterotrimer containing the G?2 subunit. These studies provide in vivo evidence as to how receptors influence the localization of the G-protein complex prior to and after ligand binding. Previous work has shown that the state of the heterotrimer could be monitored by changes in fluorescence (or Förster) resonance energy transfer (FRET) between the ?2- and ?-subunits of D. discoideum. We now report the kinetics of G-protein activation as a loss of FRET prior to and after cAMP addition by using total internal reflection fluorescence microscopy (TIRFM). We also performed photobleaching experiments to measure G-protein recovery times. Our data show that inactive and active G-proteins cycle between the cytosol and plasma membrane. These data suggest that cAR1 activation slows the membrane dissociation (`off') rate of the ?2 subunit, while simultaneously promoting ??-subunit dissociation. Class Descriptors: NAL: QH301.J6

Elzie, C. A. and C. Janetopoulos (2009). "FRAP Analysis of Chemosensory Components of Dictyostelium." Meth Mol Biol 571: 349-369.
	Dictyostelium discoideum is a useful cell model for studying protein-protein interactions and deciphering complex signaling pathways similar to those found in mammalian systems. Many of these interactions were analyzed using classical in vitro biochemical techniques. However, with the accessibility of fluorescently tagged proteins, extensive protein networks are now being mapped out in living cells using a variety of microscopic techniques. One such technique, fluorescent recovery after photobleaching (FRAP), has been used in Dictyostelium to investigate a number of cellular processes including actin and cytoskeleton dynamics during chemotaxis and cytokinesis (J. Muscle Res. Cell Motil. 23:639-649, 2002; Biophys. J. 81:2010-2019, 2001; Mol. Biol. Cell 16:4256-4266, 2005), to follow trafficking of proteins to organelles such as the membrane, nucleus, and endoplasmic reticulum (Development 130:797-804, 2003; J. Cell Biol. 154:137-146, 2001), and to understand the role of proteins in cell adhesion during motility and division (Mol. Biol. Cell 18:4074-4084, 2007; J. Cell Sci. 120:4302-4309, 2007). FRAP is a powerful tool that should provide a vast amount of information on the mobility of a number of proteins, not only in Dictyostelium, but in many organisms. This study will lay out the methods of conducting FRAP experiments in Dictyostelium and discuss the large amount of knowledge which can be gained by adopting this as a common technique.

Fedorov, R., M. Bohl, et al. (2009). "The mechanism of pentabromopseudilin inhibition of myosin motor activity." Nat Struct Mol Biol 16(1): 80-88.
	We have identified pentabromopseudilin (PBP) as a potent inhibitor of myosin-dependent processes such as isometric tension development and unloaded shortening velocity. PBP-induced reductions in the rate constants for ATP binding, ATP hydrolysis and ADP dissociation extend the time required per myosin ATPase cycle in the absence and presence of actin. Additionally, coupling between the actin and nucleotide binding sites is reduced in the presence of the inhibitor. The selectivity of PBP differs from that observed with other myosin inhibitors. To elucidate the binding mode of PBP, we crystallized the Dictyostelium myosin-2 motor domain in the presence of Mg(2+)-ADP-meta-vanadate and PBP. The electron density for PBP is unambiguous and shows PBP to bind at a previously unknown allosteric site near the tip of the 50-kDa domain, at a distance of 16 A from the nucleotide binding site and 7.5 A away from the blebbistatin binding pocket.

Fey, P., P. Gaudet, et al. (2009). "dictyBase--a Dictyostelium bioinformatics resource update." Nucl Acids Res 37(Database issue): D515-D519.
	dictyBase (http://dictybase.org) is the model organism database for Dictyostelium discoideum. It houses the complete genome sequence, ESTs and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome. This dictyBase update describes the annotations and features implemented since 2006, including improved strain and phenotype representation, integration of predicted transcriptional regulatory elements, protein domain information, biochemical pathways, improved searching and a wiki tool that allows members of the research community to provide annotations.

Fountain, S. J. (2009). "Neurotransmitter Receptor Homologues of Dictyostelium discoideum." J Mol Neurosci.
	The social amoeba Dictyostelium discoideum is a genetically amenable eukaryotic cell which displays many animal cell traits and has been used to study cellular signalling for over 30 years. Recently studies have highlighted the roles that molecules associated with synaptic transmission in animals, such as glutamate, GABA and ATP play in cellular differentiation and homeostasis in this simple organism. This short review summarises the evidence for the existence of both ionotropic and metabotropic families of neurotransmitter receptors in Dictyostelium.

Fountain, S. J. and G. Burnstock (2009). "An evolutionary history of P2X receptors." Purinergic Signal 5(3): 269-272.
	Adenosine triphosphate (ATP) is an ancient and fundamentally important biological molecule involved in both intracellular and extracellular activities. P2X ionotropic and P2Y metabotropic receptors have been cloned and characterised in mammals. ATP plays a central physiological role as a transmitter molecule in processes including the sensation of pain, taste, breathing and inflammation via the activation of P2X receptors. P2X receptors are structurally distinct from glutamate and Cys-loop/nicotinic receptors and form the third major class of ligand-gated ion channel. Yet, despite the importance of P2X receptors, both as physiological mediators and therapeutic targets, the evolutionary origins and phylogenicity of ATP signalling via P2X receptors remain unclear.

Francione, L., P. K. Smith, et al. (2009). "Legionella pneumophila multiplication is enhanced by chronic AMPK signalling in mitochondrially diseased Dictyostelium cells." Dis Model Mech 2(9-10): 479-489.
	Human patients with mitochondrial diseases are more susceptible to bacterial infections, particularly of the respiratory tract. To investigate the susceptibility of mitochondrially diseased cells to an intracellular bacterial respiratory pathogen, we exploited the advantages of Dictyostelium discoideum as an established model for mitochondrial disease and for Legionella pneumophila pathogenesis. Legionella infection of macrophages involves recruitment of mitochondria to the Legionella-containing phagosome. We confirm here that this also occurs in Dictyostelium and investigate the effect of mitochondrial dysfunction on host cell susceptibility to Legionella. In mitochondrially diseased Dictyostelium strains, the pathogen was taken up at normal rates, but it grew faster and reached counts that were twofold higher than in the wild-type host. We reported previously that other mitochondrial disease phenotypes for Dictyostelium are the result of the activity of an energy-sensing cellular alarm protein, AMP-activated protein kinase (AMPK). Here, we show that the increased ability of mitochondrially diseased cells to support Legionella proliferation is suppressed by antisense-inhibiting expression of the catalytic AMPKalpha subunit. Conversely, mitochondrial dysfunction is phenocopied, and intracellular Legionella growth is enhanced, by overexpressing an active form of AMPKalpha in otherwise normal cells. These results indicate that AMPK signalling in response to mitochondrial dysfunction enhances Legionella proliferation in host cells.

Friedberg, F. and F. Rivero (2009). "Single and multiple CH (calponin homology) domain containing multidomain proteins in Dictyostelium discoideum: an inventory." Mol Biol Rep.
	We present an inventory of single or multiple calponin homology (CH) domain containing proteins of Dictyostelium discoideum. A multiple alignment and a phylogenetic tree of all 60 CH domains found in 36 proteins showed that most CH domains can be assigned to one of 6 types. We have then distributed the proteins into several classes according to the type and arrangement of the CH domains. Most proteins belong to the class of ABD (actin-binding domain)-forming CH tandems (CH1-CH2) of the alpha-actinin and fimbrin families or to the class of CH3 domain-bearing proteins. There are a few examples of proteins with a single CH1 or CH2 domain, one with a CH1-CH1 doublet and a single representative of the CHe class of microtubule-binding proteins. A comparison with CH domain proteins in Homo sapiens suggests that while the individual domains are available in both species, the existence of identical multidomain proteins in toto is rare. Fimbrin 1, alpha-actinin and EB1 appear as perfect orthologs in both species, whereas filamin and interaptin may represent ancestral forms of human filamin and nesprins. In four more cases (NAV/Unc-53-, smoothelin-, transgelin- and Gas2-related proteins) functional data are needed in order to establish a potential relationship with a human counterpart. Although extensive data exist for a few of the D. discoideum CH proteins, most remain to be characterized and our analysis may help predicting some of their properties.

Froquet, R., E. Lelong, et al. (2009). "Dictyostelium discoideum: a model host to measure bacterial virulence." Nature Protoc 4(1): 25-30.
	Dictyostelium amoebae have been used as a host model to measure virulence of a wide range of bacterial pathogens. The simple protocol described here takes advantage of the ability of Dictyostelium to grow and form plaques on a lawn of nonpathogenic bacteria but not on virulent bacteria. This assay can be modulated to measure the virulence of different bacterial pathogens. By adjusting various parameters such as cell numbers or media, a more quantitative measure of bacterial virulence can also be obtained. The entire procedure takes about 5 h to compete, and up to 2 further weeks may be required for plaques to form on the bacterial lawn.

Garcia, G. L., E. C. Rericha, et al. (2009). "The Group Migration of Dictyostelium Cells Is Regulated by Extracellular Chemoattractant Degradation." Mol Biol Cell 66(11): 929-939.
	Monitoring Editor: Jean E. Schwarzbauer Starvation of Dictyostelium induces a developmental program where cells form an aggregate that eventually differentiates into a multicellular structure. The aggregate formation is mediated by directional migration of individual cells that quickly transition to group migration where cells align in a head-to-tail manner to form streams. Cyclic AMP acts as a chemoattractant and its production, secretion, and degradation are highly regulated. A key protein is the extracellular phosphodiesterase, PdsA. In this study we examine the role and localization of PdsA during chemotaxis and streaming. We find that pdsA(-) cells respond chemotactically to a narrower range of chemoattractant concentrations compared with WT cells. Moreover, unlike WT cells, pdsA(-) cells do not form streams at low cell densities and form unusual thick and transient streams at high cell densities. We find that the intracellular pool of PdsA is localized to the ER, which may provide a compartment for storage and secretion of PdsA. As we find that cAMP synthesis is normal in cells lacking PdsA, we conclude that signal degradation regulates the external cAMP gradient field generation and that the group migration behavior of these cells is compromised even though their signaling machinery is intact.

Gateva, G., M. Schleicher, et al. (2009). The Ste20-like kinase DstC regulates phagocytosis in Dictyostelium discoideum. Eur J Cell Biol, Konstanz.
	Dictyostelium discoideum, a soil amoeba and professional phagocyte that mainly feeds on bacteria, can be seen as a primitive form of macrophage. To engulf particles phagocytic cells depend mainly on the dynamics of the actin cytoskeleton. Here we describe the Ste20-like kinase DstC as a regulator of the actin driven process of phagocytosis. Different members of the Ste20-like serine/threonine kinases were shown to finely tune chemotaxis (Arasada et al. (2006) Eur. J. Cell Biol., 85, 1059-1068) and to regulate late stages of cytokinesis (Rohlfs et al. (2007) J. Cell Sci., 120, 4345-4354) in D. discoideum. The catalytic domain of DstC is most similar to the mammalian kinases Mst1/Krs2 and Mst2/Krs1, which were shown to modulate cell growth and apoptosis. DstC localizes to actin-rich phagocytic cups during bacteria and yeast uptake. In contrast to actin, which usually disappears as soon as the particle is completely engulfed, the kinase DstC stays at the membrane of the phagosome for several minutes. We could map the
sorting-signal that localizes DstC to phagocytic cups and early phagosomes to about 90 amino acids in the Cterminal half of the protein. In addition, we show that the gene knockout for DstC has a severe phagocytosis defect. The data suggest that DstC is an important regulator of phagocytosis in D. discoideum.

Gaudet, P., L. Lane, et al. (2009). "Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase." Database (Oxford) 2009: bap016.
	UniProtKB/Swiss-Prot, a curated protein database, and dictyBase, the Model Organism Database for Dictyostelium discoideum, have established a collaboration to improve data sharing. One of the major steps in this effort was the 'Dicty annotation marathon', a week-long exercise with 30 annotators aimed at achieving a major increase in the number of D. discoideum proteins represented in UniProtKB/Swiss-Prot. The marathon led to the annotation of over 1000 D. discoideum proteins in UniProtKB/Swiss-Prot. Concomitantly, there were a large number of updates in dictyBase concerning gene symbols, protein names and gene models. This exercise demonstrates how UniProtKB/Swiss-Prot can work in very close cooperation with model organism databases and how the annotation of proteins can be accelerated through those collaborations.

Geberth, D. and M. T. Hutt (2009). "Predicting the distribution of spiral waves from cell properties in a developmental-path model of Dictyostelium pattern formation." PLoS Comput Biol 5(7): e1000422.
	The slime mold Dictyostelium discoideum is one of the model systems of biological pattern formation. One of the most successful answers to the challenge of establishing a spiral wave pattern in a colony of homogeneously distributed D. discoideum cells has been the suggestion of a developmental path the cells follow (Lauzeral and coworkers). This is a well-defined change in properties each cell undergoes on a longer time scale than the typical dynamics of the cell. Here we show that this concept leads to an inhomogeneous and systematic spatial distribution of spiral waves, which can be predicted from the distribution of cells on the developmental path. We propose specific experiments for checking whether such systematics are also found in data and thus, indirectly, provide evidence of a developmental path.

Gerisch, G. (2009). "Imaging actin cytoskeleton dynamics in Dictyostelium chemotaxis." Meth Mol Biol 571: 385-400.
	This chapter will focus on responses that the chemoattractant cyclic AMP elicits in the motility system of Dictyostelium. These cells can be permanently transfected to express cytoskeleton-associated proteins tagged with fluorescent proteins. Multiple proteins that are distinguishable by the excitation and emission spectra of their tags can be simultaneously expressed. This makes it possible to relate the spatial and temporal patterns of their chemoattractant-induced translocation to each other in one cell by a single recording. Since actin polymerization in live cells progresses with velocities of about 3 mum/s, high image frequencies and short acquisition times in the millisecond range are required. Techniques of total internal reflection fluorescence (TIRF) and spinning-disc confocal microscopy provide appropriate temporal and spatial resolution for the analysis of actin dynamics.

Gilbert, O. M., D. C. Queller, et al. (2009). "Discovery of a large clonal patch of a social amoeba: implications for social evolution." Mol Ecol 18(6): 1273-1281.
	Studies of genetic population structures of clonally reproducing macro-organisms have revealed large areas where only one clone is found. These areas, referred to as clonal patches, have not been shown to occur in free-living microbes until now. In free-living microbes, high genetic diversity at local scales is usually maintained by high rates of dispersal. We report, however, a highly dense, 12-m clonal patch of the social amoeba Dictyostelium discoideum in a cattle pasture located in a Texas Gulf Coast prairie. We confirm the presence of only one clone by the analysis of 65 samples and amplification of 10 polymorphic microsatellite loci. Samplings of additional cattle pastures nearby showed higher clonal diversity, but with a density of D. discoideum isolates lower than in the clonal patch. These findings show that high rates of microbial dispersal do not always produce genetic diversity at local scales, contrary to the findings of previous studies. The existence of clonal patches may be particularly important for microbial social evolution.

Giusti, C., M. F. Luciani, et al. (2009). "Necrotic cell death: From reversible mitochondrial uncoupling to irreversible lysosomal permeabilization." Exp Cell Res 315(1): 26-38.
	Dictyostelium atg1- mutant cells provide an experimentally and genetically favorable model to study necrotic cell death (NCD) with no interference from apoptosis or autophagy. In such cells subjected to starvation and cAMP, induction by the differentiation-inducing factor DIF or by classical uncouplers led within minutes to mitochondrial uncoupling, which causally initiated NCD. We now report that (1) in this model, NCD included a mitochondrial-lysosomal cascade of events, (2) mitochondrial uncoupling and therefore initial stages of death showed reversibility for a surprisingly long time, (3) subsequent lysosomal permeabilization could be demonstrated using Lysosensor blue, acridin orange, Texas red-dextran and cathepsin B substrate, (4) this lysosomal permeabilization was irreversible, and (5) the presence of the uncoupler was required to maintain mitochondrial lesions but also to induce lysosomal lesions, suggesting that signaling from mitochondria to lysosomes must be sustained by the continuous presence of the uncoupler. These results further characterized the NCD pathway in this priviledged model, contributed to a definition of NCD at the lysosomal level, and suggested that in mammalian NCD even late reversibility attempts by removal of the inducer may be of therapeutic interest.

Glockner, G. and A. J. Heidel (2009). "Centromere sequence and dynamics in Dictyostelium discoideum." Nucl Acids Res 37(6): 1809-1816.
	Centromeres play a pivotal role in the life of a eukaryote cell, perform an essential and conserved function, but this has not led to a standard centromere structure. It remains currently unclear, how the centromeric function is achieved by widely differing structures. Since centromeres are often large and consist mainly of repetitive sequences they have only been analyzed in great detail in a handful of organisms. The genome of Dictyostelium discoideum, a valuable model organism, was described a few years ago but its centromere organization remained largely unclear. Using available sequence information we reconstructed the putative centromere organization in three of the six chromosomes of D. discoideum. They mainly consist of one type of transposons that is confined to centromeric regions. Centromeres are dynamic due to transposon integration, but an optimal centromere size seems to exist in D. discoideum. One centromere probably has expanded recently, whereas another underwent major rearrangements. In addition to insights into the centromere organization and dynamics of a protist eukaryote, this work also provides a starting point for the analysis of the evolution of centromere structures in social amoebas by comparative genomics.

Gross, J. D. (2009). "Acidic Ca2+ stores, excitability and cell patterning in Dictyostelium discoideum." Euk Cell 8(5): 696-702.
	Dictyostelium discoideum is best known for its self-organising behaviour as seen in the striking wave patterns formed during cell-to-cell relay of chemotactic cyclic AMP signals, and in the stable division of the resulting aggregates into distinct anterior and posterior zones.

Hagedorn, M., K. H. Rohde, et al. (2009). "Infection by tubercular mycobacteria is spread by nonlytic ejection from their amoeba hosts." Science 323(5922): 1729-1733.
	To generate efficient vaccines and cures for Mycobacterium tuberculosis, we need a far better understanding of its modes of infection, persistence, and spreading. Host cell entry and the establishment of a replication niche are well understood, but little is known about how tubercular mycobacteria exit host cells and disseminate the infection. Using the social amoeba Dictyostelium as a genetically tractable host for pathogenic mycobacteria, we discovered that M. tuberculosis and M. marinum, but not M. avium, are ejected from the cell through an actin-based structure, the ejectosome. This conserved nonlytic spreading mechanism requires a cytoskeleton regulator from the host and an intact mycobacterial ESX-1 secretion system. This insight offers new directions for research into the spreading of tubercular mycobacteria infections in mammalian cells.

Hanel, F., N. Pawolleck, et al. (2009). Characterization of LC-FACS proteins in Dictyostelium discoideum. Eur J Cell Biol, Konstanz.
	Long-Chain-Fatty Acyl-CoA Synthetases (LC-FACS) catalyze the activation of fatty acids (FAs) consisting of 16 to 22 C-atoms by adding a Coenzyme A to the C1 atom of the FA. This activation is required for storage of FAs as triacylgylcerol or their degradation in the β-oxidation to provide energy for the cell. In Dictyostelium we have identified two LC-FACS proteins, LC-FACS 1 and LC-FACS 2 encoded by the genes fcsA and fcsB respectively. LC-FACS 1 is associated with the cytosolic side of the endosomal membrane for the first few minutes of endosome formation and remains bound to it until the endosomes are neutralised. Cells deficient in LC-FACS 1 that were constructed by homologous recombination and carry the disrupted fcsAgene show a decreased uptake of FAs from endosomes but no other conspicuous defect. LC-FACS 2 is a transmembrane protein which contains an N-terminal ER-targeting sequence. GFP fused to the C-terminus of LC-FACS 2 localizes in the ER whereas the LC-FACS 2 bearing an internal mycepitope is transported to peroxisomes. Mutants lacking LC-FACS 2 show wildtype-like uptake of FAs from endosomes but show reduced phagocytosis instead. To verify these results and to better understand the function of LC-FACS proteins in Dictyostelium further research will be done on the double mutant (fcsA-/fcsB-) and a fcsA-overexpressor strain in a fcsB--background.

Heise, N., D. Singh, et al. (2009). "Molecular analysis of a UDP-GlcNAc:polypeptide {alpha}-N-acetylglucosaminyltransferase implicated in the initiation of mucin-type O-glycosylation in Trypanosoma cruzi." Glycobiology 19(8): 918-933.
	Trypanosoma cruzi, the causative agent of Chagas disease, is surrounded by a mucin coat that plays important functions in parasite survival/invasion and is extensively O-glycosylated by Golgi and cell surface glycosyltransferases. Addition of the first sugar, alpha-N-acetylglucosamine (GlcNAc) linked to Threonine (Thr), is catalyzed by a polypeptide alpha-GlcNAc-transferase (pp-alphaGlcNAcT) which is unstable to purification. Here, a comparison of the genomes of T. cruzi and Dictyostelium discoideum, an amoebazoan which also forms this linkage, identified two T. cruzi genes (TcOGNT1 and TcOGNT2) that might encode this activity. Though neither was able to complement the Dictyostelium gene, expression in the trypanosomatid Leishmania tarentolae resulted in elevated levels of UDP-[(3)H]GlcNAc:Thr-peptide GlcNAc-transferase activity and UDP-[(3)H]GlcNAc breakdown activity. The ectodomain of TcOGNT2 was expressed and the secreted protein found to retain both activities after extensive purification away from other proteins and the endogenous activity. Product analysis showed that (3)H was transferred as GlcNAc to a hydroxyamino acid, and breakdown was due to hydrolysis. Both activities were specific for UDP-GlcNAc relative to UDP-GalNAc, and were abolished by active site point mutations that inactivate a related Dictyostelium enzyme and distantly related animal pp-alphaGalNAcTs. The peptide preference and the alkaline pH optimum were indistinguishable from that of the native activity in T. cruzi microsomes. The results suggest that mucin-type O-glycosylation in T. cruzi is initiated by conserved members of CAZy family GT60, which is homologous to the GT27 family of animal pp-alphaGalNAcTs that initiate mucin-type O-glycosylation in animals.

Hillen, T. and K. J. Painter (2009). "A user's guide to PDE models for chemotaxis." J Math Biol 58(1-2): 183-217.
	Mathematical modelling of chemotaxis (the movement of biological cells or organisms in response to chemical gradients) has developed into a large and diverse discipline, whose aspects include its mechanistic basis, the modelling of specific systems and the mathematical behaviour of the underlying equations. The Keller-Segel model of chemotaxis (Keller and Segel in J Theor Biol 26:399-415, 1970; 30:225-234, 1971) has provided a cornerstone for much of this work, its success being a consequence of its intuitive simplicity, analytical tractability and capacity to replicate key behaviour of chemotactic populations. One such property, the ability to display "auto-aggregation", has led to its prominence as a mechanism for self-organisation of biological systems. This phenomenon has been shown to lead to finite-time blow-up under certain formulations of the model, and a large body of work has been devoted to determining when blow-up occurs or whether globally existing solutions exist. In this paper, we explore in detail a number of variations of the original Keller-Segel model. We review their formulation from a biological perspective, contrast their patterning properties, summarise key results on their analytical properties and classify their solution form. We conclude with a brief discussion and expand on some of the outstanding issues revealed as a result of this work.

Honma, S., M. Saito, et al. (2009). "A reduction of epidermal growth factor receptor is involved in brefelamide-induced inhibition of phosphorylation of ERK in human astrocytoma cells." Eur J Pharmacol 616(1-3): 38-42.
	Brefelamide is an aromatic amide isolated from Dictyostelium cellular slime molds. We found that brefelamide has a potent inhibitory growth effect measured by MTT assay in 1321N1 human astrocytoma cells. The inhibition was associated with reduced phosphorylation of extracellular signal-regulated kinase (ERK). Brefelamide inhibited epidermal growth factor (EGF)-induced phosphorylation of ERK in a concentration-dependent manner. Furthermore, brefelamide diminished EGF-induced phosphorylation of EGF receptor at Tyr(1068), a Grb2 binding site that leads to an activation of the Ras/Raf/ERK system. Brefelamide also reduced the expression level of the EGF receptor. These results suggest that one of the mechanisms of action of brefelamide is assumed to be inhibition of phosphorylation of ERK through a reduction of EGF receptor activity in 1321N1 human astrocytoma cells.

Hsu, S. T., L. D. Cabrita, et al. (2009). "1H, 15N and 13C assignments of domain 5 of Dictyostelium discoideum gelation factor (ABP-120) in its native and 8M urea-denatured states." Biomol NMR Assign 3(1): 29-31.
	The gelation factor from Dictyostelium discoideum (ABP-120) is an actin binding protein consisting of six immunoglobulin (Ig) domains in the C-terminal rod domain. We have recently used the pair of domains 5 and 6 of ABP-120 as a model system for studying multi-domain nascent chain folding on the ribosome. Here we present the NMR assignments of domain 5 in its native and 8M urea-denatured states.

Hsu, S. T., L. D. Cabrita, et al. (2009). "Structure, Dynamics and Folding of an Immunoglobulin Domain of the Gelation Factor (ABP-120) from Dictyostelium discoideum." J Mol Biol 388(4): 865-879.
	We have carried out a detailed structural and dynamical characterisation of the isolated fifth repeat of the gelation factor (ABP-120) from Dictyostelium discoideum (ddFLN5) by NMR spectroscopy to provide a basis for studies of co-translational folding on the ribosome of this immunoglobulin-like domain. The isolated ddFLN5 can fold autonomously in solution into a structure that resembles very closely the crystal structure of the domain in a construct in which the adjacent sixth repeat (ddFLN6) is covalently linked to its C-terminus in tandem but deviates locally from a second crystal structure in which ddFLN5 is flanked by ddFLN4 and ddFLN6 at both N- and C-termini. Conformational fluctuations were observed via (15)N relaxation methods and are primarily localised in the interstrand loops that encompass the C-terminal hemisphere. These fluctuations are distinct in location from the region where line broadening is observed in ddFLN5 when attached to the ribosome as part of a nascent chain. This observation supports the conclusion that the broadening is associated with interactions with the ribosome surface [Hsu, S. T. D., Fucini, P., Cabrita, L. D., Launay, H., Dobson, C. M. & Christodoulou, J. (2007). Structure and dynamics of a ribosome-bound nascent chain by NMR spectroscopy. Proc. Natl. Acad. Sci. USA, 104, 16516-16521]. The unfolding of ddFLN5 induced by high concentrations of urea shows a low population of a folding intermediate, as inferred from an intensity-based analysis, a finding that differs from that of ddFLN5 as a ribosome-bound nascent chain. These results suggest that interesting differences in detail may exist between the structure of the domain in isolation and when linked to the ribosome and between protein folding in vitro and the folding of a nascent chain as it emerges from the ribosome.

Huber, R. and D. H. O'Day (2009). "An EGF-like peptide sequence from Dictyostelium enhances cell motility and chemotaxis." Biochem Biophys Res Commun 379(2): 470-475.
	Dictyostelium discoideum possesses more EGF-like (EGFL) domains than any other sequenced eukaryote. Here we show that a synthetic EGFL peptide (DdEGFL1) based upon an amino acid sequence from a cysteine-rich Dictyostelium protein, functions extracellularly to enhance random cell motility and cAMP-mediated chemotaxis in Dictyostelium by 625% and 85%, respectively, in strain NC4 and by 620% and 80% in strain AX3. Quinacrine inhibited peptide-enhanced random motility but not chemotaxis in strain AX3 providing evidence that PLA2 is the predominant regulator of this process. While LY294002 alone had no significant effect on either event, in combination with quinacrine it dramatically inhibited both processes suggesting that both PI3K and PLA2-mediated signaling are required for EGFL peptide-enhanced cell movement. DdEGFL1 also sustained the threonine phosphorylation of a 210kDa protein that is dephosphorylated during Dictyostelium starvation. Taken together, these results suggest an important role for certain EGFL peptides in Dictyostelium cell movement.

Hwang, R. D., C. C. Chen, et al. (2009). "ReAsH: another viable option for in vivo protein labelling in Dictyostelium." J Microsc 234(1): 9-15.
	Biarsenical-tetracysteine fluorescent protein tagging has been effectively used in a variety of cell types. It has the advantage of requiring a much smaller peptide alteration to existing proteins than fusion to green fluorescent protein (GFP) or monomeric red fluorescent protein (mRFP). However, there are no reports of the tetracysteine tagging system being used in Dictyostelium. In order to establish this tagging system in Dictyostelium, the filamin gene (FLN) was modified to express a C-terminal tetracysteine sequence and then transfected into cells. After addition of either FlAsH-EDT(2) or ReAsH-EDT(2), the fluorescence intensity of cells increased in a time-dependent manner and reached a plateau after 3 h of incubation. ReAsH had a much stronger and more specifically localized fluorescent signal compared with FlAsH. After removal of the ReAsH-EDT(2) reagent, the fluorescence signal remained detectable for at least 24 h. The localization of filamin labelled by ReAsH was similar to that of an FLN-mRFP fusion protein, but the fluorescence signal from the ReAsH-labelled protein was stronger. Our findings suggest that the ReAsH-tetracysteine tagging system can be a useful alternative for in vivo protein tagging in Dictyostelium.

Iglesias, P. A. (2009). "Spatial regulation of PI3K signaling during chemotaxis." Wiley Interdiscip Rev Syst Biol Med 1(2): 247-253.
	Phosphoinositide 3-kinases (PI3Ks) are a family of lipid kinases that phosphorylate the 3' OH position of the inositol ring of phosphoinositides on the inner leaf of the plasma membrane. Receptor-mediated activation of the PI3K pathway plays a crucial role in numerous signaling pathways and regulates a number of critical cellular processes, including growth, differentiation, survival and directed migration. In this focus article, we review the temporal and spatial regulation of PI3K in chemotaxing cells with particular emphasis on the amoeba Dictyostelium as well as neutrophils. We also briefly discuss one model used to elucidate the PI3K pathway.

Isberg, R. R., T. J. O'Connor, et al. (2009). "The Legionella pneumophila replication vacuole: making a cosy niche inside host cells." Nature Rev Microbiol 7(1): 12-24.
	The pathogenesis of Legionella pneumophila is derived from its growth within lung macrophages after aerosols are inhaled from contaminated water sources. Interest in this bacterium stems from its ability to manipulate host cell vesicular-trafficking pathways and establish a membrane-bound replication vacuole, making it a model for intravacuolar pathogens. Establishment of the replication compartment requires a specialized translocation system that transports a large cadre of protein substrates across the vacuolar membrane. These substrates regulate vesicle traffic and survival pathways in the host cell. This Review focuses on the strategies that L. pneumophila uses to establish intracellular growth and evaluates why this microorganism has accumulated an unprecedented number of translocated substrates that are targeted at host cells.

Ishii, K., Y. Nakao, et al. (2009). "Novel functions of ribosomal protein S6 in growth and differentiation of Dictyostelium cells." Devel Growth Differ 51(6): 533-546.
	We have previously shown that in Dictyostelium cells a 32 kDa protein is rapidly and completely dephosphorylated in response to starvation that is essential for the initiation of differentiation ( Akiyama & Maeda 1992 ). In the present work, this phosphoprotein was identified as a homologue (Dd-RPS6) of ribosomal protein S6 (RPS6) that is an essential member for protein synthesis. As expected, Dd-RPS6 seems to be absolutely required for cell survival, because we failed to obtain antisense-RNA mediated cells as well as Dd-rps6-null cells by homologous recombination in spite of many trials. In many kinds of cell lines, RPS6 is known to be located in the nucleus and cytosol, but Dd-RPS6 is predominantly located in the cell cortex with cytoskeletons, and in the contractile ring of just-dividing cells. In this connection, the overexpression of Dd-RPS6 greatly impairs cytokinesis during axenic shake-cultures in growth medium, resulting in the formation of multinucleate cells. Much severe impairment of cytokinesis was observed when Dd-RPS6-overexpressing cells (Dd-RPS6OE cells) were incubated on a living Escherichia coli lawn. The initiation of differentiation triggered by starvation was also delayed in Dd-RPS6OE cells. In addition, Dd-RPS6OE cells exhibit defective differentiation into prespore cells and spores during late development. Thus, it is likely that the proper expression of Dd-RPS6 may be of importance for the normal progression of late differentiation as well as for the initiation of differentiation. Class Descriptors: NAL: QL951.E4

Ito, K., Y. Yamaguchi, et al. (2009). "Unique charge distribution in surface loops confers high velocity on the fast motor protein Chara myosin." Proc Natl Acad Sci U S A 106(51): 21585-21590.
	Most myosins have a positively charged loop 2 with a cluster of lysine residues that bind to the negatively charged N-terminal segment of actin. However, the net charge of loop 2 of very fast Chara myosin is zero and there is no lysine cluster in it. In contrast, Chara myosin has a highly positively charged loop 3. To elucidate the role of these unique surface loops of Chara myosin in its high velocity and high actin-activated ATPase activity, we have undertaken mutational analysis using recombinant Chara myosin motor domain. It was found that net positive charge in loop 3 affected V(max) and K(app) of actin activated ATPase activity, while it affected the velocity only slightly. The net positive charge in loop 2 affected K(app) and the velocity, although it did not affect V(max). Our results suggested that Chara myosin has evolved to have highly positively charged loop 3 for its high ATPase activity and have less positively charged loop 2 for its high velocity. Since high positive charge in loop 3 and low positive charge in loop 2 seem to be one of the reasons for Chara myosin's high velocity, we manipulated charge contents in loops 2 and 3 of Dictyostelium myosin (class II). Removing positive charge from loop 2 and adding positive charge to loop 3 of Dictyostelium myosin made its velocity higher than that of the wild type, suggesting that the charge strategy in loops 2 and 3 is widely applicable.

Iwadate, Y. and S. Yumura (2009). "Cyclic stretch of the substratum using a shape-memory alloy induces directional migration in Dictyostelium cells." Biotechniques 47(3): 757-767.
	Living cells are constantly subjected to various mechanical stimulations. They must sense the mechanical aspects of their environment and respond appropriately for proper cell function. In general, cells adhere to substrata. Thus, the cells must receive and respond to mechanical stimuli mainly from the substrata. For example, migrating cells can create their own polarity and migrate in a certain direction even in the absence of any attractive substance. In order to generate such polarity, cells must sense mechanical stimuli from the substrata and transduce these stimuli into intracellular signals. To investigate the relationship between signals derived from mechanical stimuli and related cell functions, one of the most commonly used techniques is the application of mechanical stimuli via stretching of elastic substrata. Here, we developed a new stretching device using a shape-memory alloy (SMA). An SMA has three advantages as an actuator of stretching devices: (i) the cost of the SMA required for the device is inexpensive, approximately 30 USD, (ii) the size of an SMA is very small (0.62 mm in diameter and 22 mm in length), and (iii) an SMA does not generate any vibrating noise, which can negatively affect cells. In response to the cyclic stretching by the new stretching device, Dictyostelium discoideum cells migrated perpendicular to the stretching direction and the migrating speed increased significantly. To our knowledge, this is the first report indicating that migrating cells can create their own polarity by the mechanical stimuli from the substrata.

Jang, W., O. G. Schwartz, et al. (2009). "A cell number counting factor alters cell metabolism." Commun Integr Biol 2(4): 293-297.
	It is still not clear how organisms regulate the size of appendages or organs during development. During development, Dictyostelium discoideum cells form groups of approximately 2 x 10(4) cells. The cells secrete a protein complex called counting factor (CF) that allows them to sense the local cell density. If there are too many cells in a group, as indicated by high extracellular concentrations of CF, the cells break up the group by decreasing cell-cell adhesion and increasing random cell motility. As a part of the signal transduction pathway, CF decreases the activity of glucose-6-phosphatase to decrease internal glucose levels. CF also decreases the levels of fructose-1,6-bisphosphate and increases the levels of glucose-6-phosphate and fructose-6-phosphate. In this report, we focus on how a secreted signal used to regulate the size of a group of cells regulates many basic aspects of cell metabolism, including the levels of pyruvate, lactate, and ATP, and oxygen consumption.

Jeon, T. J., S. Lee, et al. (2009). "Regulation of Dictyostelium morphogenesis by RapGAP3." Dev Biol 328(2): 210-220.
	Rap1 is a key regulator of cell adhesion and cell motility in Dictyostelium. Here, we identify a Rap1-specific GAP protein (RapGAP3) and provide evidence that Rap1 signaling regulates cell-cell adhesion and cell migration within the multicellular organism. RapGAP3 mediates the deactivation of Rap1 at the late mound stage of development and plays an important role in regulating cell sorting during apical tip formation, when the anterior-posterior axis of the organism is formed, by controlling cell-cell adhesion and cell migration. The loss of RapGAP3 results in a severely altered morphogenesis of the multicellular organism at the late mound stage. Direct measurement of cell motility within the mound shows that rapGAP3(-) cells have a reduced speed of movement and, compared to wild-type cells, have a reduced motility towards the apex. rapGAP3(-) cells exhibit some increased EDTA/EGTA sensitive cell-cell adhesion at the late mound stage. RapGAP3 transiently and rapidly translocates to the cell cortex in response to chemoattractant stimulation, which is dependent on F-actin polymerization. We suggest that the altered morphogenesis and the cell-sorting defect of rapGAP3(-) cells may result in reduced directional movement of the mutant cells to the apex of the mound.

Jia, K., C. Thomas, et al. (2009). "Autophagy genes protect against Salmonella typhimurium infection and mediate insulin signaling-regulated pathogen resistance." Proc Natl Acad Sci U S A 106(34): 14564-14569.
	A conserved insulin-like pathway modulates both aging and pathogen resistance in Caenorhabditis elegans. However, the specific innate effector functions that mediate this pathogen resistance are largely unknown. Autophagy, a lysosomal degradation pathway, plays a role in controlling intracellular bacterial pathogen infections in cultured cells, but less is known about its role at the organismal level. We examined the effects of autophagy gene inactivation on Salmonella enterica Serovar Typhimurium (Salmonella typhimurium) infection in 2 model organisms, Caenorhabditis elegans and Dictyostelium discoideum. In both organisms, genetic inactivation of the autophagy pathway increases bacterial intracellular replication, decreases animal lifespan, and results in apoptotic-independent death. In C. elegans, genetic knockdown of autophagy genes abrogates pathogen resistance conferred by a loss-of-function mutation, daf-2(e1370), in the insulin-like tyrosine kinase receptor or by over-expression of the DAF-16 FOXO transcription factor. Thus, autophagy genes play an essential role in host defense in vivo against an intracellular bacterial pathogen and mediate pathogen resistance in long-lived mutant nematodes. Class Descriptors: NAL: 500 N21P

Jin, T., X. Xu, et al. (2009). "How human leukocytes track down and destroy pathogens: lessons learned from the model organism Dictyostelium discoideum." Immunol Res 43(1-3): 118-127.
	Human leukocytes, including macrophages and neutrophils, are phagocytic immune cells that capture and engulf pathogens and subsequently destroy them in intracellular vesicles. To accomplish this vital task, these leukocytes utilize two basic cell behaviors-chemotaxis for chasing down infectious pathogens and phagocytosis for destroying them. The molecular mechanisms controlling these behaviors are not well understood for immune cells. Interestingly, a soil amoeba, Dictyostelium discoideum, uses these same behaviors to pursue and injest its bacterial food source and to organize its multi-cellular development. Consequently, studies of this model system have provided and will continue to provide us with mechanistic insights into the chemotaxis and phagocytosis of immune cells. Here, we review recent research in these areas that have been conducted in the Chemotaxis Signal Section of NIAID's Laboratory of Immunogenetics.

Jung, G., M. A. Titus, et al. (2009). "The Dictyostelium type V myosin MyoJ is responsible for the cortical association and motility of contractile vacuole membranes." J Cell Biol 186(4): 555-570.
	The contractile vacuole (CV) complex in Dictyostelium is a tubulovesicular osmoregulatory organelle that exhibits extensive motility along the actin-rich cortex, providing a useful model for investigating myosin-dependent membrane transport. Here, we show that the type V myosin myoJ localizes to CV membranes and is required for efficient osmoregulation, the normal accumulation of CV membranes in the cortex, and the conversion of collapsed bladder membranes into outwardly radiating cortical CV tubules. Complementation of myoJ-null cells with a version of myoJ containing a shorter lever arm causes these radiating tubules to move at a slower speed, confirming myoJ's role in translocating CV membranes along the cortex. MyoJ-null cells also exhibit a dramatic concentration of CV membranes around the microtubule-organizing center. Consistently, we demonstrate that CV membranes also move bi-directionally on microtubules between the cortex and the centrosome. Therefore, myoJ cooperates with plus and minus end-directed microtubule motors to drive the normal distribution and dynamics of the CV complex in DICTYOSTELIUM: Class Descriptors: NAL: 442.8 J828

Kamimura, Y., M. Tang, et al. (2009). "Assays for Chemotaxis and Chemoattractant-Stimulated TorC2 Activation and PKB Substrate Phosphorylation in Dictyostelium." Meth Mol Biol 571: 255-270.
	Chemotaxis is a highly coordinated biological system where chemoattractants trigger multiple signal transduction pathways which act in concert to bring about directed migration. A signaling pathway acting through PIP(3), which accumulates at the leading edge of the cell, has been extensively characterized. However, chemotaxis still remains in cells depleted of PIP(3), suggesting there are PIP(3)-independent pathways. We have identified a pathway involving TorC2-PKBR1 as well as another containing PLA2 activity that act in parallel with PIP(3). Activation of PKBR1, a myristoylated Protein Kinase B homolog, is dependent on TorC2 (Rapamycin-insensitive Tor complex 2) kinase but is completely independent of PIP(3). In response to chemoattractant, PKBs rapidly phosphorylate at least eight proteins, including Talin B, PI4P 5-kinase, two RasGefs, and a RhoGap. These studies help to link the signaling pathways to specific effectors and provide a more complete understanding of chemotaxis.

Kastner, P., M. Schleicher, et al. (2009). Characterization of NDR kinases in Dictyostelium discoideum. Eur J Cell Biol, Konstanz.
	NDR (nuclear Dbf2-related) kinases are a subgroup of the
AGC class of protein kinases. The genome of
Dictyostelium discoideum encodes four NDR group
kinases, NdrA, B, C and D, and three potential NDR
activators, MobA, B and C. In Schizosaccharomyces
pombe the NDR kinase Sid2 is part of the septation
initiation network (SIN), which is essential for the final
stages of cytokinesis. We recently found a SIN-related
pathway to be involved in the regulation of cytokinesis in
D. discoideum. Upstream components of this pathway
include a polo-like kinase (PLK), a GAP (Bub2), a GTPase
(Spg1), and a Ser/Thr-kinase (SepA) homologous to the
SIN-kinase Cdc7. The effectors downstream of SepA are
not specified yet, but may include members of the Ste20-
like and NDR group of kinases. Therefore, we started to
explore the D. discoideum NDR kinases in order to test
their potential involvement in cytokinesis.
NdrA and NdrB were shown to localize to centrosomes.
NdrA-null cells have defects in growth and phagocytosis,
but cytokinesis is unaffected. By immunoprecipitation and
tandem affinity purification MobB was found to interact
with NdrB. Knockout mutants lacking NdrC are
multinucleated indicating an involvement of NdrC in
cytokinesis. Our data suggest that NdrC may be a
component downstream of SepA which was shown to
regulate cleavage furrow formation in a SIN-related
pathway of D. discoideum.

Kawabe, Y., T. Morio, et al. (2009). "Activated cAMP receptors switch encystation into sporulation." Proc Natl Acad Sci U S A 106(17): 7089-7094.
	Metazoan embryogenesis is controlled by a limited number of signaling modules that are used repetitively at successive developmental stages. The development of social amoebas shows similar reiterated use of cAMP-mediated signaling. In the model Dictyostelium discoideum, secreted cAMP acting on 4 cAMP receptors (cARs1-4) coordinates cell movement during aggregation and fruiting body formation, and induces the expression of aggregation and sporulation genes at consecutive developmental stages. To identify hierarchy in the multiple roles of cAMP, we investigated cAR heterogeneity and function across the social amoeba phylogeny. The gene duplications that yielded cARs 2-4 occurred late in evolution. Many species have only a cAR1 ortholog that duplicated independently in the Polysphondylids and Acytostelids. Disruption of both cAR genes of Polysphondylium pallidum (Ppal) did not affect aggregation, but caused complete collapse of fruiting body morphogenesis. The stunted structures contained disorganized stalk cells, which supported a mass of cysts instead of spores; cAMP triggered spore gene expression in Ppal, but not in the cAR null mutant, explaining its sporulation defect. Encystation is the survival strategy of solitary amoebas, and lower taxa, like Ppal, can still encyst as single cells. Recent findings showed that intracellular cAMP accumulation suffices to trigger encystation, whereas it is a complementary requirement for sporulation. Combined, the data suggest that cAMP signaling in social amoebas evolved from cAMP-mediated encystation in solitary amoebas; cAMP secretion in aggregates prompted the starving cells to form spores and not cysts, and additionally organized fruiting body morphogenesis. cAMP-mediated aggregation was the most recent innovation.

Kay, R. R. and C. R. L. Thompson (2009). "Forming patterns in development without morphogen gradients: scattered differentiation and sorting out." CSH Persp. Biol.
	 Few mechanisms provide alternatives to morphogen gradients for producing spatial patterns of cells in development. One possibility is based on the sorting out of cells that initially differentiate in a salt and pepper mixture and then physically move to create coherent tissues. Here, we describe the evidence suggesting this is the major mode of patterning in Dictyostelium. In addition, we discuss whether convergent evolution could have produced a conceptually similar mechanism in other organisms. 

Khare, A., L. A. Santorelli, et al. (2009). "Cheater-resistance is not futile." Nature 461(7266): 980-982.
	Cooperative social systems are susceptible to cheating by individuals that reap the benefits of cooperation without incurring the costs(1). There are various theoretical mechanisms for the repression of cheating(2) and many have been tested experimentally. One possibility that has not been tested rigorously is the evolution of mutations that confer resistance to cheating. Here we show that the presence of a cheater in a population of randomly mutated social amoebae can select for cheater-resistance. Furthermore, we show that this cheater-resistance can be a noble strategy because the resister strain does not necessarily exploit other strains. Thus, the evolution of resisters may be instrumental in preserving cooperative behaviour in the face of cheating.

Kihara, K., K. Mori, et al. (2009). "Global/temporal gene expression analysis of Escherichia coli in the early stages of symbiotic relationship development with the cellular slime mold Dictyostelium discoideum." Biosystems 96(2): 141-164.
	Escherichia coli and the cellular slime mold Dictyostelium discoideum form stable viscous symbiotic colonies in the laboratory. To examine changes in E. coli gene expression during establishment of this symbiotic relationship, cells of symbiotic co-cultures and monocultures at various time points were subjected to microarrays analysis. Genes changed significantly over time compared to the initial gene expression level were determined as characteristics of GO function categories. The categories that appeared significantly at the same sampling time points between the two cultures were also identified. Up-regulation of genes from several GO categories associated with polysaccharide synthesis, cell wall degradation, and iron acquisition as well as down-regulation of genes from GO categories associated with biosynthesis through starvation response were observed in co-cultures, indicating exchange of molecules between the two organisms. Up-regulation of genes from several GO categories associated with anaerobic respiration and flagella biosynthesis were also observed, indicating that the environment inside symbiotic colonies was similar to that in developed biofilms. Up-regulation of genes associated with energy-generating systems indicated that E. coli prolonged survival within the symbiotic colony. Thus, E. coli showed not only molecule exchange but also altered expression of various genes in symbiosis with D. discoideum.

Kim, D. H., R. C. Davis, et al. (2009). "Autophagy contributes to degradation of Hirano bodies." Autophagy 5(1): 44-51.
	Hirano bodies are actin-rich inclusions reported most frequently in the hippocampus in association with a variety of conditions including neurodegenerative diseases, and aging. We have developed a model system for formation of Hirano bodies in Dictyostelium and cultured mammalian cells to permit detailed studies of the dynamics of these structures in living cells. Model Hirano bodies are frequently observed in membrane-enclosed vesicles in mammalian cells consistent with a role of autophagy in the degradation of these structures. Clearance of Hirano bodies by an exocytotic process is supported by images from electron microscopy showing extracellular release of Hirano bodies, and observation of Hirano bodies in the culture medium of Dictyostelium and mammalian cells. An autophagosome marker protein Atg8-GFP, was co-localized with model Hirano bodies in wild type Dictyostelium cells, but not in atg5(-) or atg1-1 autophagy mutant strains. Induction of model Hirano bodies in Dictyostelium with a high level expression of 34 kDa DeltaEF1 from the inducible discoidin promoter resulted in larger Hirano bodies and a cessation of cell doubling. The degradation of model Hirano bodies still occurred rapidly in autophagy mutant (atg5(-)) Dictyostelium, suggesting that other mechanisms such as the ubiquitin-mediated proteasome pathway could contribute to the degradation of Hirano bodies. Chemical inhibition of the proteasome pathway with lactacystin, significantly decreased the turnover of Hirano bodies in Dictyostelium providing direct evidence that autophagy and the proteasome can both contribute to degradation of Hirano bodies. Short term treatment of mammalian cells with either lactacystin or 3-methyl adenine results in higher levels of Hirano bodies and a lower level of viable cells in the cultures, supporting the conclusion that both autophagy and the proteasome contribute to degradation of Hirano bodies.

King, J. S. and R. H. Insall (2009). "Chemotaxis: finding the way forward with Dictyostelium." Trends Cell Biol 19(10): 523-530.
	Understanding cell migration is centrally important to modern cell biology. However, despite years of study, progress has been hindered by experimental limitations and the complexity of the process. This has led to the popularity of Dictyostelium discoideum, with its experimentally-friendly lifestyle and small, haploid genome, as a tool to dissect the pathways involved in migration. This humble amoeba is now established at the centre of dramatic changes in our understanding of cell movement. In this review we describe the recent reinterpretation of the role of phosphatidylinositol trisphosphate (PIP(3)) and other intracellular messengers that connect signalling and migration, and the transition to models of chemotaxis driven by multiple, intertwined signalling pathways. In shallow gradients, pseudopods are generated with random directions, and we discuss how chemotaxis can operate by biasing this process. Overall we describe how Dictyostelium has the potential to unlock many fundamental questions in the cell motility field.

King, J. S., R. Teo, et al. (2009). "The mood stabiliser lithium suppresses PIP3 signalling in Dictyostelium and human cells." Dis Model Mech 2(5-6): 306-312.
	Bipolar mood disorder (manic depression) is a major psychiatric disorder whose molecular origins are unknown. Mood stabilisers offer patients both acute and prophylactic treatment, and experimentally, they provide a means to probe the underlying biology of the disorder. Lithium and other mood stabilisers deplete intracellular inositol and it has been proposed that bipolar mood disorder arises from aberrant inositol (1,4,5)-trisphosphate [IP(3), also known as Ins(1,4,5)P(3)] signalling. However, there is no definitive evidence to support this or any other proposed target; a problem exacerbated by a lack of good cellular models. Phosphatidylinositol (3,4,5)-trisphosphate [PIP(3), also known as PtdIns(3,4,5)P(3)] is a prominent intracellular signal molecule within the central nervous system (CNS) that regulates neuronal survival, connectivity and synaptic function. By using the genetically tractable organism Dictyostelium, we show that lithium suppresses PIP(3)-mediated signalling. These effects extend to the human neutrophil cell line HL60. Mechanistically, we show that lithium attenuates phosphoinositide synthesis and that its effects can be reversed by overexpression of inositol monophosphatase (IMPase), consistent with the inositol-depletion hypothesis. These results demonstrate a lithium target that is compatible with our current knowledge of the genetic predisposition for bipolar disorder. They also suggest that lithium therapy might be beneficial for other diseases caused by elevated PIP(3) signalling.

Konotop, G., I. Muller, et al. (2009). Possible components of the signalling cascade between endosomes and the cytoskeleton in Dictyostelium discoideum. Eur J Cell Biol, Konstanz.
	A novel class of lysozymes was recently identified in
D. discoideum. The knock-out of its main member, AlyA,
leads to increased phagocytic rates without affecting
macropinocytosis. The esterase Gp70 was found to be upregulated
in the AlyA-null cells, and over-expression of
Gp70 in wild type cells (AX2) leads to the same phenotype
as AlyA knock-out. These results raised the idea of a
signalling pathway between reduced lysozyme levels,
elevated Gp70 content, and increased phagocytosis. A
cDNA-microarray analysis on both mutants revealed a
series of genes up-regulated in AlyA-null cells, but not in
Gp70 over-expressing cells, as well as eight equally 
down-regulated genes in both strains. These genes seem
to be possible candidates for the signalling cascade from
phagosomes to the cytoskeletal machinery. Our current
data shows the involvement of SSE346, SSJ758 and
SLB350 in the signalling cascade between Gp70 and
increased particle internalization. Interestingly, the knockout
of these proteins led to divergent phenotypes. The
SSE346-KO strains are characterized by increased
phagocytic rates as well as enlarged plaques on bacterial
lawns, when compared to the wild type. SSJ758-KO leads
to enlarged plaques but exhibit normal phagocytosis. On
the contrary, SLB350-KO show increased phagocytosis
but no variation in plaque size. We are currently analysing
other candidates in order to understand the succession of
events linking the lysosomal defect with the cytoskeletal
adaptation.

Kourtis, N. and N. Tavernarakis (2009). "Autophagy and cell death in model organisms." Cell Death Differ 16(1): 21-30.
	Autophagy evolved in unicellular eukaryotes as a means for surviving nutrient stress. During the course of evolution, as multicellular organisms developed specialized cell types and complex intracellular signalling networks, autophagy has been summoned to serve additional cellular functions. Numerous recent studies indicate that apart from its pro-survival role under nutrient limitation, autophagy also participates in cell death. However, the precise role of this catabolic process in dying cells is not fully understood. Although in certain situations autophagy has a protective function, in other types of cell death it actually contributes to cellular destruction. Simple model organisms ranging from the unicellular Saccharomyces cerevisiae to the soil amoeba Dictyostelium discoideum and the metazoans Caenorhabditis elegans and Drosophila melanogaster provide clearly defined cell death paradigms that can be used to dissect the involvement of autophagy in cell death, at the molecular level. In this review, we survey current research in simple organisms, linking autophagy to cell death and discuss the complex interplay between autophagy, cell survival and cell death.

Kriebel, P. W. (2009). Vesicle trafficking and protein synthesis, target adenylyl cyclase A to the back of migrating cells, localizing the release of chemoattractant to the trailing edge. United States -- District of Columbia, The George Washington University.
	Adenylyl cyclases and their product, 3'-5'-cyclic adenosine monophosphate (cAMP), are critical signaling molecules fundamental to many signaling pathways found throughout eukaryotes and mammals. This importance arises from the ability to not only transduce signals from receptors to downstream effectors but also to amplify the initial signaling response. In Dictyostelium, the binding of the chemoattractant cAMP to its G protein coupled receptor activates a variety of effectors including the adenylyl cyclase A (ACA). We demonstrate using the gene fusion product ACA-YFP (ACA and yellow fluorescent protein) that ACA is enriched at the back of chemotaxing cells and propose that this enrichment provides a compartment from which cAMP is released, relaying the chemotactic signal to neighboring cells and allowing the cells to align head-to-tail, forming streams during chemotaxis. Interestingly, we find that this enrichment of ACA is composed of many smaller vesicles containing ACA and that ACA containing vesicles are observed rapidly moving throughout the cell. We investigated the role of ACA vesicle trafficking in the enrichment of ACA at the back of cells. Using Fluorescence Recovery After Photobleaching (FRAP), we find that vesicle delivery of ACA-YFP to the plasma membrane is required for the asymmetric enrichment of ACA at the back of cells. When actin fibers and microtubules are disrupted with latrunculin A or nocodazole, respectively, ACA vesicle trafficking is strongly inhibited resulting in the loss of ACA enrichment at the back of cells. We find that ACA vesicles co-localize with microtubules and that nocodazole-treated cells have streaming defects. Together, these findings suggest that vesicle trafficking is required for cAMP release. Intriguingly, we also observe that migrating cells leave behind trails containing ACA. Since migrating cells maintain a polarized distribution of ACA, we reason that ACA must be replenished by protein synthesis to maintain its asymmetric distribution. To investigate this, we completely bleached migrating ACA-YFP expressing cells and monitored the fluorescence recovery over time. We observe a 40% recovery within 7 minutes, presumably due to protein synthesis. Indeed, we find that cycloheximide treatment reduces ACA levels, abolishes its enrichment specifically at the back of migrating cells and prevents streaming. Our findings provide a novel model to explain group cell migration, where vesicles containing de novo enzymes involved in the synthesis of chemoattractants are delivered to the back of migrating cells, thereby creating a compartment from which chemoattractants are specifically released. We propose that similar methods of enzyme compartmentalization exist in mammalian cells allowing for cells to migrate collectively to sites of inflammation, to metastasize to new tissues and to form neural networks.

Kriebel, P. W. and C. A. Parent (2009). "Group migration and signal relay in Dictyostelium." Meth Mol Biol 571: 111-124.
	The ability of cells to migrate directionally in gradients of chemoattractant is a fundamental biological response that is essential for the survival of the social amoebae Dictyostelium discoideum. In Dictyostelium, cAMP is the most potent chemoattractant and the detection, synthesis, and degradation of cAMP is exquisitely regulated. Interestingly, as Dictyostelium cells migrate directionally, they do so in a head-to-tail fashion, forming characteristic streams. This group behavior is acquired through the relay of the cAMP signals to neighboring cells. This chapter describes experimental procedures used to obtain synchronized populations of chemotactically competent cells and to assess their streaming behavior. In addition, we provide a detailed account of the method used to measure the ability of chemoattractants to directly stimulate adenylyl cyclase activity. Together, these techniques provide a way to combine cell biological and biochemical approaches to the study of signal relay.

Kuwayama, H. and Y. Kubohara (2009). "Differentiation-inducing factor-1 and -2 function also as modulators for Dictyostelium chemotaxis." PLoS One 4(8): e6658.
	BACKGROUND: In the early stages of development of the cellular slime mold Dictyostelium discoideum, chemotaxis toward cAMP plays a pivotal role in organizing discrete cells into a multicellular structure. In this process, a series of signaling molecules, such as G-protein-coupled cell surface receptors for cAMP, phosphatidylinositol metabolites, and cyclic nucleotides, function as the signal transducers for controlling dynamics of cytoskeleton. Differentiation-inducing factor-1 and -2 (DIF-1 and DIF-2) were originally identified as the factors (chlorinated alkylphenones) that induce Dictyostelium stalk cell differentiation, but it remained unknown whether the DIFs had any other physiologic functions. METHODOLOGY/PRINCIPAL FINDINGS: To further elucidate the functions of DIFs, in the present study we investigated their effects on chemotaxis under various conditions. Quite interestingly, in shallow cAMP gradients, DIF-1 suppressed chemotaxis whereas DIF-2 promoted it greatly. Analyses with various mutants revealed that DIF-1 may inhibit chemotaxis, at least in part, via GbpB (a phosphodiesterase) and a decrease in the intracellular cGMP concentration ([cGMP](i)). DIF-2, by contrast, may enhance chemotaxis, at least in part, via RegA (another phosphodiesterase) and an increase in [cGMP](i). Using null mutants for DimA and DimB, the transcription factors that are required for DIF-dependent prestalk differentiation, we also showed that the mechanisms for the modulation of chemotaxis by DIFs differ from those for the induction of cell differentiation by DIFs, at least in part. CONCLUSIONS/SIGNIFICANCE: Our findings indicate that DIF-1 and DIF-2 function as negative and positive modulators for Dictyostelium chemotaxis, respectively. To our knowledge, this is the first report in any organism of physiologic modulators (small molecules) for chemotaxis having differentiation-inducing activity.

Kuzmic, P., T. Lorenz, et al. (2009). "Analysis of residuals from enzyme kinetic and protein folding experiments in the presence of correlated experimental noise." Anal Biochem 395(1): 1-7.
	Experimental data from continuous enzyme assays or protein folding experiments often contain hundreds, or even thousands, of densely spaced data points. When the sampling interval is extremely short, the experimental data points might not be statistically independent. The resulting neighborhood correlation invalidates important theoretical assumptions of nonlinear regression analysis. As a consequence, certain goodness-of-fit criteria, such as the runs-of-signs test and the autocorrelation function, might indicate a systematic lack of fit even if the experiment does agree very well with the underlying theoretical model. A solution to this problem is to analyze only a subset of the residuals of fit, such that any excessive neighborhood correlation is eliminated. Substrate kinetics of the HIV protease and the unfolding kinetics of UMP/CMP kinase, a globular protein from Dictyostelium discoideum, serve as two illustrative examples. A suitable data-reduction algorithm has been incorporated into software DYNAFIT [P. Kuzmic, Anal. Biochem. 237 (1996) 260-273], freely available to all academic researchers from http://www.biokin.com.

Lavialle, F., S. Deshayes, et al. (2009). "Nanovesicles released by Dictyostelium cells: a potential carrier for drug delivery." Int J Pharm 380(1-2): 206-215.
	Nanovesicles released by Dictyostelium discoideum cells grown in the presence of the DNA-specific dye Hoechst 33342 have been previously shown to mediate the transfer of the dye into the nuclei of Hoechst-resistant cells. The present investigation extends this work by conducting experiments in the presence of hypericin, a fluorescent therapeutic photosensitizer assayed for antitumoral photodynamic therapy. Nanovesicles released by Dictyostelium cells exhibit an averaged diameter between 50 and 150 nm, as measured by transmission cryoelectron microscopy. A proteomic analysis reveals a predominance of actin and actin-related proteins. The detection of a lysosomal membrane protein (LIMP II) indicates that these vesicles are likely generated in the late endosomal compartment. The use of the hypericin-containing nanovesicles as nanodevices for in vitro drug delivery was investigated by fluorescence microscopy. The observed signal was almost exclusively located in the perinuclear area of two human cell lines, skin fibroblasts (HS68) and cervix carcinoma (HeLa) cells. Studies by confocal microscopy with specific markers of cell organelles, provided evidence that hypericin was accumulated in the Golgi apparatus. All these data shed a new light on in vitro drug delivery by using cell-released vesicles as carriers.

Le, P., P. R. Fisher, et al. (2009). "Transcription of the Dictyostelium discoideum mitochondrial genome occurs from a single initiation site." RNA.
	Transcription of the mitochondrial genome in Dictyostelium discoideum gives rise to eight major polycistronic RNA species that can be detected by Northern hybridization. In order to determine whether these transcripts could possibly derive from processing of even larger transcripts, reverse transcriptase polymerase chain reactions (RT-PCRs) were performed in an attempt to amplify the intervening regions between the eight major transcripts. All but one intervening region were successfully reverse transcribed and amplified, indicating that even larger transcripts existed and that the eight major transcripts detected previously may be the products of transcript processing. Southern hybridization analyses of DNA fragments representing the sequences between the eight major transcripts with in vitro capped mitochondrial RNA identified the 5' end of only one of the eight major transcripts as a genuine transcription start site. The ability to initiate transcription from DNA sequences upstream of the identified transcription initiation site was demonstrated in bacterial cells expressing the Dictyostelium mitochondrial RNA polymerase. We conclude that transcription of the Dictyostelium mitochondrial genome is initiated at a single site, generating a large polycistronic transcript that is very efficiently, probably cotranscriptionally processed into mature RNA species. This is the first report on a protist mitochondrial DNA that is, although much larger in size than its metazoan counterparts, transcribed from a single transcription initiation site.

Lee, S., J. W. Han, et al. (2009). "Regulation of the formation and trafficking of vesicles from Golgi by PCH family proteins during chemotaxis." Biochim Biophys Acta 1793(7): 1199-1209.
	Previous study demonstrated that WASP localizes on vesicles during Dictyostelium chemotaxis and these vesicles appear to be preferentially distributed at the leading and trailing edge of migrating cells. In this study, we have examined the role of PCH family proteins, Nwk/Bzz1p-like protein (NLP) and Syndapin-like protein (SLP), in the regulation of the formation and trafficking of WASP-vesicles during chemotaxis. NLP and SLP appear to be functionally redundant and deletion of both nlp and slp genes causes the loss of polarized F-actin organization and significant defects in chemotaxis. WASP and NLP are colocalized on vesicles and interactions between two molecules via the SH3 domain of NLP/SLP and the proline-rich repeats of WASP are required for vesicle formation from Golgi. Microtubules are required for polarized trafficking of these vesicles as vesicles showing high directed mobility are absent in cells treated with nocodazole. Our results suggest that interaction of WASP with NLP/SLP is required for the formation and trafficking of vesicles from Golgi to the membrane, which might play a central role in the establishment of cell polarity during chemotaxis.

Li, Z., A. S. Dugan, et al. (2009). "The amoebal MAP kinase response to Legionella pneumophila is regulated by DupA." Cell Host Microbe 6(3): 253-267.
	The amoeba Dictyostelium discoideum can support replication of Legionella pneumophila. Here we identify the dupA gene, encoding a putative tyrosine kinase/dual-specificity phosphatase, in a screen for D. discoideum mutants altered in allowing L. pneumophila intracellular replication. Inactivation of dupA resulted in depressed L. pneumophila growth and sustained hyperphosphorylation of the amoebal MAP kinase ERK1, consistent with loss of a phosphatase activity. Bacterial challenge of wild-type amoebae induced dupA expression and resulted in transiently increased ERK1 phosphorylation, suggesting that dupA and ERK1 are part of a response to bacteria. Indeed, over 500 of the genes misregulated in the dupA(-) mutant were regulated in response to L. pneumophila infection, including some thought to have immune-like functions. MAP kinase phosphatases are known to be highly upregulated in macrophages challenged with L. pneumophila. Thus, DupA may regulate a MAP kinase response to bacteria that is conserved from amoebae to mammals.

Liao, X. H. and A. R. Kimmel (2009). "Biochemical responses to chemoattractants in Dictyostelium: ligand-receptor interactions and downstream kinase activation." Meth Mol Biol 571: 271-281.
	Dictyostelium discoideum is one of the most facile eukaryotic systems for the study of chemotactic response to secreted chemical ligands. Dictyostelium grow as individual cells, using bacteria and fungi as primary nutrient sources; during growth, Dictyostelium moves directionally toward folate, a bacterial byproduct. Upon nutrient depletion Dictyostelium initiates a multicellular development program characterized by the production and secretion of cAMP. Cell surface receptors specifically recognize extracellular cAMP, which serves as both a morphogen to promote development and a chemoattractant to organize multicellularity. We discuss several approaches for the study of ligand-receptor interaction, with focus on affinity class determination and quantification of ligand binding sites (i.e., receptors) per cell. We further present examples for the application of biochemical assays to characterize the ligand-induced kinase activation of PI3K, GSK3, and ERK2.

Lozupone, F., M. Perdicchio, et al. (2009). "The human homologue of Dictyostelium discoideum phg1A is expressed by human metastatic melanoma cells." EMBO Rep 10(12): 1348-1354.
	Tumour cannibalism is a characteristic of malignancy and metastatic behaviour. This atypical phagocytic activity is a crucial survival option for tumours in conditions of low nutrient supply, and has some similarities to the phagocytic activity of unicellular microorganisms. In fact, Dictyostelium discoideum has been used widely as a model to study phagocytosis. Recently, phg1A has been described as a protein that is primarily involved in the phagocytic process of this microorganism. The closest human homologue to phg1A is transmembrane 9 superfamily protein member 4 (TM9SF4). Here, we report that TM9SF4 is highly expressed in human malignant melanoma cells deriving from metastatic lesions, whereas it is undetectable in healthy human tissues and cells. TM9SF4 is predominantly expressed in acidic vesicles of melanoma cells, in which it co-localizes with the early endosome antigens Rab5 and early endosome antigen 1. TM9SF4 silencing induced marked inhibition of cannibal activity, which is consistent with a derangement of intracellular pH gradients, with alkalinization of acidic vesicles and acidification of the cell cytosol. We propose TM9SF4 as a new marker of malignancy, representing a potential new target for anti-tumour strategies with a specific role in tumour cannibalism and in the establishment of a metastatic phenotype.

Lucas, J., A. Bilzer, et al. (2009). "The carboxy-terminal domain of Dictyostelium C-module-binding factor is an independent gene regulatory entity." PLoS One 4(4): e5012.
	The C-module-binding factor (CbfA) is a multidomain protein that belongs to the family of jumonji-type (JmjC) transcription regulators. In the social amoeba Dictyostelium discoideum, CbfA regulates gene expression during the unicellular growth phase and multicellular development. CbfA and a related D. discoideum CbfA-like protein, CbfB, share a paralogous domain arrangement that includes the JmjC domain, presumably a chromatin-remodeling activity, and two zinc finger-like (ZF) motifs. On the other hand, the CbfA and CbfB proteins have completely different carboxy-terminal domains, suggesting that the plasticity of such domains may have contributed to the adaptation of the CbfA-like transcription factors to the rapid genome evolution in the dictyostelid clade. To support this hypothesis we performed DNA microarray and real-time RT-PCR measurements and found that CbfA regulates at least 160 genes during the vegetative growth of D. discoideum cells. Functional annotation of these genes revealed that CbfA predominantly controls the expression of gene products involved in housekeeping functions, such as carbohydrate, purine nucleoside/nucleotide, and amino acid metabolism. The CbfA protein displays two different mechanisms of gene regulation. The expression of one set of CbfA-dependent genes requires at least the JmjC/ZF domain of the CbfA protein and thus may depend on chromatin modulation. Regulation of the larger group of genes, however, does not depend on the entire CbfA protein and requires only the carboxy-terminal domain of CbfA (CbfA-CTD). An AT-hook motif located in CbfA-CTD, which is known to mediate DNA binding to A+T-rich sequences in vitro, contributed to CbfA-CTD-dependent gene regulatory functions in vivo.

Luciani, M. F., Y. Kubohara, et al. (2009). "Autophagic or necrotic cell death triggered by distinct motifs of the differentiation factor DIF-1." Cell Death Differ 16(4): 564-570.
	Autophagic or necrotic cell death (ACD and NCD, respectively), studied in the model organism Dictyostelium which offers unique advantages, require triggering by the same differentiation-inducing factor DIF-1. To initiate these two types of cell death, does DIF-1 act through only one or through two distinct recognition structures? Such distinct structures may recognize distinct motifs of DIF-1. To test this albeit indirectly, DIF-1 was modified at one or two of several positions, and the corresponding derivatives were tested for their abilities to induce ACD or NCD. The results strongly indicated that distinct biochemical motifs of DIF-1 were required to trigger ACD or NCD, and that these motifs were separately recognized at the onset of ACD or NCD. In addition, both ACD and NCD were induced more efficiently by DIF-1 than by either its precursors or its immediate catabolite. These results showed an unexpected relation between a differentiation factor, the cellular structures that recognize it, the cell death types it can trigger and the metabolic state of the cell. The latter seems to guide the choice of the signaling pathway to cell death, which in turn imposes the cell death type and the recognition pattern of the differentiation factor.

Luo, J., M. Teng, et al. (2009). "Evaluating the evolution of G. lamblia based on the small nucleolar RNAs identified from Archaea and unicellular eukaryotes." Parasitol Res 104(6): 1543-1546.
	The evolutionary position of Giardia lamblia has been challenged in recent years. Comparison of the snoRNAs identified from Archaea and unicellular eukaryotes shows that G. lamblia snoRNAs are more similar in most respects to the counterparts identified from Dictyostelium discoideum, Plasmodium falciparum, fungi, and some metazoans, remarkably differently from those of Euglenozoa protozoans. We propose that G. lamblia emerged somewhat later than Trypanosoma and Euglena during the early evolution of excavata eukaryotes. Class Descriptors: NAL: QL757.P377

Lusche, D. F., D. Wessels, et al. (2009). "The effects of extracellular calcium on motility, pseudopod and uropod formation, chemotaxis, and the cortical localization of myosin II in Dictyostelium discoideum." Cell Motil Cytoskeleton 66(8): 567-587.
	Extracellular Ca(++), a ubiquitous cation in the soluble environment of cells both free living and within the human body, regulates most aspects of amoeboid cell motility, including shape, uropod formation, pseudopod formation, velocity, and turning in Dictyostelium discoideum. Hence it affects the efficiency of both basic motile behavior and chemotaxis. Extracellular Ca(++) is optimal at 10 mM. A gradient of the chemoattractant cAMP generated in the absence of added Ca(++) only affects turning, but in combination with extracellular Ca(++), enhances the effects of extracellular Ca(++). Potassium, at 40 mM, can partially substitute for Ca(++). Mg(++), Mn(++), Zn(++), and Na(+) cannot. Extracellular Ca(++), or K(+), also induce the cortical localization of myosin II in a polar fashion. The effects of Ca(++), K(+) or a cAMP gradient do not appear to be similarly mediated by an increase in the general pool of free cytosolic Ca(++). These results suggest a model, in which each agent functioning through different signaling systems, converge to affect the cortical localization of myosin II, which in turn effects the behavioral changes leading to efficient cell motility and chemotaxis. Cell Motil. Cytoskeleton 2009. (c) 2009 Wiley-Liss, Inc.

Maeda, Y., T. Mayanagi, et al. (2009). "Folic Acid is A Potent Chemoattractant of Free-Living Amoebae in A New and Amazing Species of Protist, Vahlkampfia sp." Zoolog Sci 26(3): 179-186.
	Folic acid (folate; vitamin Bc) is well recognized as essential for the proper metabolism of the essential amino acid methionine as well as for the synthesis of adenine and thymine. A folate deficiency has been Implicated in a wide variety of disorders from Alzheimer's disease to depression and neural tube defects. In the cellular slime molds, including Dictyostelium, vegetative growthphase cells are known to chemotactically move toward folate that is secreted by bacterial food sources such as Escherichia coli. Intracellular folate signal transductlon, including G proteins, Ca(2+)channels, and the PIP3 pathway, has been reported in D. discoideum. To our surprise, the genuine chemoattractant(s) of free-living protozoan amoebae have remained to be determined, possibly because of lack of a pertinent method for assaying chemotaxis. We recently isolated a primitive free-living amoeba from the soil of Costa Rica and identified it as a new species of the genus Vahlkampfia belonging to Subclass Gymnamoebia, which includes Entamoeba and Acanthamoeba. The amoebae can grow and multiply quite rapidly, engulfing nearby bacteria such as E. coli. Importantly, we have demonstrated here using a quite simple but finely designed chemotaxis assay that the Vahlkampfia amoebae exhibit chemotaxis toward higher folate concentrations. Riboflavin and cyanocobalamin were also found to serve as positive chemoattractants. Among these chemoattractants, folate is of particular importance because its function seems to be evolutionarily conserved as a potent chemoattractant of amoeboid cells in a wide range of organisms as well as in the Protista and cellular slime molds.

Mahowald, J., D. Arcizet, et al. (2009). "Impact of external stimuli and cell micro-architecture on intracellular transport states." Chemphyschem 10(9-10): 1559-1566.
	A living cell is a complex out-of-equilibrium system, in which a great variety of biochemical and physical processes have to be coordinated to ensure viability. We investigate properties of intracellular transport in single cells of the amoeba Dictyostelium discoideum, a relevant model organism due to its cytoskeleton simplicity. In the cells, vesicles undergo two types of motion: directed transport, driven by molecular motors on filaments, or thermal diffusion in a crowded active medium. We present results obtained with our recently developed TRAnSpORT algorithm, which performs a high-resolution temporal analysis of the track of endosomal superparamagnetic particles and splits intracellular transport into different motion states. It results in a two-state model, distinguishing active and passive transport phenomena. We can extract the precise effect of cellular micro- and nanoarchitecture on endosomal transport by disturbing the cytoskeleton through the use of depolymerizing drugs (Benomyl for microtubules, and Latrunculin A for F-actin). Further, we investigate how cytoskeleton filaments act together in order to maintain cell integrity, by applying external mechanical force on the magnetic particle and influencing its motion.

Mana-Capelli, S., R. Graf, et al. (2009). "Dictyostelium discoideum CenB is a bona fide centrin essential for nuclear architecture and centrosome stability." Euk Cell 8(8): 1106-1117.
	Centrins are a family of proteins within the calcium-binding EF-hand superfamily. In addition to the archetypical role at the MTOC, centrins have acquired multiple functionalities throughout the course of evolution. For example, centrins have been linked to different nuclear activities, including mRNA export and DNA repair. Dictyostelium discoideum centrin B is a divergent member of the centrin family. At the amino acid level, DdCenB shows 51 % identity with its closest relative and only paralog, DdCenA. Phylogenetic analysis revealed that DdCenB and DdCenA form a well supported monophyletic and divergent group within the centrin family of proteins. Interestingly, fluorescently-tagged versions of DdCenB were not found at the centrosome (in whole cells or isolated centrosomes). Instead, DdCenB localized to the nuclei of interphase cells. This localization disappeared as cells entered mitosis, although Dictyostelium cells undergo a closed mitosis in which the NE does not breakdown. DdCenB knockout cells exhibited aberrant nuclear architecture, characterized by enlarged and deformed nuclei, and loss of proper centrosome-nucleus anchoring (observed as NE protrusions). At the centrosome, loss of DdCenB resulted in defects in the organization and morphology of the MTOC, supernumerary centrosomes, and centrosome-related bodies. The multiple defects that loss of DdCenB generated at the centrosome can be explained by its atypical division cycle, transitioning into the NE as it divides at mitosis. On the basis of these findings, we propose that DdCenB is required at interphase to maintain proper nuclear architecture, and, before delocalizing from the nucleus, DdCenB is part of the centrosome duplication machinery.

Marchetti, A., E. Lelong, et al. (2009). "A measure of endosomal pH by flow cytometry in Dictyostelium." BMC Res Notes 2: 7.
	ABSTRACT: BACKGROUND: Dictyostelium amoebae are frequently used to study the organization and function of the endocytic pathway, and specific protocols are essential to measure the dynamics of endocytic compartments and their internal pH. FINDINGS: We have revisited these classical protocols to measure more accurately endosomal pH, making use of a fluorescent probe (Oregon green) more adequate for very acidic pH values. This pH-sensitive probe was combined with a pH-insensitive marker, in order to visualize simultaneously endosome dynamics and pH changes. Finally, a flow cytometer was used to measure endosomal pH in individual cells. CONCLUSION: Using these simple protocols the endosomal pH of endocytic compartments can be assessed accurately, revealing the extreme acidity of Dictyostelium lysosomes (pH <3.5).

Mason, D. A., D. E. Stage, et al. (2009). "Evolution of the Metazoan-Specific Importin alpha Gene Family." J Mol Evol 68(4): 351-365.
	Importin ?s are import receptors for nuclear localization signal-containing proteins. Most animal importin ?s assort into ?1, ?2, and ?3 groups. Studies in Drosophila melanogaster, Caenorhabditis elegans, and mouse suggest that the animal importin ? gene family evolved from ancestral plant-like genes to serve paralog-specific roles in gametogenesis. To explore this hypothesis we extended the phylogenetic analysis of the importin ? gene family to nonbilateral animals and investigated whether animal-like genes occur in premetazoan taxa. Maximum likelihood analysis suggests that animal-like importin ? genes occur in the Choanoflaggelate Monosiga brevicollis and the amoebozoan Dictyostelium; however, both of these results are caused by long-branch attraction effects. The absence of animal-like ? genes in premetazoan taxa is consistent with the hypothesis that they duplicated and then specialized to function in animal gametogenesis. The gene structures of the importin ?s provide insight into how the animal importin ? gene family may have evolved from the most likely ancestral gene. Interestingly, animal ?1s are more similar to plant and fungal ?1-like sequences than they are to animal ?2s or ?3s. We show that animal ?1 genes share most of their introns with plant ?1-like genes, and ?2s and ?3s share many more intron positions with each other than with the ?1s. Together, phylogenetics and gene structure analysis suggests a parsimonious path for the evolution of the mammalian importin ? gene family from an ancestral ?1-like progenitor. Finally, these results establish a rational basis for a unified nomenclature of the importin ? gene family. Class Descriptors: NAL: QH359.J6

Masson, P., D. Lundin, et al. (2009). "Characterization of a REG/PA28 proteasome activator homolog in Dictyostelium discoideum indicates that the ubiquitin- and ATP-independent REGgamma proteasome is an ancient nuclear protease." Euk Cell 8(6): 844-851.
	The nuclear proteasome activator REGgamma/PA28gamma is an ATP- and ubiquitin-independent activator of the 20S proteasome and has been proposed to degrade and thereby regulate both a key human oncogene, encoding the coactivator SRC-3/AIB1, and the cyclin-dependent kinase inhibitor p21 (Waf/Cip1). We report the identification and characterization of a PA28/REG homolog in Dictyostelium. Association of a recombinant Dictyostelium REG with the purified Dictyostelium 20S proteasome led to the preferential stimulation of the trypsin-like proteasome peptidase activity. Immunolocalization studies demonstrated that the proteasome activator is localized to the nucleus and is present in growing as well as starving Dictyostelium cells. Our results indicate that the Dictyostelium PA28/REG activator can stimulate both the trypsin-like and chymotrypsin-like activities of the 20S proteasome and supports the idea that the REGgamma-20S proteasome represents an early unique nuclear degradation pathway for eukaryotic cells.

Mehdiabadi, N. J., M. R. Kronforst, et al. (2009). "Phylogeny, reproductive isolation and kin recognition in the social amoeba Dictyostelium purpureum." Evolution 63(2): 542-548.
	Little is known about the population structure of social microorganisms, yet such studies are particularly interesting for the ways that genetic variation impacts their social evolution. Dictyostelium, a eukaryotic microbe widely used as a developmental model, has a social fruiting stage in which some formerly independent individuals die to help others. To assess genetic variation within the social amoeba Dictyostelium purpureum, we sequenced approximately 4000 base pairs of ribosomal DNA (rDNA) from 37 isolates collected in Texas, Virginia, and Japan. Our analysis showed extensive genetic variation between populations and clear evidence of phylogenetic structure. We identified three major phylogenetic groups that were more different than other accepted species pairs. Tests using pairs of clones showed that both sexual macrocyst and asexual fruiting body formation were influenced by genetic divergence. Macrocysts were less likely to form between pairs of clones from different groups than from the same group. There was also a correlation between the genetic divergence of a pair of clones and their degree of mixing within fruiting bodies. These observations suggest that cryptic species might occur within D. purpureum and, more importantly, reveal how genetic variation impacts social interactions.

Middlemist, S. (2009). Mutational processes in Dictyostelium discoideum: How mutations affect social behaviors and fitness. United States -- Texas, Rice University: 146.
	Part I. Mutation is the most important biological force as it generates the variation that drives evolution and may play an important role in maintaining social structure in the social amoeba Dictyostelium discoideum. Using mutation accumulation lines of the social amoeba, I estimated the rate and degree of mutational effects on the social ability to form spores in chimeras by mixing equal proportions of cells of the ancestral clone with a mutated line and determining if the resultant spore proportion differs. Through the use of assays measuring growth, migration ability, and rates of spore germination, I assessed the fitness effects of mutation. In agreement with evidence that the majority of mutations are deleterious, I have found that the ability to get into the reproductive spores is diminished following mutation accumulation. Measuring growth rates on the selective medium revealed that approximately half of the lines showing a significant deviation from the ancestor have increased growth rates, possibly indicating the presence of beneficial mutations, while growth in a non-selective medium resulted in a loss of fitness. Additionally, spore germination decreased in lines with an abundance of mutations. Part II. Restriction Enzyme Mediated Integration (REMI) is a method of transformation that generates tagged mutations. We employed the REMI mutants to select for cheaters by competing pools of mutants over many generations, allowing the lines to fruit each time. We plated out high densities of spores in order to facilitate the lines bypassing the vegetative cycle but still allowing the social cycle. This process was repeated 20 times. At the end of this process, the frequency of each line was assessed and each line was sequenced to identify the genes that were affected by REMI mutagenesis. Once we had obligate cheaters, we assessed fitness in a variety of ways: axenic growth and growth on bacteria, rate of spore germination, and distance traveled by migrating slugs. We then looked for a correlation between cheating and fitness. We expect to see a tradeoff between the ability to preferentially produce spores in chimeric mixtures and other aspects of fitness.

Miyanaga, Y., S. Matsuoka, et al. (2009). "Single-molecule imaging techniques to visualize chemotactic signaling events on the membrane of living Dictyostelium cells." Meth Mol Biol 571: 417-435.
	In this chapter, we describe methods to monitor signaling events at the single-molecule level on the membrane of living cells by using total internal reflection fluorescence microscopy (TIRFM). The techniques provide a powerful tool for elucidating the stochastic properties of signaling molecules involved in chemotaxis of the cellular slime mold Dictyostelium discoideum. Taking cAMP receptor 1 (cAR1) as an example of a target protein for single-molecule imaging, we describe the experimental setup of TIRFM, a method for labeling cAR1 with a fluorescent dye, and a method for investigating the receptor's lateral mobility. We discuss how the developmental progression of cells modulates both cAR1 behavior and the phenotypic variability in cAR1 mobility for different cell populations.

Moreno, S. N. J. and R. Docampo (2009). "The Role of Acidocalcisomes in Parasitic Protists." J. Euk. Microbiol. 56(3): 208-213.
	Acidocalcisomes are acidic organelles with a high concentration of phosphorus present as pyrophosphate (PPi) and polyphosphate (poly P) complexed with calcium and other cations. The acidocalcisome membrane contains a number of pumps (Ca2+-ATPase, V-H+-ATPase, H+-PPase), exchangers (Na+/H+, Ca2+/H+), and channels (aquaporins), while its matrix contains enzymes related to PPi and poly P metabolism. Acidocalcisomes have been observed in pathogenic, as well as non-pathogenic prokaryotes and eukaryotes, e.g. Chlamydomonas reinhardtii, and Dictyostelium discoideum. Some of the potential functions of the acidocalcisome are the storage of cations and phosphorus, the participation of phosphorus in PPi and poly P metabolism, calcium homeostasis, maintenance of intracellular pH homeostasis, and osmoregulation. In addition, acidocalcisomes resemble lysosome-related organelles (LRO) from mammalian cells in many of their properties. For example, we found that platelet dense granules, which are LROs, are very similar to acidocalcisomes. They share a similar size, acidic properties, and both contain PPi, poly P, and calcium. Recent work that indicates that they also share the system for targeting of their membrane proteins through adaptor protein 3 reinforces this concept. The fact that acidocalcisomes interact with other organelles in parasitic protists, e.g. the contractile vacuole in Trypanosoma cruzi, and other vacuoles observed in Toxoplasma gondii, suggests that these cellular compartments may be associated with the endosomal/lysosomal pathway. Class Descriptors: NAL: QL366.J67

Mujumdar, N., K. Inouye, et al. (2009). "The trishanku gene and terminal morphogenesis in Dictyostelium discoideum." Evol Dev 11(6): 697-709.
	Multicellular development in the social amoeba Dictyostelium discoideum is triggered by starvation. It involves a series of morphogenetic movements, among them being the rising of the spore mass to the tip of the stalk. The process requires precise coordination between two distinct cell types-presumptive (pre-) spore cells and presumptive (pre-) stalk cells. Trishanku (triA) is a gene expressed in prespore cells that is required for normal morphogenesis. The triA(-) mutant shows pleiotropic effects that include an inability of the spore mass to go all the way to the top. We have examined the cellular behavior required for the normal ascent of the spore mass. Grafting and mixing experiments carried out with tissue fragments and cells show that the upper cup, a tissue that derives from prestalk cells and anterior-like cells (ALCs), does not develop properly in a triA(-) background. A mutant upper cup is unable to lift the spore mass to the top of the fruiting body, likely due to defective intercellular adhesion. If wild-type upper cup function is provided by prestalk and ALCs, trishanku spores ascend all the way. Conversely, Ax2 spores fail to do so in chimeras in which the upper cup is largely made up of mutant cells. Besides proving that under these conditions the wild-type phenotype of the upper cup is necessary and sufficient for terminal morphogenesis in D. discoideum, this study provides novel insights into developmental and evolutionary aspects of morphogenesis in general. Genes that are active exclusively in one cell type can elicit behavior in a second cell type that enhances the reproductive fitness of the first cell type, thereby showing that morphogenesis is a cooperative process.

Muller-Taubenberger, A., H. C. Ishikawa-Ankerhold, et al. (2009). "The STE group kinase sepA controls cleavage furrow formation in Dictyostelium." Cell Motil Cytoskeleton 66(11): 929-939.
	During a REMI screen for proteins regulating cytokinesis in Dictyostelium discoideum we isolated a mutant forming multinucleate cells. The gene affected in this mutant encoded a kinase, SepA, which is an ortholog of Cdc7, a serine-threonine kinase essential for septum formation in Schizosaccharomyces pombe. Localization of SepA-GFP in live cells and its presence in isolated centrosomes indicated that SepA, like its upstream regulator Spg1, is associated with centrosomes. Knockout mutants of SepA showed a severe cytokinesis defect and a delay in development. In multinucleate SepA-null cells nuclear division proceeded normally and synchronously. However, often cleavage furrows were either missing or atypical: they were extremely asymmetric and constriction was impaired. Cortexillin-I, a marker localizing strictly to the furrow in wild-type cells, demonstrated that large, crescent-shaped furrows expanded and persisted long after the spindle regressed and nuclei returned to the interphase state. Outside the furrow the filamentous actin system of the cell cortex showed strong ruffling activity. These data suggest that SepA is involved in the spatial and temporal control system organizing cortical activities in mitotic and postmitotic cells. Cell Motil. Cytoskeleton, 2009. (c) 2009 Wiley-Liss, Inc.

Myre, M. A., K. Washicosky, et al. (2009). "Reduced amyloidogenic processing of the amyloid beta-protein precursor by the small-molecule Differentiation Inducing Factor-1." Cell Signal 21(4): 567-576.
	The detection of cell cycle proteins in Alzheimer's disease (AD) brains may represent an early event leading to neurodegeneration. To identify cell cycle modifiers with anti-Abeta properties, we assessed the effect of Differentiation-Inducing Factor-1 (DIF-1), a unique, small-molecule from Dictyostelium discoideum, on the proteolysis of the amyloid beta-protein precursor (APP) in a variety of different cell types. We show that DIF-1 slows cell cycle progression through G0/G1 that correlates with a reduction in cyclin D1 protein levels. Western blot analysis of DIF-treated cells and conditioned medium revealed decreases in the levels of secreted APP, mature APP, and C-terminal fragments. Assessment of conditioned media by sandwich ELISA showed reduced levels of Abeta40 and Abeta42, also demonstrating that treatment with DIF-1 effectively decreases the ratio of Abeta42 to Abeta40. In addition, DIF-1 significantly diminished APP phosphorylation at residue T668. Interestingly, site-directed mutagenesis of APP residue Thr668 to alanine or glutamic acid abolished the effect of DIF-1 on APP proteolysis and restored secreted levels of Abeta. Finally, DIF-1 prevented the accumulation of APP C-terminal fragments induced by the proteasome inhibitor lactacystin, and calpain inhibitor N-acetyl-leucyl-leucyl-norleucinal (ALLN). Our findings suggest that DIF-1 affects G0/G1-associated amyloidogenic processing of APP by a gamma-secretase-, proteasome- and calpain-insensitive pathway, and that this effect requires the presence of residue Thr668.

Nagasaki, A., M. Kanada, et al. (2009). "Cell adhesion molecules regulate contractile ring-independent cytokinesis in Dictyostelium discoideum." Cell Res 19(2): 236-246.
	To investigate the roles of substrate adhesion in cytokinesis, we established cell lines lacking paxillin (PAXB) or vinculin (VINA), and those expressing the respective GFP fusion proteins in Dictyostelium discoideum. As in mammalian cells, GFP-PAXB and GFP-VINA formed focal adhesion-like complexes on the cell bottom. paxB(-) cells in suspension grew normally, but on substrates, often failed to divide after regression of the furrow. The efficient cytokinesis of paxB(-) cells in suspension is not because of shear forces to assist abscission, as they divided normally in static suspension culture as well. Double knockout strains lacking mhcA, which codes for myosin II, and paxB or vinA displayed more severe cytokinetic defects than each single knockout strain. In mitotic wild-type cells, GFP-PAXB was diffusely distributed on the basal membrane, but was strikingly condensed along the polar edges in mitotic mhcA(-) cells. These results are consistent with our idea that Dictyostelium displays two forms of cytokinesis, one that is contractile ring-dependent and adhesion-independent, and the other that is contractile ring-independent and adhesion-dependent, and that the latter requires PAXB and VINA. Furthermore, that paxB(-) cells fail to divide normally in the presence of substrate adhesion suggests that this adhesion molecule may play additional signaling roles.

Nguyen, H. N. and J. A. Hadwiger (2009). "The Galpha4 G protein subunit interacts with the MAP kinase ERK2 using a D-motif that regulates developmental morphogenesis in Dictyostelium." Dev Biol 335(2): 385-395.
	G protein Galpha subunits contribute to the specificity of different signal transduction pathways in Dictyostelium discoideum but Galpha subunit-effector interactions have not been previously identified. The requirement of the Dictyostelium Galpha4 subunit for MAP kinase (MAPK) activation and the identification of a putative MAPK docking site (D-motif) in this subunit suggested a possible interaction between the Galpha4 subunit and MAPKs. In vivo association of the Galpha4 subunit and ERK2 was demonstrated by pull-down and co-immunoprecipitation assays. Alteration of the D-motif reduced Galpha4 subunit-ERK2 interactions but only slightly altered MAPK activation in response to folate. Expression of the Galpha4 subunit with the altered D-motif in galpha4(-)cells allowed for slug formation but not the morphogenesis associated with culmination. Expression of this mutant Galpha4 subunit was sufficient to rescue chemotactic movement to folate. Alteration of the D-motif also reduced the aggregation defect associated with constitutively active Galpha4 subunits. These results suggest Galpha4 subunit-MAPK interactions are necessary for developmental morphogenesis but not for chemotaxis to folate.

Nordstrom, K. J., M. C. Lagerstrom, et al. (2009). "The Secretin GPCRs descended from the family of Adhesion GPCRs." Mol Biol Evol 26(1): 71-84.
	The Adhesion G-protein-coupled receptors (GPCRs) are the most complex gene family among GPCRs with large genomic size, multiple introns, and a fascinating flora of functional domains, though the evolutionary origin of this family has been obscure. Here we studied the evolution of all class B (7tm2)-related genes, including the Adhesion, Secretin, and Methuselah families of GPCRs with a focus on nine genomes. We found that the cnidarian genome of Nematostella vectensis has a remarkably rich set of Adhesion GPCRs with a broad repertoire of N-terminal domains although this genome did not have any Secretin GPCRs. Moreover, the single-celled and colony-forming eukaryotes Monosiga brevicollis and Dictyostelium discoideum contain Adhesion-like GPCRs although these genomes do not have any Secretin GPCRs suggesting that the Adhesion types of GPCRs are the most ancient among class B GPCRs. Phylogenetic analysis found Adhesion group V (that contains GPR133 and GPR144) to be the closest relative to the Secretin family in the Adhesion family. Moreover, Adhesion group V sequences in N. vectensis share the same splice site setup as the Secretin GPCRs. Additionally, one of the most conserved motifs in the entire Secretin family is only found in group V of the Adhesion family. We suggest therefore that the Secretin family of GPCRs could have descended from group V Adhesion GPCRs. We found a set of unique Adhesion-like GPCRs in N. vectensis that have long N-termini containing one Somatomedin B domain each, which is a domain configuration similar to that of a set of Adhesion-like GPCRs found in Branchiostoma floridae. These sequences show slight similarities to Methuselah sequences found in insects. The extended class B GPCRs have a very complex evolutionary history with several species-specific expansions, and we identified at least 31 unique N-terminal domains originating from other protein classes. The overall N-terminal domain structure, however, concurs with the phylogenetic analysis of the transmembrane domains, thus enabling us to track the origin of most of the subgroups.

O'Day, D. H., Y. Poloz, et al. (2009). "Differentiation inducing factor-1 (DIF-1) induces gene and protein expression of the Dictyostelium nuclear calmodulin-binding protein nucleomorphin." Cell Signal 21(2): 317-323.
	The nucleomorphin gene numA1 from Dictyostelium codes for a multi-domain, calmodulin binding protein that regulates nuclear number. To gain insight into the regulation of numA, we assessed the effects of the stalk cell differentiation inducing factor-1 (DIF-1), an extracellular signalling molecule, on the expression of numA1 RNA and protein. For comparison, the extracellular signalling molecules cAMP (mediates chemotaxis, prestalk and prespore differentiation) and ammonia (NH(3)/NH(4)(+); antagonizes DIF) were also studied. Starvation, which is a signal for multicellular development, results in a greater than 80% decrease in numA1 mRNA expression within 4 h. Treatment with ammonium chloride led to a greater than 90% inhibition of numA1 RNA expression within 2 h. In contrast, the addition of DIF-1 completely blocked the decrease in numA1 gene expression caused by starvation. Treatment of vegetative cells with cAMP led to decreases in numA1 RNA expression that were equivalent to those seen with starvation. Western blotting after various morphogen treatments showed that the maintenance of vegetative levels of numA1 RNA by DIF-1 in starved cells was reflected in significantly increased numA1 protein levels. Treatment with cAMP and/or ammonia led to decreased protein expression and each of these morphogens suppressed the stimulatory effects of DIF-1. Protein expression levels of CBP4a, a calcium-dependent binding partner of numA1, were regulated in the same manner as numA1 suggesting this potential co-regulation may be related to their functional relationship. NumA1 is the first calmodulin binding protein shown to be regulated by developmental morphogens in Dictyostelium being upregulated by DIF-1 and down-regulated by cAMP and ammonia.

Ogasawara, S., N. Shimada, et al. (2009). "Role of an expansin-like molecule in Dictyostelium morphogenesis and regulation of its gene expression by the signal transducer and activator of transcription protein Dd-STATa." Dev Growth Differ 51(2): 109-122.
	Expansins are proteins involved in plant morphogenesis, exerting their effects on cellulose to extend cell walls. Dictyostelium is an organism that possesses expansin-like molecules, but their functions are not known. In this study, we analyzed the expL7 (expansin-like 7) gene, which has been identified as a putative target of Dd-STATa, a Dictyostelium homolog of the metazoan signal transducer and activator of transcription (STAT) proteins. Promoter fragments of the expL7 were fused to a lacZ reporter and the expression patterns determined. As expected from the behavior of the endogenous expL7 gene, the expL7/lacZ fusion gene was downregulated in Dd-STATa null slugs. In the parental strain, the expL7 promoter was activated in the anterior tip region. Mutational analysis of the promoter identified a sequence that was necessary for expression in tip cells. In addition, an activator sequence for pstAB cells was identified. These sequences act in combination with the repressor region to prevent ectopic expL7 expression in the prespore and prestalk regions of the slug and culminant. Although the expL7 null mutant showed no phenotypic change, the expL7 overexpressor showed aberrant stalk formation. These results indicate that the expansin-like molecule is important for morphogenesis in Dictyostelium.

Oohata, A. A., M. Fukuzawa, et al. (2009). "Differentiation inducing factors in Dictyostelium discoideum: A novel low molecular factor functions at an early stage(s) of differentiation." Dev Growth Differ.
	There are reports that secreted factor(s) are involved in prespore cell differentiation in Dictyostelium discoideum, but the structures and functions of the various factors have not been elucidated. Previously, we described two prespore cell-inducing factors in conditioned medium; one was a glycoprotein named prespore cell-inducing factor (psi factor, or PSI-1), and the other, a heat stable dialyzable factor(s). In the present paper, we purified and characterized the most potent prespore cell-inducing activity in dialysates. The factor began to be secreted after the onset of starvation and stopped being secreted once the cells had aggregated, which was earlier than the onset of the psi factor gene expression. In addition, unlike psi factor, its secretion did not appear to depend on activation of protein kinase A. Interestingly, the purified factor not only induced prespore cell specific genes such as pspA and cotC but also a prestalk-cell specific gene, ecmB in vitro. The purified factor is tentatively designated polyketide-like factor (PLF), because it seems to be a novel polyketide with 208 Da. Half maximal induction of prespore cell was obtained with 26 nmol/L of PLF. We propose that PLF plays a key role in the acquisition of differentiation commitment, before the psi factor induces specifically prespore cell differentiation.

Painter, K. J. (2009). "Continuous Models for Cell Migration in Tissues and Applications to Cell Sorting via Differential Chemotaxis." Bull Math Biol 71(5): 1117-1147.
	Chemotaxis, the guided migration of cells in response to chemical gradients, is vital to a wide variety of biological processes, including patterning of the slime mold Dictyostelium, embryonic morphogenesis, wound healing, and tumor invasion. Continuous models of chemotaxis have been developed to describe many such systems, yet few have considered the movements within a heterogeneous tissue composed of multiple subpopulations. In this paper, a partial differential equation (PDE) model is developed to describe a tissue formed from two distinct chemotactic populations. For a "crowded" (negligible extracellular space) tissue, it is demonstrated that the model reduces to a simpler one-species system while for an "uncrowded" tissue, it captures both movement of the entire tissue (via cells attaching to/migrating within an extracellular substrate) and the within-tissue rearrangements of the separate cellular subpopulations. The model is applied to explore the sorting of a heterogeneous tissue, where it is shown that differential-chemotaxis not only generates classical sorting patterns previously seen via differential-adhesion, but also demonstrates new classes of behavior. These new phenomena include temporal dynamics consisting of a traveling wave composed of spatially sorted subpopulations reminiscent of Dictyostelium slugs.

Palsson, E. (2009). "A cAMP signaling model explains the benefit of maintaining two forms of phosphodiesterase in Dictyostelium." Biophys J 97(9): 2388-2398.
	Starving Dictyostelium cells respond chemotactically to cell-generated waves of cyclic adenosine -3',5'- monophosphate (cAMP) that guide cell aggregation toward a signaling center. In this process, a large number of cells are recruited, resulting in the formation of aggregation territories that are essential for fruiting body formation. The enzyme PdsA phosphodiesterase (PDE), a crucial component of the signaling system, breaks down the external cAMP and can be either membrane-bound or secreted. The existence of two such forms is unusual in cell biology, and it remains to be determined why they have both been maintained through evolution. Here, using a model of the cAMP signaling system, I show that colonies can successfully organize into aggregates over a wider range of initial cell densities when both forms of PDE are present in an appropriately tuned ratio than when only a single form is present. The model indicates that membrane-bound PDE maintains aggregation-territory integrity in colonies with high initial cell density, whereas the secreted form is important for wave propagation at low cell densities. Thus, the ultimate retention of both forms can increase territory size. These findings have implications for other excitable media, including Ca(2+) propagation in cardiac cells and propagation of electrical excitation in nerve axons, since these systems have similar features of spatial nonuniform "release" and "degradation" of the relevant signals.

Para, A., M. Krischke, et al. (2009). "Dictyostelium Dock180-related RacGEFs regulate the actin cytoskeleton during cell motility." Mol Biol Cell 20(2): 699-707.
	Cell motility of amoeboid cells is mediated by localized F-actin polymerization that drives the extension of membrane protrusions to promote forward movements. We show that deletion of either of two members of the Dictyostelium Dock180 family of RacGEFs, DockA and DockD, causes decreased speed of chemotaxing cells. The phenotype is enhanced in the double mutant and expression of DockA or DockD complements the reduced speed of randomly moving DockD null cells' phenotype, suggesting that DockA and DockD are likely to act redundantly and to have similar functions in regulating cell movement. In this regard, we find that overexpressing DockD causes increased cell speed by enhancing F-actin polymerization at the sites of pseudopod extension. DockD localizes to the cell cortex upon chemoattractant stimulation and at the leading edge of migrating cells and this localization is dependent on PI3K activity, suggesting that DockD might be part of the pathway that links PtdIns(3,4,5)P(3) production to F-actin polymerization. Using a proteomic approach, we found that DdELMO1 is associated with DockD and that Rac1A and RacC are possible in vivo DockD substrates. In conclusion, our work provides a further understanding of how cell motility is controlled and provides evidence that the molecular mechanism underlying Dock180-related protein function is evolutionarily conserved.

Park, S. J., H. S. Yim, et al. (2009). Analysis of cell cycle regulation during vegetative cell growth in Dictyostelium discoideum. The 48th MSK Annual Meeting.
	
Parkinson, K., P. Bolourani, et al. (2009). "Regulation of Rap1 activity is required for differential adhesion, cell-type patterning and morphogenesis in Dictyostelium." J Cell Sci 122(Pt 3): 335-344.
	Regulated cell adhesion and motility have important roles during growth, development and tissue homeostasis. Consequently, great efforts have been made to identify genes that control these processes. One candidate is Rap1, as it has been implicated in the regulation of adhesion and motility in cell culture. To further study the role of Rap1 during multicellular development, we generated a mutant in a potential Rap1 GTPase activating protein (RapGAPB) in Dictyostelium. rapGAPB(-) cells have increased levels of active Rap1 compared with wild-type cells, indicating that RapGAPB regulates Rap1 activity. Furthermore, rapGAPB(-) cells exhibit hallmark phenotypes of other known mutants with hyperactivated Rap1, including increased substrate adhesion and abnormal F-actin distribution. However, unlike these other mutants, rapGAPB(-) cells do not exhibit impaired motility or chemotaxis, indicating that RapGAPB might only regulate specific roles of Rap1. Importantly, we also found that RapGAPB regulates Rap1 activity during multicellular development and is required for normal morphogenesis. First, streams of aggregating rapGAPB(-) cells break up as a result of decreased cell-cell adhesion. Second, rapGAPB(-) cells exhibit cell-autonomous defects in prestalk cell patterning. Using cell-type-specific markers, we demonstrate that RapGAPB is required for the correct sorting behaviour of different cell types. Finally, we show that inactivation of RapGAPB affects prestalk and prespore cell adhesion. We therefore propose that a possible mechanism for RapGAPB-regulated cell sorting is through differential adhesion.

Patel, H. and V. G. Brunton (2009). "Loss of FrmA leads to increased cell-cell adhesion and impaired multi-cellular development of Dictyostelium cells." Cell Mol Life Sci 66(1): 145-155.
	Cell-cell adhesion is a critical property of all multi-cellular organisms and its correct regulation is critical during development, differentiation, tissue building and maintenance, and many immune responses. The multi-talin-like FERM domain containing protein, FrmA, is required during starvation-induced multi-cellular development of Dictyostelium cells. Loss of FrmA leads to increased cell-cell adhesion and results in impaired multi-cellular development, slug migration and fruiting bodies. Further, mixing experiments show that FrmA null cells are excluded from the apex of wild-type mounds, to which cells that normally form the organising centre known as the tip sort. These data suggest a critical role for FrmA in regulating cell-cell adhesion, multi-cellular development and, in particular, the formation of the organising centre known as the tip.

Pawolleck, N. and R. S. Williams (2009). "Quantifying in vivo phosphoinositide turnover in chemotactically competent Dictyostelium cells." Meth Mol Biol 571: 283-290.
	Phosphoinositide (PI) signalling is one of multiple signalling cascades involved in chemotaxis in Dictyostelium discoideum. PI signalling comprises a complex interaction of multiple enzymes, each with multiple phospholipid substrates and thus products, often relying upon several enzymes in series to produce a signal. PI turnover, controlled by both kinases and phosphatases, is also rapidly triggered and spatially constricted. This complexity makes understanding acute regulation of these signalling components problematic. However, the ubiquitous and extensive roles of phospholipids, including phosphatidylinositol-4,5-diphosphate (PI(4,5)P(2)), in cell signalling and developmental processes make understanding the production of these compounds of great importance. We have shown the acute reduction of PI phosphorylation in response to a widely used bipolar disorder and epilepsy treatment, valproic acid, as a potential therapeutic role for the drug using chemotactically competent Dictyostelium. Here we describe a means for measuring acute in vivo phospholipid labelling in Dictyostelium.

Pennisi, E. (2009). "Origins. On the origin of cooperation." Science 325(5945): 1196-1199.
	
Pollitt, A. Y. and R. H. Insall (2009). "Loss of Dictyostelium HSPC300 causes a scar-like phenotype and loss of SCAR protein." BMC Cell Biol 10: 13.
	BACKGROUND: SCAR/WAVE proteins couple signalling to actin polymerization, and are thus fundamental to the formation of pseudopods and lamellipods. They are controlled as part of a five-membered complex that includes the tiny HSPC300 protein. It is not known why SCAR/WAVE is found in such a large assembly, but in Dictyostelium the four larger subunits have different, clearly delineated functions. RESULTS: We have generated Dictyostelium mutants in which the HSPC300 gene is disrupted. As has been seen in other regulatory complex mutants, SCAR is lost in these cells, apparently by a post-translational mechanism, though PIR121 levels do not change. HSPC300 knockouts resemble scar mutants in slow migration, roundness, and lack of large pseudopods. However hspc300-colonies on bacteria are larger and more similar to wild type, suggesting that some SCAR function can survive without HSPC300. We find no evidence for functions of HSPC300 outside the SCAR complex. CONCLUSION: HSPC300 is essential for most SCAR complex functions. The phenotype of HSPC300 knockouts is most similar to mutants in scar, not the other members of the SCAR complex, suggesting that HSPC300 acts most directly on SCAR itself.

Postma, M. and P. J. van Haastert (2009). "Mathematics of experimentally generated chemoattractant gradients." Meth Mol Biol 571: 473-488.
	Many eukaryotic cells move in the direction of a chemical gradient. Several assays have been developed to measure this chemotactic response, but no complete mathematical models of the spatial and temporal gradients are available to describe the fundamental principles of chemotaxis. Here we provide analytical solutions for the gradients formed by release of chemoattractant from a point source by passive diffusion or forced flow (micropipettes) and gradients formed by laminar diffusion in a Zigmond chamber. The results show that gradients delivered with a micropipette are formed nearly instantaneous, are very steep close to the pipette, and have a steepness that is strongly dependent on the distance from the pipette. In contrast, gradients in a Zigmond chamber are formed more slowly, are nearly independent of the distance from the source, and resemble the temporal and spatial properties of the natural cAMP wave that Dictyostelium cells experience during cell aggregation.

Powell, A. (2009). Disruption of three PP2A regulatory subunits in Dictyostelium discoideum and phenotypic analysis of null strains. United States -- California, University of California, San Diego: 65.
	The Dictyostelium discoideum genome has been found to encode three PP2A regulatory subunits (B, B', and B"). In order to study their function, the genes were individually disrupted and the resulting null strains' phenotypes were analyzed. Our results suggested that the PP2A-B' regulatory subunit was essential for proper multicellular development. Additionally, when exposed to a gradient of cAMP, both the PP2A-B and -B' regulatory subunit null strains showed some significant chemotaxis defects. Null strains expressing GFP and the previously knocked out subunits showed that the PP2A-B and -B' subunits are globally distributed throughout chemotaxing cells. Finally, analysis of cAMP-induced F-actin polymerization and myosin assembly revealed that there were noticeable deficits in all of the analyzed null strains' actin profiles (especially that of PP2A-B and -B') when compared to the wild type. Also, there were significant increases in myosin filament formation in PP2A-B". The results suggest that the PP2A-B and -B' regulatory subunits positively regulate F-actin polymerization, although probably through different effector proteins. On the other hand, PP2A-B" appears to negatively regulate myosin filament formation. Therefore, the specificity of PP2A in de-phosphorylating its effector proteins is different depending on the regulatory subunit within the holoenzyme. Also, these differing specificities appear to cause the phosphatase to have unique protein-protein interactions with other effector proteins involved in F-actin polymerization.

Pramanik, M. K., M. Iijima, et al. (2009). "PTEN is a mechanosensing signal transducer for myosin II localization in Dictyostelium cells." Genes to Cells 14(7): 821-834.
	To investigate the role of PTEN in regulation of cortical motile activity, especially in myosin II localization, eGFP-PTEN and mRFP-myosin II were simultaneously expressed in Dictyostelium cells. PTEN and myosin II co-localized at the posterior of migrating cells and furrow region of dividing cells. In suspension culture, PTEN knockout (pten-) cells became multinucleated, and myosin II significantly decreased in amount at the furrow. During pseudopod retraction and cell aspiration by microcapillary, PTEN accumulated at the tips of pseudopods and aspirated lobes prior to the accumulation of myosin II. In pten- cells, only a small amount of myosin II accumulated at the retracting pseudopods and aspirated cell lobes. PTEN accumulated at the retracting pseudopods and aspirated lobes even in myosin II null cells and latrunculin B-treated cells though in reduced amounts, indicating that PTEN accumulates partially depending on myosin II and cortical actin. Accumulation of PTEN prior to myosin II suggests that PTEN is an upstream component in signaling pathway to localize myosin II, possibly with mechanosensing signaling loop where actomyosin-driven contraction further augments accumulation of PTEN and myosin II by a positive feedback mechanism. Class Descriptors: NAL: QH441.5

Price, C. T., S. Al-Khodor, et al. (2009). "Molecular mimicry by an F-box effector of Legionella pneumophila hijacks a conserved polyubiquitination machinery within macrophages and protozoa." PLoS Pathog 5(12): e1000704.
	The ability of Legionella pneumophila to proliferate within various protozoa in the aquatic environment and in macrophages indicates a remarkable evolution and microbial exploitation of evolutionarily conserved eukaryotic processes. Ankyrin B (AnkB) of L. pneumophila is a non-canonical F-box-containing protein, and is the only known Dot/Icm-translocated effector of L. pneumophila essential for intra-vacuolar proliferation within both macrophages and protozoan hosts. We show that the F-box domain of AnkB and the (9)L(10)P conserved residues are essential for intracellular bacterial proliferation and for rapid acquisition of polyubiquitinated proteins by the Legionella-containing vacuole (LCV) within macrophages, Dictyostelium discoideum, and Acanthamoeba. Interestingly, translocation of AnkB and recruitment of polyubiquitinated proteins in macrophages and Acanthamoeba is rapidly triggered by extracellular bacteria within 5 min of bacterial attachment. Ectopically expressed AnkB within mammalian cells is localized to the periphery of the cell where it co-localizes with host SKP1 and recruits polyubiquitinated proteins, which results in restoration of intracellular growth to the ankB mutant similar to the parental strain. While an ectopically expressed AnkB-(9)L(10)P/AA variant is localized to the cell periphery, it does not recruit polyubiquitinated proteins and fails to trans-rescue the ankB mutant intracellular growth defect. Direct in vivo interaction of AnkB but not the AnkB-(9)L(10)P/AA variant with the host SKP1 is demonstrated. Importantly, RNAi-mediated silencing of expression of SKP1 renders the cells non-permissive for intracellular proliferation of L. pneumophila. The role of AnkB in exploitation of the polyubiquitination machinery is essential for intrapulmonary bacterial proliferation in the mouse model of Legionnaires' disease. Therefore, AnkB exhibits a novel molecular and functional mimicry of eukaryotic F-box proteins that exploits conserved polyubiquitination machinery for intracellular proliferation within evolutionarily distant hosts.

Pujic, Z., D. Mortimer, et al. (2009). "Assays for Eukaryotic Cell Chemotaxis." Combinatorial Chemistry & High Throughput Screening 12(6): 580-588.
	Chemotaxis is essential for many biological processes. Much of our understanding of the mechanisms underlying chemotaxis is based on a variety of in vitro assays. We review these assays, dividing them into groups depending on the process used to generate the gradient. We describe how each method works, its strengths and limitations, and provide some information about the kinds of cells that have been studied with each assay.

Raghu, P., M. Manifava, et al. (2009). "Emerging findings from studies of phospholipase D in model organisms (and a short update on phosphatidic acid effectors)." Biochim Biophys Acta 1791(9): 889-897.
	Phospholipase D (PLD) catalyses the hydrolysis of phosphatidylcholine to generate phosphatidic acid and choline. Historically, much PLD work has been conducted in mammalian settings although genes encoding enzymes of this family have been identified in all eukaryotic organisms. Recently, important insights on PLD function are emerging from work in yeast, but much less is known about PLD in other organisms. In this review we will summarize what is known about phospholipase D in several model organisms, including C. elegans, D. discoideum, D. rerio and D. melanogaster. In the cases where knockouts are available (C. elegans, Dictyostelium and Drosophila) the PLD gene(s) appear not to be essential, but several studies are beginning to identify pathways where this activity has a role. Given that the proteins are very similar, we expect that future studies in model organisms will complement and extend ongoing work in mammalian settings. At the end of this review we will also provide a short update on phosphatidic acid targets, a topic last reviewed in 2006.

Rao, N. N. and M. R. Gomez-Garcia (2009). "Inorganic polyphosphate: essential for growth and survival." Annu Rev Biochem 78: 605-647.
	Inorganic polyphosphate (Poly P) is a polymer of tens to hundreds of phosphate residues linked by "high-energy" phosphoanhydride bonds as in ATP. Found in abundance in all cells in nature, it is unique in its likely role in the origin and survival of species. Here, we present extensive evidence that the remarkable properties of Poly P as a polyanion have made it suited for a crucial role in the emergence of cells on earth. Beyond that, Poly P has proved in a variety of ways to be essential for growth of cells, their responses to stresses and stringencies, and the virulence of pathogens. In this review, we pay particular attention to the enzyme, polyphosphate kinase 1 (Poly P kinase 1 or PPK1), responsible for Poly P synthesis and highly conserved in a many bacterial species, including 20 or more of the major pathogens. Mutants lacking PPK1 are defective in motility, quorum sensing, biofilm formation, and virulence. Structural studies are cited that reveal the conserved ATP-binding site of PPK1 at atomic resolution and reveal that the site can be blocked with minute concentrations of designed inhibitors. Another widely conserved enzyme is PPK2 with distinctive kinetic properties and also implicated in the virulence of some pathogens. Thus, these enzymes, absent in yeast and animals, are novel attractive targets for treatment of many microbial diseases. Still another enzyme featured in this review is one discovered in Dictyostelium discoideum that becomes an actin-like fiber concurrent with the synthesis, step by step, of a Poly P chain made from ATP. The Poly P-actin fiber complex, localized in the cell, lengthens and recedes in response to metabolic signals. Homologs of DdPPK2 are found in pathogenic protozoa and in the alga, Chlamydomonas. Beyond the immediate relevance of Poly P as a target for anti-infective drugs, a large variety of cellular operations that rely on Poly P will be considered. Expected final online publication date for the Annual Review of Biochemistry Volume 78 is June 02, 2009. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.

Rappel, W. J. and W. F. Loomis (2009). "Eukaryotic chemotaxis." WIREs Systems Biology and Medicine 1(1): 141-149.
	During eukaryotic chemotaxis, external chemical gradients guide the crawling motion of cells. This process plays an important role in a large variety of biological systems and has wide ranging medical implications. New experimental techniques including confocal microscopy and microfluidics have advanced our understanding of chemotaxis while numerical modeling efforts are beginning to offer critical insights. In this short review, we survey the current experimental status of the field by dividing chemotaxis into three distinct ‘modules’: directional sensing, polarity and motility. For each module, we attempt to point out potential new directions of research and discuss how modeling studies interact with experimental investigations.

Ren, Y., J. C. Effler, et al. (2009). "Mechanosensing through Cooperative Interactions between Myosin II and the Actin Crosslinker Cortexillin I." Curr Biol 19(17): 1421-1428.
	BACKGROUND: Mechanosensing governs many processes from molecular to organismal levels, including during cytokinesis where it ensures successful and symmetrical cell division. Although many proteins are now known to be force sensitive, myosin motors with their ATPase activity and force-sensitive mechanical steps are well poised to facilitate cellular mechanosensing. For a myosin motor to experience tension, the actin filament must also be anchored. RESULTS: Here, we find a cooperative relationship between myosin II and the actin crosslinker cortexillin I where both proteins are essential for cellular mechanosensory responses. Although many functions of cortexillin I and myosin II are dispensable for cytokinesis, all are required for full mechanosensing. Our analysis demonstrates that this mechanosensor has three critical elements: the myosin motor where the lever arm acts as a force amplifier, a force-sensitive bipolar thick-filament assembly, and a long-lived actin crosslinker, which anchors the actin filament so that the motor may experience tension. We also demonstrate that a Rac small GTPase inhibits this mechanosensory module during interphase, allowing the module to be primarily active during cytokinesis. CONCLUSIONS: Overall, myosin II and cortexillin I define a cellular-scale mechanosensor that controls cell shape during cytokinesis. This system is exquisitely tuned through the enzymatic properties of the myosin motor, its lever arm length, and bipolar thick-filament assembly dynamics. The system also requires cortexillin I to stably anchor the actin filament so that the myosin motor can experience tension. Through this cross-talk, myosin II and cortexillin I define a cellular-scale mechanosensor that monitors and corrects shape defects, ensuring symmetrical cell division.

Rey, S. M., B. Povazay, et al. (2009). "Three- and four-dimensional visualization of cell migration using optical coherence tomography." J Biophotonics 2(6-7): 370-379.
	Conventionally, cell chemotaxis is studied on two-dimensional (2D) transparent surfaces, due to limitations in optical and image data-collection techniques. However, surfaces that more closely mimic the natural environment of cells are often opaque. Optical coherence tomography (OCT) is a noninvasive label-free imaging technique, which offers the potential to visualize moving cells on opaque surfaces and in three dimensions (3D). Here, we demonstrate that OCT is an effective means of time-lapse videomicroscopy of Dictyostelium cells undergoing 3D (2D+time) cell migration on nitrocellulose substrates and 4D (3D+time) chemotaxis within low-density agarose gels. The generated image sequences are compatible with current computer-based image-analysis software for quantification of cell motility. This demonstrates the utility of OCT for cell tracking and analysis of cell chemotaxis in complex environments. ((c) 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim).

Reyes, J., K. Stone, et al. (2009). "Formation of Hirano Bodies After Inducible Expression of a Modified Form of an Actin-Crosslinking Protein." Euk Cell 8(6): 852-857.
	Hirano bodies are cytoplasmic inclusions composed mainly of actin and actin associated proteins. The formation of Hirano bodies has been reported in various neurodegenerative disorders including Alzheimer's Disease and amyotrophic lateral sclerosis. Although the underlying molecular mechanisms that lead to the formation of these inclusions in the brain is not known, expression of the C-terminal fragment (CT, aa 124-295) from the endogenous 34 kDa actin binding protein of Dictyostelium discoideum leads to the formation of actin inclusions in vivo. In the current study, we report the development of an inducible expression system to study the early phases of Hirano Body formation using an inducible promoter system (rnrB). By fusing the CT fragment to a fluorescent probe (CT-GFP), we monitored protein expression and localization by fluorescence microscopy, flow cytometry and western blot analysis. We observed an increase in the number and size of inclusions formed following induction of the CT-GFP vector system. Time-lapse microscopy studies revealed that the CT-GFP foci associated with the cell cortex and fuse to form a single large aggregate. Transmission electron microscopy (TEM) further demonstrates that these inclusions have a highly ordered ultrastructure, a pathological hallmark of Hirano Bodies observed in post-mortem brain samples from patients with various neurodegenerative disorders. Collectively, this system provides a method to visualize and characterize the events that surround early actin inclusion formation in a eukaryotic model.

Rieu, J. P., T. Saito, et al. (2009). "Migration of Dictyostelium slugs: Anterior-like cells may provide the motive force for the prespore zone." Cell Motil Cytoskeleton.
	The collective motion of cells in a biological tissue originates from their individual responses to chemical and mechanical signals. The Dictyostelium slug moves as a collective of up to 100,000 cells with prestalk cells in the anterior 10-30% and prespore cells, intermingled with anterior-like cells (AL cells), in the posterior. We used traction force microscopy to measure the forces exerted by migrating slugs. Wild-type slugs exert frictional forces on their substratum in the direction of motion in their anterior, balanced by motive forces dispersed down their length. StlB- mutants lack the signal molecule DIF-1 and hence a subpopulation of AL cells. They produce little if any motive force in their rear and immediately break up. This argues that AL cells, but not prespore cells, are the motive cells in the posterior zone. Slugs also exert large outward radial forces, which we have analyzed during "looping" movement. Each time the anterior touches down after a loop, the outward forces rapidly develop, approximately normal to the almost stationary contact lines. We postulate that these forces result from the immediate binding of the sheath to the substratum and the subsequent application of outward "pressure," which might be developed in several different ways. Cell Motil. Cytoskeleton 2009. (c) 2009 Wiley-Liss, Inc.

Roberts, A. J., N. Numata, et al. (2009). "AAA+ Ring and linker swing mechanism in the dynein motor." Cell 136(3): 485-495.
	Dynein ATPases power diverse microtubule-based motilities. Each dynein motor domain comprises a ring-like head containing six AAA+ modules and N- and C-terminal regions, together with a stalk that binds microtubules. How these subdomains are arranged and generate force remains poorly understood. Here, using electron microscopy and image processing of tagged and truncated Dictyostelium cytoplasmic dynein constructs, we show that the heart of the motor is a hexameric ring of AAA+ modules, with the stalk emerging opposite the primary ATPase site (AAA1). The C-terminal region is not an integral part of the ring but spans between AAA6 and near the stalk base. The N-terminal region includes a lever-like linker whose N terminus swings by approximately 17 nm during the ATPase cycle between AAA2 and the stalk base. Together with evidence of stalk tilting, which may communicate changes in microtubule binding affinity, these findings suggest a model for dynein's structure and mechanism.

Romeralo, M., S. L. Baldauf, et al. (2009). "A new species of cellular slime mold from southern Portugal based on morphology, ITS and SSU sequences." Mycologia 101(2): 269-274.
	Sampling soils to look for dictyostelids in southern Portugal we found an isolate that has a morphology that differed from any previously described species of the group. We sequenced the internally transcribed spacer (ITS) and small subunit (SSU) genes of the nuclear ribosomal RNA and found that both sequences are distinct from all previously described sequences. Phylogenetic analyses place the new species in dictyostelid Group 3 (Rhizostelids) together with D. potamoides, with which it shares 65.8% identity for ITS and 96.6% for SSU. In this paper we describe a new species of cellular slime mold, Dictyostelium ibericum, based on morphological and molecular characters. It is a small species with polar granules in its spores.

Rot, G., A. Parikh, et al. (2009). "dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface." BMC Bioinformatics 10: 265.
	BACKGROUND: Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. RESULTS: We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. CONCLUSION: dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms.

Saedler, R., M. Jakoby, et al. (2009). "The cell morphogenesis gene SPIRRIG in Arabidopsis encodes a WD/BEACH domain protein." Plant J. 59(4): 612-621.
	WD40/BEACH domain proteins have been implicated in membrane trafficking and membrane composition events in Dictyostelium and Drosophila. In this paper, we show that the Arabidopsis SPIRRIG (SPI) gene encodes a WD40/BEACH domain protein. The cellular analysis revealed fragmented vacuoles in root hairs similar to those found in the corresponding Dictyostelium mutants, suggesting a related cellular function. The phenotypic analysis revealed that spi mutants share all phenotypic aspects of mutants in the actin polymerization-regulating ARP2/3 pathway, including distorted trichomes, less lobing of epidermal pavement cells, disconnected epidermal cells on various organs, and shorter root hairs. This complete phenotypic overlap suggests that this WD40/BEACH domain protein and the actin-regulating ARP2/3 pathway are involved in similar growth processes. Class Descriptors: NAL: QK710.P68

Salah, I. B., E. Ghigo, et al. (2009). "Free-living amoebae, a training field for macrophage resistance of mycobacteria." Clin Microbiol Infect 15(10): 894-905.
	Mycobacterium species evolved from an environmental recent common ancestor by reductive evolution and lateral gene transfer. Strategies selected through evolution and developed by mycobacteria resulted in resistance to predation by environmental unicellular protists, including free-living amoebae. Indeed, mycobacteria are isolated from the same soil and water environments as are amoebae, and experimental models using Acanthamoeba spp. and Dictyostelium discoideum were exploited to analyse the mechanisms for intracellular survival. Most of these mechanisms have been further reproduced in macrophages for mycobacteria regarded as opportunistic and obligate pathogens. Amoebal cysts may protect intracellular mycobacteria against adverse conditions and may act as a vector for mycobacteria. The latter hypothesis warrants further environmental and clinical studies to better assess the role of free-living amoebae in the epidemiology of infections caused by mycobacteria.

Sasaki, A. T. and R. A. Firtel (2009). "Spatiotemporal Regulation of Ras-GTPases During Chemotaxis." Meth Mol Biol 571: 333-348.
	Many eukaryotic cells can elicit intracellular signaling relays to produce pseudopodia and move up to the chemoattractant gradient (chemotaxis) or move randomly in the absence of extracellular stimuli and nutrients (random movement). A precise spatiotemporal regulation of Ras-GTPases, such as Ras and Rap, is crucial to induce pseudopodia formation and cellular adhesion during the chemotaxis and random movement. Here, we describe biochemical and real-time imaging methods for using Dictyostelium to understand the signaling events important for chemotaxis and random cell movement. The chapter includes (1) a biochemical method to assess Ras and Rap1 activation in response to chemoattractant, (2) an imaging method to detect endogenous Ras and Rap1 activation in moving cells, and (3) a simultaneous imaging method to decipher the precise order and localization of these signaling events. With a combination of powerful Dictyostelium genetics, these methods will facilitate to elucidate a dynamic activation of Ras proteins and their inter relay with other signaling molecules during chemotaxis and random movement.

Sato, M. J., H. Kuwayama, et al. (2009). "Switching direction in electric-signal-induced cell migration by cyclic guanosine monophosphate and phosphatidylinositol signaling." Proc Natl Acad Sci U S A 106(16): 6667-6672.
	Switching between attractive and repulsive migration in cell movement in response to extracellular guidance cues has been found in various cell types and is an important cellular function for translocation during cellular and developmental processes. Here we show that the preferential direction of migration during electrotaxis in Dictyostelium cells can be reversed by genetically modulating both guanylyl cyclases (GCases) and the cyclic guanosine monophosphate (cGMP)-binding protein C (GbpC) in combination with the inhibition of phosphatidylinositol-3-OH kinases (PI3Ks). The PI3K-dependent pathway is involved in cathode-directed migration under a direct-current electric field. The catalytic domains of soluble GCase (sGC) and GbpC also mediate cathode-directed signaling via cGMP, whereas the N-terminal domain of sGC mediates anode-directed signaling in conjunction with both the inhibition of PI3Ks and cGMP production. These observations provide an identification of the genes required for directional switching in electrotaxis and suggest that a parallel processing of electric signals, in which multiple-signaling pathways act to bias cell movement toward the cathode or anode, is used to determine the direction of migration.

Sawarkar, R., S. S. Visweswariah, et al. (2009). "Histone deacetylases regulate multicellular development in the social amoeba Dictyostelium discoideum." J Mol Biol 391(5): 833-848.
	Epigenetic modifications of histones regulate gene expression and lead to the establishment and maintenance of cellular phenotypes during development. Histone acetylation depends on a balance between the activities of histone acetyltransferases and histone deacetylases (HDACs) and influences transcriptional regulation. In this study, we analyse the roles of HDACs during growth and development of one of the cellular slime moulds, the social amoeba Dictyostelium discoideum. The inhibition of HDAC activity by trichostatin A results in histone hyperacetylation and a delay in cell aggregation and differentiation. Cyclic AMP oscillations are normal in starved amoebae treated with trichostatin A but the expression of a subset of cAMP-regulated genes is delayed. Bioinformatic analysis indicates that there are four genes encoding putative HDACs in D. discoideum. Using biochemical, genetic and developmental approaches, we demonstrate that one of these four genes, hdaB, is dispensable for growth and development under laboratory conditions. A knockout of the hdaB gene results in a social context-dependent phenotype: hdaB(-) cells develop normally but sporulate less efficiently than the wild type in chimeras. We infer that HDAC activity is important for regulating the timing of gene expression during the development of D. discoideum and for defining aspects of the phenotype that mediate social behaviour in genetically heterogeneous groups.

Schiller, B., A. Hykollari, et al. (2009). "Development of Dictyostelium discoideum is associated with alteration of fucosylated N-glycan structures." Biochem J 423(1): 41-52.
	The social amoeba Dictyostelium discoideum has become established as a simple model for the examination of cell-cell interactions, and early studies suggested that shifts in glycosylation profiles take place during its life cycle. In the present study, we have applied HPLC and mass spectrometric methods to show that the major N-glycans in axenic cultures of the AX3 strain are oligomannosidic forms, most of which carry core fucose and/or intersecting and bisecting N-acetylglucosamine residues, including the major structure with the composition Man8GlcNAc4Fuc1. The postulated alpha1,3-linkage of the core fucose correlates with the cross-reactivity of Dictyostelium glycoproteins with a horseradish peroxidase antiserum; a corresponding core alpha1,3-fucosyltransferase activity capable of modifying oligomannosidic N-glycans was detected in axenic Dictyostelium extracts. The presence of fucose on the N-glycans and the reactivity to the antiserum, but not the fucosyltransferase activity, are abolished in the fucose-deficient HL250 strain. In later stages of development, N-glycans at the mound and culmination stages show a reduction in both the size and the degree of modification by intersecting/bisecting residues compared with mid-exponential phase cultures, consistent with the hypothesis that glycosidase and glycosyltransferase expression levels are altered during the slime mould life cycle.

Schmauch, C., S. Claussner, et al. (2009). "Targeting the actin-binding protein VASP to late endosomes induces the formation of giant actin aggregates." Eur J Cell Biol 88(7): 385-396.
	In vitro, the vasodilator-stimulated phosphoprotein (VASP) acts as a regulator of actin filament assembly in many ways. In cells it localizes to sites where actin is rapidly polymerized such as filopodia, lamellipodia, and focal adhesions. We have mistargeted VASP to the surface of the late endosome in Dictyostelium cells thereby inducing the formation of a dense actin aggregate which sequesters various actin-binding proteins and endosomal components. Depletion of these proteins from the cytoplasm leads to phenotypes mimicking the corresponding knockout cells. Some properties of the actin aggregate are reminiscent of Hirano bodies that are often observed in nerve tissue from patients suffering from neurodegenerative diseases, opening the possibility that protein sequestration contributes to neuronal malfunction.

Schroth-Diez, B., S. Gerwig, et al. (2009). "Propagating waves separate two states of actin organization in living cells." HFSP J 3(6): 412-427.
	Propagating actin waves are dynamic supramolecular structures formed by the self-assembly of proteins within living cells. They are built from actin filaments together with single-headed myosin, the Arp23 complex, and coronin in a defined three-dimensional order. The function of these waves in structuring the cell cortex is studied on the substrate-attached surface of Dictyostelium cells by the use of total internal reflection fluorescence (TIRF) microscopy. Actin waves separate two areas of the cell cortex from each other, which are distinguished by the arrangement of actin filaments. The Arp23 complex dominates in the area enclosed by a wave, where it has the capacity of building dendritic structures, while the proteins prevailing in the external area, cortexillin I and myosin-II, bundle actin filaments and arrange them in antiparallel direction. Wave propagation is accompanied by transitions in the state of actin with a preferential period of 5 min. Wave generation is preceded by local fluctuations in actin assembly, some of the nuclei of polymerized actin emanating from clathrin-coated structures, others emerging independently. The dynamics of phase transitions has been analyzed to provide a basis for modeling the nonlinear interactions that produce spatio-temporal patterns in the actin system of living cells.

Schulz, I., O. Baumann, et al. (2009). "Dictyostelium Sun1 is a dynamic membrane protein of both nuclear membranes and required for centrosomal association with clustered centromeres." Eur J Cell Biol 88(11): 621-638.
	Centrosomal attachment to nuclei is crucial for proper mitosis and nuclear positioning in various organisms, and generally involves Sun-family proteins located at the inner nuclear envelope. There is still no common scheme for the outer nuclear membrane proteins interacting with Sun1 in centrosome/nucleus attachment. Here we propose a model in which Sun1 mediates a physical link between centrosomes and clustered centromeres through both nuclear membranes in Dictyostelium. For the first time we provide a detailed microscopic analysis of the centrosomal and nuclear envelope localization of endogenous Dictyostelium Sun1 during interphase and mitosis. By immunogold electron microscopy we show that Sun1 is a resident of both nuclear membranes. Disruption of Sun1 function by overexpression of full-length GFP-Sun1 or a GFP-Sun-domain deletion construct revealed not only the established function in centrosome/nucleus attachment and maintenance of ploidy, but also a requirement of Sun1 for the association of the centromere cluster with the centrosome. Live-cell imaging visualized the occurrence of mitotic defects, and demonstrated the requirement of microtubules for dynamic distance changes between centrosomes and nuclei. FRAP analysis revealed at least two populations of Sun1, with an immobile fraction associated with the centrosome, and a mobile fraction in the nuclear envelope.

Schulz, I., A. Erle, et al. (2009). "Identification and cell cycle-dependent localization of nine novel, genuine centrosomal components in Dictyostelium discoideum." Cell Motil Cytoskeleton 66(11): 915-928.
	The centrosome is the main microtubule-organizing center and constitutes the largest protein complex in a eukaryotic cell. The Dictyostelium centrosome is an established model for acentriolar centrosomes and it consists of a layered core structure surrounded by a so-called corona, which harbors microtubule nucleation complexes. We have identified 34 new centrosomal candidate proteins through mass spectrometrical analysis of the proteome of isolated Dictyostelium centrosomes. Here we present a characterization of 12 centrosomal candidate proteins all featuring coiled coil regions and low expression levels, which are the most common attributes of centrosomal proteins. We used GFP fusion proteins to localize the candidate proteins in whole cells and on microtubule-free, isolated centrosomes. Thus we were able to identify nine new genuine centrosomal proteins including a putative orthologue of Cep192, an interaction partner of polo-like kinase 4 in human centriole biogenesis. In this respect, centrosomal localization of the only polo-like kinase in Dictyostelium, Plk, is also shown in this work. Using confocal deconvolution microscopy, four components, CP39, CP55, CP75, and CP91 could be clearly assigned to the so far almost uncharacterized centrosomal core structure, while CP148 and Cep192 localized to a zone between that of corona marker and core proteins. Finally, CP103 and CP248 were constituents of the corona. In contrast, NE81 was localized at the nuclear envelope and three others, an orthologue of the spindle checkpoint component Mad1, the novel Cenp68, and the centrosomal CP248 were observed at the centromeres, which are clustered and linked to the centrosome throughout the entire cell cycle. Cell Motil. Cytoskeleton 2009. (c) 2009 Wiley-Liss, Inc.

Schulz, I., A. Erle, et al. (2009). Cell cycle-dependent localization of novel centrosomal and centromeric proteins in Dictyostelium. Eur J Cell Biol, Konstanz.
	In Dictyostelium the centrosome consists of a layered core
structure surrounded by a so-called corona, which harbors
microtubule nucleation complexes. We used GFP fusion
proteins to localize novel centrosomal candidate proteins
previously identified in a proteomic screen in whole cells
and at microtubule-free, isolated centrosomes. We were
able to verify eight new proteins including a putative
orthologue of Cep192 as genuine centrosomal
components. Four components, DdCP39, DdCP55,
DdCP75 and DdCP91 could be clearly assigned to the
almost uncharacterized centrosomal core structure. By
contrast, DdCP148 and DdCep192 localized to a zone
between that of corona marker and core proteins.
Overexpression of DdCP39, DdCP75, DdCP91 and
DdCep192 resulted in centrosome amplification
suggesting a function of these proteins in centrosome
biogenesis. DdCP39, DdCP75, DdCP91 and DdCP148
exhibited a cell cycle-dependent localization. These
proteins disappeared from the spindle poles during
mitosis. Two further proteins, an orthologue of the spindle
checkpoint component Mad1 and the novel DdCenp68,
were observed at the centromeres, which are clustered
and tightly linked to the centrosome during the entire cell
cycle. Live cell imaging revealed that GFP-Mad1 appears
at centromeres in late G2 and starts to disappear in
metaphase, while GFP-DdCenp68 is a permanent
centromeric resident.

Shanina, N. A., E. M. Lazareva, et al. (2009). "A high molecular weight polypeptide cross-reacting with the antibodies to the dynein heavy chain localizes to the subset of Golgi complex in higher plant cells." Cell Biol Int 33(3): 290-300.
	Antibodies were produced against fragments of the microtubule-binding domain and the motor domain of the dynein heavy chain from Dictyostelium discoideum to probe whole cell extracts of root meristem cells of wheat Triticum aestivum. In plant extracts, these antibodies cross-reacted with a polypeptide of high molecular weight (>500kDa). The antibodies bound to protein A-Sepharose precipitated high molecular weight polypeptide from cell extracts. Immunofluorescence showed that the antibodies identified various aggregates inside cells, localized at the perinuclear area during interphase to early prophase, at the spindle periphery and polar area during mitosis, and in the interzonal region during phragmoplast development. Some aggregates were also co-labeled by markers for the Golgi apparatus. Thus, we found in higher plant cells a high molecular weight antigen cross-reacting with the antibodies to motor and microtubule-binding domains of dynein heavy chains. This antigen is associated with aggregates distributed in the cytoplasm in cell cycle-dependent manner. A subset of these aggregates belongs to the Golgi complex.

Shemarova, I. V. (2009). "cAMP-dependent signal pathways in unicellular eukaryotes." Crit Rev Microbiol 35(1): 23-42.
	The review summarizes current data about mechanisms of signal transduction with participation of cAMP (cyclic adenosine monophosphate) and elements of the complex cAMP-protein kinase A (PKA) signal pathway in unicellular eukaryotes. Conceptions of evolutionary origin of eukaryotic signal transduction systems are developed.

Shevchuk, O., C. Batzilla, et al. (2009). "Proteomic analysis of Legionella-containing phagosomes isolated from Dictyostelium." Int J Med Microbiol 299(7): 489-508.
	Legionella pneumophila, the agent of Legionnaires' disease, replicates intracellularly within specialized phagosomes of human macrophages and amoebae. In this study, we have developed a protocol for the isolation of Legionella-containing phagosomes from Dictyostelium discoideum. Cell fractionation, two-dimensional gel electrophoresis and MALDI-TOF MS combined with genomic data identified 157 phagosome host proteins. In addition to proteins with an evident role in phagosome maturation, we identified proteins for which a function remains to be elucidated. Possible interactions of coronin with cytosolic NADPH oxidase components and protein kinase C inhibitors which together may lead to an inhibition of phagosomal superoxide generation are discussed. Comparative proteomics of phagosomes containing highly virulent L. pneumophila Corby versus less virulent L. hackeliae revealed distinctive protein expression patterns, e.g., an abundance of RhoGDI in L. hackeliae degrading phagosomes versus little RhoGDI in L. pneumophila Corby replicative phagosomes. We present a kinetic dissection of phagosome maturation including the complex alterations of the phagosome protein composition. A reference flow chart suggests so far unrecognized consequences of infection for host cell physiology, actin degradation on phagosomes, and a putative cysteine proteinase inhibitor interference with lysosomal enzyme sorting and activation processes.

Shevchuk, O. and M. Steinert (2009). "Screening of virulence traits in Legionella pneumophila and analysis of the host susceptibility to infection by using the Dictyostelium host model system." Meth Mol Biol 470: 47-56.
	The social soil amoeba Dictyostelium discoideum has been established as a host model for several human pathogens including Legionella pneumophila. The complete genome sequence, the genetic tractability, and the phagocytic characteristics of Dictyostelium generate many opportunities for the study of host-pathogen interactions. Important applications of this haploid model organism are (i) the use of Dictyostelium cells as a screening system for bacterial virulence, (ii) the use of Dictyostelium mutant cells to identify genetic host determinants of susceptibility and resistance to infection, and (iii) experiments that allow the dissection of the complex cross-talk with infectious agents. Accordingly, this chapter describes a plaque assay to identify attenuated pathogens, an infection assay for the analysis of host cell mutants and pathogens, and a screening method for the isolation of Legionella mutants that are defective in the reprogramming of the phagolysosomal maturation of the host.

Shimizu, K., T. Murata, et al. (2009). "Characterization of phosphodiesterase 1 in human malignant melanoma cell lines." Anticancer Res 29(4): 1119-1122.
	BACKGROUND: Differentiation-inducing factor 1 [DIF-1; 1-(3,5-dichloro-2,6-dihydroxy-4-methoxyphenyl) hexan-1-one] from Dictyostelium discoideum exhibits antiproliferative activity in mammalian cells. We have previously shown that phosphodiesterase 1 (PDE1) is a pharmacological target of DIF-1, but there are no reports of PDE1 in human malignant melanoma cells. Therefore, we characterized PDE1 in human malignant melanoma MAA cells. MATERIALS AND METHODS: PDE1 mRNA expression was investigated in MAA cells. The full open reading frames for human PDE1C1 and PDE1C3 were cloned. Cell growth was determined by MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tet razolium, inner salt] assay. RESULTS: PDE1C mRNA expression was detected in MAA cells. The nucleotide sequence of PDE1C1 was identical to that of human PDE1C1, previously published. At nucleotide 2246 in PDE1C3, A was replaced by G, but this did not change the encoded amino acid. Cell growth was inhibited by the PDE1 inhibitor vinpocetin. CONCLUSION: PDE1C mRNA is expressed and may play an important role in human malignant melanoma MAA cells.

Shkilnyy, A., R. Graf, et al. (2009). "Unprecedented, low cytotoxicity of spongelike calcium phosphate/poly(ethylene imine) hydrogel composites." Macromol Biosci 9(2): 179-186.
	Covalently crosslinked PEI hydrogels are efficient templates for calcium phosphate mineralization in SBF. In contrast to the PEI hydrogels, non-crosslinked PEI does not lead to calcium phosphate nucleation and growth in SBF. The precipitate is a mixture of brushite and hydroxyapatite. The PEI/calcium phosphate composite material exhibits a sponge like morphology and a chemical composition that is interesting for implants. Cytotoxicity tests using Dictyostelium discoideum amoebae show that both the non-mineralized and mineralized hydrogels have a very low cytotoxicity. This suggests that next generation PEI hydrogels, where also the degradation products are non-toxic, could be interesting for biomedical applications.

Skoge, M. (2009). Receptor-receptor interactions in gradient sensing. United States -- New Jersey, Princeton University: 149.
	The ability to detect and process chemical signals is one of the most ancient and widespread biological functions. Underlying this ability are membrane-bound receptors that specifically bind the signaling molecule and undergo conformational, dynamical and/or organizational changes to transduce the signal to intracellular biochemical networks. We study both theoretically and experimentally the roles of cooperative interactions and spatial organization of receptors in signal transduction, focusing on chemotaxis receptors, whose function is to infer chemical gradients. We study two very different model organisms, namely the bacterium, Escherichia coli , and the social ameoba, Dictyostelium discoideum (Dicty), which are both remarkably sensitive to chemical gradients over a wide range of background concentration. We extend a two-state model of E. coli chemotaxis receptors to include cooperative interactions among receptors and use recent experimental data to infer their topological organization. We study two proposed microscopic models of cooperativity among receptors: a large extended lattice of weakly-coupled receptors as described by the high-temperature Ising model, and an ensemble of small strongly-coupled clusters as described by the Monod-Wyman-Changeaux (MWC) model, and show that current experimental data supports the MWC model of receptor coupling. We also show that in any physical model, receptor-receptor interactions greatly increase the conformational switching time of a receptor cluster, which negatively affects its signal-processing capabilities. We explicitly calculate the signal-to-noise ratio for coupled two-state receptors with a constrained averaging time, taking into account both intrinsic and extrinsic sources of noise, and determine the optimal cluster size and coupling strength. We then experimentally probe the organization of chemotaxis receptors in Dicty. We discuss the evidence suggesting the receptors exhibit complex dynamics and use fluorescence resonance energy transfer to look for interactions among receptors in living cells. Our results do not show any evidence for direct physical interactions or clustering among the chemotaxis receptors in this system. Finally, we end with a diversion from the theme of receptor signal transduction, and study a model many-body system, hard spheres. We present the first study of disordered jammed packings of hard spheres in four, five and six dimensions using collision-driven molecular dynamics, and show that short-range ordering appreciably decreases with increasing dimension.

Soll, D. R., D. Wessels, et al. (2009). "How a cell crawls and the role of cortical myosin II." Euk Cell 8(9): 1381-1396.
	The movements of Dictyostelium discoideum amoebae translocating on a glass surface in the absence of chemoattractant have been reconstructed at 5-second intervals and motion analyzed by employing 3D-DIAS software. A morphometric analysis of pseudopods, the main cell body, and the uropod provides a comprehensive description of the basic motile behavior of a cell in four dimensions (4D), resulting in a list of 18 characteristics. A similar analysis of the myosin II phosphorylation mutant 3XASP reveals a role for the cortical localization of myosin II in the suppression of lateral pseudopods, formation of the uropod, cytoplasmic distribution of cytoplasm in the main cell body, and efficient motility. The results of the morphometric analysis suggest that pseudopods, the main cell body, and the uropod represent three motility compartments that are coordinated for efficient translocation. It provides a contextual framework for interpreting the effects of mutations, inhibitors, and chemoattractants on the basic motile behavior of D. discoideum. The generality of the characteristics of the basic motile behavior of D. discoideum must now be tested by similar 4D analyses of the motility of amoeboid cells of higher eukaryotic cells, in particular human polymorphonuclear leukocytes.

Soppina, V., A. Rai, et al. (2009). "Simple non-fluorescent polarity labeling of microtubules for molecular motor assays." Biotechniques 46(7): 543-549.
	Transport of intracellular organelles along the microtubule cytoskeleton occurs in a bidirectional manner due to opposing activity of microtubule-associated motor proteins of the kinesin and dynein families. Regulation of this opposing activity and the resultant motion is believed to generate a polarized distribution of many organelles within the cell. The bidirectional motion can be reconstituted on in vitro assembled microtubules using organelles extracted from cells. This provides an opportunity to understand the regulation of intracellular transport through quantitative analysis of the motion of organelles in a controlled environment. Such analysis requires the use of polarity-labeled microtubules to resolve the plus and minus components of bidirectional motion. However, existing methods of in vitro microtubule polarity labeling are unsuitable for high-resolution recording of motion. Here we present a simple and reliable method that uses avidin-coated magnetic beads to prepare microtubules labeled at the minus end. The microtubule polarity can be identified without any need for fluorescence excitation. We demonstrate video-rate high-resolution imaging of single cellular organelles moving along plus and minus directions on labeled microtubules. Quantitative analysis of this motion indicates that these organelles are likely to be driven by multiple dynein motors in vivo.

Soppina, V., A. K. Rai, et al. (2009). "Tug-of-war between dissimilar teams of microtubule motors regulates transport and fission of endosomes." Proc Natl Acad Sci U S A.
	Intracellular transport is interspersed with frequent reversals in direction due to the presence of opposing kinesin and dynein motors on organelles that are carried as cargo. The cause and the mechanism of reversals are unknown, but are a key to understanding how cargos are delivered in a regulated manner to specific cellular locations. Unlike established single-motor biophysical assays, this problem requires understanding of the cooperative behavior of multiple interacting motors. Here we present measurements inside live Dictyostelium cells, in a cell extract and with purified motors to quantify such an ensemble function of motors. We show through precise motion analysis that reversals during endosome motion are caused by a tug-of-war between kinesin and dynein. Further, we use a combination of optical trap-based force measurements and Monte Carlo simulations to make the surprising discovery that endosome transport uses many (approximately four to eight) weak and detachment-prone dyneins in a tug-of-war against a single strong and tenacious kinesin. We elucidate how this clever choice of dissimilar motors and motor teams achieves net transport together with endosome fission, both of which are important in controlling the balance of endocytic sorting. To the best of our knowledge, this is a unique demonstration that dynein and kinesin function differently at the molecular level inside cells and of how this difference is used in a specific cellular process, namely endosome biogenesis. Our work may provide a platform to understand intracellular transport of a variety of organelles in terms of measurable quantities.

Sriskanthadevan, S., T. Lee, et al. (2009). "The cell adhesion molecule DdCAD-1 is imported into contractile vacuoles by membrane invagination in a Ca2+- and conformation-dependent manner." J Biol Chem.
	The cadA gene in Dictyostelium encodes a Ca2+-dependent cell adhesion molecule DdCAD-1 which contains two beta-sandwich domains. DdCAD-1 is synthesized in the cytoplasm as a soluble protein and then transported by contractile vacuoles to the plasma membrane for surface presentation or secretion. DdCAD-1-GFP3 fusion protein was expressed in cadA-null cells for further investigation of this unconventional protein transport pathway. Both morphological and biochemical characterizations showed that DdCAD-1-GFP was imported into contractile vacuoles. Time-lapse microscopy of transfectants revealed the transient appearance of DdCAD-1-GFP-filled vesicular structures in the lumen of contractile vacuoles, suggesting that DdCAD-1 could be imported by invagination of contractile vacuole membrane. To assess the structural requirements in this transport process, the N-terminal and C-terminal domains of DdCAD-1 were expressed separately in cells as GFP-fusion proteins. Both fusion proteins failed to enter the contractile vacuole, suggesting that the integrity of DdCAD-1 is required for import. Such a requirement was also observed in in vitro reconstitution assays using His6-tagged fusion proteins and purified contractile vacuoles. Import of DdCAD-1 was compromised when two of its three Ca2+-binding sites were mutated, indicating a role for Ca2+ in the import process. Spectral analysis showed that mutations in the Ca2+-binding sites resulted in subtle conformational changes. Indeed, proteins with altered conformation failed to enter the contractile vacuole, suggesting that the import signal is somehow integrated in the three-dimensional structure of DdCAD-1.

Sultana, H., G. Neelakanta, et al. (2009). "Microarray phenotyping places cyclase associated protein CAP at the crossroad of signaling pathways reorganizing the actin cytoskeleton in Dictyostelium." Exp Cell Res 315(2): 127-140.
	Large-scale gene expression analysis has been applied recently to uncover groups of genes that are co-regulated in particular processes. Here we undertake such an analysis on CAP, a protein that participates in the regulation of the actin cytoskeleton and in cAMP signaling in Dictyostelium. microarray analysis revealed that loss of CAP altered the expression of many cytoskeletal components. One of these, the Rho GDP-dissociation inhibitor RhoGDI1, was analyzed further. RhoGDI1 null cells expressed lower amounts of CAP, which failed to accumulate predominantly at the cell cortex. To further position CAP in the corresponding signal transduction pathways we studied CAP localization and cellular functioning in mutants that have defects in several signaling components. CAP showed correct localization and dynamics in all analyzed strains except in mutants with deficient cAMP dependent protein kinase A activity, where CAP preferentially accumulated in crown shaped structures. Ectopic expression of CAP improved the efficiency of phagocytosis in Gbeta-deficient cells and restored the pinocytosis, morphology and actin distribution defects in a PI3 kinase double mutant (pi3k1/2 null). Our results show that CAP acts at multiple crossroads and links signaling pathways to the actin cytoskeleton either by physical interaction with cytoskeletal components or through regulation of their gene expression.

Swarbrick, J. D., L. Cubeddu, et al. (2009). "NMR assignment of prespore specific antigen--a cell surface adhesion glycoprotein from Dictyostelium discoideum." Biomol NMR Assign 3(1): 1-3.
	Presopore-specific antigen (PsA) is a cell surface glycoprotein of the cellular slime mould Dictyostelium discoidum implicated in cell adhesion. The (15)N, (13)C and (1)H chemical shift assignments of PsA were determined from multidimensional, multinuclear NMR experiments. Resonance assignments have been made for both the N-terminal globular domain and its attached O-glycosylated PTVT linker motif.

Szabo, Z. B., H. Mihaly, et al. (2009). "Synthesis of three regioisomers of the pentasaccharide part of the Skp1 glycoprotein of Dictyostelium discoideum." Tetrahedron-Asymmetry 20(6-8): 808-820.
	Three regioisomers of the linear pentasaccharide part of the Skp1 glycoprotein, found in Dictyostelium discorideum, were prepared in the form of (2-trimethylsilyl)ethyl glycosides by means of 2+3 block syntheses using the disaccharide donor at the non-reducing end, and three different trisaccharide acceptors at the reducing end. Fucosylation of (2-trimethylsilyl)ethyl 3,4,6-tri-O-benzyl-beta-D-galactopyranosyl-(1 -> 3)-4,6-O-benzylidene-2-deoxy-2-NPhth-beta-D-glucopyranoside with different fucosyl donors carrying an O-(2-naphthyl)methyl ether as a temporary-protecting group at positions C2, C3 or C4 gave rise to the protected core trisaccharides. After selective removal of the (2-naphthyl)methyl group, the resulting acceptors were glycosylated with the alpha(1 -> 6) linked digalactosyl donor to yield the respective three regioisomeric pentasaccharides. Transformation of the phthalimido moiety into an N-acetyl group, followed by catalytic hydrogenation of the reducible-protecting groups furnished the free target pentasaccharides, which should be able to assist during the elucidation of the exact structure of the natural pentasaccharide. (C) 2009 Elsevier Ltd. All rights reserved.

Takahashi, K., M. Murakami, et al. (2009). "Regulation of IL-2 production in Jurkat cells by Dictyostelium-derived factors." Life Sci 85(11-12): 438-443.
	AIMS: Differentiation-inducing factors (DIFs) are chlorinated alkylphenones found in the cellular slime mold Dictyostelium discoideum. DIF derivatives exhibit antiproliferative activities and promote glucose consumption in mammalian cells in vitro. In this study, we assessed the ability of DIFs to regulate the immune system and investigated their mechanisms of action. MAIN METHODS: We examined the effects of 30 DIF derivatives on concanavalin A-induced IL-2 production (CIIP) in Jurkat T-cells. We also examined the effects of some DIF derivatives on the activity of AP-1 (activator protein-1), NFAT (nuclear factor of activated T-cells), and NFkappaB (nuclear factor kappa B), which are transcription factors required for CIIP. KEY FINDINGS: Of the derivatives tested, some compounds suppressed CIIP as well as the known immunosuppressants cyclosporine A and FK506. A reporter gene assay revealed that 4 DIF derivatives tested suppressed CIIP, at least in part, by inhibiting the activity of AP-1, NFAT, and/or NFkappaB. Unlike cyclosporine A and FK506, the DIF derivatives had little effect on concanavalin A-induced interferon-gamma production in Jurkat cells. SIGNIFICANCE: The present results suggest that DIF derivatives could be developed as novel immunosuppressive drugs.

Takahashi-Yanaga, F. and T. Sasaguri (2009). "Drug development targeting the glycogen synthase kinase-3beta (GSK-3beta)-mediated signal transduction pathway: inhibitors of the Wnt/beta-catenin signaling pathway as novel anticancer drugs." J Pharmacol Sci 109(2): 179-183.
	Accumulating evidence suggests that the Wnt/beta-catenin signaling pathway is often involved in oncogenesis and cancer development. Accordingly, a novel anticancer drug can be developed using inhibitors of this pathway. However, at present, there is no selective inhibitor of this pathway available as a therapeutic agent. Although all the components of the Wnt/beta-catenin signaling pathway can be a target for drug development, glycogen synthase kinase-3beta (GSK-3beta), in particular, may be a good target because GSK-3beta is an essential component of the pathway, and activation of this kinase results in the inhibition of the Wnt signaling pathway. We found that the differentiation-inducing factors (DIFs), putative morphogens for Dictyostelium discoideum, inhibit the Wnt/beta-catenin signaling pathway via the activation of GSK-3beta, resulting in the cell-cycle arrest of human cancer cell lines. In this review, we summarize our recent findings on the antiproliferative effect of DIFs and show the possibility for development of a novel anticancer drug from DIFs and their derivatives.

Tikhonenko, I., D. K. Nag, et al. (2009). "Microtubule-nucleus interactions in Dictyostelium discoideum mediated by central motor kinesins." Euk Cell 8(5): 723-731.
	Kinesins are a diverse superfamily of motor proteins that drive organelles and other microtubule-based movements in eukaryotic cells. These motors play important roles in multiple events during both interphase and cell division. Dictyostelium discoideum contains 13 kinesin motors, 12 of which are grouped into nine families, plus one orphan. Functions for 11 of the 13 motors have been previously investigated; we address here the activities of the two remaining kinesins, both isoforms with central motor domains. Kif6 (of the kinesin-13 family) appears to be essential for cell viability. The partial knockdown of Kif6 with RNA interference generates mitotic defects (lagging chromosomes and aberrant spindle assemblies) that are consistent with kinesin-13 disruptions in other organisms. However, the orphan motor Kif9 participates in a completely novel kinesin activity, one that maintains a connection between the microtubule-organizing center (MTOC) and nucleus during interphase. kif9 null cell growth is impaired, and the MTOC appears to disconnect from its normally tight nuclear linkage. Mitotic spindles elongate in a normal fashion in kif9(-) cells, but we hypothesize that this kinesin is important for positioning the MTOC into the nuclear envelope during prophase. This function would be significant for the early steps of cell division and also may play a role in regulating centrosome replication.

Tinsley, M. R., A. F. Taylor, et al. (2009). "Emergence of collective behavior in groups of excitable catalyst-loaded particles: spatiotemporal dynamical quorum sensing." Phys Rev Lett 102(15): 158301.
	Spontaneous spatiotemporal wave activity occurs in groups of excitable particles for groups larger than a critical size. Experiments are carried out with particles loaded with the catalyst of the Belousov-Zhabotinsky reaction that are immersed in catalyst-free reaction mixture. The particles diffusively exchange activator and inhibitor species with the surrounding solution. All particles are nonoscillatory when separated from the other particles; however, target and spiral waves are exhibited in sufficiently large groups. A cellular particle model of the system also exhibits transitions from excitable steady state behavior to spatiotemporal wave activity with increasing group size.

Tokuraku, K., R. Kurogi, et al. (2009). "Novel mode of cooperative binding between myosin and Mg2+ -actin filaments in the presence of low concentrations of ATP." J Mol Biol 386(1): 149-162.
	Cooperative interaction between myosin and actin filaments has been detected by a number of different methods, and has been suggested to have some role in force generation by the actomyosin motor. In this study, we observed the binding of myosin to actin filaments directly using fluorescence microscopy to analyze the mechanism of the cooperative interaction in more detail. For this purpose, we prepared fluorescently labeled heavy meromyosin (HMM) of rabbit skeletal muscle myosin and Dictyostelium myosin II. Both types of HMMs formed fluorescent clusters along actin filaments when added at substoichiometric amounts. Quantitative analysis of the fluorescence intensity of the HMM clusters revealed that there are two distinct types of cooperative binding. The stronger form was observed along Ca(2+)-actin filaments with substoichiometric amounts of bound phalloidin, in which the density of HMM molecules in the clusters was comparable to full decoration. The novel, weaker form was observed along Mg(2+)-actin filaments with and without stoichiometric amounts of phalloidin. HMM density in the clusters of the weaker form was several-fold lower than full decoration. The weak cooperative binding required sub-micromolar ATP, and did not occur in the absence of nucleotides or in the presence of ADP and ADP-Vi. The G680V mutant of Dictyostelium HMM, which over-occupies the ADP-Pi bound state in the presence of actin filaments and ATP, also formed clusters along Mg(2+)-actin filaments, suggesting that the weak cooperative binding of HMM to actin filaments occurs or initiates at an intermediate state of the actomyosin-ADP-Pi complex other than that attained by adding ADP-Vi.

Underwood, J. (2009). An analysis of the mechanism of Dictyostelium myosin heavy chain kinase B in substrate targeting. United States -- North Carolina, The University of North Carolina at Greensboro: 49.
	Previous studies have shown that myosin heavy chain kinase A and B (MHKA and MHKB) are able to phosphorylate and disassemble Dictyostelium discoideum myosin II bipolar filaments by directly targeting myosin II via a conserved region of WD repeats, also referred to as the WD repeat domain. MHKA lacking this domain is unable to phosphorylate myosin II. By comparison, MHKB lacking this same domain is able to phosphorylate myosin II, albeit at a significantly reduced level compared to the full-length protein. The main difference between the MHKA and MHKB proteins is the presence of a region of MHKB in which the amino acid asparagine is repeated 25 times, called the asparagine-rich (pN) region. The function of this region has not been well studied. The research described in this thesis focuses on the asparagine-rich and WD repeat domains of MHKB and their roles in targeting myosin II for phosphorylation. My studies revealed that overexpressing full-length MHKB in Dictyostelium cells resulted in slowed growth rates due to cytokinesis defects in which cells become large and multinucleated. MHKB lacking the WD repeat domain (MHKB-”WD) also showed this large multinucleated phenotype and slowed growth rate. However, cells overexpressing a truncation of MHKB lacking both the WD and pN regions (MHKB-”pN-WD) grew normally and did not become multi-nucleated; indicating that the WD repeat domain is not the only targeting region of MHKB. Triton X-100 cytoskeleton fractionation assays revealed that cells overexpressing full-length MHKB or MHKB-”WD have more myosin II in the cytosol than in the cytoskeleton, which is indicative of myosin II being phosphorylated and disassembled by these two versions of MHKB. By contrast, the myosin II in cells overexpressing the MHKB-”pN-WD truncation was located primarily in the cytoskeletal fraction, suggesting that the poly-asparagine region of MHKB may be involved in targeting the kinase to phosphorylate myosin II heavy chain (MHC). Biochemical assays of kinase activity toward myosin II substrate revealed that while full-length MHKB and the MHKB-”WD truncation were able to phosphorylate myosin II, the activity of the MHKB-”pN-WD truncation toward myosin II substrate was below the limits of detection. This is despite the fact that all three versions of the kinase phosphorylate a peptide substrate to essentially the same level. In summary, MHKB has two major regions involved in targeting myosin II for phosphorylation. The WD-repeat domain is known to directly target myosin II, but is not necessary for the kinase to function. My studies of this system have revealed that the pN region, in combination with the WD-repeat domain, is necessary for MHKB to target myosin II for phosphorylation.

Urushihara, H. (2009). "The cellular slime mold: eukaryotic model microorganism." Exp Anim 58(2): 97-104.
	Cellular slime molds are eukaryotic microorganisms in the soil. They feed on bacteria as solitary amoebae but conditionally construct multicellular forms in which cell differentiation takes place. Therefore, they are attractive for the study of fundamental biological phenomena such as phagocytosis, cell division, chemotactic movements, intercellular communication, cell differentiation, and morphogenesis. The most widely used species, Dictyostelium discoideum, is highly amenable to experimental manipulation and can be used with most recent molecular biological techniques. Its genome and cDNA analyses have been completed and well-annotated data are publicly available. A larger number of orthologues of human disease-related genes were found in D. discoideum than in yeast. Moreover, some pathogenic bacteria infect Dictyostelium amoebae. Thus, this microorganism can also offer a good experimental system for biomedical research. The resources of cellular slime molds, standard strains, mutants, and genes are maintained and distributed upon request by the core center of the National BioResource Project (NBRP-nenkin) to support Dictyostelium community users as well as new users interested in new platforms for research and/or phylogenic consideration.

Urwyler, S., Y. Nyfeler, et al. (2009). "Proteome analysis of Legionella vacuoles purified by magnetic immunoseparation reveals secretory and endosomal GTPases." Traffic 10(1): 76-87.
	Legionella pneumophila, the causative agent of Legionnaires' disease, replicates in macrophages and amoebae within 'Legionella-containing vacuoles' (LCVs), which communicate with the early secretory pathway and the endoplasmic reticulum. Formation of LCVs requires the bacterial Icm/Dot type IV secretion system. The Icm/Dot-translocated effector protein SidC selectively anchors to LCVs by binding the host lipid phosphatidylinositol-4-phosphate (PtdIns(4)P). Here, we describe a novel and simple approach to purify intact vacuoles formed by L. pneumophila within Dictyostelium discoideum by using magnetic immunoseparation with an antibody against SidC, followed by density gradient centrifugation. To monitor LCV purification by fluorescence microscopy, we used Dictyostelium producing the LCV marker calnexin-GFP and L. pneumophila labeled with the red fluorescent protein DsRed. A proteome analysis of purified LCVs by liquid chromatography coupled to tandem mass spectrometry revealed 566 host proteins, including known LCV components, such as the small GTPases Arf1, Rab1 and Rab7. Rab8, an endosomal regulator of the late secretory pathway originating from the trans Golgi network, and the endosomal GTPase Rab14 were identified as novel LCV components, which were found to be present on vacuoles harboring wild-type but not Icm/Dot-deficient L. pneumophila. Thus, LCVs also communicate with the late secretory and endosomal pathways. Depletion of Rab8 or Arf1 by RNA interference reduced the amount of SidC on LCVs, indicating that the GTPases promote the recruitment of Legionella effectors by regulating the level of PtdIns(4)P.

Valeyev, N. V., J. S. Kim, et al. (2009). "Computational modelling suggests dynamic interactions between Ca2+, IP3 and G protein-coupled modules are key to robust Dictyostelium aggregation." Mol Biosyst 5(6): 612-628.
	Under conditions of starvation, Dictyostelium cells begin a programme of development during which they aggregate to form a multicellular structure by chemotaxis, guided by propagating waves of cyclic AMP that are relayed robustly from cell to cell. In this paper, we develop and analyse a new model for the intracellular and extracellular cAMP dependent processes that regulate Dictyostelium migration. The model allows, for the first time, a quantitative analysis of the dynamic interactions between calcium, IP(3) and G protein-dependent modules that are shown to be key to the generation of robust cAMP oscillations in Dictyostelium cells. The model provides a mechanistic explanation for the transient increase in cytosolic free Ca(2+) concentration seen in recent experiments with the application of the calmodulin inhibitor calmidazolium (R24571) to Dictyostelium cells, and also allows elucidation of the effects of varying both the conductivity of stretch-activated channels and the concentration of external phosphodiesterase on the oscillatory regime of an individual cell. A rigorous analysis of the robustness of the new model shows that interactions between the different modules significantly reduce the sensitivity of the resulting cAMP oscillations to variations in the kinetics of different Dictyostelium cells, an essential requirement for the generation of the spatially and temporally synchronised chemoattractant cAMP waves that guide Dictyostelium aggregation.

Van Haastert, P. J. and L. Bosgraaf (2009). "Food searching strategy of amoeboid cells by starvation induced run length extension." PLoS One 4(8): e6814.
	Food searching strategies of animals are key to their success in heterogeneous environments. The optimal search strategy may include specialized random walks such as Levy walks with heavy power-law tail distributions, or persistent walks with preferred movement in a similar direction. We have investigated the movement of the soil amoebae Dictyostelium searching for food. Dictyostelium cells move by extending pseudopodia, either in the direction of the previous pseudopod (persistent step) or in a different direction (turn). The analysis of approximately 4000 pseudopodia reveals that step and turn pseudopodia are drawn from a probability distribution that is determined by cGMP/PLA2 signaling pathways. Starvation activates these pathways thereby suppressing turns and inducing steps. As a consequence, starved cells make very long nearly straight runs and disperse over approximately 30-fold larger areas, without extending more or larger pseudopodia than vegetative cells. This 'win-stay/lose-shift' strategy for food searching is called Starvation Induced Run-length Extension. The SIRE walk explains very well the observed differences in search behavior between fed and starving organisms such as bumble-bees, flower bug, hoverfly and zooplankton.

Van Haastert, P. J. M. and L. Bosgraaf (2009). "The local cell curvature guides pseudopodia towards chemoattractants." Hfsp Journal 3(4): 282-286.
	Many eukaryotic cells use pseudopodia for movement towards chemoattractants. We developed a computer algorithm to identify pseudopodia, and analyzed how pseudopodia of Dictyostelium cells are guided toward cAMP. Surprisingly, the direction of a pseudopod is not actively oriented toward the gradient, but is always perpendicular to the local cell curvature. The gradient induces a bias in the position where the pseudopod emerges: pseudopodia more likely emerge at the side of the cell closer to the gradient where perpendicular pseudopodia are pointed automatically toward the chemoattractant. A mutant lacking the formin dDia2 is not spherical but has many invaginations. Although pseudopodia still emerge at the side closer to the gradient, the surface curvature is so irregular that many pseudopodia are not extended toward cAMP. The results imply that the direction of the pseudopod extension, and therefore also the direction of cell movement, is dominated by two aspects: the position at the cell surface where a pseudopod emerges, and the local curvature of the membrane at that position. [DOI: 10.2976/1.3185725]

Vanag, V. K. and I. R. Epstein (2009). "Pattern formation mechanisms in reaction-diffusion systems." Int J Dev Biol 53(5-6): 673-681.
	In systems undergoing chemical reaction and diffusion, a remarkable variety of spatially structured patterns, stationary or moving, local or global, can arise, many of them reminiscent of forms and phenomena seen in living systems. Chemical systems offer the advantage that one can often control the parameters that determine the patterns formed and can thereby probe fundamental issues about pattern formation, with possible insights into biologically relevant phenomena. We present experimental examples and discuss several mechanisms by which such spatiotemporal structure may arise, classifying the mechanisms according to the type of instability that results in pattern formation. In some systems, the pattern that emerges depends not only on the chemical and physical parameters but also on the initial state of the system. Interactions between instabilities can result in particularly complex patterns.

Vats, B. and H. Padh (2009). "DNA passage to nuclei: role of endo-lysosomal circuit in eukaryotic Dictyostelium." Can J Microbiol 55(5): 617-621.
	The understanding of DNA passage in eukaryotic cells is still very ambiguous. The route to the nucleus is difficult owing to the barriers, metabolic as well as membranous, posed by the eukaryotic cells. Endocytosis appears to be the most likely process responsible for the transport but is also the major culprit of low transfection efficiencies. Here, we report a study on a eukaryotic amoeba, Dictyostelium discoideum, where by disruption of the endocytic process at the opportune moment, the transformant number increased. We have observed that by disruption of fluid-phase uptake of calcium phosphate DNA nanoparticles, the number of clones increased with the probable increase in number of foreign genes integrating in the host genome. The method described here leads to the possibility of safe and inexpensive methods for transfer of genes required for heterologous recombinant protein production as well as generating therapeutic recombinant cells.

Vats, B. and H. Padh (2009). "Efficient cell lysis method for isolation of total RNA from slime mold Dictyostelium: 
Applicability in preparation of cDNA." Int. J. Biotechnol. Biochem. 5(1): 51-62.
	Dictyostelium is a model organism for understanding of many cellular processes, 
evolutionary studies, behavioral analysis, gene expression and now even drug 
metabolism. RNA analysis is vital to most studies at molecular level. Extracting 
RNA is no easy task due to the omnipresence of robust RNases. Attaining full 
length mRNAs is the chief task in isolation of pure RNA. Stable ribonucleases 
are the major obstacle in isolating RNA of any kind. Many methods and kits are 
available for different organisms with differing efficiency, utility and expense. 
For isolation of RNA from Dictyostelium, Blumberg and Lodish devised a simple, 
in-expensive yet effective method, though for identification of mRNA use of 
DNase and poly-dT columns were required. We modified the cell 
homogenization process and isolated total RNA with the method. The 
modification enables us to detect specific mRNA from the total RNA pool 
without purifying through poly-dT columns or processing for DNA removal. The 
integrity of RNA isolated by the modified method was similar to that of RNA 
extracted with Qiagen RNAasy Mini kit indicative of the quality of the total RNA
 extracted. With this modification, we have been able to identify three mRNA 
transcripts and specifically amplify the cDNA using sequence specific primers.

Veltman, D. M., G. Akar, et al. (2009). "A new set of small, extrachromosomal expression vectors for Dictyostelium discoideum." Plasmid 61(2): 110-118.
	A new set of extrachromosomal Dictyostelium expression vectors is presented that can be modified according to the experimental needs with minimal cloning efforts. To achieve this, the vector consists of four functional regions that are separated by unique restriction sites, (1) an Escherichia coli replication region, and regions for (2) replication, (3) selection and (4) protein expression in Dictyostelium. Each region was trimmed down to its smallest possible size. A basic expression vector can be constructed from these modules with a size of only 6.8 kb. By exchanging modules, a large number of vectors with different properties can be constructed. The resulting set of vectors allows most basic expression needs, such as immuno blotting, protein purification, visualization of protein localization and identification of protein-protein interactions. In addition, two genes can be simultaneously expressed on one vector, which yields far more synchronous levels of expression than when expressing two genes on separate plasmids.

Veltman, D. M., I. Keizer-Gunnink, et al. (2009). "An extrachromosomal, inducible expression system for Dictyostelium discoideum." Plasmid 61(2): 119-125.
	Inducible expression systems are essential for the expression of toxic proteins and are very convenient for proteins that induce strong side effects such as retardation of growth or development. Currently available systems for use in Dictyostelium either do not have a very tight control over expression levels or use a combination of an integrating and an extrachromosomal vector. We designed a new vector in which all components of the available 2-plasmid tetracycline-inducible system were combined onto a single extrachromosomal vector. Two types of inducible plasmids are presented, in which transcription is induced by adding or removing doxycycline, respectively. The location and orientation of the components was optimized in order to obtain a low background expression combined with high inducibility. The resulting vectors have a very low expression in the uninduced state (>1000-fold lower expression compared to that resulting from the act15 promoter), show a 10,000-fold induction of gene expression in a doxycycline concentration-dependent manner and are comparatively small (8.5 kb). With these new vectors, inducible gene expression is as easy as constitutive gene expression.

Vial, L., M. C. Groleau, et al. (2009). "Phase variation has a role in Burkholderia ambifaria niche adaptation." ISME J.
	Members of the Burkholderia cepacia complex (Bcc), such as B. ambifaria, are effective biocontrol strains, for instance, as plant growth-promoting bacteria; however, Bcc isolates can also cause severe respiratory infections in people suffering from cystic fibrosis (CF). No distinction is known between isolates from environmental and human origins, suggesting that the natural environment is a potential source of infectious Bcc species. While investigating the presence and role of phase variation in B. ambifaria HSJ1, an isolate recovered from a CF patient, we identified stable variants that arose spontaneously irrespective of the culture conditions. Phenotypic and proteomic approaches revealed that the transition from wild-type to variant types affects the expression of several putative virulence factors. By using four different infection models (Drosophila melanogaster, Galleria mellonella, macrophages and Dictyostelium discoideum), we showed that the wild-type was more virulent than the variant. It may be noted that the variant showed reduced replication in a human monocyte cell line when compared with the wild-type. On the other hand, the variant of isolate HSJ1 was more competitive in colonizing plant roots than the wild-type. Furthermore, we observed that only clinical B. ambifaria isolates generated phase variants, and that these variants showed the same phenotypes as observed with the HSJ1 variant. Finally, we determined that environmental B. ambifaria isolates showed traits that were characteristic of variants derived from clinical isolates. Our study therefore suggest that B. ambifaria uses phase variation to adapt to drastically different environments: the lung of patients with CF or the rhizosphere.The ISME Journal advance online publication, 27 August 2009; doi:10.1038/ismej.2009.95.

Vlahou, G., O. Schmidt, et al. (2009). "Yersinia outer protein YopE affects the actin cytoskeleton in Dictyostelium discoideum through targeting of multiple Rho family GTPases." BMC Microbiol 9: 138.
	BACKGROUND: All human pathogenic Yersinia species share a virulence-associated type III secretion system that translocates Yersinia effector proteins into host cells to counteract infection-induced signaling responses and prevent phagocytosis. Dictyostelium discoideum has been recently used to study the effects of bacterial virulence factors produced by internalized pathogens. In this study we explored the potential of Dictyostelium as model organism for analyzing the effects of ectopically expressed Yersinia outer proteins (Yops). RESULTS: The Yersinia pseudotuberculosis virulence factors YopE, YopH, YopM and YopJ were expressed de novo within Dictyostelium and their effects on growth in axenic medium and on bacterial lawns were analyzed. No severe effect was observed for YopH, YopJ and YopM, but expression of YopE, which is a GTPase activating protein for Rho GTPases, was found to be highly detrimental. GFP-tagged YopE expressing cells had less conspicuous cortical actin accumulation and decreased amounts of F-actin. The actin polymerization response upon cAMP stimulation was impaired, although chemotaxis was unaffected. YopE also caused reduced uptake of yeast particles. These alterations are probably due to impaired Rac1 activation. We also found that YopE predominantly associates with intracellular membranes including the Golgi apparatus and inhibits the function of moderately overexpressed RacH. CONCLUSION: The phenotype elicited by YopE in Dictyostelium can be explained, at least in part, by inactivation of one or more Rho family GTPases. It further demonstrates that the social amoeba Dictyostelium discoideum can be used as an efficient and easy-to-handle model organism in order to analyze the function of a translocated GAP protein of a human pathogen.

Wang, F. (2009). "The signaling mechanisms underlying cell polarity and chemotaxis." CSH Persp. Biol. 1(4): a002980 (002916 pages).
	Chemotaxis—the directed movement of cells in a gradient of chemoattractant—is essential for neutrophils to crawl to sites of inflammation and infection and for Dictyostelium discoideum (D. discoideum) to aggregate during morphogenesis. Chemoattractant-induced activation of spatially localized cellular signals causes cells to polarize and move toward the highest concentration of the chemoattractant. Extensive studies have been devoted to achieving a better understanding of the mechanism(s) used by a neutrophil to choose its direction of polarity and to crawl effectively in response to chemoattractant gradients. Recent technological advances are beginning to reveal many fascinating details of the intracellular signaling components that spatially direct the cytoskeleton of neutrophils and D. discoideum and the complementary mechanisms that make the cell's front distinct from its back. 

Wang, H. Y. and J. G. Williams (2009). "Identification of a target for CudA, the transcription factor which directs formation of the Dictyostelium tip organiser." Int J Dev Biol.
	The tip of the Dictyostelium slug functions much like an embryonic organiser; when grafted onto the flank of a recipient slug, it recruits a mass of prespore cells and leads them away as part of a secondary slug. CudA is a nuclear protein which is expressed in prespore cells where it acts as a specific transcription factor. CudA is also expressed in an anteriorly located group of cells, the tip-organiser, that is believed to constitute the functional tip. We identify an expansin-like gene, expl7, that is expressed within the tip-organiser region and which is not expressed in a cudA null strain. The expl7 promoter contains a region that binds to CudA in vitro and this region is necessary for expression in the tip-organiser. These results provide an end-point for a previously defined signal transduction pathway in which regionalised expression of the ACA adenylyl cyclase within the tip-organiser leads to localised cAMP-induced activation of STATa and consequent binding of STATa to the cudA promoter. STATa then induces expression of cudA and cudA directs the transcription of target genes such as expl7.

Wang, Z. A., X. Jin, et al. (2009). Skp1 mediates O2-dependent development in Dictyostelium. 34th Annual Graduate Student Research Symposium, University of Oklahoma, Health Sciences Center.
	When starved, the soil amoeba Dictyostelium aggregates at an air-water interface to form a slug that subsequently culminates into a fruiting body consisting of a stalk and aerial spores. We have previously shown that culmination requires high oxygen by a mechanism that depends on the Skp1 prolyl 4-hydroxylase (P4H1). As a subunit of E3(SCF) ubiquitin ligases, Skp1 may influence the cellular proteome via protein turnover. Two almost identical Skp1 genes are expressed in Dictyostelium. To investigate the role of Skp1, we created strains harboring 1, 2, or 3 Skp1 genes, and a strain in which one of the Skp1s carried an amino acid substitution at the hydroxyproline site. Developmental analysis showed that increased Skp1 gene dosage correlated with an increased oxygen requirement for culmination, in a proline-dependent fashion. Biochemical analysis showed that Skp1 gene dosage partially correlated with protein level in the cell. In contrast, cells that under or overexpress P4H1 exhibit the opposite pattern of oxygen requirement. Since Skp1 likely functions through its associated E3-ubiquitin ligase, we propose that increased Skp1 degrades an activator of culmination. Since P4H1 acts in the opposite direction, we propose that hydroxylation (and dependent glycosylation) inhibit Skp1. O2 activates P4H1 as its substrate. These interpretations lead to the following signaling model for O2-dependent regulation of development in Dictyostelium, and other organisms that this pathway is found: O2àP4H1—I Skp1—I activators àculmination.

Wang, Z. A., H. van der Wel, et al. (2009). "Role of a cytoplasmic dual-function glycosyltransferase in O2 regulation of development in Dictyostelium." J Biol Chem 284(42): 28896-28904.
	In the social amoeba Dictyostelium, a terminal step in development is regulated by environmental O(2). Prolyl 4-hydroxylase-1 (P4H1) was previously implicated in mediating the O(2) signal, and P4H1-null cells require elevated O(2) to culminate. The E3-ubiquitin ligase adaptor Skp1 is a P4H1 substrate, and here we investigate the function of PgtA, a dual function beta3-galactosyltransferase/alpha2-fucosyltransferase that contributes the 2nd and 3rd sugars of the pentasaccharide cap formed on Skp1 hydroxyproline. Although pgtA-null cells, whose Skp1 contains only a single sugar (N-acetylglucosamine or GlcNAc), show wild-type O(2) dependence of culmination, cells lacking AgtA, an alpha3-galactosyltransferase required to extend the trisaccharide, require elevated O(2) as for P4H1-null cells. Skp1 is the only detectable protein modified by purified PgtA added to pgtA-null extracts. The basis for specificity of PgtA was investigated using native Skp1 acceptor glycoforms and a novel synthetic peptide containing GlcNAcalpha1,4-hydroxy(trans)proline. Cysteine-alkylation of Skp1 strongly inhibited modification by the PgtA galactosyltransferase but not the fucosyltransferase. Furthermore, native and synthetic Skp1 glycopeptides were poorly galactosylated, not processively fucosylated, and negligibly inhibitory, whereas the fucosyltransferase was active toward small substrates. In addition, the galactosyltransferase exhibited an atypical concentration dependence on UDP-galactose. The results provide the first evidence that Skp1 is the functional target of P4H1 in O(2) regulation, indicate a gatekeeper function for the beta3-galactosyltransferase in the PgtA dual reaction, and identify an unexpected P4H1-dependent yet antagonistic function for PgtA that is reversed by AgtA.

Weber, S. S., C. Ragaz, et al. (2009). "The inositol polyphosphate 5-phosphatase OCRL1 restricts intracellular growth of Legionella, localizes to the replicative vacuole and binds to the bacterial effector LpnE." Cell Microbiol 11(3): 442-460.
	Legionella pneumophila, the causative agent of Legionnaires' disease, replicates within a specific vacuole in amoebae and macrophages. To form these 'Legionella-containing vacuoles' (LCVs), the bacteria employ the Icm/Dot type IV secretion system and effector proteins, some of which anchor to the LCV membrane via the host glycolipid phosphatidylinositol 4-phosphate [PtdIns(4)P]. Here we analysed the role of inositol polyphosphate 5-phosphatases (IP5Ps) during L. pneumophila infections. Bacterial replication and LCV formation occurred more efficiently in Dictyostelium discoideum amoebae lacking the IP5P Dd5P4, a homologue of human OCRL1 (Oculocerebrorenal syndrome of Lowe), implicated in retrograde endosome to Golgi trafficking. The phenotype was complemented by Dd5P4 but not the catalytically inactive 5-phosphatase. Ectopically expressed Dd5P4 or OCRL1 localized to LCVs in D. discoideum via an N-terminal domain previously not implicated in membrane targeting, and OCRL1 was also identified on LCVs in macrophages. Dd5P4 was catalytically active on LCVs and accumulated on LCVs harbouring wild-type but not DeltaicmT mutant L. pneumophila. The N-terminal domain of OCRL1 bound L. pneumophila LpnE, a Sel1-like repeat protein involved in LCV formation, which localizes to LCVs and selectively binds PtdIns(3)P. Our results indicate that OCRL1 restricts intracellular growth of L. pneumophila and binds to LCVs in association with LpnE.

Weijer, C. J. (2009). "Collective cell migration in development." J Cell Sci 122(18): 3215-3223.
	Collective cell migration is a key process during the development of most organisms. It can involve either the migration of closely packed mesenchymal cells that make dynamic contacts with frequently changing neighbour cells, or the migration of epithelial sheets that typically display more stable cell-cell interactions and less frequent changes in neighbours. These collective movements can be controlled by short-or long-range dynamic gradients of extracellular signalling molecules, depending on the number of cells involved and their distance of migration. These gradients are sensed by some or all of the migrating cells and translated into directed migration, which in many settings is further modulated by cell-contact-mediated attractive or repulsive interactions that result in contact-following or contact-inhibition of locomotion, respectively. Studies of collective migration of groups of epithelial cells during development indicate that, in some cases, only leader cells sense and migrate up an external signal gradient, and that adjacent cells follow through strong cell-cell contacts. In this Commentary, I review studies of collective cell migration of differently sized cell populations during the development of several model organisms, and discuss our current understanding of the molecular mechanisms that coordinate this migration.

Wen, Y., I. Stavrou, et al. (2009). "AP180-Mediated Trafficking of Vamp7B Limits Homotypic Fusion of Dictyostelium Contractile Vacuoles." Mol Biol Cell 20(20): 4278-4288.
	Clathrin-coated vesicles play an established role in endocytosis from the plasma membrane, but they are also found on internal organelles. We examined the composition of clathrin-coated vesicles on an internal organelle responsible for osmoregulation, the Dictyostelium discoideum contractile vacuole. Clathrin puncta on contractile vacuoles contained multiple accessory proteins typical of plasma membrane-coated pits, including AP2, AP180, and epsin, but not Hip1r. To examine how these clathrin accessory proteins influenced the contractile vacuole, we generated cell lines that carried single and double gene knockouts in the same genetic background. Single or double mutants that lacked AP180 or AP2 exhibited abnormally large contractile vacuoles. The enlarged contractile vacuoles in AP180-null mutants formed because of excessive homotypic fusion among contractile vacuoles. The SNARE protein Vamp7B was mislocalized and enriched on the contractile vacuoles of AP180-null mutants. In vitro assays revealed that AP180 interacted with the cytoplasmic domain of Vamp7B. We propose that AP180 directs Vamp7B into clathrin-coated vesicles on contractile vacuoles, creating an efficient mechanism for regulating the internal distribution of fusion-competent SNARE proteins and limiting homotypic fusions among contractile vacuoles. Dictyostelium contractile vacuoles offer a valuable system to study clathrin-coated vesicles on internal organelles within eukaryotic cells.

Wessels, D., S. Kuhl, et al. (2009). "2D and 3D Quantitative Analysis of Cell Motility and Cytoskeletal Dynamics." Meth Mol Biol 586: 315-335.
	2D- and 3D-Dynamic Image Analysis Systems (2D- and 3D-DIAS) for quantitative analysis of cell motility and chemotaxis are described. Particular attention is given to protocols that have proven useful in the quantitation of cell shape changes and pseudopod dynamics during basic cell motility (i.e. crawling in the absence of a chemotactic or other type of extracellular signal) and directed motion. In addition, methods provided, highlight the applicability of this approach to the accurate phenotypic characterizations of cytoskeletal mutations in Dictyostelium discoideum, cytoskeletal alterations in metastatic cells, and cytoskeletal defects in chemotactically defective polymorphonuclear neutrophils.

Wessels, D. J., S. Kuhl, et al. (2009). "Light microscopy to image and quantify cell movement." Meth Mol Biol 571: 455-471.
	For decades, Dictyostelium discoideum has been an efficacious and attractive model system for the study of cell motility, primarily because cells become highly motile during the transition from growth phase to aggregation competence and because the haploid genome is readily amenable to mutation. These crawling amoebae, as well as other motile cells such as polymorphonuclear neutrophils (PMNs), extend pseudopodia, retract pseudopodia, and translocate across a substratum even in the absence of chemoattractant. This phenomenon, referred to as basic motile behavior, has been investigated in Dictyostelium through analysis of cytoskeletal mutants. Likewise, many chemotactic signal transduction pathways and networks have been inferred from studies of Dictyostelium mutants. However, before concluding from mutational analyses that a particular molecule or protein plays a role in chemotaxis, it is imperative to first precisely define its contribution, if any, to basic motile behavior. Here, we describe two-dimensional and three-dimensional technologies that can be coupled with 2D and 3D Dynamic Image Analysis System (2D and 3D-DIAS) software for the analysis of cell motility, shape changes, pseudopod formation, and localization of tagged molecules during basic motile behavior. In addition, we describe a method to analyze the 3D trajectories of microspheres attached to the surface of crawling Dictyostelium cells. We include information on microscopy, image acquisition techniques, and computer hardware that could be reproduced in a typical laboratory setting for motion analysis using 2D and 3D-DIAS software. Finally, we highlight features available in DIAS that have proven insightful in identifying defects in basic motile behavior exhibited by various cytoskeletal and putative signal transduction mutants.

West, C. M., P. Nguyen, et al. (2009). "Dependence of stress resistance on a spore coat heteropolysaccharide in Dictyostelium." Euk Cell 8(1): 27-36.
	In Dictyostelium, sporulation occurs synchronously as prespore cells approach the apex of the aerial stalk during culmination. Each prespore cell becomes surrounded by its own coat comprised of a core of crystalline cellulose and a branched heteropolysaccharide sandwiched between heterogeneous cysteine-rich glycoproteins. The function of the heteropolysaccharide, which consists of galactose and N-acetylgalactosamine, is unknown. Two glycosyltransferase-like genes encoding multifunctional proteins, each with predicted features of a heteropolysaccharide synthase, were identified in the Dictyostelium discoideum genome. pgtB and pgtC transcripts were modestly upregulated during early development, and pgtB was further intensely upregulated at the time of heteropolysaccharide accumulation. Disruption of either gene reduced synthase-like activity and blocked heteropolysaccharide formation, based on loss of cytological labeling with a lectin and absence of component sugars after acid hydrolysis. Cell mixing experiments showed that heteropolysaccharide expression is spore cell autonomous, suggesting a physical association with other coat molecules during assembly. Mutant coats expressed reduced levels of crystalline cellulose based on chemical analysis after acid degradation, and cellulose was heterogeneously affected based on flow cytometry and electron microscopy. Mutant coats also contained elevated levels of selected coat proteins but not others and were sensitive to shear. Mutant spores were unusually susceptible to hypertonic collapse and damage by detergent or hypertonic stress. Thus, the heteropolysaccharide is essential for spore integrity, which can be explained by a role in the formation of crystalline cellulose and regulation of the protein content of the coat.

Whitelam, S., T. Bretschneider, et al. (2009). "Transformation from spots to waves in a model of actin pattern formation." Phys Rev Lett 102(19): 198103.
	Actin networks in certain single-celled organisms exhibit a complex pattern-forming dynamics that starts with the appearance of static spots of actin on the cell cortex. Spots soon become mobile, executing persistent random walks, and eventually give rise to traveling waves of actin. Here we describe a possible physical mechanism for this distinctive set of dynamic transformations, by equipping an excitable reaction-diffusion model with a field describing the spatial orientation of its chief constituent (which we consider to be actin). The interplay of anisotropic actin growth and spatial inhibition drives a transformation at fixed parameter values from static spots to moving spots to waves.

Xu, X., J. A. Brzostowski, et al. (2009). "Monitoring Dynamic GPCR Signaling Events Using Fluorescence Microscopy, FRET Imaging, and Single-Molecule Imaging." Meth Mol Biol 571: 371-383.
	How a eukaryotic cell translates a small concentration difference of a chemoattractant across the length of its surface into highly polarized intracellular responses is a fundamental question in chemotaxis. Chemoattractants are detected by G-protein-coupled receptors (GPCRs). Binding of chemoattractants to GPCRs induces the dissociation of heterotrimeric G-proteins into Galpha and Gbetagamma subunits, which in turn, activate downstream signaling networks. To fully understand the molecular mechanisms of chemotaxis, it is essential to quantitatively measure the dynamic changes of chemoattractant concentrations around cells, activation of heterotrimeric G-proteins, and the mobility of GPCR and G-protein subunits in the cell membrane. Here, we outline fluorescence imaging methods including Forster resonance energy transfer (FRET) imaging and a single-molecule analysis that allow us to measure the dynamic properties of GPCR signaling in single live cells.

Yang, L. and P. A. Iglesias (2009). "Modeling spatial and temporal dynamics of chemotactic networks." Meth Mol Biol 571: 489-505.
	When stimulated by chemoattractants, eukaryotic cells respond through a combination of temporal and spatial dynamics. These responses come about because of the interaction of a large number of signaling components. The complexity of these systems makes it hard to understand without a means of systematically generating and testing hypotheses. Computer simulations have proved to be useful in testing conceptual models. Here we outline the steps required to develop these models.

Ying, M., Z. Zhan, et al. (2009). "Origin and evolution of ubiquitin-conjugating enzymes from Guillardia theta nucleomorph to hominoid." Gene 447(2): 72-85.
	The origin of eukaryotic ubiquitin-conjugating enzymes (E2s) can be traced back to the Guillardia theta nucleomorph about 2500 million years ago (Mya). E2s are largely vertically inherited over eukaryotic evolution [Lespinet, O., Wolf, Y.I., Koonin, E.V., Aravind, L., 2002. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 1048-1059], while mammal E2s experienced evolution of multigene families by gene duplications which have been accompanied by the increase in the species complexity. Because of alternatively splicing, primate-specific expansions of E2s happened once again at a transcriptional level. Both of them resulted in increasing genomic complexity and diversity of primate E2 proteomic function. The evolutionary processes of human E2 gene structure during expansions were accompanied by exon duplication and exonization of intronic sequences. Exonizations of Transposable Elements (TEs) in UBE2D3, UBE2L3 and UBE2V1 genes from primates indicate that exaptation of TEs also plays important roles in the structural innovation of primate-specific E2s and may create alternative splicing isoforms at a transcriptional level. Estimates for the ratio of dN/dS suggest that a strong purifying selection had acted upon protein-coding sequences of their orthologous UBE2D2, UBE2A, UBE2N, UBE2I and Rbx1 genes from animals, plants and fungi. The similar rates of synonymous substitutions are in accordance with the neutral mutation-random drift hypothesis of molecular evolution. Systematic detection of the origin and evolution of E2s, analyzing the evolution of E2 multigene families by gene duplications and the evolutionary processes of E2s during expansions, and testing its evolutionary force using E2s from distant phylogenetic lineages may advance our distinguishing of ancestral E2s from created E2s, and reveal previously unknown relationships between E2s and metazoan complexity. Analysis of these conserved proteins provides strong support for a close relationship between social amoeba and eukaryote, choanoflagellate and metazoan, and for the central roles of social amoeba and choanoflagellate in the origin and evolution of eukaryote and metazoan. Retracing the different stages of primate E2 exonization by monitoring genomic events over 63 Myr of primate evolution will advance our understanding of how TEs dynamically modified primate transcriptome and proteome in the past, and continue to do so.

Yue, Z. (2009). "LRRK2 in Parkinson's disease: in vivo models and approaches for understanding pathogenic roles." FEBS J.
	The recent discovery of the genetic causes for Parkinson's disease (PD) is fruitful; however, the continuing revelation of PD-related genes is rapidly outpacing the functional characterization of the gene products. Although the discovery of multiple PD-related genes places PD as one of the most complex multigenetic diseases of the brain, it will undoubtedly facilitate the unfolding of a central pathogenic pathway and an understanding of the etiology of PD. Recent findings of pathogenic mutations in leucine-rich repeat kinase 2 (LRRK2) (PARK8) that are linked to the most common familial forms and some sporadic forms of PD provide a unique opportunity to gain insight into the pathogenesis of PD. Despite rapid growth in biochemical, structural and in vitro cell culture studies of LRRK2, the in vivo characterizations of LRRK2 function generally fall short and are largely limited to invertebrates. The investigation of LRRK2 or homologs of LRRK2 in nonmammalian models provides important clues with respect to the cellular functions of LRRK2, but an elucidation of the physiology and pathophysiology of LRRK2 relevant to PD would still depend on mammalian models established by multiple genetic approaches, followed by rigorous examination of the models for pathological process. This minireview summarizes previous studies of genes for ROCO and LRRK2 homologs in slime mold, nematode worms and fruit flies. It also discusses the results obtained from available mouse models of LRRK2 that begin to provide information for understanding LRRK2-mediated pathogenesis in PD.

Zhang, C. and A. Kuspa (2009). "Transcriptional down-regulation and rRNA cleavage in Dictyostelium discoideum mitochondria during Legionella pneumophila infection." PLoS One 4(5): e5706.
	Bacterial pathogens employ a variety of survival strategies when they invade eukaryotic cells. The amoeba Dictyostelium discoideum is used as a model host to study the pathogenic mechanisms that Legionella pneumophila, the causative agent of Legionnaire's disease, uses to kill eukaryotic cells. Here we show that the infection of D. discoideum by L. pneumophila results in a decrease in mitochondrial messenger RNAs, beginning more than 8 hours prior to detectable host cell death. These changes can be mimicked by hydrogen peroxide treatment, but not by other cytotoxic agents. The mitochondrial large subunit ribosomal RNA (LSU rRNA) is also cleaved at three specific sites during the course of infection. Two LSU rRNA fragments appear first, followed by smaller fragments produced by additional cleavage events. The initial LSU rRNA cleavage site is predicted to be on the surface of the large subunit of the mitochondrial ribosome, while two secondary sites map to the predicted interface with the small subunit. No LSU rRNA cleavage was observed after exposure of D. discoideum to hydrogen peroxide, or other cytotoxic chemicals that kill cells in a variety of ways. Functional L. pneumophila type II and type IV secretion systems are required for the cleavage, establishing a correlation between the pathogenesis of L. pneumophila and D. discoideum LSU rRNA destruction. LSU rRNA cleavage was not observed in L. pneumophila infections of Acanthamoeba castellanii or human U937 cells, suggesting that L. pneumophila uses distinct mechanisms to interrupt metabolism in different hosts. Thus, L. pneumophila infection of D. discoideum results in dramatic decrease of mitochondrial RNAs, and in the specific cleavage of mitochondrial rRNA. The predicted location of the cleavage sites on the mitochondrial ribosome suggests that rRNA destruction is initiated by a specific sequence of events. These findings suggest that L. pneumophila specifically disrupts mitochondrial protein synthesis in D. discoideum during the course of infection.

Zhang, X. Y., J. Langenick, et al. (2009). "Xpf and not the Fanconi anaemia proteins or Rev3 accounts for the extreme resistance to cisplatin in Dictyostelium discoideum." PLoS Genet 5(9): e1000645.
	Organisms like Dictyostelium discoideum, often referred to as DNA damage "extremophiles", can survive exposure to extremely high doses of radiation and DNA crosslinking agents. These agents form highly toxic DNA crosslinks that cause extensive DNA damage. However, little is known about how Dictyostelium and the other "extremophiles" can tolerate and repair such large numbers of DNA crosslinks. Here we describe a comprehensive genetic analysis of crosslink repair in Dictyostelium discoideum. We analyse three gene groups that are crucial for a replication-coupled repair process that removes DNA crosslinks in higher eukarya: The Fanconi anaemia pathway (FA), translesion synthesis (TLS), and nucleotide excision repair. Gene disruption studies unexpectedly reveal that the FA genes and the TLS enzyme Rev3 play minor roles in tolerance to crosslinks in Dictyostelium. However, disruption of the Xpf nuclease subcomponent results in striking hypersensitivity to crosslinks. Genetic interaction studies reveal that although Xpf functions with FA and TLS gene products, most Xpf mediated repair is independent of these two gene groups. These results suggest that Dictyostelium utilises a distinct Xpf nuclease-mediated repair process to remove crosslinked DNA. Other DNA damage-resistant organisms and chemoresistant cancer cells might adopt a similar strategy to develop resistance to DNA crosslinking agents.

Abedin, M. and N. King (2010). "Diverse evolutionary paths to cell adhesion." Trends Cell Biol 20(12): 734-742.
	The morphological diversity of animals, fungi, plants, and other multicellular organisms stems from the fact that each lineage acquired multicellularity independently. A prerequisite for each origin of multicellularity was the evolution of mechanisms for stable cell-cell adhesion or attachment. Recent advances in comparative genomics and phylogenetics provide critical insights into the evolutionary foundations of cell adhesion. Reconstructing the evolution of cell junction proteins in animals and their unicellular relatives exemplifies the roles of co-option and innovation. Comparative studies of volvocine algae reveal specific molecular changes that accompanied the evolution of multicellularity in Volvox. Comparisons between animals and Dictyostelium show how commonalities and differences in the biology of unicellular ancestors influenced the evolution of adhesive mechanisms. Understanding the unicellular ancestry of cell adhesion helps illuminate the basic cell biology of multicellular development in modern organisms.

Adiba, S., C. Nizak, et al. (2010). "From grazing resistance to pathogenesis: the coincidental evolution of virulence factors." PLoS One 5(8): e11882.
	To many pathogenic bacteria, human hosts are an evolutionary dead end. This begs the question what evolutionary forces have shaped their virulence traits. Why are these bacteria so virulent? The coincidental evolution hypothesis suggests that such virulence factors result from adaptation to other ecological niches. In particular, virulence traits in bacteria might result from selective pressure exerted by protozoan predator. Thus, grazing resistance may be an evolutionarily exaptation for bacterial pathogenicity. This hypothesis was tested by subjecting a well characterized collection of 31 Escherichia coli strains (human commensal or extra-intestinal pathogenic) to grazing by the social haploid amoeba Dictyostelium discoideum. We then assessed how resistance to grazing correlates with some bacterial traits, such as the presence of virulence genes. Whatever the relative population size (bacteria/amoeba) for a non-pathogenic bacteria strain, D. discoideum was able to phagocytise, digest and grow. In contrast, a pathogenic bacterium strain killed D. discoideum above a certain bacteria/amoeba population size. A plating assay was then carried out using the E. coli collection faced to the grazing of D. discoideum. E. coli strains carrying virulence genes such as iroN, irp2, fyuA involved in iron uptake, belonging to the B2 phylogenetic group and being virulent in a mouse model of septicaemia were resistant to the grazing from D. discoideum. Experimental proof of the key role of the irp gene in the grazing resistance was evidenced with a mutant strain lacking this gene. Such determinant of virulence may well be originally selected and (or) further maintained for their role in natural habitat: resistance to digestion by free-living protozoa, rather than for virulence per se.

Aguirre, J. and J. D. Lambeth (2010). "Nox enzymes from fungus to fly to fish and what they tell us about Nox function in mammals." Free Radic Biol Med 49(9): 1342-1353.
	The production of reactive oxygen species (ROS) in a highly regulated fashion is a hallmark of members of the NADPH oxidase (Nox) family of enzymes. Nox enzymes are present in most eukaryotic groups such as the amebozoid, fungi, algae and plants, and animals, in which they are involved in seemingly diverse biological processes. However, a comprehensive survey of Nox functions throughout biology reveals common functional themes. Noxes are often activated in response to stressful conditions such as nutrient starvation, physical damage, or pathogen attack. Although the end result varies depending on the organism and tissue, Nox-produced ROS mediate the response to the adverse stimuli, such as innate immunity responses in plants and animals or cell differentiation in Dictyostelium, fungi, and plants. These responses involve ROS-mediated signaling mechanisms occurring at intracellular or cell-to-cell levels and sometimes involve cell wall or extracellular matrix cross-linking. Indeed, Noxes are involved in local and systemic signaling from plants to fish and in cross-linking of the plant hair-cell wall, synthesis of the nematode cuticle, and formation of the sea urchin fertilization envelope. The extensive use of Nox enzymes in biology to regulate cell-to-cell signaling and morphogenesis suggests that additional functions in mammalian signaling and development remain to be discovered.

Alam-Nazki, A. and J. Krishnan (2010). "A mathematical modelling framework for understanding chemorepulsive signal transduction in Dictyostelium." J Theor Biol 266(1): 140-153.
	Chemorepulsion is the process by which an organism or a cell moves in the direction of decreasing chemical concentration. While a few experimental studies have been performed, no mathematical models exist for this process. In this paper we have modelled gradient sensing, the first subprocess of chemorepulsion, in Dictyostelium discoideum-a well characterized model eukaryotic system. We take the first steps towards achieving a comprehensive mechanistic understanding of chemorepulsion in this system. We have used, as a basis, the biochemical network of the Keizer-Gunnink et al. (2007) to develop the mathematical modelling framework. This network describes the underlying pathways of chemorepellent gradient sensing in D. discoideum. Working within this modelling framework we address whether the postulated interactions of the pathways and species in this network can lead to a chemorepulsive response. We also analyse the possible role of additional regulatory effects (such as additional receptor regulation of enzymes in this network) and if this is necessary to achieve this behaviour. Thus we have investigated the receptor regulation of important enzymes and feedback effects in the network. This modelling framework generates important insights into and testable predictions regarding the role of key components and feedback loops in regulating chemorepulsive gradient sensing, and what factors might be important for generating a chemorepulsive response; it serves as a first step towards a comprehensive mechanistic understanding of this process.

Apri, M., J. Molenaar, et al. (2010). "Efficient estimation of the robustness region of biological models with oscillatory behavior." PLoS One 5(4): e9865.
	Robustness is an essential feature of biological systems, and any mathematical model that describes such a system should reflect this feature. Especially, persistence of oscillatory behavior is an important issue. A benchmark model for this phenomenon is the Laub-Loomis model, a nonlinear model for cAMP oscillations in Dictyostelium discoideum. This model captures the most important features of biomolecular networks oscillating at constant frequencies. Nevertheless, the robustness of its oscillatory behavior is not yet fully understood. Given a system that exhibits oscillating behavior for some set of parameters, the central question of robustness is how far the parameters may be changed, such that the qualitative behavior does not change. The determination of such a "robustness region" in parameter space is an intricate task. If the number of parameters is high, it may be also time consuming. In the literature, several methods are proposed that partially tackle this problem. For example, some methods only detect particular bifurcations, or only find a relatively small box-shaped estimate for an irregularly shaped robustness region. Here, we present an approach that is much more general, and is especially designed to be efficient for systems with a large number of parameters. As an illustration, we apply the method first to a well understood low-dimensional system, the Rosenzweig-MacArthur model. This is a predator-prey model featuring satiation of the predator. It has only two parameters and its bifurcation diagram is available in the literature. We find a good agreement with the existing knowledge about this model. When we apply the new method to the high dimensional Laub-Loomis model, we obtain a much larger robustness region than reported earlier in the literature. This clearly demonstrates the power of our method. From the results, we conclude that the biological system underlying is much more robust than was realized until now.

Arai, Y., T. Shibata, et al. (2010). "Self-organization of the phosphatidylinositol lipids signaling system for random cell migration." Proc Natl Acad Sci U S A 107(27): 12399-12404.
	Phosphatidylinositol (PtdIns) lipids have been identified as key signaling mediators for random cell migration as well as chemoattractant-induced directional migration. However, how the PtdIns lipids are organized spatiotemporally to regulate cellular motility and polarity remains to be clarified. Here, we found that self-organized waves of PtdIns 3,4,5-trisphosphate [PtdIns(3,4,5)P(3)] are generated spontaneously on the membrane of Dictyostelium cells in the absence of a chemoattractant. Characteristic oscillatory dynamics within the PtdIns lipids signaling system were determined experimentally by observing the phenotypic variability of PtdIns lipid waves in single cells, which exhibited characteristics of a relaxation oscillator. The enzymes phosphatase and tensin homolog (PTEN) and phosphoinositide-3-kinase (PI3K), which are regulators for PtdIns lipid concentrations along the membrane, were essential for wave generation whereas functional actin cytoskeleton was not. Defects in these enzymes inhibited wave generation as well as actin-based polarization and cell migration. On the basis of these experimental results, we developed a reaction-diffusion model that reproduced the characteristic relaxation oscillation dynamics of the PtdIns lipid system, illustrating that a self-organization mechanism provides the basis for the PtdIns lipids signaling system to generate spontaneous spatiotemporal signals for random cell migration and that molecular noise derived from stochastic fluctuations within the signaling components gives rise to the variability of these spontaneous signals.

Araki, T., W. N. van Egmond, et al. (2010). "Dual regulation of a Dictyostelium STAT by cGMP and Ca2+ signalling." J Cell Sci 123(Pt 6): 837-841.
	When cells are exposed to hyperosmotic stress, the Dictyostelium STAT orthologue STATc is rapidly tyrosine phosphorylated. Previous observations suggest a non-paradigmatic mode of STAT activation, whereby stress-induced serine phosphorylation of the PTP3 protein tyrosine phosphatase inhibits its activity towards STATc. We show that two serine residues in PTP3, S448 and S747, are rapidly phosphorylated after osmotic stress. cGMP is a second messenger for hyperosmotic stress response and 8-bromo-cGMP, a membrane-permeable form of cGMP, is a known activator of STATc. GbpC, a cGMP-binding Ras guanine nucleotide exchange factor protein, is a founder member of a protein family that includes LRRK2, the gene commonly mutated in familial Parkinson's disease. Genetic ablation of gbpC prevents STATc activation by 8-bromo-cGMP. However, osmotic-stress-induced activation of STATc occurs normally in the gbpC null mutant. Moreover, 8-bromo-cGMP does not stimulate phosphorylation of S448 and S747 of PTP3 in a wild-type strain. These facts imply the occurrence of redundant activation pathways. We present evidence that intracellular Ca(2+) is a parallel second messenger, by showing that agents that elevate intracellular Ca(2+) levels are potent STATc activators that stimulate phosphorylation of S448 and S747. We propose that stress-induced cGMP signalling exerts its stimulatory effect by potentiating the activity of a semi-constitutive tyrosine kinase that phosphorylates STATc, whereas parallel, stress-induced Ca(2+) signalling represses STATc dephosphorylation through its inhibitory effect on PTP3.

Bae, A. J. and E. Bodenschatz (2010). "On the swimming of Dictyostelium amoebae." Proc Natl Acad Sci U S A 107(44): E165-166.
	
Baek, S. H., Y. C. Kwon, et al. (2010). "Rho-family small GTPases are required for cell polarization and directional sensing in Drosophila wound healing." Biochem Biophys Res Commun 394(3): 488-492.
	A wound induces cell polarization, in which myosin II is localized at the rear end of individual cells in a migrating epithelial sheet of the Drosophila larval epidermis. Here, we use myosin localization to demonstrate that Rac1, Cdc42, and Rho1 are each required for cell polarization and directional sensing of the wound. The three GTPases are also required for actin cable formation at the wound leading edge. Rac1, Cdc42, and Rho1 act upstream of c-Jun N-terminal kinase (JNK) to organize actin assembly. These results highlight the similarities between the molecular mechanism of Drosophila wound healing and those of Drosophila embryonic dorsal closure and the chemotactic response of Dictyostelium and leukocytes.

Bakthavatsalam, D. and R. H. Gomer (2010). "The secreted proteome profile of developing Dictyostelium discoideum cells." Proteomics 10(13): 2556-2559.
	Dictyostelium discoideum is a unicellular eukaryote that, when starved, aggregates to form multicellular structures. In this report, we identified the proteins secreted by developing Dictyostelium cells using MS-based proteomics. A total of 349 different secreted proteins were identified, indicating that at least 2.6% of the 13 600 predicted proteins in the Dictyostelium genome are secreted. Gene ontology analysis suggests that many of the secreted proteins are involved in protein and carbohydrate metabolism, and proteolysis.

Barry, N. P. and M. S. Bretscher (2010). "Dictyostelium amoebae and neutrophils can swim." Proc Natl Acad Sci U S A 107(25): 11376-11380.
	Animal cells migrating over a substratum crawl in amoeboid fashion; how the force against the substratum is achieved remains uncertain. We find that amoebae and neutrophils, cells traditionally used to study cell migration on a solid surface, move toward a chemotactic source while suspended in solution. They can swim and do so with speeds similar to those on a solid substrate. Based on the surprisingly rapidly changing shape of amoebae as they swim and earlier theoretical schemes for how suspended microorganisms can migrate (Purcell EM (1977) Life at low Reynolds number. Am J Phys 45:3-11), we suggest the general features these cells use to gain traction with the medium. This motion requires either the movement of the cell's surface from the cell's front toward its rear or protrusions that move down the length of the elongated cell. Our results indicate that a solid substratum is not a prerequisite for these cells to produce a forward thrust during movement and suggest that crawling and swimming are similar processes, a comparison we think is helpful in understanding how cells migrate.

Beta, C. (2010). "Bistability in the actin cortex." PMC Biophys 3(1): 12.
	Multi-color fluorescence imaging experiments of wave forming Dictyostelium cells have revealed that actin waves separate two domains of the cell cortex that differ in their actin structure and phosphoinositide composition. We propose a bistable model of actin dynamics to account for these experimental observation. The model is based on the simplifying assumption that the actin cytoskeleton is composed of two distinct network types, a dendritic and a bundled network. The two structurally different states that were observed in experiments correspond to the stable fixed points in the bistable regime of this model. Each fixed point is dominated by one of the two network types. The experimentally observed actin waves can be considered as trigger waves that propagate transitions between the two stable fixed points.PACS Codes: 87.16.Ln, 87.17.Aa, 89.75.Fb.

Bloomfield, G., J. Skelton, et al. (2010). "Sex determination in the social amoeba Dictyostelium discoideum." Science 330(6010): 1533-1536.
	The genetics of sex determination remain mysterious in many organisms, including some that are otherwise well studied. Here we report the discovery and analysis of the mating-type locus of the model organism Dictyostelium discoideum. Three forms of a single genetic locus specify this species' three mating types: two versions of the locus are entirely different in sequence, and the third resembles a composite of the other two. Single, unrelated genes are sufficient to determine two of the mating types, whereas homologs of both these genes are required in the composite type. The key genes encode polypeptides that possess no recognizable similarity to established protein families. Sex determination in the social amoebae thus appears to use regulators that are unrelated to any others currently known.

Bolourani, P., G. Spiegelman, et al. (2010). "Ras proteins have multiple functions in vegetative cells of Dictyostelium." Eukaryot Cell 9(11): 1728-1733.
	During the aggregation of Dictyostelium cells, signaling through RasG is more important in regulating cyclic AMP (cAMP) chemotaxis, whereas signaling through RasC is more important in regulating the cAMP relay. However, RasC is capable of substituting for RasG for chemotaxis, since rasG cells are only partially deficient in chemotaxis, whereas rasC/rasG cells are totally incapable of chemotaxis. In this study we have examined the possible functional overlap between RasG and RasC in vegetative cells by comparing the vegetative cell properties of rasG, rasC, and rasC/rasG cells. In addition, since RasD, a protein not normally found in vegetative cells, is expressed in vegetative rasG and rasC/rasG cells and appears to partially compensate for the absence of RasG, we have also examined the possible functional overlap between RasG and RasD by comparing the properties of rasG and rasC/rasG cells with those of the mutant cells expressing higher levels of RasD. The results of these two lines of investigation show that RasD is capable of totally substituting for RasG for cytokinesis and growth in suspension, whereas RasC is without effect. In contrast, for chemotaxis to folate, RasC is capable of partially substituting for RasG, but RasD is totally without effect. Finally, neither RasC nor RasD is able to substitute for the role that RasG plays in regulating actin distribution and random motility. These specificity studies therefore delineate three distinct and none-overlapping functions for RasG in vegetative cells.

Bolourani, P., G. Spiegelman, et al. (2010). "Determinants of RasC specificity during Dictyostelium aggregation." J Biol Chem 285(53): 41374-41379.
	RasC is required for optimum activation of adenylyl cyclase A and for aggregate stream formation during the early differentiation of Dictyostelium discoideum. RasG is unable to substitute for this requirement despite its sequence similarity to RasC. A critical question is which amino acids in RasC are required for its specific function. Each of the amino acids within the switch 1 and 2 domains in the N-terminal portion of RasG was changed to the corresponding amino acid from RasC, and the ability of the mutated RasG protein to reverse the phenotype of rasC(-) cells was determined. Only the change from aspartate at position 30 of RasG to alanine (the equivalent position 31 in RasC) resulted in a significant increase in adenylyl cyclase A activation and a partial reversal of the aggregation-deficient phenotype of rasC(-) cells. All other single amino acid changes were without effect. Expression of a chimeric protein, RasG(1-77)-RasC(79-189), also resulted in a partial reversal of the rasC(-) cell phenotype, indicating the importance of the C-terminal portion of RasC. Furthermore, expression of the chimeric protein, with alanine changed to aspartate (RasG(1-77(D30A))-RasC(79-189)), resulted in a full rescue the rasC(-) aggregation-deficient phenotype. Finally, the expression of either a mutated RasC, with the aspartate 31 replaced by alanine, or the chimeric protein, RasC(1-78)-RasG(78-189), only generated a partial rescue. These results emphasize the importance of both the single amino acid at position 31 and the C-terminal sequence for the specific function of RasC during Dictyostelium aggregation.

Bosgraaf, L. and P. J. Van Haastert (2010). "Quimp3, an automated pseudopod-tracking algorithm." Cell Adh Migr 4(1): 46-55.
	To understand movement of amoeboid cells we have developed an information tool that automatically detects protrusions of moving cells. The algorithm uses digitized cell recordings at a speed of approximately 1 image per second that are analyzed in three steps. In the first part, the outline of a cell is defined as a polygon of approximately 150 nodes, using the previously published Quimp2 program. By comparing the position of the nodes in place and time, each node contains information on position, local curvature and speed of movement. The second part uses rules for curvature and movement to define the position and time of start and end of a growing pseudopod. This part of the algorithm produces quantitative data on size, surface area, lifetime, frequency and direction of pseudopod extension. The third part of the algorithm assigns qualitative properties to each pseudopod. It decides on the origin of a pseudopod as splitting of an existing pseudopod or as extension de novo. It also decides on the fate of each pseudopod as merged with the cell body or retracted. Here we describe the pseudopod tool and present the first data based on the analysis of approximately 1,000 pseudopodia extended by Dictyostelium cells in the absence of external cues.

Brady, R. J., C. K. Damer, et al. (2010). "Regulation of Hip1r by epsin controls the temporal and spatial coupling of actin filaments to clathrin-coated pits." J Cell Sci 123(Pt 21): 3652-3661.
	Recently, it has become clear that the actin cytoskeleton is involved in clathrin-mediated endocytosis. During clathrin-mediated endocytosis, clathrin triskelions and adaptor proteins assemble into lattices, forming clathrin-coated pits. These coated pits invaginate and detach from the membrane, a process that requires dynamic actin polymerization. We found an unexpected role for the clathrin adaptor epsin in regulating actin dynamics during this late stage of coated vesicle formation. In Dictyostelium cells, epsin is required for both the membrane recruitment and phosphorylation of the actin- and clathrin-binding protein Hip1r. Epsin-null and Hip1r-null cells exhibit deficiencies in the timing and organization of actin filaments at clathrin-coated pits. Consequently, clathrin structures persist on the membranes of epsin and Hip1r mutants and the internalization of clathrin structures is delayed. We conclude that epsin works with Hip1r to regulate actin dynamics by controlling the spatial and temporal coupling of actin filaments to clathrin-coated pits. Specific residues in the ENTH domain of epsin that are required for the membrane recruitment and phosphorylation of Hip1r are also required for normal actin and clathrin dynamics at the plasma membrane. We propose that epsin promotes the membrane recruitment and phosphorylation of Hip1r, which in turn regulates actin polymerization at clathrin-coated pits.

Breshears, L. M., D. Wessels, et al. (2010). "An unconventional myosin required for cell polarization and chemotaxis." Proc Natl Acad Sci U S A 107(15): 6918-6923.
	MyTH/FERM (myosin tail homology 4/band 4.1, ezrin, radixin, and moesin) myosins have roles in cellular adhesion, extension of actin-filled projections such as filopodia and stereocilia, and directional migration. The amoeba Dictyostelium discoideum expresses a simple complement of MyTH/FERM myosins, a class VII (M7) myosin required for cell-substrate adhesion and a unique myosin named MyoG. Mutants lacking MyoG exhibit a wide range of normal actin-based behaviors, including chemotaxis to folic acid, but have a striking defect in polarization and chemotaxis to cAMP. Although the myoG mutants respond to cAMP stimulation by increasing persistence and weakly increasing levels of cortical F-actin, they do not polarize; instead, they maintain a round shape and move slowly and randomly when exposed to a chemotactic gradient. The mutants also fail to activate and localize PI3K to the membrane closest to the source of chemoattractant. These data reveal a role for a MyTH/FERM myosin in mediating early chemotactic signaling and suggest that MyTH/FERM proteins have conserved roles in signaling and the generation of cell polarity.

Buenemann, M., H. Levine, et al. (2010). "The role of cell contraction and adhesion in dictyostelium motility." Biophys J 99(1): 50-58.
	The crawling motion of Dictyostelium discoideum on substrata involves a number of coordinated events including cell contractions and cell protrusions. The mechanical forces exerted on the substratum during these contractions have recently been quantified using traction force experiments. Based on the results from these experiments, we present a biomechanical model of the contraction phase of Dictyostelium discoideum motility with an emphasis on the adhesive properties of the cell-substratum contact. Our model assumes that the cell contracts at a constant rate and is bound to the substratum by adhesive bridges that are modeled as elastic springs. These bridges are established at a spatially uniform rate while detachment occurs at a spatially varying, load-dependent rate. Using Monte Carlo simulations and assuming a rigid substratum, we find that the cell speed depends only weakly on the detachment kinetics of the cell-substratum interface, in agreement with experimental data. By varying the parameters that control the adhesive and contractile properties of the cell, we are able to make testable predictions. We also extend our model to include a flexible substrate and show that our model is able to produce substratum deformations and force patterns that are quantitatively and qualitatively in agreement with experimental data.

Bullerwell, C. E., G. Burger, et al. (2010). "Abundant 5S rRNA-like transcripts encoded by the mitochondrial genome in amoebozoa." Eukaryot Cell 9(5): 762-773.
	5S rRNAs are ubiquitous components of prokaryotic, chloroplast, and eukaryotic cytosolic ribosomes but are apparently absent from mitochondrial ribosomes (mitoribosomes) of many eukaryotic groups including animals and fungi. Nevertheless, a clearly identifiable, mitochondrion-encoded 5S rRNA is present in Acanthamoeba castellanii, a member of Amoebozoa. During a search for additional mitochondrial 5S rRNAs, we detected small abundant RNAs in other members of Amoebozoa, namely, in the lobose amoeba Hartmannella vermiformis and in the myxomycete slime mold Physarum polycephalum. These RNAs are encoded by mitochondrial DNA (mtDNA), cosediment with mitoribosomes in glycerol gradients, and can be folded into a secondary structure similar to that of bona fide 5S rRNAs. Further, in the mtDNA of another slime mold, Didymium nigripes, we identified a region that in sequence, potential secondary structure, and genomic location is similar to the corresponding region encoding the Physarum small RNA. A mtDNA-encoded small RNA previously identified in Dictyostelium discoideum is here shown to share several characteristics with known 5S rRNAs. Again, we detected genes encoding potential homologs of this RNA in the mtDNA of three other species of the genus Dictyostelium as well as in a related genus, Polysphondylium. Taken together, our results indicate a widespread occurrence of small, abundant, mtDNA-encoded RNAs with 5S rRNA-like structures that are associated with the mitoribosome in various amoebozoan taxa. Our working hypothesis is that these novel small abundant RNAs represent radically divergent mitochondrial 5S rRNA homologs. We posit that currently unrecognized 5S-like RNAs may exist in other mitochondrial systems in which a conventional 5S rRNA cannot be identified.

Buttery, N. J., C. R. Thompson, et al. (2010). "Complex genotype interactions influence social fitness during the developmental phase of the social amoeba Dictyostelium discoideum." J Evol Biol 23(8): 1664-1671.
	When individuals interact, phenotypic variation can be partitioned into direct genetic effects (DGEs) of the individuals' own genotypes, indirect genetic effects (IGEs) of their social partners' genotypes and epistatic interactions between the genotypes of interacting individuals ('genotype-by-genotype (GxG) epistasis'). These components can all play important roles in evolutionary processes, but few empirical studies have examined their importance. The social amoeba Dictyostelium discoideum provides an ideal system to measure these effects during social interactions and development. When starved, free-living amoebae aggregate and differentiate into a multicellular fruiting body with a dead stalk that holds aloft viable spores. By measuring interactions among a set of natural strains, we quantify DGEs, IGEs and GxG epistasis affecting spore formation. We find that DGEs explain most of the phenotypic variance (57.6%) whereas IGEs explain a smaller (13.3%) but highly significant component. Interestingly, GxG epistasis explains nearly a quarter of the variance (23.0%), highlighting the complex nature of genotype interactions. These results demonstrate the large impact that social interactions can have on development and suggest that social effects should play an important role in developmental evolution in this system.

Cabral, M., C. Anjard, et al. (2010). "Unconventional secretion of AcbA in Dictyostelium discoideum through a vesicular intermediate." Eukaryot Cell 9(7): 1009-1017.
	The acyl coenzyme A (CoA) binding protein AcbA is secreted unconventionally and processed into spore differentiation factor 2 (SDF-2), a peptide that coordinates sporulation in Dictyostelium discoideum. We report that AcbA is localized in vesicles that accumulate in the cortex of prespore cells just prior to sporulation. These vesicles are not observed after cells are stimulated to release AcbA but remain visible after stimulation in cells lacking the Golgi reassembly stacking protein (GRASP). Acyl-CoA binding is required for the inclusion of AcbA in these vesicles, and the secretion of AcbA requires N-ethylmaleimide-sensitive factor (NSF). About 1% of the total cellular AcbA can be purified within membrane-bound vesicles. The yield of vesicles decreases dramatically when purified from wild-type cells that were stimulated to release AcbA, whereas the yield from GRASP mutant cells was only modestly altered by stimulation. We suggest that these AcbA-containing vesicles are secretion intermediates and that GRASP functions at a late step leading to the docking/fusion of these vesicles at the cell surface.

Cai, H., S. Das, et al. (2010). "Ras-mediated activation of the TORC2-PKB pathway is critical for chemotaxis." J Cell Biol 190(2): 233-245.
	In chemotactic cells, G protein-coupled receptors activate Ras proteins, but it is unclear how Ras-associated pathways link extracellular signaling to cell migration. We show that, in Dictyostelium discoideum, activated forms of RasC prolong the time course of TORC2 (target of rapamycin [Tor] complex 2)-mediated activation of a myristoylated protein kinase B (PKB; PKBR1) and the phosphorylation of PKB substrates, independently of phosphatidylinositol-(3,4,5)-trisphosphate. Paralleling these changes, the kinetics of chemoattractant-induced adenylyl cyclase activation and actin polymerization are extended, pseudopodial activity is increased and mislocalized, and chemotaxis is impaired. The effects of activated RasC are suppressed by deletion of the TORC2 subunit PiaA. In vitro RasC(Q62L)-dependent PKB phosphorylation can be rapidly initiated by the addition of a PiaA-associated immunocomplex to membranes of TORC2-deficient cells and blocked by TOR-specific inhibitor PP242. Furthermore, TORC2 binds specifically to the activated form of RasC. These results demonstrate that RasC is an upstream regulator of TORC2 and that the TORC2-PKB signaling mediates effects of activated Ras proteins on the cytoskeleton and cell migration.

Calovi, D. S., L. G. Brunnet, et al. (2010). "cAMP diffusion in Dictyostelium discoideum: a Green's function method." Phys Rev E Stat Nonlin Soft Matter Phys 82(1 Pt 1): 011909.
	A Green's function method is developed to approach the spatiotemporal equations describing the cAMP production in Dictyostelium discoideum, markedly reducing numerical calculations times: cAMP concentrations and gradients are calculated just at the amoeba locations. A single set of parameters is capable of reproducing the different observed behaviors, from cAMP synchronization, spiral waves and reaction-diffusion patterns to streaming and mound formation. After aggregation, the emergence of a circular motion of amoebas, breaking the radial cAMP field symmetry, is observed.

Calvo-Garrido, J., S. Carilla-Latorre, et al. (2010). "Autophagy in Dictyostelium: genes and pathways, cell death and infection." Autophagy 6(6): 686-701.
	The use of simple organisms to understand the molecular and cellular function of complex processes is instrumental for the rapid development of biomedical research. A remarkable example has been the discovery in S. cerevisiae of a group of proteins involved in the pathways of autophagy. Orthologues of these proteins have been identified in humans and experimental model organisms. Interestingly, some mammalian autophagy proteins do not seem to have homologues in yeast but are present in Dictyostelium, a social amoeba with two distinctive life phases, a unicellular stage in nutrient-rich conditions that differentiates upon starvation into a multicellular stage that depends on autophagy. This review focuses on the identification and annotation of the putative Dictyostelium autophagy genes and on the role of autophagy in development, cell death and infection by bacterial pathogens.

Calvo-Garrido, J. and R. Escalante (2010). "Autophagy dysfunction and ubiquitin-positive protein aggregates in Dictyostelium cells lacking Vmp1." Autophagy 6(1): 100-109.
	Ubiquitin-positive protein aggregates are a hallmark of many degenerative diseases. Their presence can be induced by dysfunction in protein degradation pathways such as proteasome and autophagy. We now report several lines of evidence suggesting a defect in autophagy in Dictyostelium cells lacking Vmp1 (vacuole membrane protein 1), an endoplasmic reticulum (ER)-resident protein involved in pathological processes such as cancer and pancreatitis. vmp1- null cells are unable to survive starvation or undergo autophagic cell death under the appropriate inductive signals. Moreover, confocal studies using the autophagy marker Atg8 and previous transmission electron microscopy analysis showed defects in autophagosome formation. Although Vmp1 is localized in the ER, we found colocalization with Atg8 suggesting a contribution of both Vmp1 and ER in autophagosome biogenesis or maturation. Interestingly, vmp1- mutant cells showed accumulation of huge ubiquitin-positive protein aggregates containing the autophagy marker GFP-Atg8 and the putative Dictyostelium p62 homologue as described in many degenerative human diseases. The analysis of other Dictyostelium autophagic mutants (atg1-, atg5-, atg6-, atg7- and atg8-) showed a correlation in the severity of their corresponding phenotypes and the presence of ubiquitin-positive protein aggregates suggesting that the deleterious effects associated with development of these aggregates might contribute to the complex phenotypes observed in autophagy deficient mutants. Our results suggest that Vmp1 is required for the clearance of these ubiquitinated protein aggregates through autophagy and highlight a potential role for Vmp1 in protein-aggregation diseases.

Camarena, L., V. Bruno, et al. (2010). "Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing." PLoS Pathog 6(4): e1000834.
	Acinetobacter baumannii is a common pathogen whose recent resistance to drugs has emerged as a major health problem. Ethanol has been found to increase the virulence of A. baumannii in Dictyostelium discoideum and Caenorhabditis elegans models of infection. To better understand the causes of this effect, we examined the transcriptional profile of A. baumannii grown in the presence or absence of ethanol using RNA-Seq. Using the Illumina/Solexa platform, a total of 43,453,960 reads (35 nt) were obtained, of which 3,596,474 mapped uniquely to the genome. Our analysis revealed that ethanol induces the expression of 49 genes that belong to different functional categories. A strong induction was observed for genes encoding metabolic enzymes, indicating that ethanol is efficiently assimilated. In addition, we detected the induction of genes encoding stress proteins, including upsA, hsp90, groEL and lon as well as permeases, efflux pumps and a secreted phospholipase C. In stationary phase, ethanol strongly induced several genes involved with iron assimilation and a high-affinity phosphate transport system, indicating that A. baumannii makes a better use of the iron and phosphate resources in the medium when ethanol is used as a carbon source. To evaluate the role of phospholipase C (Plc1) in virulence, we generated and analyzed a deletion mutant for plc1. This strain exhibits a modest, but reproducible, reduction in the cytotoxic effect caused by A. baumannii on epithelial cells, suggesting that phospholipase C is important for virulence. Overall, our results indicate the power of applying RNA-Seq to identify key modulators of bacterial pathogenesis. We suggest that the effect of ethanol on the virulence of A. baumannii is multifactorial and includes a general stress response and other specific components such as phospholipase C.

Carilla-Latorre, S., M. E. Gallardo, et al. (2010). "MidA is a putative methyltransferase that is required for mitochondrial complex I function." J Cell Sci 123(Pt 10): 1674-1683.
	Dictyostelium and human MidA are homologous proteins that belong to a family of proteins of unknown function called DUF185. Using yeast two-hybrid screening and pull-down experiments, we showed that both proteins interact with the mitochondrial complex I subunit NDUFS2. Consistent with this, Dictyostelium cells lacking MidA showed a specific defect in complex I activity, and knockdown of human MidA in HEK293T cells resulted in reduced levels of assembled complex I. These results indicate a role for MidA in complex I assembly or stability. A structural bioinformatics analysis suggested the presence of a methyltransferase domain; this was further supported by site-directed mutagenesis of specific residues from the putative catalytic site. Interestingly, this complex I deficiency in a Dictyostelium midA(-) mutant causes a complex phenotypic outcome, which includes phototaxis and thermotaxis defects. We found that these aspects of the phenotype are mediated by a chronic activation of AMPK, revealing a possible role of AMPK signaling in complex I cytopathology.

Catalano, A., W. Luo, et al. (2010). "Synthesis and biological activity of peptides equivalent to the IP22 repeat motif found in proteins from Dictyostelium and Mimivirus." Peptides 31(10): 1799-1805.
	A novel IP22 repeat motif of unknown function was discovered previously that comprises almost the entire structure of cmbB, a calmodulin-binding protein from Dictyostelium discoideum. An analysis of over 2000 IP22 repeats across 130 different proteins from different species allowed us to define a prototypical IP22 repeat: I/LPxxhxxhxhxxxhxxxhxxxx (where L=leucine, I=isoleucine, h=any hydrophobic amino acid, x=any amino acid). Here we describe the synthesis of three peptide variants of the IP22 motif: IP22-1 (IPNSVTSLKFGDGFNQPLTPGT; 22aa); IP22-2 (LPSTLKTISLSNSTDKKIFKNS; 22aa); and, IP22-3 (IPKSLRSLFLGKGYNQPLEF; 20aa) plus a control peptide from the N-term of cmbB (HNMNPFSPQLDEKKNSHIVEY; 21aa). The structure and purity of synthesized peptides were verified by HPLC and mass spectrometry. The peptides all dose-dependently enhanced random cell motility and cAMP-mediated chemotaxis in Dictyostelium but IP22-3 was most effective peaking in activity around 50 muM. Fluorescein isothiocyanate (FITC)-conjugated IP22 peptides did not penetrate cells suggesting these peptides affect cell motility via cell surface interactions. Treatment of cells with FITC-IP22 peptides also led to enhanced cell motility equivalent to the non-conjugated peptides. Treatment of IP22-3-stimulated cells with 50 muM LY294002, 20 muM quinacrine or both suggests that IP22-3 requires both phosphoinositol 3-kinase and phospholipase A2 signaling to elicit its effects, a mechanism unique from EGFL motility enhancing peptides. The mechanism of action and potential uses of IP22 repeat peptides are discussed.

Cha, I., S. H. Lee, et al. (2010). "Chemoattractant-mediated Rap1 activation requires GPCR/G proteins." Mol Cells 30(6): 563-567.
	Rap1 is rapidly activated upon chemoattractant stimulation and plays an important role in cell adhesion and cytoskeletal reorganization during chemotaxis. Here, we demonstrate that G-protein coupled receptors and G-proteins are essential for chemoattractant-mediated Rap1 activation in Dictyostelium. The rapid Rap1 activation upon cAMP chemoattractant stimulation was absent in cells lacking chemoattractant cAMP receptors cAR1/cAR3 or a subunit of the heterotrimeric G-protein complex Galpha2. Loss of guanylyl cyclases GCA/SGC or a cGMP-binding protein GbpC exhibited no effect on Rap1 activation kinetics. These results suggest that Rap1, a key regulator for the regulation of cytoskeletal reorganization during cell movement, is activated through the G-protein coupled receptors cAR1/cAR3 and Galpha2 proteins in a way independent of the cGMP signaling pathway.

Charest, P. G., Z. Shen, et al. (2010). "A Ras signaling complex controls the RasC-TORC2 pathway and directed cell migration." Dev Cell 18(5): 737-749.
	Ras was found to regulate Dictyostelium chemotaxis, but the mechanisms that spatially and temporally control Ras activity during chemotaxis remain largely unknown. We report the discovery of a Ras signaling complex that includes the Ras guanine exchange factor (RasGEF) Aimless, RasGEFH, protein phosphatase 2A (PP2A), and a scaffold designated Sca1. The Sca1/RasGEF/PP2A complex is recruited to the plasma membrane in a chemoattractant- and F-actin-dependent manner and is enriched at the leading edge of chemotaxing cells where it regulates F-actin dynamics and signal relay by controlling the activation of RasC and the downstream target of rapamycin complex 2 (TORC2)-Akt/protein kinase B (PKB) pathway. In addition, PKB and PKB-related PKBR1 phosphorylate Sca1 and regulate the membrane localization of the Sca1/RasGEF/PP2A complex, and thereby RasC activity, in a negative feedback fashion. Thus, our study uncovered a molecular mechanism whereby RasC activity and the spatiotemporal activation of TORC2 are tightly controlled at the leading edge of chemotaxing cells.

Cheli, V. T. and E. C. Dell'Angelica (2010). "Early origin of genes encoding subunits of biogenesis of lysosome-related organelles complex-1, -2 and -3." Traffic 11(5): 579-586.
	Biogenesis of lysosome-related organelles complex (BLOC)-1, -2 and -3 are three multi-subunit protein complexes that are deficient in various forms of Hermansky-Pudlak syndrome, a human disease characterized by abnormal formation of lysosome-related organelles. Contrasting views have arisen on the evolutionary origin of these protein complexes. One view is that the BLOCs represent a recent evolutionary 'acquisition' unique to metazoans. However, the yeast proteins Mon1, Ccz1 and She3 have been reported to display homology to the HPS1 and HPS4 subunits of BLOC-3 and the BLOS2 subunit of BLOC-1, respectively. In this work, we have systematically searched for orthologs of BLOC subunits in the annotated genomes of over 160 species of eukaryotes, including metazoans and fungi in the Opisthokonta group as well as highly divergent organisms. We have found orthologs of six of the eight BLOC-1 subunits, two of the three BLOC-2 subunits, and the two BLOC-3 subunits, in some non-opisthokonts such as Dictyostelium discoideum, suggesting an early evolutionary origin for these complexes. On the other hand, we have obtained no evidence in support of the notion that yeast She3 would be an ortholog of BLOS2, and found that yeast Mon1 and Ccz1, despite displaying restricted homology to portions of HPS1 and HPS4, are unlikely to represent the orthologs of these BLOC-3 subunits. Potential orthologs of Mon1 and Ccz1 were found in humans and several other eukaryotes.

Chen, P. W., P. A. Randazzo, et al. (2010). "ACAP-A/B are ArfGAP homologs in dictyostelium involved in sporulation but not in chemotaxis." PLoS One 5(1): e8624.
	Arfs and Arf GTPase-activating proteins (ArfGAPs) are regulators of membrane trafficking and actin dynamics in mammalian cells. In this study, we identified a primordial Arf, ArfA, and two ArfGAPs (ACAP-A/B) containing BAR, PH, ArfGAP and Ankyrin repeat domains in the eukaryote Dictyostelium discoideum. In vitro, ArfA has similar nucleotide binding properties as mammalian Arfs and, with GTP bound, is a substrate for ACAP-A and B. We also investigated the physiological functions of ACAP-A/B by characterizing cells lacking both ACAP-A and B. Although ACAP-A/B knockout cells showed no defects in cell growth, migration or chemotaxis, they exhibited abnormal actin protrusions and approximately 50% reduction in spore yield. We conclude that while ACAP-A/B have a conserved biochemical mechanism and effect on actin organization, their role in migration is not conserved. The absence of an effect on Dictyostelium migration may be due to a specific requirement for ACAPs in mesenchymal migration, which is observed in epithelial cancer cells where most studies of mammalian ArfGAPs were performed.

Chen, Z. H., C. Schilde, et al. (2010). "Functional dissection of adenylate cyclase R, an inducer of spore encapsulation." J Biol Chem 285(53): 41724-41731.
	Cyclic AMP acting on protein kinase A controls sporulation and encystation in social and solitary amoebas. In Dictyostelium discoideum, adenylate cyclase R (ACR), is essential for spore encapsulation. In addition to its cyclase (AC) domain, ACR harbors seven transmembrane helices, a histidine kinase domain, and two receiver domains. We investigated the role of these domains in the regulation of AC activity. Expression of an ACR-YFP fusion protein in acr(-) cells rescued their sporulation defective phenotype and revealed that ACR is associated with the nuclear envelope and endoplasmic reticulum. Loss of the transmembrane helices (DeltaTM) caused a 60% reduction of AC activity, but DeltaTM-ACR still rescued the acr(-) phenotype. The isolated AC domain was properly expressed but inactive. Mutation of three essential ATP-binding residues in the histidine kinase domain did not affect the AC activity or phenotypic rescue. Mutation of the essential phosphoryl-accepting aspartate in receivers 1, 2, or both had only modest effects on AC activity and did not affect phenotypic rescue, indicating that AC activity is not critically regulated by phosphorelay. Remarkably, the dimerizing histidine phosphoacceptor subdomain, which in ACR lacks the canonical histidine for autophosphorylation, was essential for AC activity. Transformation of wild-type cells with an ACR allele (DeltaCRA) that is truncated after this domain inhibited AC activity of endogenous ACR and replicated the acr(-) phenotype. Combined with the observation that the isolated AC domain was inactive, the dominant-negative effect of DeltaCRA strongly suggests that the defunct phosphoacceptor domain acquired a novel role in enforcing dimerization of the AC domain.

Choi, C. H., H. Patel, et al. (2010). "Expression of actin-interacting protein 1 suppresses impaired chemotaxis of Dictyostelium cells lacking the Na+-H+ exchanger NHE1." Mol Biol Cell 21(18): 3162-3170.
	Increased intracellular pH is an evolutionarily conserved signal necessary for directed cell migration. We reported previously that in Dictyostelium cells lacking H(+) efflux by a Na(+)-H(+) exchanger (NHE; Ddnhe1(-)), chemotaxis is impaired and the assembly of filamentous actin (F-actin) is attenuated. We now describe a modifier screen that reveals the C-terminal fragment of actin-interacting protein 1 (Aip1) enhances the chemotaxis defect of Ddnhe1(-) cells but has no effect in wild-type Ax2 cells. However, expression of full-length Aip1 mostly suppresses chemotaxis defects of Ddnhe1(-) cells and restores F-actin assembly. Aip1 functions to promote cofilin-dependent actin remodeling, and we found that although full-length Aip1 binds cofilin and F-actin, the C-terminal fragment binds cofilin but not F-actin. Because pH-dependent cofilin activity is attenuated in mammalian cells lacking H(+) efflux by NHE1, our current data suggest that full-length Aip1 facilitates F-actin assembly when cofilin activity is limited. We predict the C-terminus of Aip1 enhances defective chemotaxis of Ddnhe1(-) cells by sequestering the limited amount of active cofilin without promoting F-actin assembly. Our findings indicate a cooperative role of Aip1 and cofilin in pH-dependent cell migration, and they suggest defective chemotaxis in Ddnhe1(-) cells is determined primarily by loss of cofilin-dependent actin dynamics.

Clarke, M. (2010). "Recent insights into host-pathogen interactions from Dictyostelium." Cell Microbiol 12(3): 283-291.
	To protect themselves from predation by amoebae and protozoa in the natural environment, some bacteria evolved means of escaping killing. The same mechanisms allow survival in mammalian phagocytes, producing opportunistic human pathogens. The social amoeba Dictyostelium discoideum is a powerful system for analysis of conserved host-pathogen interactions. This report reviews recent insights gained for several bacterial pathogens using Dictyostelium as host.

Clarke, M., U. Engel, et al. (2010). "Curvature recognition and force generation in phagocytosis." BMC Biol 8: 154.
	BACKGROUND: The uptake of particles by actin-powered invagination of the plasma membrane is common to protozoa and to phagocytes involved in the immune response of higher organisms. The question addressed here is how a phagocyte may use geometric cues to optimize force generation for the uptake of a particle. We survey mechanisms that enable a phagocyte to remodel actin organization in response to particles of complex shape. RESULTS: Using particles that consist of two lobes separated by a neck, we found that Dictyostelium cells transmit signals concerning the curvature of a surface to the actin system underlying the plasma membrane. Force applied to a concave region can divide a particle in two, allowing engulfment of the portion first encountered. The phagosome membrane that is bent around the concave region is marked by a protein containing an inverse Bin-Amphiphysin-Rvs (I-BAR) domain in combination with an Src homology (SH3) domain, similar to mammalian insulin receptor tyrosine kinase substrate p53. Regulatory proteins enable the phagocyte to switch activities within seconds in response to particle shape. Ras, an inducer of actin polymerization, is activated along the cup surface. Coronin, which limits the lifetime of actin structures, is reversibly recruited to the cup, reflecting a program of actin depolymerization. The various forms of myosin-I are candidate motor proteins for force generation in particle uptake, whereas myosin-II is engaged only in retracting a phagocytic cup after a switch to particle release. Thus, the constriction of a phagocytic cup differs from the contraction of a cleavage furrow in mitosis. CONCLUSIONS: Phagocytes scan a particle surface for convex and concave regions. By modulating the spatiotemporal pattern of actin organization, they are capable of switching between different modes of interaction with a particle, either arresting at a concave region and applying force in an attempt to sever the particle there, or extending the cup along the particle surface to identify the very end of the object to be ingested. Our data illustrate the flexibility of regulatory mechanisms that are at the phagocyte's disposal in exploring an environment of irregular geometry.

Clarke, M., L. Maddera, et al. (2010). "Retrieval of the vacuolar H-ATPase from phagosomes revealed by live cell imaging." PLoS One 5(1): e8585.
	BACKGROUND: The vacuolar H+-ATPase, or V-ATPase, is a highly-conserved multi-subunit enzyme that transports protons across membranes at the expense of ATP. The resulting proton gradient serves many essential functions, among them energizing transport of small molecules such as neurotransmitters, and acidifying organelles such as endosomes. The enzyme is not present in the plasma membrane from which a phagosome is formed, but is rapidly delivered by fusion with endosomes that already bear the V-ATPase in their membranes. Similarly, the enzyme is thought to be retrieved from phagosome membranes prior to exocytosis of indigestible material, although that process has not been directly visualized. METHODOLOGY: To monitor trafficking of the V-ATPase in the phagocytic pathway of Dictyostelium discoideum, we fed the cells yeast, large particles that maintain their shape during trafficking. To track pH changes, we conjugated the yeast with fluorescein isothiocyanate. Cells were labeled with VatM-GFP, a fluorescently-tagged transmembrane subunit of the V-ATPase, in parallel with stage-specific endosomal markers or in combination with mRFP-tagged cytoskeletal proteins. PRINCIPAL FINDINGS: We find that the V-ATPase is commonly retrieved from the phagosome membrane by vesiculation shortly before exocytosis. However, if the cells are kept in confined spaces, a bulky phagosome may be exocytosed prematurely. In this event, a large V-ATPase-rich vacuole coated with actin typically separates from the acidic phagosome shortly before exocytosis. This vacuole is propelled by an actin tail and soon acquires the properties of an early endosome, revealing an unexpected mechanism for rapid recycling of the V-ATPase. Any V-ATPase that reaches the plasma membrane is also promptly retrieved. CONCLUSIONS/SIGNIFICANCE: Thus, live cell microscopy has revealed both a usual route and alternative means of recycling the V-ATPase in the endocytic pathway.

Conte, D., H. K. MacWilliams, et al. (2010). "BTG interacts with retinoblastoma to control cell fate in Dictyostelium." PLoS One 5(3): e9676.
	BACKGROUND: In the genesis of many tissues, a phase of cell proliferation is followed by cell cycle exit and terminal differentiation. The latter two processes overlap: genes involved in the cessation of growth may also be important in triggering differentiation. Though conceptually distinct, they are often causally related and functional interactions between the cell cycle machinery and cell fate control networks are fundamental to coordinate growth and differentiation. A switch from proliferation to differentiation may also be important in the life cycle of single-celled organisms, and genes which arose as regulators of microbial differentiation may be conserved in higher organisms. Studies in microorganisms may thus contribute to understanding the molecular links between cell cycle machinery and the determination of cell fate choice networks. METHODOLOGY/PRINCIPAL FINDINGS: Here we show that in the amoebozoan D. discoideum, an ortholog of the metazoan antiproliferative gene btg controls cell fate, and that this function is dependent on the presence of a second tumor suppressor ortholog, the retinoblastoma-like gene product. Specifically, we find that btg-overexpressing cells preferentially adopt a stalk cell (and, more particularly, an Anterior-Like Cell) fate. No btg-dependent preference for ALC fate is observed in cells in which the retinoblastoma-like gene has been genetically inactivated. Dictyostelium btg is the only example of non-metazoan member of the BTG family characterized so far, suggesting that a genetic interaction between btg and Rb predated the divergence between dictyostelids and metazoa. CONCLUSIONS/SIGNIFICANCE: While the requirement for retinoblastoma function for BTG antiproliferative activity in metazoans is known, an interaction of these genes in the control of cell fate has not been previously documented. Involvement of a single pathway in the control of mutually exclusive processes may have relevant implication in the evolution of multicellularity.

Cox, A. D., F. St Michael, et al. (2010). "Investigating the candidacy of LPS-based glycoconjugates to prevent invasive meningococcal disease: chemical strategies to prepare glycoconjugates with good carbohydrate loading." Glycoconj J 27(4): 401-417.
	In previous studies protective antibodies that could facilitate bactericidal killing of Neisseria meningitidis (Nm) serogroup B strains were derived from immunisation with glycoconjugates prepared from O-deacylated lipopolysaccharide (LPS-OH) via direct reductive amination between the reducing end of the oligosaccharide molecule, created by treatment with alkaline phosphatase, and amino functionalities on the CRM(197) carrier protein. These glycoconjugates proved difficult to prepare because the presence of amide linked fatty-acyl groups results in glycolipids that are relatively insoluble and aggregate. Therefore, we have examined several strategies to prepare glycoconjugates in order to identify a robust, consistently reproducible strategy that produces glycoconjugates with a high loading of LPS derived oligosaccharides. Initially we used completely deacylated LPS molecules, but lacking phosphoethanolamine (PEtn) from the core OS as the strong basic conditions required to completely deacylate the LPS would modify the PEtn residue. We utilised a squarate linker and conjugated via the reducing end of the carbohydrate antigen following removal of the glycosidic phosphate to amino groups on CRM(197), however carbohydrate loading on the carrier protein was low. Glycoconjugates were then produced utilising amidases produced by Dictyostelium discoideum (Dd), which partially remove N-linked fatty acids from the lipid A region of the Nm LPS molecule, which enabled the retention of the PEtn residue. LPS-OH was treated with Dd amidase, the reducing glycosidic phosphate removed, and using a cystamine linker strategy, conjugated to the carrier protein. Carbohydrate loading was somewhat improved but still not high. Finally, we have developed a novel conjugation strategy that targets the amino functionality created by the amidase activity as the attachment point. The amino functionality on the PEtn residue of the inner core was protected via a novel blocking and unblocking strategy with t-butyl oxycarbonyl. A maleimide-thiol linker strategy, targeting lysine residues on the carrier protein did not result in high loading of the carbohydrate molecules, however when we targeted the carboxyl residues we have consistently obtained a high loading of carbohydrate antigens per CRM(197), which can be controlled by variation in the amount of activated carbohydrate utilised in the conjugation reaction.

Czarna, M., G. Mathy, et al. (2010). "Dynamics of the Dictyostelium discoideum mitochondrial proteome during vegetative growth, starvation and early stages of development." Proteomics 10(1): 6-22.
	In this study, a quantitative comparative proteomics approach has been used to analyze the Dictyostelium discoideum mitochondrial proteome variations during vegetative growth, starvation and the early stages of development. Application of 2-D DIGE technology allowed the detection of around 2000 protein spots on each 2-D gel with 180 proteins exhibiting significant changes in their expression level. In total, 96 proteins (51 unique and 45 redundant) were unambiguously identified. We show that the D. discoideum mitochondrial proteome adaptations mainly affect energy metabolism enzymes (the Krebs cycle, anaplerotic pathways, the oxidative phosphorylation system and energy dissipation), proteins involved in developmental and signaling processes as well as in protein biosynthesis and fate. The most striking observations were the opposite regulation of expression of citrate synthase and aconitase and the very large variation in the expression of the alternative oxidase that highlighted the importance of citrate and alternative oxidase in the physiology of the development of D. discoideum. Mitochondrial energy states measured in vivo with MitoTracker Orange CM Ros showed an increase in mitochondrial membrane polarization during D. discoideum starvation and starvation-induced development.

Delanoe-Ayari, H., J. P. Rieu, et al. (2010). "4D traction force microscopy reveals asymmetric cortical forces in migrating Dictyostelium cells." Phys Rev Lett 105(24): 248103.
	We present a 4D (x; y; z; t) force map of Dictyostelium cells crawling on a soft gel substrate. Vertical forces are of the same order as the tangential ones. The cells pull the substratum upward along the cell, medium, or substratum contact line and push it downward under the cell except for the pseudopods. We demonstrate quantitatively that the variations in the asymmetry in cortical forces correlates with the variations of the direction and speed of cell displacement.

Dieckmann, R., Y. von Heyden, et al. (2010). "A myosin IK-Abp1-PakB circuit acts as a switch to regulate phagocytosis efficiency." Mol Biol Cell 21(9): 1505-1518.
	Actin dynamics and myosin (Myo) contractile forces are necessary for formation and closure of the phagocytic cup. In Dictyostelium, the actin-binding protein Abp1 and myosin IK are enriched in the closing cup and especially at an actin-dense constriction furrow formed around the neck of engulfed budded yeasts. This phagocytic furrow consists of concentric overlapping rings of MyoK, Abp1, Arp3, coronin, and myosin II, following an order strikingly reminiscent of the overall organization of the lamellipodium of migrating cells. Mutation analyses of MyoK revealed that both a C-terminal farnesylation membrane anchor and a Gly-Pro-Arg domain that interacts with profilin and Abp1 were necessary for proper localization in the furrow and efficient phagocytosis. Consequently, we measured the binding affinities of these interactions and unraveled further interactions with profilins, dynamin A, and PakB. Due to the redundancy of the interaction network, we hypothesize that MyoK and Abp1 are restricted to regulatory roles and might affect the dynamic of cup progression. Indeed, phagocytic uptake was regulated antagonistically by MyoK and Abp1. MyoK is phosphorylated by PakB and positively regulates phagocytosis, whereas binding of Abp1 negatively regulates PakB and MyoK. We conclude that a MyoK-Abp1-PakB circuit acts as a switch regulating phagocytosis efficiency of large particles.

Dubin, M., J. Fuchs, et al. (2010). "Dynamics of a novel centromeric histone variant CenH3 reveals the evolutionary ancestral timing of centromere biogenesis." Nucleic Acids Res 38(21): 7526-7537.
	The centromeric histone H3 variant (CenH3) serves to target the kinetochore to the centromeres and thus ensures correct chromosome segregation during mitosis and meiosis. The Dictyostelium H3-like variant H3v1 was identified as the CenH3 ortholog. Dictyostelium CenH3 has an extended N-terminal domain with no similarity to any other known proteins and a histone fold domain at its C-terminus. Within the histone fold, alpha-helix 2 (alpha2) and an extended loop 1 (L1) have been shown to be required for targeting CenH3 to centromeres. Compared to other known and putative CenH3 histones, Dictyostelium CenH3 has a shorter L1, suggesting that the extension is not an obligatory feature. Through ChIP analysis and fluorescence microscopy of live and fixed cells, we provide here the first survey of centromere structure in amoebozoa. The six telocentric centromeres were found to mostly consist of all the DIRS-1 elements and to associate with H3K9me3. During interphase, the centromeres remain attached to the centrosome forming a single CenH3-containing cluster. Loading of Dictyostelium CenH3 onto centromeres occurs at the G2/prophase transition, in contrast to the anaphase/telophase loading of CenH3 observed in metazoans. This suggests that loading during G2/prophase is the ancestral eukaryotic mechanism and that anaphase/telophase loading of CenH3 has evolved more recently after the amoebozoa diverged from the animal linage.

Dubin, M. and W. Nellen (2010). "A versatile set of tagged expression vectors to monitor protein localisation and function in Dictyostelium." Gene 465(1-2): 1-8.
	We describe here a series of vectors for ectopic expression of tagged proteins in Dictyostelium discoideum. These vectors allow the addition of N- or C-terminal tags (GFP, mRFP, 3xFLAG, 3xHA, 6xMYC or TAP) with an optimised polylinker sequence and no additional amino acid residues at the N- or C-terminus of the protein. The expression cassettes were introduced into vectors containing Blasticidin or Geneticin resistance markers and into integrating as well as extrachromosomal plasmids. The vectors are designed as high and low copy versions and thus allow for a limited expression level control. They are also convenient with regard to complementation, co- and super-transformation. Finally the vectors share standardised cloning sites, so that a gene of interest can be easily transferred between vectors as experimental requirements evolve. These vectors were used to study the localisation of several putative RNA processing proteins including EriA and DicerB.

Duran, J. M., C. Anjard, et al. (2010). "Unconventional secretion of Acb1 is mediated by autophagosomes." J Cell Biol 188(4): 527-536.
	Starving Dictyostelium discoideum cells secrete AcbA, an acyl coenzyme A-binding protein (ACBP) that lacks a conventional signal sequence for entering the endoplasmic reticulum (ER). Secretion of AcbA in D. discoideum requires the Golgi-associated protein GRASP. In this study, we report that starvation-induced secretion of Acb1, the Saccharomyces cerevisiae ACBP orthologue, also requires GRASP (Grh1). This highlights the conserved function of GRASP in unconventional secretion. Although genes required for ER to Golgi or Golgi to cell surface transport are not required for Acb1 secretion in yeast, this process involves autophagy genes and the plasma membrane t-SNARE, Sso1. Inhibiting transport to vacuoles does not affect Acb1 secretion. In sum, our experiments reveal a unique secretory pathway where autophagosomes containing Acb1 evade fusion with the vacuole to prevent cargo degradation. We propose that these autophagosome intermediates fuse with recycling endosomes instead to form multivesicular body carriers that then fuse with the plasma membrane to release cargo.

Eder, M., U. Lutz-Meindl, et al. (2010). "Non-invasive LC-PolScope imaging of biominerals and cell wall anisotropy changes." Protoplasma 246(1-4): 49-64.
	The formation of defined shapes by cells is one of the challenging questions in biology. Due to the anisotropy of cell walls and of certain biominerals, the LC-PolScope represents a promising tool for tracking dynamic structural changes in vivo non-invasively and, to some extent, quantitatively. A complex three-dimensional biogenic system, the in vitro precipitation of calcium oxalate induced by cellulose stalks produced by Dictyostelium discoideum, was analyzed. Although the retardance values and orientation of the crystals with respect to the stalk were quickly and easily detected, this study raised a number of issues that were addressed in this work. The effect of the refractive index of the embedding medium was examined by taking advantage of the homogeneous size and shape distribution of kiwifruit raphides, a biologically controlled calcium oxalate biomineral and of cotton (Gossypium) seed fibers. The retardance remained consistent when embedding these samples in media with increasing refractive indices from 1.33 to 1.42 or 1.47 for sucrose or glycerol gradients, respectively. The general applicability of LC-PolScope image processing for biominerals and cell wall formation during development in vivo was demonstrated in a particular group of green algae, the Desmidiaceae. Various organization levels of the cell wall were identified, thus confirming earlier findings based on electron microscopy and immunostaining investigations. It can be concluded that LC-PolScope microscopy is an attractive tool for studying dynamic ordering of biomolecules, such as plant cell walls, when additional parameters regarding the structure, composition, and refractive indices of the specimen are available.

Engelke, H., D. Heinrich, et al. (2010). "Probing GFP-actin diffusion in living cells using fluorescence correlation spectroscopy." Phys Biol 7(4): 046014.
	The cytoskeleton of eukaryotic cells is continuously remodeled by polymerization and depolymerization of actin. Consequently, the relative content of polymerized filamentous actin (F-actin) and monomeric globular actin (G-actin) is subject to temporal and spatial fluctuations. Since fluorescence correlation spectroscopy (FCS) can measure the diffusion of fluorescently labeled actin it seems likely that FCS allows us to determine the dynamics and hence indirectly the structural properties of the cytoskeleton components with high spatial resolution. To this end we investigate the FCS signal of GFP-actin in living Dictyostelium discoideum cells and explore the inherent spatial and temporal signatures of the actin cytoskeleton. Using the free green fluorescent protein (GFP) as a reference, we find that actin diffusion inside cells is dominated by G-actin and slower than diffusion in diluted cell extract. The FCS signal in the dense cortical F-actin network near the cell membrane is probed using the cytoskeleton protein LIM and is found to be slower than cytosolic G-actin diffusion. Furthermore, we show that polymerization of the cytoskeleton induced by Jasplakinolide leads to a substantial decrease of G-actin diffusion. Pronounced fluctuations in the distribution of the FCS correlation curves can be induced by latrunculin, which is known to induce actin waves. Our work suggests that the FCS signal of GFP-actin in combination with scanning or spatial correlation techniques yield valuable information about the local dynamics and concomitant cytoskeletal properties.

Feasley, C. L., J. M. Johnson, et al. (2010). "Glycopeptidome of a heavily N-glycosylated cell surface glycoprotein of Dictyostelium implicated in cell adhesion." J Proteome Res 9(7): 3495-3510.
	Genetic analysis has implicated the cell surface glycoprotein gp130 in cell interactions of the social amoeba Dictyostelium, and information about the utilization of the 18 N-glycosylation sequons present in gp130 is needed to identify critical molecular determinants of its activity. Various glycomics strategies, including mass spectrometry of native and derivatized glycans, monosaccharide analysis, exoglycosidase digestion, and antibody binding, were applied to characterize a nonanchored version secreted from Dictyostelium. s-gp130 is modified by a predominant Man(8)GlcNAc(4) species containing bisecting and intersecting GlcNAc residues and additional high-mannose N-glycans substituted with sulfate, methyl-phosphate, and/or core alpha 3-fucose. Site mapping confirmed the occupancy of 15 sequons, some variably, and glycopeptide analysis confirmed 14 sites and revealed extensive heterogeneity at most sites. Glycopeptide glycoforms ranged from Man(6) to Man(9), GlcNAc(0-2) (peripheral), Fuc(0-2) (including core alpha 3 and peripheral), (SO(4))(0-1), and (MePO(4))(0-1), which represented elements of virtually the entire known cellular N-glycome as inferred from prior metabolic labeling and mass spectrometry studies. gp130, and a family of 14 related predicted glycoproteins whose polypeptide sequences are rapidly diverging in the Dictyostelium lineage, may contribute a functionally important shroud of high-mannose N-glycans at the interface of the amoebae with each other, their predators and prey, and the soil environment.

Fets, L., R. Kay, et al. (2010). "Dictyostelium." Curr Biol 20(23): R1008-1010.
	
Fiore-Donno, A. M., S. I. Nikolaev, et al. (2010). "Deep phylogeny and evolution of slime moulds (mycetozoa)." Protist 161(1): 55-70.
	Mycetozoa, characterized by spore-bearing fruiting bodies, are the most diverse Amoebozoa. They traditionally comprise three taxa: Myxogastria, Dictyostelia and Protostelia. Myxogastria and Dictyostelia typically have multispored fruiting bodies, but controversy exists whether they are related or arose independently from different unicellular ancestors. Protostelid slime moulds, with single-spored fruiting bodies, are possible evolutionary intermediates between them and typical amoebae, but have received almost no molecular study. Protostelid morphology is so varied that they might not be monophyletic. We therefore provide 38 new 18S rRNA and/or EF-1alpha gene sequences from Mycetozoa and related species, including four protostelids and the enigmatic Ceratiomyxa fruticulosa. Phylogenetic analyses support the monophyly of Dictyostelia, Myxogastria, and Ceratiomyxa (here collectively called "macromycetozoa") and show that protostelids are Amoebozoa, mostly related to non-fruiting amoebae of the class Variosea, but may not be monophyletic; some phylogenetic relationships remain poorly resolved. Ceratiomyxa fruticulosa, originally regarded as a myxogastrid, but in recent decades included in Protostelia, is a deeply diverging sister to Myxogastria. The protostelids studied here plus varipodid amoebae and the flagellates Phalansterium and Multicilia together probably form the outgroup to macromycetozoa plus Archamoebae. Thus protostelids and Variosea are especially significant for understanding the evolutionary transition from solitary amoebae to macromycetozoa.

Flowers, J. M., S. I. Li, et al. (2010). "Variation, sex, and social cooperation: molecular population genetics of the social amoeba Dictyostelium discoideum." PLoS Genet 6(7): e1001013.
	Dictyostelium discoideum is a eukaryotic microbial model system for multicellular development, cell-cell signaling, and social behavior. Key models of social evolution require an understanding of genetic relationships between individuals across the genome or possibly at specific genes, but the nature of variation within D. discoideum is largely unknown. We re-sequenced 137 gene fragments in wild North American strains of D. discoideum and examined the levels and patterns of nucleotide variation in this social microbial species. We observe surprisingly low levels of nucleotide variation in D. discoideum across these strains, with a mean nucleotide diversity (pi) of 0.08%, and no strong population stratification among North American strains. We also do not find any clear relationship between nucleotide divergence between strains and levels of social dominance and kin discrimination. Kin discrimination experiments, however, show that strains collected from the same location show greater ability to distinguish self from non-self than do strains from different geographic areas. This suggests that a greater ability to recognize self versus non-self may arise among strains that are more likely to encounter each other in nature, which would lead to preferential formation of fruiting bodies with clonemates and may prevent the evolution of cheating behaviors within D. discoideum populations. Finally, despite the fact that sex has rarely been observed in this species, we document a rapid decay of linkage disequilibrium between SNPs, the presence of recombinant genotypes among natural strains, and high estimates of the population recombination parameter rho. The SNP data indicate that recombination is widespread within D. discoideum and that sex as a form of social interaction is likely to be an important aspect of the life cycle.

Fountain, S. J. (2010). "Neurotransmitter receptor homologues of Dictyostelium discoideum." J Mol Neurosci 41(2): 263-266.
	The social amoeba Dictyostelium discoideum is a genetically amenable eukaryotic cell which displays many animal cell traits and has been used to study cellular signalling for over 30 years. Recently studies have highlighted the roles that molecules associated with synaptic transmission in animals, such as glutamate, GABA and ATP play in cellular differentiation and homeostasis in this simple organism. This short review summarises the evidence for the existence of both ionotropic and metabotropic families of neurotransmitter receptors in Dictyostelium.

Franklin, A., L. Hyatt, et al. (2010). "WD repeat domain of Dictyostelium myosin heavy chain kinase C functions in both substrate targeting and cellular localization." Eukaryot Cell 9(2): 344-349.
	Myosin II disassembly in Dictyostelium discoideum is regulated by three structurally related myosin heavy chain kinases (myosin II heavy chain kinase A [MHCK-A], -B, and -C). We show that the WD repeat domain of MHCK-C is unique in that it mediates both substrate targeting and subcellular localization, revealing a target for regulation that is distinct from those of the other MHCKs.

Frenkiel-Krispin, D., B. Maco, et al. (2010). "Structural analysis of a metazoan nuclear pore complex reveals a fused concentric ring architecture." J Mol Biol 395(3): 578-586.
	The sole gateway for molecular exchange between the cytoplasm and the nucleus is the nuclear pore complex (NPC). This large supramolecular assembly mediates transport of cargo into and out of the nucleus and fuse the inner and outer nuclear membranes to form an aqueous translocation channel. The NPC is composed of eight proteinaceous asymmetric units forming a pseudo-8-fold symmetric passage. Due to its shear size, complexity, and plastic nature, dissecting the high-resolution three-dimensional structure of the NPC in its hydrated state is a formidable challenge. Toward this goal, we applied cryo-electron tomography to spread nuclear envelopes from Xenopus oocytes. To compensate for perturbations of the 8-fold symmetry of individual NPCs, we performed symmetry-independent asymmetric unit averaging of three-dimensional tomographic NPC volumes to eventually yield a refined model at 6.4 nm resolution. This approach revealed novel structural features, particularly in the spoke-ring complex and luminal domains. Fused concentric ring architecture of the spoke-ring complex was found along the translocation channel. Additionally, a comparison of the refined Xenopus model to that of its Dictyostelium homologue yielded similar pore diameters at the level of the three canonical rings, although the Xenopus NPC was found to be 30% taller than the Dictyostelium pore. This discrepancy is attributed primarily to the relatively low homology and different organization of some nucleoporins in the Dictyostelium genome as compared to that of vertebrates. Nevertheless, the experimental conditions impose a preferred axial orientation of the NPCs within spread Xenopus oocyte nuclear envelopes. This may at least in part explain the increased height of the reconstructed vertebrate NPCs compared to those obtained from tomographic reconstruction of intact Dictyostelium nuclei.

Friedberg, F. and F. Rivero (2010). "Single and multiple CH (calponin homology) domain containing multidomain proteins in Dictyostelium discoideum: an inventory." Mol Biol Rep 37(6): 2853-2862.
	We present an inventory of single or multiple calponin homology (CH) domain containing proteins of Dictyostelium discoideum. A multiple alignment and a phylogenetic tree of all 60 CH domains found in 36 proteins showed that most CH domains can be assigned to one of 6 types. We have then distributed the proteins into several classes according to the type and arrangement of the CH domains. Most proteins belong to the class of ABD (actin-binding domain)-forming CH tandems (CH1-CH2) of the alpha-actinin and fimbrin families or to the class of CH3 domain-bearing proteins. There are a few examples of proteins with a single CH1 or CH2 domain, one with a CH1-CH1 doublet and a single representative of the CHe class of microtubule-binding proteins. A comparison with CH domain proteins in Homo sapiens suggests that while the individual domains are available in both species, the existence of identical multidomain proteins in toto is rare. Fimbrin 1, alpha-actinin and EB1 appear as perfect orthologs in both species, whereas filamin and interaptin may represent ancestral forms of human filamin and nesprins. In four more cases (NAV/Unc-53-, smoothelin-, transgelin- and Gas2-related proteins) functional data are needed in order to establish a potential relationship with a human counterpart. Although extensive data exist for a few of the D. discoideum CH proteins, most remain to be characterized and our analysis may help predicting some of their properties.

Frye, J. J., V. A. Klenchin, et al. (2010). "Insights into the importance of hydrogen bonding in the gamma-phosphate binding pocket of myosin: structural and functional studies of serine 236." Biochemistry 49(23): 4897-4907.
	The active site of myosin contains a group of highly conserved amino acid residues whose roles in nucleotide hydrolysis and energy transduction might appear to be obvious from the initial structural and kinetic analyses but become less clear on deeper investigation. One such residue is Ser236 (Dictyostelium discoideum myosin II numbering) which was proposed to be involved in a hydrogen transfer network during gamma-phosphate hydrolysis of ATP, which would imply a critical function in ATP hydrolysis and motility. The S236A mutant protein shows a comparatively small decrease in hydrolytic activity and motility, and thus this residue does not appear to be essential. To understand better the contribution of Ser236 to the function of myosin, structural and kinetic studies have been performed on the S236A mutant protein. The structures of the D. discoideum motor domain (S1dC) S236A mutant protein in complex with magnesium pyrophosphate, MgAMPPNP, and MgADP.vanadate have been determined. In contrast to the previous structure of wild-type S1dC, the S236A.MgAMPPNP complex crystallized in the closed state. Furthermore, transient-state kinetics showed a 4-fold reduction of the nucleotide release step, suggesting that the mutation stabilizes a closed active site. The structures show that a water molecule approximately adopts the location of the missing hydroxyl of Ser236 in the magnesium pyrophosphate and MgAMPPNP structures. This study suggests that the S236A mutant myosin proceeds via a different structural mechanism than wild-type myosin, where the alternate mechanism is able to maintain near normal transient-state kinetic values.

Fuller, D., W. Chen, et al. (2010). "External and internal constraints on eukaryotic chemotaxis." Proc Natl Acad Sci U S A 107(21): 9656-9659.
	Chemotaxis, the chemically guided movement of cells, plays an important role in several biological processes including cancer, wound healing, and embryogenesis. Chemotacting cells are able to sense shallow chemical gradients where the concentration of chemoattractant differs by only a few percent from one side of the cell to the other, over a wide range of local concentrations. Exactly what limits the chemotactic ability of these cells is presently unclear. Here we determine the chemotactic response of Dictyostelium cells to exponential gradients of varying steepness and local concentration of the chemoattractant cAMP. We find that the cells are sensitive to the steepness of the gradient as well as to the local concentration. Using information theory techniques, we derive a formula for the mutual information between the input gradient and the spatial distribution of bound receptors and also compute the mutual information between the input gradient and the motility direction in the experiments. A comparison between these quantities reveals that for shallow gradients, in which the concentration difference between the back and the front of a 10-mum-diameter cell is &lt;5%, and for small local concentrations (&lt;10 nM) the intracellular information loss is insignificant. Thus, external fluctuations due to the finite number of receptors dominate and limit the chemotactic response. For steeper gradients and higher local concentrations, the intracellular information processing is suboptimal and results in a smaller mutual information between the input gradient and the motility direction than would have been predicted from the ligand-receptor binding process.

Galardi-Castilla, M., A. Garciandia, et al. (2010). "The Dictyostelium discoideum acaA gene is transcribed from alternative promoters during aggregation and multicellular development." PLoS One 5(10): e13286.
	BACKGROUND: Extracellular cAMP is a key extracellular signaling molecule that regulates aggregation, cell differentiation and morphogenesis during multi-cellular development of the social amoeba Dictyostelium discoideum. This molecule is produced by three different adenylyl cyclases, encoded by the genes acaA, acrA and acgA, expressed at different stages of development and in different structures. METHODOLOGY/PRINCIPAL FINDINGS: This article describes the characterization of the promoter region of the acaA gene, showing that it is transcribed from three different alternative promoters. The distal promoter, promoter 1, is active during the aggregation process while the more proximal promoters are active in tip-organiser and posterior regions of the structures. A DNA fragment containing the three promoters drove expression to these same regions and similar results were obtained by in situ hybridization. Analyses of mRNA expression by quantitative RT-PCR with specific primers for each of the three transcripts also demonstrated their different temporal patterns of expression. CONCLUSIONS/SIGNIFICANCE: The existence of an aggregation-specific promoter can be associated with the use of cAMP as chemo-attractant molecule, which is specific for some Dictyostelium species. Expression at late developmental stages indicates that adenylyl cyclase A might play a more important role in post-aggregative development than previously considered.

Gerisch, G. (2010). "Self-organizing actin waves that simulate phagocytic cup structures." PMC Biophys 3(1): 7.
	This report deals with actin waves that are spontaneously generated on the planar, substrate-attached surface of Dictyostelium cells. These waves have the following characteristics. (1) They are circular structures of varying shape, capable of changing the direction of propagation. (2) The waves propagate by treadmilling with a recovery of actin incorporation after photobleaching of less than 10 seconds. (3) The waves are associated with actin-binding proteins in an ordered 3-dimensional organization: with myosin-IB at the front and close to the membrane, the Arp2/3 complex throughout the wave, and coronin at the cytoplasmic face and back of the wave. Coronin is a marker of disassembling actin structures. (4) The waves separate two areas of the cell cortex that differ in actin structure and phosphoinositide composition of the membrane. The waves arise at the border of membrane areas rich in phosphatidylinositol (3,4,5) trisphosphate (PIP3). The inhibition of PIP3 synthesis reversibly inhibits wave formation. (5) The actin wave and PIP3 patterns resemble 2-dimensional projections of phagocytic cups, suggesting that they are involved in the scanning of surfaces for particles to be taken up.PACS Codes: 87.16.Ln, 87.19.lp, 89.75.Fb.

Giusti, C., M. F. Luciani, et al. (2010). "A second signal for autophagic cell death?" Autophagy 6(6): 823-824.
	Dictyostelium cells in monolayers in vitro lend themselves well to a study of autophagic cell death (ACD). There is no apoptosis machinery in the protist Dictyostelium, no caspase nor Bcl-2 family members (except a paracaspase whose inactivation does not alter cell death), thus there is no apoptosis that could interfere with, or substitute for, nonapoptotic cell death. Also, Dictyostelium, a eukaryote, has a haploid genome, which facilitates random insertional mutagenesis.

Giusti, C., M. F. Luciani, et al. (2010). "Autophagic cell death in Dictyostelium requires the receptor histidine kinase DhkM." Mol Biol Cell 21(11): 1825-1835.
	Dictyostelium constitutes a genetically tractable model for the analysis of autophagic cell death (ACD). During ACD, Dictyostelium cells first transform into paddle cells and then become round, synthesize cellulose, vacuolize, and die. Through random insertional mutagenesis, we identified the receptor histidine kinase DhkM as being essential for ACD. Surprisingly, different DhkM mutants showed distinct nonvacuolizing ACD phenotypes. One class of mutants arrested ACD at the paddle cell stage, perhaps through a dominant-negative effect. Other mutants, however, progressed further in the ACD program. They underwent rounding and cellulose synthesis but stopped before vacuolization. Moreover, they underwent clonogenic but not morphological cell death. Exogenous 8-bromo-cAMP restored vacuolization and death. A role for a membrane receptor at a late stage of the ACD pathway is puzzling, raising questions as to which ligand it is a receptor for and which moieties it phosphorylates. Together, DhkM is the most downstream-known molecule required for this model ACD, and its distinct mutants genetically separate previously undissociated late cell death events.

Glenn, A. E., E. P. Karagianni, et al. (2010). "Comparative genomic and phylogenetic investigation of the xenobiotic metabolizing arylamine N-acetyltransferase enzyme family." FEBS Lett 584(14): 3158-3164.
	Arylamine N-acetyltransferases (NATs) are xenobiotic metabolizing enzymes characterized in several bacteria and eukaryotic organisms. We report a comprehensive phylogenetic analysis employing an exhaustive dataset of NAT-homologous sequences recovered through inspection of 2445 genomes. We describe the first NAT homologues in viruses, archaea, protists, many fungi and invertebrates, providing complete annotations in line with the consensus nomenclature. Contrary to the NAT genes of vertebrates, introns are commonly found within the homologous coding regions of lower eukaryotes. The NATs of fungi and higher animals are distinctly monophyletic, but evidence supports a mixed phylogeny of NATs among bacteria, protists and possibly some invertebrates.

Greene, D. M., D. W. Hsu, et al. (2010). "Control of cyclin C levels during development of Dictyostelium." PLoS One 5(5): e10543.
	BACKGROUND: Cdk8 and its partner cyclin C form part of the mediator complex which links the basal transcription machinery to regulatory proteins. The pair are required for correct regulation of a subset of genes and have been implicated in control of development in a number of organisms including the social amoeba Dictyostelium discoideum. When feeding, Dictyostelium amoebae are unicellular but upon starvation they aggregate to form a multicellular structure which develops into a fruiting body containing spores. Cells in which the gene encoding Cdk8 has been deleted fail to enter aggregates due to a failure of early gene expression. PRINCIPAL FINDINGS: We have monitored the expression levels of cyclin C protein during development and find levels decrease after the multicellular mound is formed. This decrease is triggered by extracellular cAMP that, in turn, is working in part through an increase in intracellular cAMP. The loss of cyclin C is coincident with a reduction in the association of Cdk8 with a high molecular weight complex in the nucleus. Overexpression of cyclin C and Cdk8 lead to an increased rate of early development, consistent with the levels being rate limiting. CONCLUSIONS: Overall these results show that both cyclin C and Cdk8 are regulated during development in response to extracellular signals and the levels of these proteins are important in controlling the timing of developmental processes. These findings have important implications for the role of these proteins in controlling development, suggesting that they are targets for developmental signals to regulate gene expression.

Gregor, T., K. Fujimoto, et al. (2010). "The onset of collective behavior in social amoebae." Science 328(5981): 1021-1025.
	In the social amoebae Dictyostelium discoideum, periodic synthesis and release of extracellular cyclic adenosine 3',5'-monophosphate (cAMP) guide cell aggregation and commitment to form fruiting bodies. It is unclear whether these oscillations are an intrinsic property of individual cells or if they exist only as a population-level phenomenon. Here, we showed by live-cell imaging of intact cell populations that pulses originate from a discrete location despite constant exchange of cells to and from the region. In a perfusion chamber, both isolated single cells and cell populations switched from quiescence to rhythmic activity depending on the concentration of extracellular cAMP. A quantitative analysis showed that stochastic pulsing of individual cells below the threshold concentration of extracellular cAMP plays a critical role in the onset of collective behavior.

Gruver, J. S., A. A. Potdar, et al. (2010). "Bimodal analysis reveals a general scaling law governing nondirected and chemotactic cell motility." Biophys J 99(2): 367-376.
	Cell motility is a fundamental process with relevance to embryonic development, immune response, and metastasis. Cells move either spontaneously, in a nondirected fashion, or in response to chemotactic signals, in a directed fashion. Even though they are often studied separately, both forms of motility share many complex processes at the molecular and subcellular scale, e.g., orchestrated cytoskeletal rearrangements and polarization. In addition, at the cellular level both types of motility include persistent runs interspersed with reorientation pauses. Because there is a great range of variability in motility among different cell types, a key challenge in the field is to integrate these multiscale processes into a coherent framework. We analyzed the motility of Dictyostelium cells with bimodal analysis, a method that compares time spent in persistent versus reorientation mode. Unexpectedly, we found that reorientation time is coupled with persistent time in an inverse correlation and, surprisingly, the inverse correlation holds for both nondirected and chemotactic motility, so that the full range of Dictyostelium motility can be described by a single scaling relationship. Additionally, we found an identical scaling relationship for three human cell lines, indicating that the coupling of reorientation and persistence holds across species and making it possible to describe the complexity of cell motility in a surprisingly general and simple manner. With this new perspective, we analyzed the motility of Dictyostelium mutants, and found four in which the coupling between two modes was altered. Our results point to a fundamental underlying principle, described by a simple scaling law, unifying mechanisms of eukaryotic cell motility at several scales.

Guetta, D., K. Langou, et al. (2010). "FYVE-dependent endosomal targeting of an arrestin-related protein in amoeba." PLoS One 5(12): e15249.
	BACKGROUND: Visual and beta-arrestins are scaffolding proteins involved in the regulation of receptor-dependent intracellular signaling and their trafficking. The arrestin superfamilly includes several arrestin domain-containing proteins and the structurally related protein Vps26. In Dictyostelium discoideum, the arrestin-domain containing proteins form a family of six members, namely AdcA to -F. In contrast to canonical arrestins, Dictyostelium Adc proteins show a more complex architecture, as they possess, in addition to the arrestin core, other domains, such as C2, FYVE, LIM, MIT and SAM, which potentially mediate selective interactions with either lipids or proteins. METHODOLOGY AND PRINCIPAL FINDINGS: A detailed analysis of AdcA has been performed. AdcA extends on both sides of the arrestin core, in particular by a FYVE domain which mediates selective interactions with PI(3)P, as disclosed by intrinsic fluorescence measurements and lipid overlay assays. Localization studies showed an enrichment of tagged- and endogenous AdcA on the rim of early macropinosomes and phagosomes. This vesicular distribution relies on a functional FYVE domain. Our data also show that the arrestin core binds the ADP-ribosylation factor ArfA, the unique amoebal Arf member, in its GDP-bound conformation. SIGNIFICANCE: This work describes one of the 6 arrestin domain-containing proteins of Dictyostelium, a novel and atypical member of the arrestin clan. It provides the basis for a better understanding of arrestin-related protein involvement in trafficking processes and for further studies on the expanding roles of arrestins in eukaryotes.

Hatayama, M. and J. Aruga (2010). "Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions." BMC Evol Biol 10: 53.
	BACKGROUND: The C2H2 zinc finger (ZF) domain is widely conserved among eukaryotic proteins. In Zic/Gli/Zap1 C2H2 ZF proteins, the two N-terminal ZFs form a single structural unit by sharing a hydrophobic core. This structural unit defines a new motif comprised of two tryptophan side chains at the center of the hydrophobic core. Because each tryptophan residue is located between the two cysteine residues of the C2H2 motif, we have named this structure the tandem CWCH2 (tCWCH2) motif. RESULTS: Here, we characterized 587 tCWCH2-containing genes using data derived from public databases. We categorized genes into 11 classes including Zic/Gli/Glis, Arid2/Rsc9, PacC, Mizf, Aebp2, Zap1/ZafA, Fungl, Zfp106, Twincl, Clr1, and Fungl-4ZF, based on sequence similarity, domain organization, and functional similarities. tCWCH2 motifs are mostly found in organisms belonging to the Opisthokonta (metazoa, fungi, and choanoflagellates) and Amoebozoa (amoeba, Dictyostelium discoideum). By comparison, the C2H2 ZF motif is distributed widely among the eukaryotes. The structure and organization of the tCWCH2 motif, its phylogenetic distribution, and molecular phylogenetic analysis suggest that prototypical tCWCH2 genes existed in the Opisthokonta ancestor. Within-group or between-group comparisons of the tCWCH2 amino acid sequence identified three additional sequence features (site-specific amino acid frequencies, longer linker sequence between two C2H2 ZFs, and frequent extra-sequences within C2H2 ZF motifs). CONCLUSION: These features suggest that the tCWCH2 motif is a specialized motif involved in inter-zinc finger interactions.

Hayashi, Y., S. Nakamura, et al. (2010). "Host range of obligate intracellular bacterium Parachlamydia acanthamoebae." Microbiol Immunol 54(11): 707-713.
	The obligate intracellular bacterium Parachlamydia acanthamoebae is a potential human pathogen, but the host range of the bacteria remains unknown. Hence, the growth of P. acanthamoebae Bn in protozoa (Tetrahymena, Acanthamoeba, Dictyostelium) and mammalian cells (HEp-2, Vero, THP-1, PMA-stimulated THP-1, Jurkat) was assessed using an AIU assay which had been previously established by the current authors. P. acanthamoebae grew in Acanthamoeba but not in the other cell types. The growth was also confirmed using DAPI staining, FISH and TEM. These results indicate that the host range of P. acanthamoebae is limited.

Hu, B., D. Fuller, et al. (2010). "Phenomenological approach to eukaryotic chemotactic efficiency." Phys Rev E Stat Nonlin Soft Matter Phys 81(3 Pt 1): 031906.
	Eukaryotic cells are capable of detecting small chemical gradients for a wide range of background concentrations. Ultimately, fluctuations place a limit on gradient sensing and recent work has focused on the role of stochastic receptor occupancy as one possible limiting factor. Here, we use a phenomenological approach to add spontaneous motility fluctuations to receptor noise and predict the directional statistics of eukaryotic chemotaxis. Specifically, an Ito diffusion equation with direction-dependent multiplicative noise is developed and analytically studied. We show that our approach can naturally accommodate recent experimental data for the chemotaxis of the social amoeba Dictyostelium.

Ishikawa-Ankerhold, H. C., G. Gerisch, et al. (2010). "Genetic evidence for concerted control of actin dynamics in cytokinesis, endocytic traffic, and cell motility by coronin and Aip1." Cytoskeleton (Hoboken) 67(7): 442-455.
	Coronin and actin-interacting protein 1 (Aip1) are actin-binding proteins that by different mechanisms inhibit actin polymerization or enhance the disassembly of actin filaments. Cells of Dictyostelium discoideum lacking both proteins are retarded in growth and early development and often fail to proceed to fruiting body formation. Coronin/Aip1-null cells show numerous surface protrusions enriched in filamentous actin and cofilin. We show that the double-null cells are characterized by an increase in filamentous actin that causes a thickening of the cell cortex. This imbalance has severe consequences for processes that rely on the dynamic reorganization of the actin cytoskeleton, such as cell motility, cytokinesis and endocytosis. Although cell motility is considerably slowed down, the double-mutant cells are still capable of orientating in a gradient of chemoattractant. The cytokinesis defect is caused by the lack of proper cleavage furrow formation, a defect that is partially rescued by low concentrations of latrunculin A, an inhibitor of actin polymerization. Furthermore, we demonstrate that the disassembly of the actin coat after phagocytic or macropinocytic uptake is significantly delayed in the double-mutant cells. Our results prove that coronin and Aip1 are important effectors that act together in maintaining the balance of actin polymerization and depolymerization in living cells.

Iwai, S. and T. Q. Uyeda (2010). "Myosin-actin interaction in Dictyostelium cells revealed by GFP-based strain sensor and validated linear spectral unmixing." Cytometry A 77(8): 743-750.
	Myosin is an actin-based motor protein that is involved in a wide range of cellular motile processes. Although in vitro properties of the myosin-actin interaction have been extensively studied, the interaction in vivo remains poorly understood. Recently, we developed a GFP-based strain sensor termed PriSSM (PRIM-based strain sensor module), by using the proximity imaging (PRIM) technique, which detects spectral changes of two GFP molecules that are in direct contact. Using PriSSM-myosin II fusion proteins, the interaction between myosin II and F-actin can be detected in Dictyostelium cells. In the spectroscopic measurements of PriSSM, to decompose the measured spectra of the cells expressing the sensor proteins into the contributions from the sensor and the background autofluorescence, we applied the linear spectral unmixing approach, which was based on the assumption that the errors at each wavelength were independent. Cellular autofluorescence, however, often includes systematic errors, so that the unmixing procedures might lead to biased estimates. Here, to validate our spectral unmixing procedures, we estimate the possible maximum errors in the fluorescence ratio values that are obtained by unmixing spectra including such systematic errors. This estimation provided a general criterion to validate the results obtained by linear unmixing of spectra including serially correlated error terms. Using the proposed criterion and PriSSM-myosin II fusion proteins, we examined the interaction between myosin II and F-actin in Dictyostelium cells under several different conditions. The spectroscopic results, together with the microscopic observations of the cells expressing the proteins, suggest that the formation of myosin filaments through the tail region has only a slight effect on binding to F-actin but has significant effects on the cortical localization of myosin II.

Jowhar, D., G. Wright, et al. (2010). "Open access microfluidic device for the study of cell migration during chemotaxis." Integr Biol (Camb) 2(11-12): 648-658.
	Cells sense and interpret chemical gradients, and respond by localized responses that lead to directed migration. An open microfluidic device (OMD) was developed to provide quantitative information on both the gradient and morphological changes that occurred as cells crawled through various microfabricated channels. This device overcame problems that many current devices have been plagued with, such as complicated cell loading, media evaporation and channel blockage by air bubbles. We used a micropipette to set up stable gradients formed by passive diffusion and thus avoided confounding cellular responses produced by shear forces. Two versions of the OMD are reported here: one device that has channels with widths of 6, 8, 10 and 12 mum, while the other has two large 100 mum channels to minimize cellular interaction with lateral walls. These experiments compared the migration rates and qualitative behavior of Dictyostelium discoideum cells responding to measurable cAMP and folic acid gradients in small and large channels. We report on the influence that polarity has on a cell's ability to migrate when confined in a channel. Polarized cells that migrated to cAMP were significantly faster than the unpolarized cells that crawled toward folic acid. Unpolarized cells in wide channels often strayed off course, yet migrated faster than unpolarized cells in confined channels. Cells in channels farthest from the micropipette migrated through the channels at rates similar to cells in channels with higher concentrations, suggesting that cell speed was independent of mean concentration. Lastly, it was found that the polarized cells could easily change migration direction even when only the leading edge of the cell was exposed to a lateral gradient.

Kabir, M., N. Noman, et al. (2010). "Reverse engineering gene regulatory network from microarray data using linear time-variant model." BMC Bioinformatics 11 Suppl 1: S56.
	BACKGROUND: Gene regulatory network is an abstract mapping of gene regulations in living cells that can help to predict the system behavior of living organisms. Such prediction capability can potentially lead to the development of improved diagnostic tests and therapeutics. DNA microarrays, which measure the expression level of thousands of genes in parallel, constitute the numeric seed for the inference of gene regulatory networks. In this paper, we have proposed a new approach for inferring gene regulatory networks from time-series gene expression data using linear time-variant model. Here, Self-Adaptive Differential Evolution, a versatile and robust Evolutionary Algorithm, is used as the learning paradigm. RESULTS: To assess the potency of the proposed work, a well known nonlinear synthetic network has been used. The reconstruction method has inferred this synthetic network topology and the associated regulatory parameters with high accuracy from both the noise-free and noisy time-series data. For validation purposes, the proposed approach is also applied to the simulated expression dataset of cAMP oscillations in Dictyostelium discoideum and has proved it's strength in finding the correct regulations. The strength of this work has also been verified by analyzing the real expression dataset of SOS DNA repair system in Escherichia coli and it has succeeded in finding more correct and reasonable regulations as compared to various existing works. CONCLUSION: By the proposed approach, the gene interaction networks have been inferred in an efficient manner from both the synthetic, simulated cAMP oscillation expression data and real expression data. The computational time of this approach is also considerably smaller, which makes it to be more suitable for larger network reconstruction. Thus the proposed approach can serve as an initiate for the future researches regarding the associated area.

Kamimura, Y. and P. N. Devreotes (2010). "Phosphoinositide-dependent protein kinase (PDK) activity regulates phosphatidylinositol 3,4,5-trisphosphate-dependent and -independent protein kinase B activation and chemotaxis." J Biol Chem 285(11): 7938-7946.
	Chemotactic cells must sense shallow extracellular gradients and produce localized intracellular responses. We previously showed that the temporal and spatial activation of two protein kinase B (PKB) homologues, PkbA and PkbR1, in Dictyostelium discoideum by phosphorylation of activation loops (ALs) and hydrophobic motifs had important roles in chemotaxis. We found that hydrophobic motif phosphorylation depended on regulation of TorC2 (target of rapamycin complex 2); however, the regulation of AL phosphorylation remains to be determined at a molecular level. Here, we show that two PDK (phosphoinositide-dependent protein kinase) homologues, PdkA and PdkB, function as the key AL kinases. Cells lacking both PdkA and PdkB are defective in PKB activation, chemotaxis, and fruiting body formation upon nutrient deprivation. The pleckstrin homology domain of PdkA is sufficient to localize it to the membrane, but transient activation of PdkA is independent of PIP(3) as well as TorC2 and dispensable for full function. These results confirm the importance of the TorC2-PDK-PKB pathway in chemotaxis and point to a novel mechanism of regulation of PDKs by chemoattractant.

Kessin, R. H. (2010). "Two different genomes that produce the same result." Genome Biol 11(4): 114.
	Despite considerable differences in genomic sequence, the developmental program of gene expression between two similar Dictyostelium species is remarkably similar.

Khare, A. and G. Shaulsky (2010). "Cheating by exploitation of developmental prestalk patterning in Dictyostelium discoideum." PLoS Genet 6(2): e1000854.
	The cooperative developmental system of the social amoeba Dictyostelium discoideum is susceptible to exploitation by cheaters-strains that make more than their fair share of spores in chimerae. Laboratory screens in Dictyostelium have shown that the genetic potential for facultative cheating is high, and field surveys have shown that cheaters are abundant in nature, but the cheating mechanisms are largely unknown. Here we describe cheater C (chtC), a strong facultative cheater mutant that cheats by affecting prestalk differentiation. The chtC gene is developmentally regulated and its mRNA becomes stalk-enriched at the end of development. chtC mutants are defective in maintaining the prestalk cell fate as some of their prestalk cells transdifferentiate into prespore cells, but that defect does not affect gross developmental morphology or sporulation efficiency. In chimerae between wild-type and chtC mutant cells, the wild-type cells preferentially give rise to prestalk cells, and the chtC mutants increase their representation in the spore mass. Mixing chtC mutants with other cell-type proportioning mutants revealed that the cheating is directly related to the prestalk-differentiation propensity of the victim. These findings illustrate that a cheater can victimize cooperative strains by exploiting an established developmental pathway.

Kimura, K., H. Kuwayama, et al. (2010). "Developmental significance of cyanide-resistant respiration under stressed conditions: experiments in Dictyostelium cells." Dev Growth Differ 52(7): 645-656.
	We have previously reported that benzohydroxamic acid (BHAM), a potent inhibitor of cyanide (CN)-resistant respiration mediated by alternative oxidase (AOX), induces formation of unique cell masses (i.e., stalk-like cells with a large vacuole and thick cell wall) in starved Dictyostelium cells. Unexpectedly, however, aox-null cells prepared by homologous recombination exhibited normal development under normal culture conditions on agar, indicating that BHAM-induced stalk formation is not solely attributable to inhibition of CN-resistant respiration. This also suggests that a series of pharmacological approaches in the field of life science has serious limitations. Under stress (e.g., in submerged culture), starved aox-null cells exhibited slightly delayed aggregation compared with parental Ax-2 cells; most cells remained as loose aggregates even after prolonged incubation. Also, the developmental defects of aox-null cells became more marked upon incubation for 30 min just after starvation in the presence of &gt;/= 1.75 mmol/L H(2)O(2). This seems to indicate that CN-resistant respiration could mitigate cellular damage through reactive oxygen species (ROS), because AOX has a potential role in reduction of ROS production. Starved aox-null cells did not develop in the presence of 5 mmol/L KCN (which completely inhibited the conventional cytochrome-mediated respiration) and remained as non-aggregated single cells on agar even after prolonged incubation. Somewhat surprisingly, however, parental Ax-2 cells were found to develop normally, forming fruiting bodies even in the presence of 10 mmol/L KCN. Taken together, these results suggest that CN-resistant respiration might compensate for the production of adenosine tri-phosphate via oxidative phosphorylation.

King, J., M. Keim, et al. (2010). "Genetic control of lithium sensitivity and regulation of inositol biosynthetic genes." PLoS One 5(6): e11151.
	Lithium (Li(+)) is a common treatment for bipolar mood disorder, a major psychiatric illness with a lifetime prevalence of more than 1%. Risk of bipolar disorder is heavily influenced by genetic predisposition, but is a complex genetic trait and, to date, genetic studies have provided little insight into its molecular origins. An alternative approach is to investigate the genetics of Li(+) sensitivity. Using the social amoeba Dictyostelium, we previously identified prolyl oligopeptidase (PO) as a modulator of Li(+) sensitivity. In a link to the clinic, PO enzyme activity is altered in bipolar disorder patients. Further studies demonstrated that PO is a negative regulator of inositol(1,4,5)trisphosphate (IP(3)) synthesis, a Li(+) sensitive intracellular signal. However, it was unclear how PO could influence either Li(+) sensitivity or risk of bipolar disorder. Here we show that in both Dictyostelium and cultured human cells PO acts via Multiple Inositol Polyphosphate Phosphatase (Mipp1) to control gene expression. This reveals a novel, gene regulatory network that modulates inositol metabolism and Li(+) sensitivity. Among its targets is the inositol monophosphatase gene IMPA2, which has also been associated with risk of bipolar disorder in some family studies, and our observations offer a cellular signalling pathway in which PO activity and IMPA2 gene expression converge.

King, J. S., D. M. Veltman, et al. (2010). "SCAR/WAVE is activated at mitosis and drives myosin-independent cytokinesis." J Cell Sci 123(Pt 13): 2246-2255.
	Cell division requires the tight coordination of multiple cytoskeletal pathways. The best understood of these involves myosin-II-dependent constriction around the cell equator, but both Dictyostelium and mammalian cells also use a parallel, adhesion-dependent mechanism to generate furrows. We show that the actin nucleation factor SCAR/WAVE is strongly activated during Dictyostelium cytokinesis. This activation localises to large polar protrusions, driving separation of the daughter cells. This continues for 10 minutes after division before the daughter cells revert to normal random motility, indicating that this is a tightly regulated process. We demonstrate that SCAR activity is essential to drive myosin-II-independent cytokinesis, and stabilises the furrow, ensuring symmetrical division. SCAR is also responsible for the generation of MiDASes, mitosis-specific actin-rich adhesions. Loss of SCAR in both Dictyostelium and Drosophila leads to a similar mitotic phenotype, with severe mitotic blebbing, indicating conserved functionality. We also find that the microtubule end-binding protein EB1 is required to restrict SCAR localisation and direct migration. EB1-null cells also exhibit decreased adhesion during mitosis. Our data reveal a spindle-directed signalling pathway that regulates SCAR activity, migration and adhesion at mitosis.

Knecht, D. A., R. A. LaFleur, et al. (2010). "Cucurbitacin I inhibits cell motility by indirectly interfering with actin dynamics." PLoS One 5(11): e14039.
	BACKGROUND: Cucurbitacins are plant natural products that inhibit activation of the Janus kinase 2 (JAK2)/signal transducer and activator of transcription 3 (STAT3) pathway by an unknown mechanism. They are also known to cause changes in the organization of the actin cytoskeleton. METHODOLOGY/PRINCIPAL FINDINGS: We show that cucurbitacin I potently inhibits the migration of Madin-Darby canine kidney (MDCK) cell sheets during wound closure, as well as the random motility of B16-F1 mouse melanoma cells, but has no effect on movement of Dictyostelium discoideum amoebae. Upon treatment of MDCK or B16-F1 cells with cucurbitacin I, there is a very rapid cessation of motility and gradual accumulation of filamentous actin aggregates. The cellular effect of the compound is similar to that observed when cells are treated with the actin filament-stabilizing agent jasplakinolide. However, we found that, unlike jasplakinolide or phallacidin, cucurbitacin I does not directly stabilize actin filaments. In in vitro actin depolymerization experiments, cucurbitacin I had no effect on the rate of actin filament disassembly at the nanomolar concentrations that inhibit cell migration. At elevated concentrations, the depolymerization rate was also unaffected, although there was a delay in the initiation of depolymerization. Therefore, cucurbitacin I targets some factor involved in cellular actin dynamics other than actin itself. Two candidate proteins that play roles in actin depolymerization are the actin-severing proteins cofilin and gelsolin. Cucurbitacin I possesses electrophilic reactivity that may lead to chemical modification of its target protein, as suggested by structure-activity relationship data. However, mass spectrometry revealed no evidence for modification of purified cofilin or gelsolin by cucurbitacin I. CONCLUSIONS/SIGNIFICANCE: Cucurbitacin I results in accumulation of actin filaments in cells by a unique indirect mechanism. Furthermore, the proximal target of cucurbitacin I relevant to cell migration is unlikely to be the same one involved in activation of the JAK2/STAT3 pathway.

Koonce, M. P. and R. Graf (2010). "Dictyostelium discoideum: a model system for ultrastructural analyses of cell motility and development." Methods Cell Biol 96: 197-216.
	Dictyostelium occupies an interesting niche in the grand scheme of model organisms. On the one hand, it is a compact, highly motile single cell that presents numerous opportunities to investigate the fundamental mechanisms of signal transduction, cell movement, and pathogen infection. However, upon starvation, individual cells enter a developmental pathway that involves cell aggregation, cell-cell adhesion, pattern formation, and differentiation. Thus, Dictyostelium is also well known as a basic model for studying developmental processes. Electron microscopy (EM) has played a large role in both the unicellular and the multicellular life stages, for example, providing image detail for structure/function relationships of cytoskeletal proteins, the deposition of cellulose fibrils in maturing spores, and the identification of intercellular junctional complexes. Powerful combinations of robust molecular genetic tools, high-resolution light microscopy, and EM methods make this organism an attractive model for imaging dynamic cell processes. This chapter serves to highlight the past and current EM approaches that have advanced our understanding of how cells and proteins function.

Kortholt, A., P. Bolourani, et al. (2010). "A Rap/phosphatidylinositol 3-kinase pathway controls pseudopod formation [corrected]." Mol Biol Cell 21(6): 936-945.
	GbpD, a Dictyostelium discoideum guanine exchange factor specific for Rap1, has been implicated in adhesion, cell polarity, and chemotaxis. Cells overexpressing GbpD are flat, exhibit strongly increased cell-substrate attachment, and extend many bifurcated and lateral pseudopodia. Phg2, a serine/threonine-specific kinase, mediates Rap1-regulated cell-substrate adhesion, but not cell polarity or chemotaxis. In this study we demonstrate that overexpression of GbpD in pi3k1/2-null cells does not induce the adhesion and cell morphology phenotype. Furthermore we show that Rap1 directly binds to the Ras binding domain of PI3K, and overexpression of GbpD leads to strongly enhanced PIP3 levels. Consistently, upon overexpression of the PIP3-degradating enzyme PTEN in GbpD-overexpressing cells, the strong adhesion and cell morphology phenotype is largely lost. These results indicate that a GbpD/Rap/PI3K pathway helps control pseudopod formation and cell polarity. As in Rap-regulated pseudopod formation in Dictyostelium, mammalian Rap and PI3K are essential for determining neuronal polarity, suggesting that the Rap/PI3K pathway is a conserved module regulating the establishment of cell polarity.

Kubohara, Y., H. Kikuchi, et al. (2010). "Preparation of an antibody that recognizes and neutralizes Dictyostelium differentiation-inducing factor-1." Biochem Biophys Res Commun 396(2): 364-369.
	In the development of the cellular slime mold Dictyostelium discoideum, the differentiation-inducing factor-1 (DIF-1; 1-(3,5-dichloro-2,6-dihydroxy-4-methoxyphenyl)hexan-1-one) plays an important role in the regulation of cell differentiation and chemotaxis; however, the cellular signaling systems involving DIF-1 remain to be elucidated. To obtain a probe for DIF-1, we synthesized a DIF derivative (DIF-1-NH(2); 6-amino-1-(3,5-dichloro-2,6-dihydroxy-4-methoxyphenyl)hexan-1-one), and prepared an anti-DIF-1 antibody using a DIF-1-NH(2)-conjugated macromolecule as the immunogen. A 100-fold dilution of the antibody bound to DIF-1-NH(2)-conjugated resin, and this binding was inhibited by co-addition of 20 microM DIF-1 or DIF-1-NH(2). In a monolayer culture of HM44 cells, a DIF-deficient D. discoideum strain, 0.5 nM exogenous DIF-1 induced stalk cell formation in approximately 60% of the cells; this induction was dose-dependently inhibited by the antibody (diluted 12.5- or 25-fold). Furthermore, this inhibition by the antibody was recovered by co-addition of 2.5 or10 nM DIF-1. The results indicate that the anti-DIF-1 antibody recognizes DIF-1 and neutralizes its function.

Kubohara, Y. and H. Kuwayama (2010). "[Low molecular compounds that regulate cell differentiation and chemotaxis in Dictyostelium discoideum]." Seikagaku 82(12): 1132-1137.
	
Kuzdzal-Fick, J. J., D. C. Queller, et al. (2010). "An invitation to die: initiators of sociality in a social amoeba become selfish spores." Biol Lett 6(6): 800-802.
	Greater size and strength are common attributes of contest winners. Even in social insects with high cooperation, the right to reproduce falls to the well-fed queens rather than to poorly fed workers. In Dictyostelium discoideum, formerly solitary amoebae aggregate when faced with starvation, and some cells die to form a stalk which others ride up to reach a better location to sporulate. The first cells to starve have lower energy reserves than those that starve later, and previous studies have shown that the better-fed cells in a mix tend to form disproportionately more reproductive spores. Therefore, one might expect that the first cells to starve and initiate the social stage should act altruistically and form disproportionately more of the sterile stalk, thereby enticing other better-fed cells into joining the aggregate. This would resemble caste determination in social insects, where altruistic workers are typically fed less than reproductive queens. However, we show that the opposite result holds: the first cells to starve become reproductive spores, presumably by gearing up for competition and outcompeting late starvers to become prespore first. These findings pose the interesting question of why others would join selfish organizers.

Lee, S., Z. Shen, et al. (2010). "Involvement of the cytoskeleton in controlling leading-edge function during chemotaxis." Mol Biol Cell 21(11): 1810-1824.
	In response to directional stimulation by a chemoattractant, cells rapidly activate a series of signaling pathways at the site closest to the chemoattractant source that leads to F-actin polymerization, pseudopod formation, and directional movement up the gradient. Ras proteins are major regulators of chemotaxis in Dictyostelium; they are activated at the leading edge, are required for chemoattractant-mediated activation of PI3K and TORC2, and are one of the most rapid responders, with activity peaking at approximately 3 s after stimulation. We demonstrate that in myosin II (MyoII) null cells, Ras activation is highly extended and is not restricted to the site closest to the chemoattractant source. This causes elevated, extended, and spatially misregulated activation of PI3K and TORC2 and their effectors Akt/PKB and PKBR1, as well as elevated F-actin polymerization. We further demonstrate that disruption of specific IQGAP/cortexillin complexes, which also regulate cortical mechanics, causes extended activation of PI3K and Akt/PKB but not Ras activation. Our findings suggest that MyoII and IQGAP/cortexillin play key roles in spatially and temporally regulating leading-edge activity and, through this, the ability of cells to restrict the site of pseudopod formation.

Liao, X. H., J. Buggey, et al. (2010). "Chemotactic activation of Dictyostelium AGC-family kinases AKT and PKBR1 requires separate but coordinated functions of PDK1 and TORC2." J Cell Sci 123(Pt 6): 983-992.
	Protein kinases AKT and PKBR1 of Dictyostelium belong to the AGC protein kinase superfamily. AKT and PKBR1 are phosphorylated at similar sites by phosphoinositide-dependent kinase 1 (PDK1) and TORC2 kinases; however, they have different subcellular localizing domains. AKT has a phosphoinositide 3-kinase (PI3K)/phosphatidylinositol (3,4,5)-trisphosphate [PtdIns(3,4,5)P(3)]-regulated PH (pleckstrin homology) domain whereas PKBR1 is myristoylated and persistently membrane localized. Using strains defective for PI3K/PtdIns(3,4,5)P(3)-, PDK1- and TORC2-signaling or strains that express phospho-site mutants of AKT and PKBR1, we dissect the different roles of PI3K/PtdIns(3,4,5)P(3), PDK1 and TORC2. We show that activation of AKT and PKBR1 requires PDK1-site phosphorylation, but that phosphorylation by TORC2 is insufficient for AKT or PKBR1 activation. However, PDK1-site phosphorylation is dependent on phosphorylation by TORC2, which suggests that there is regulatory coordination among PDK1, TORC2 and their phospho-site targets. This defines a separate input for signaling in control of chemotaxis and dependency on PDK1 function. We also demonstrate that PDK1 in Dictyostelium functions independently of PI3K/PtdIns(3,4,5)P(3). Finally, we show that AKT and PKBR1 exhibit substrate selectivity and identify two novel lipid-interacting proteins preferentially phosphorylated by AKT. Despite certain similarities, AKT and PKBR1 have distinct regulatory paths that impact activation and effector targeting, with PDK1 serving a central role.

Lin, W. H., S. E. Nelson, et al. (2010). "Functional roles of VASP phosphorylation in the regulation of chemotaxis and osmotic stress response." Cytoskeleton (Hoboken) 67(4): 259-271.
	Vasodilator-stimulated phosphoprotein (VASP) plays crucial roles in controlling F-actin-driven processes and growing evidence indicates that VASP function is modulated by phosphorylation at multiple sites. However, the complexity of mammalian system prevents the clear understanding of the role of VASP phosphorylation. In this study, we took advantage of Dictyostelium which possesses only one member of the Ena/VASP family to investigate the functional roles of VASP phosphorylation. Our results demonstrated that hyperosmotic stress and cAMP stimulation cause VASP phosphorylation. VASP phosphorylation plays a negative role for the early steps of filopodia/microspikes formation. VASP phosphorylation appears to modulate VASP localization at the membrane cortex and its interactions with WASP and WIPa. Analysis of chemotaxis of cells expressing VASP mutants showed that VASP phosphorylation is required for the establishment of cell polarity under a cAMP gradient.

Linares, J. F., R. Moreno, et al. (2010). "The global regulator Crc modulates metabolism, susceptibility to antibiotics and virulence in Pseudomonas aeruginosa." Environ Microbiol 12(12): 3196-3212.
	The capacity of a bacterial pathogen to produce a disease in a treated host depends on the former's virulence and resistance to antibiotics. Several scattered pieces of evidence suggest that these two characteristics can be influenced by bacterial metabolism. This potential relationship is particularly important upon infection of a host, a situation that demands bacteria adapt their physiology to their new environment, making use of newly available nutrients. To explore the potential cross-talk between bacterial metabolism, antibiotic resistance and virulence, a Pseudomonas aeruginosa model was used. This species is an important opportunistic pathogen intrinsically resistant to many antibiotics. The role of Crc, a global regulator that controls the metabolism of carbon sources and catabolite repression in Pseudomonas, was analysed to determine its contribution to the intrinsic antibiotic resistance and virulence of P. aeruginosa. Using proteomic analyses, high-throughput metabolic tests and functional assays, the present work shows the virulence and antibiotic resistance of this pathogen to be linked to its physiology, and to be under the control (directly or indirectly) of Crc. A P. aeruginosa strain lacking the Crc regulator showed defects in type III secretion, motility, expression of quorum sensing-regulated virulence factors, and was less virulent in a Dictyostelium discoideum model. In addition, this mutant strain was more susceptible to beta-lactams, aminoglycosides, fosfomycin and rifampin. Crc might therefore be a good target in the search for new antibiotics.

Liu, X., S. Shu, et al. (2010). "Mutation of actin Tyr-53 alters the conformations of the DNase I-binding loop and the nucleotide-binding cleft." J Biol Chem 285(13): 9729-9739.
	All but 11 of the 323 known actin sequences have Tyr at position 53, and the 11 exceptions have the conservative substitution Phe, which raises the following questions. What is the critical role(s) of Tyr-53, and, if it can be replaced by Phe, why has this happened so infrequently? We compared the properties of purified endogenous Dictyostelium actin and mutant constructs with Tyr-53 replaced by Phe, Ala, Glu, Trp, and Leu. The Y53F mutant did not differ significantly from endogenous actin in any of the properties assayed, but the Y53A and Y53E mutants differed substantially; affinity for DNase I was reduced, the rate of nucleotide exchange was increased, the critical concentration for polymerization was increased, filament elongation was inhibited, and polymerized actin was in the form of small oligomers and imperfect filaments. Growth and/or development of cells expressing these actin mutants were also inhibited. The Trp and Leu mutations had lesser but still significant effects on cell phenotype and the biochemical properties of the purified actins. We conclude that either Tyr or Phe is required to maintain the functional conformations of the DNase I-binding loop (D-loop) in both G- and F-actin, and that the conformation of the D-loop affects not only the properties that directly involve the D-loop (binding to DNase I and polymerization) but also allosterically modifies the conformation of the nucleotide-binding cleft, thus increasing the rate of nucleotide exchange. The apparent evolutionary "preference" for Tyr at position 53 may be the result of Tyr allowing dynamic modification of the D-loop conformation by phosphorylation (Baek, K., Liu, X., Ferron, F., Shu, S., Korn, E. D., and Dominguez, R. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 11748-11753) with effects similar, but not identical, to those of the Ala and Glu mutations.

Loomis, W. F., M. M. Behrens, et al. (2010). "Pregnenolone sulfate and cortisol induce secretion of acyl-CoA-binding protein and its conversion into endozepines from astrocytes." J Biol Chem 285(28): 21359-21365.
	Acyl-CoA-binding protein (ACBP) functions both intracellularly as part of fatty acid metabolism and extracellularly as diazepam binding inhibitor, the precursor of endozepine peptides. Two of these peptides, ODN and TTN, bind to the GABA(A) receptor and modulate its sensitivity to gamma-aminobutyric acid (GABA). We have found that depolarization of mouse primary astrocytes induces the rapid release and processing of ACBP to the active peptides. We previously showed that ODN can trigger the rapid sporulation of the social amoeba Dictyostelium. Using this bioassay, we now show that astrocytes release the endozepine peptides within 10 min of exposure to the steroids cortisol, pregnenolone, pregnenolone sulfate, or progesterone. ACBP lacks a signal sequence for secretion through the endoplasmic reticulum/Golgi pathway and its secretion is not affected by addition of brefeldin A, a well known inhibitor of the classical secretion pathway, suggesting that it follows an unconventional pathway for secretion. Moreover, induction of autophagy by addition of rapamycin also resulted in rapid release of ACBP indicating that this protein uses components of the autophagy pathway for secretion. Following secretion, ACBP is proteolytically cleaved to the active neuropeptides by protease activity on the surface of astrocytes. Neurosteroids, such as pregnenolone sulfate, were previously shown to modulate the excitatory/inhibitory balance in brain through increased release of glutamate and decreased release of GABA. These effects of steroids in neurons will be reinforced by the release of endozepines from astrocytes shown here, and suggest an orchestrated astrocyte-neuron cross-talk that can affect a broad spectrum of behavioral functions.

MacIntyre, D. L., S. T. Miyata, et al. (2010). "The Vibrio cholerae type VI secretion system displays antimicrobial properties." Proc Natl Acad Sci U S A 107(45): 19520-19524.
	The acute diarrheal disease cholera is caused by the marine bacterium Vibrio cholerae. A type VI secretion system (T6SS), which is structurally similar to the bacteriophage cell-puncturing device, has been recently identified in V. cholerae and is used by this organism to confer virulence toward phagocytic eukaryotes, such as J774 murine macrophages and Dictyostelium discoideum. We tested the interbacterial virulence of V. cholerae strain V52, an O37 serogroup with a constitutively active T6SS. V52 was found to be highly virulent toward multiple Gram-negative bacteria, including Escherichia coli and Salmonella Typhimurium, and caused up to a 100,000-fold reduction in E. coli survival. Because the T6SS-deficient mutants V52DeltavasK and V52DeltavasH showed toxicity defects that could be complemented, virulence displayed by V. cholerae depends on a functional T6SS. V. cholerae V52 and strains of the O1 serogroup were resistant to V52, suggesting that V. cholerae has acquired immunity independently of its serogroup. We hypothesize that the T6SS, in addition to targeting eukaryotic host cells, confers toxicity toward other bacteria, providing a means of interspecies competition to enhance environmental survival. Thus, the V. cholerae T6SS may enhance the survival of V. cholerae in its aquatic ecosystem during the transmission of cholera and between epidemics.

Mana-Capelli, S., R. Graf, et al. (2010). "Dictyostelium centrin B localization during cell cycle progression." Commun Integr Biol 3(1): 39-41.
	Recently, we have reported the initial characterization of a novel centrin from Dictyostelium discoideum (DdCenB).1 Sequence and phylogenetic analyses clearly establish DdCenB as a centrin, yet further characterization revealed some interesting peculiarities about this novel centrin. Figure 1 depicts the localization of DdCenB at three points in the cell cycle: interphase, mitosis and cytokinesis. In interphase DdCenB primarily localizes to the nuclear envelope (NE). Although the NE remains intact during mitosis and cytokinesis in Dictyostelium, DdCenB disappears from the NE at these two stages of the cell cycle. In addition to localization at the NE, we also see weak localization in the nucleoplasm and cytoplasm (weakest). Although the nucleoplasmic concentration appears constant throughout the cell cycle, the very faint localization in the cytoplasm does appear to increase to the level of the nucleoplasm during mitosis and cytokinesis. Unlike most centrins characterized to date, we found no evidence of DdCenB at the centrosome at any point in the cell cycle. Here we examine the importance of DdCenB localization in cell cycle progression, as well as several other roles.

Manjithaya, R., C. Anjard, et al. (2010). "Unconventional secretion of Pichia pastoris Acb1 is dependent on GRASP protein, peroxisomal functions, and autophagosome formation." J Cell Biol 188(4): 537-546.
	In contrast to the enormous advances made regarding mechanisms of conventional protein secretion, mechanistic insights into the unconventional secretion of proteins are lacking. Acyl coenzyme A (CoA)-binding protein (ACBP; AcbA in Dictyostelium discoideum), an unconventionally secreted protein, is dependent on Golgi reassembly and stacking protein (GRASP) for its secretion. We discovered, surprisingly, that the secretion, processing, and function of an AcbA-derived peptide, SDF-2, are conserved between the yeast Pichia pastoris and D. discoideum. We show that in yeast, the secretion of SDF-2-like activity is GRASP dependent, triggered by nitrogen starvation, and requires autophagy proteins as well as medium-chain fatty acyl CoA generated by peroxisomes. Additionally, a phospholipase D implicated in soluble N-ethyl-maleimide sensitive fusion protein attachment protein receptor-mediated vesicle fusion at the plasma membrane is necessary, but neither peroxisome turnover nor fusion between autophagosomes and the vacuole is essential. Moreover, yeast Acb1 and several proteins required for its secretion are necessary for sporulation in P. pastoris. Our findings implicate currently unknown, evolutionarily conserved pathways in unconventional secretion.

Manjithaya, R. and S. Subramani (2010). "Role of autophagy in unconventional protein secretion." Autophagy 6(5).
	In the secretory pathway, the secretion of proteins to the plasma membrane or to the extracellular milieu occurs via vesicular transport from the endoplasmic reticulum, via the Golgi apparatus, to the plasma membrane. This process and the players involved are understood in considerable detail. However, the mode of secretion of proteins that lack a signal sequence and do not transit through the secretory pathway has not been described, despite the fact that the literature is replete with examples of such proteins. One such protein is an evolutionarily conserved, secreted Acyl-CoA binding protein (known as AcbA in Dictyostelium discoideum, Acb1 in yeast and diazepam-binding inhibitor in mammals). Two recent papers highlighted in this punctum have elucidated the pathways required for the unconventional secretion of Acb1 in Pichia pastoris and Saccharomyces cerevisiae. Both implicate autophagy proteins and autophagosome formation in the process, while also uncovering roles for other interesting proteins in the unconventional secretion of Acb1.

Mantzouranis, L., R. Bagattini, et al. (2010). "KeaA, a Dictyostelium Kelch-domain protein that regulates the response to stress and development." BMC Dev Biol 10: 79.
	BACKGROUND: The protein kinase YakA is responsible for the growth arrest and induction of developmental processes that occur upon starvation of Dictyostelium cells. yakA- cells are aggregation deficient, have a faster cell cycle and are hypersensitive to oxidative and nitrosoative stress. With the aim of isolating members of the YakA pathway, suppressors of the death induced by nitrosoative stress in the yakA- cells were identified. One of the suppressor mutations occurred in keaA, a gene identical to DG1106 and similar to Keap1 from mice and the Kelch protein from Drosophila, among others that contain Kelch domains. RESULTS: A mutation in keaA suppresses the hypersensitivity to oxidative and nitrosoative stresses but not the faster growth phenotype of yakA- cells. The growth profile of keaA deficient cells indicates that this gene is necessary for growth. keaA deficient cells are more resistant to nitrosoative and oxidative stress and keaA is necessary for the production and detection of cAMP. A morphological analysis of keaA deficient cells during multicellular development indicated that, although the mutant is not absolutely deficient in aggregation, cells do not efficiently participate in the process. Gene expression analysis using cDNA microarrays of wild-type and keaA deficient cells indicated a role for KeaA in the regulation of the cell cycle and pre-starvation responses. CONCLUSIONS: KeaA is required for cAMP signaling following stress. Our studies indicate a role for kelch proteins in the signaling that regulates the cell cycle and development in response to changes in the environmental conditions.

Marsano, F., L. Boatti, et al. (2010). "Effects of mercury on Dictyostelium discoideum: proteomics reveals the molecular mechanisms of physiological adaptation and toxicity." J Proteome Res 9(6): 2839-2854.
	Dictyostelium discoideum amoebae were exposed to Hg 2 microM corresponding to a sublethal concentration and Hg 10 microM with the first effects on mortality and replication rate. A total of 900 spots were visualized by 2-DE electrophoresis. Two-hundred fifty single proteins were identified by mass spectrometry. Low Hg concentration (2 microM) treatment induced up-regulation of 13 spots, mainly involved in oxidative stress response/detoxification, oxidoreductase activity, and metabolic processes. High Hg concentration (10 microM) treatment showed a different PES with 12 proteins downregulated and only two up-regulated, mainly involved in cellular metabolic processes, metal ion binding, and transferase activity. The analyses for the carbonylation show no changes after 2 microM Hg(2+) treatment and 13 differentially carbonylated proteins after 10 microM Hg(2+) involved in a broad range of cellular processes. Our findings provide insight into the mechanisms of physiological adaptation and toxicity to a low and an high mercury concentration, respectively, of Dictyostelium amoebae.

Mathieu, S. V., K. S. Aragao, et al. (2010). "Discoidin I from Dictyostelium discoideum and Interactions with oligosaccharides: specificity, affinity, crystal structures, and comparison with discoidin II." J Mol Biol 400(3): 540-554.
	Discoidin I (DiscI) and discoidin II (DiscII) are N-acetylgalactosamine (GalNAc)-binding proteins from Dictyostelium discoideum. They consist of two domains: an N-terminal discoidin domain and a C-terminal H-type lectin domain. They were cloned and expressed in high yield in recombinant form in Escherichia coli. Although both lectins bind galactose (Gal) and GalNAc, glycan array experiments performed on the recombinant proteins displayed strong differences in their specificity for oligosaccharides. DiscI and DiscII bind preferentially to Gal/GalNAcbeta1-3Gal/GalNAc-containing and Gal/GalNAcbeta1-4GlcNAcbeta1-6Gal/GalNAc-containing glycans, respectively. The affinity of the interaction of DiscI with monosaccharides and disaccharides was evaluated using isothermal titration calorimetry experiments. The three-dimensional structures of native DiscI and its complexes with GalNAc, GalNAcbeta1-3Gal, and Galbeta1-3GalNAc were solved by X-ray crystallography. DiscI forms trimers with involvement of calcium at the monomer interface. The N-terminal discoidin domain presents a structural similarity to F-type lectins such as the eel agglutinin, where an amphiphilic binding pocket suggests possible carbohydrate-binding activity. In the C-terminal H-type lectin domain, the GalNAc residue establishes specific hydrogen bonds that explain the observed affinity (K(d)=3x10(-4) M). The different specificities of DiscI and DiscII for oligosaccharides were rationalized from the different structures obtained by either X-ray crystallography or molecular modeling.

Matsuda, T., F. Takahashi-Yanaga, et al. (2010). "Dictyostelium differentiation-inducing factor-1 binds to mitochondrial malate dehydrogenase and inhibits its activity." J Pharmacol Sci 112(3): 320-326.
	We have reported that the differentiation-inducing factors (DIFs) DIF-1 and DIF-3, morphogens secreted from Dictyostelium discoideum, inhibit proliferation of several cancer cells via suppression of the Wnt/beta-catenin signaling pathway. However, the target molecules of DIFs involved in the anti-proliferative effects are still unknown. In the present study, DIF-1-tethered resins were synthesized to explore the target molecules of DIFs, and mitochondrial malate dehydrogenase (mMDH) was identified as one of the target molecules. In the in vitro assay, DIF-1 and other analogs including 2-MIDIF-1, DIF-3, and 6-MIDIF-3 were found to be capable of binding to mMDH but not to cytoplasmic MDH. However, only DIF-1 and 2-MIDIF-1 inhibited the enzymatic activity of mMDH. The effects of DIF analogs on ATP content and cell proliferation were then analyzed using HeLa cells. DIF-1 and 2-MIDIF-1 were found to lower the ATP content and both chemicals inhibited HeLa cell proliferation, suggesting that inhibition of mMDH activity affected cell energy production, probably leading to the inhibition of proliferation. These results suggest that the inhibition of mMDH activity by DIF-1 and 2-MIDIF-1 could be one of the mechanisms to induce anti-proliferative effects, independent of the inhibition of the Wnt/beta-catenin signaling pathway.

McCall, K. (2010). "Genetic control of necrosis - another type of programmed cell death." Curr Opin Cell Biol 22(6): 882-888.
	Necrosis has been thought to be an accidental or uncontrolled type of cell death rather than programmed. Recent studies from diverse organisms show that necrosis follows a stereotypical series of cellular and molecular events: swelling of organelles, increases in reactive oxygen species and cytoplasmic calcium, a decrease in ATP, activation of calpain and cathepsin proteases, and finally rupture of organelles and plasma membrane. Genetic and chemical manipulations demonstrate that necrosis can be inhibited, indicating that necrosis can indeed be controlled and follows a specific 'program.' This review highlights recent findings from C. elegans, yeast, Dictyostelium, Drosophila, and mammals that collectively provide evidence for conserved mechanisms of necrosis.

McCann, C. P., P. W. Kriebel, et al. (2010). "Cell speed, persistence and information transmission during signal relay and collective migration." J Cell Sci 123(Pt 10): 1724-1731.
	Collective migration is a key feature of the social amoebae Dictyostelium discoideum, where the binding of chemoattractants leads to the production and secretion of additional chemoattractant and the relay of the signal to neighboring cells. This then guides cells to migrate collectively in a head-to-tail fashion. We used mutants that were defective in signal relay to elucidate which quantitative metrics of cell migration are most strongly affected by signal relay and collective motion. We show that neither signal relay nor collective motion markedly impact the speed of cell migration. Cells maintained a preferred overall direction of motion for several minutes with similar persistence, regardless of whether or not they were attracted to moving neighbors, moving collectively in contact with their neighbors, or simply following a fixed exogenous signal. We quantitatively establish that signal relay not only increases the number of cells that respond to a chemotactic signal, but most remarkably, also transmits information about the location of the source accurately over large distances, independently of the strength of the exogenous signal. We envision that signal relay has a similar key role in the migration of a variety of chemotaxing mammalian cells that can relay chemoattractant signals.

McMains, V. C., M. Myre, et al. (2010). "Dictyostelium possesses highly diverged presenilin/gamma-secretase that regulates growth and cell-fate specification and can accurately process human APP: a system for functional studies of the presenilin/gamma-secretase complex." Dis Model Mech 3(9-10): 581-594.
	Presenilin (PS) is the catalytic moiety of the gamma-secretase complex. PS and other gamma-secretase components are well conserved among metazoa, but their presence and function in more-distant species are not resolved. Because inappropriate gamma-secretase processing of amyloid precursor protein (APP) in humans is associated with familial Alzheimer's disease, understanding essential elements within each gamma-secretase component is crucial to functional studies. Diverged proteins have been identified in primitive plants but experiments have failed to demonstrate gamma-secretase activity. We have identified highly diverged orthologs for each gamma-secretase component in the ancient eukaryote Dictyostelium, which lacks equivalents of APP, Notch and other characterized PS/gamma-secretase substrates. We show that wild-type (WT) Dictyostelium is capable of amyloidogenic processing of ectopically expressed human APP to generate amyloid-beta peptides Abeta(40) and Abeta(42); strains deficient in gamma-secretase cannot produce Abeta peptides but accumulate processed intermediates of APP that co-migrate with the C-terminal fragments alpha- and beta-CTF of APP that are found in mammalian cells. We further demonstrate that Dictyostelium requires PS for phagocytosis and cell-fate specification in a cell-autonomous manner, and show that regulation of phagocytosis requires an active gamma-secretase, a pathway suggested, but not proven, to occur in mammalian and Drosophila cells. Our results indicate that PS signaling is an ancient process that arose prior to metazoan radiation, perhaps independently of Notch. Dictyostelium might serve to identify novel PS/gamma-secretase signaling targets and provide a unique system for high-throughput screening of small-molecule libraries to select new therapeutic targets for diseases associated with this pathway.

McNaughton, L., I. Tikhonenko, et al. (2010). "A low affinity ground state conformation for the Dynein microtubule binding domain." J Biol Chem 285(21): 15994-16002.
	Dynein interacts with microtubules through a dedicated binding domain that is dynamically controlled to achieve high or low affinity, depending on the state of nucleotide bound in a distant catalytic pocket. The active sites for microtubule binding and ATP hydrolysis communicate via conformational changes transduced through a approximately 10-nm length antiparallel coiled-coil stalk, which connects the binding domain to the roughly 300-kDa motor core. Recently, an x-ray structure of the murine cytoplasmic dynein microtubule binding domain (MTBD) in a weak affinity conformation was published, containing a covalently constrained beta(+) registry for the coiled-coil stalk segment (Carter, A. P., Garbarino, J. E., Wilson-Kubalek, E. M., Shipley, W. E., Cho, C., Milligan, R. A., Vale, R. D., and Gibbons, I. R. (2008) Science 322, 1691-1695). We here present an NMR analysis of the isolated MTBD from Dictyostelium discoideum that demonstrates the coiled-coil beta(+) registry corresponds to the low energy conformation for this functional region of dynein. Addition of sequence encoding roughly half of the coiled-coil stalk proximal to the binding tip results in a decreased affinity of the MTBD for microtubules. In contrast, addition of the complete coiled-coil sequence drives the MTBD to the conformationally unstable, high affinity binding state. These results suggest a thermodynamic coupling between conformational free energy differences in the alpha and beta(+) registries of the coiled-coil stalk that acts as a switch between high and low affinity conformations of the MTBD. A balancing of opposing conformations in the stalk and MTBD enables potentially modest long-range interactions arising from ATP binding in the motor core to induce a relaxation of the MTBD into the stable low affinity state.

McVey, M. (2010). "Strategies for DNA interstrand crosslink repair: insights from worms, flies, frogs, and slime molds." Environ Mol Mutagen 51(6): 646-658.
	DNA interstrand crosslinks (ICLs) are complex lesions that covalently link both strands of the DNA double helix and impede essential cellular processes such as DNA replication and transcription. Recent studies suggest that multiple repair pathways are involved in their removal. Elegant genetic analysis has demonstrated that at least three distinct sets of pathways cooperate in the repair and/or bypass of ICLs in budding yeast. Although the mechanisms of ICL repair in mammals appear similar to those in yeast, important differences have been documented. In addition, mammalian crosslink repair requires other repair factors, such as the Fanconi anemia proteins, whose functions are poorly understood. Because many of these proteins are conserved in simpler metazoans, nonmammalian models have become attractive systems for studying the function(s) of key crosslink repair factors. This review discusses the contributions that various model organisms have made to the field of ICL repair. Specifically, it highlights how studies performed with C. elegans, Drosophila, Xenopus, and the social amoeba Dictyostelium serve to complement those from bacteria, yeast, and mammals. Together, these investigations have revealed that although the underlying themes of ICL repair are largely conserved, the complement of DNA repair proteins utilized and the ways in which each of the proteins is used can vary substantially between different organisms.

Mehdiabadi, N. J., M. R. Kronforst, et al. (2010). "Phylogeography and sexual macrocyst formation in the social amoeba Dictyostelium giganteum." BMC Evol Biol 10: 17.
	BACKGROUND: Microorganisms are ubiquitous, yet we are only beginning to understand their diversity and population structure. Social amoebae (Dictyostelia) are a diverse group of unicellular eukaryotic microbes that display a unique social behaviour upon starvation in which cells congregate and then some die to help others survive and disperse. The genetic relationships among co-occurring cells have a major influence on the evolution of social traits and recent population genetic analysis found extensive genetic variation and possible cryptic speciation in one dictyostelid species (Dictyostelium purpureum). To further characterize the interplay among genetic variation, species boundaries, social behaviour, and reproductive isolation in the Dictyostelia, we conducted phylogenetic analyses and mating experiments with the geographically widespread social amoeba Dictyostelium giganteum. RESULTS: We sequenced approximately 4,000 basepairs of the nuclear ribosomal DNA from 24 isolates collected from Texas, Michigan, Massachusetts, Virginia, and Wisconsin and identified 16 unique haplotypes. Analyses of the sequence data revealed very little genetic differentiation among isolates and no clear evidence of phylogenetic structure, although there was evidence for some genetic differentiation between the Massachusetts and Texas populations. These results suggest that sexual mating (macrocyst formation) is not likely to correlate with either genetic or geographical distance. To test this prediction, we performed 108 mating experiments and found no association between mating probability and genetic or geographical distance. CONCLUSIONS: D. giganteum isolates from across North America display little genetic variation, phylogeographic structure, and genetic differentiation among populations relative to the cryptic species observed within D. purpureum. Furthermore, variation that does exist does not predict the probability of mating among clones. These results have important implications for our understanding of speciation and social evolution in microbes.

Melykuti, B., E. August, et al. (2010). "Discriminating between rival biochemical network models: three approaches to optimal experiment design." BMC Syst Biol 4: 38.
	BACKGROUND: The success of molecular systems biology hinges on the ability to use computational models to design predictive experiments, and ultimately unravel underlying biological mechanisms. A problem commonly encountered in the computational modelling of biological networks is that alternative, structurally different models of similar complexity fit a set of experimental data equally well. In this case, more than one molecular mechanism can explain available data. In order to rule out the incorrect mechanisms, one needs to invalidate incorrect models. At this point, new experiments maximizing the difference between the measured values of alternative models should be proposed and conducted. Such experiments should be optimally designed to produce data that are most likely to invalidate incorrect model structures. RESULTS: In this paper we develop methodologies for the optimal design of experiments with the aim of discriminating between different mathematical models of the same biological system. The first approach determines the 'best' initial condition that maximizes the L2 (energy) distance between the outputs of the rival models. In the second approach, we maximize the L2-distance of the outputs by designing the optimal external stimulus (input) profile of unit L2-norm. Our third method uses optimized structural changes (corresponding, for example, to parameter value changes reflecting gene knock-outs) to achieve the same goal. The numerical implementation of each method is considered in an example, signal processing in starving Dictyostelium amoebae. CONCLUSIONS: Model-based design of experiments improves both the reliability and the efficiency of biochemical network model discrimination. This opens the way to model invalidation, which can be used to perfect our understanding of biochemical networks. Our general problem formulation together with the three proposed experiment design methods give the practitioner new tools for a systems biology approach to experiment design.

Mercanti, V. and P. Cosson (2010). "Resistance of Dictyostelium discoideum membranes to saponin permeabilization." BMC Res Notes 3: 120.
	BACKGROUND: Saponin is a mild detergent commonly used to permeabilize cells prior to immunofluorescence labeling of intracellular proteins. It has previously been used to that effect in Dictyostelium discoideum amoebae. FINDINGS: We show that saponin, contrary to Triton X-100 or alcohol, permeabilizes at best incompletely membranes of Dictyostelium. In cells exposed to osmotic stress, almost complete resistance to saponin permeabilization was observed. CONCLUSIONS: Saponin should be used with special care to permeabilize Dictyostelium membranes. This unsusual property is presumably linked to the specific sterol composition of Dictyostelium membranes. It may also represent an adaptation of Dictyostelium to harsh conditions or to natural compounds encountered in its natural environment.

Middelbeek, J., K. Clark, et al. (2010). "The alpha-kinase family: an exceptional branch on the protein kinase tree." Cell Mol Life Sci 67(6): 875-890.
	The alpha-kinase family represents a class of atypical protein kinases that display little sequence similarity to conventional protein kinases. Early studies on myosin heavy chain kinases in Dictyostelium discoideum revealed their unusual propensity to phosphorylate serine and threonine residues in the context of an alpha-helix. Although recent studies show that some members of this family can also phosphorylate residues in non-helical regions, the name alpha-kinase has remained. During evolution, the alpha-kinase domains combined with many different functional subdomains such as von Willebrand factor-like motifs (vWKa) and even cation channels (TRPM6 and TRPM7). As a result, these kinases are implicated in a large variety of cellular processes such as protein translation, Mg(2+) homeostasis, intracellular transport, cell migration, adhesion, and proliferation. Here, we review the current state of knowledge on different members of this kinase family and discuss the potential use of alpha-kinases as drug targets in diseases such as cancer.

Mondal, S., B. Burgute, et al. (2010). "Regulation of the actin cytoskeleton by an interaction of IQGAP related protein GAPA with filamin and cortexillin I." PLoS One 5(11): e15440.
	Filamin and Cortexillin are F-actin crosslinking proteins in Dictyostelium discoideum allowing actin filaments to form three-dimensional networks. GAPA, an IQGAP related protein, is required for cytokinesis and localizes to the cleavage furrow during cytokinesis. Here we describe a novel interaction with Filamin which is required for cytokinesis and regulation of the F-actin content. The interaction occurs through the actin binding domain of Filamin and the GRD domain of GAPA. A similar interaction takes place with Cortexillin I. We further report that Filamin associates with Rac1a implying that filamin might act as a scaffold for small GTPases. Filamin and activated Rac associate with GAPA to regulate actin remodelling. Overexpression of filamin and GAPA in the various strains suggests that GAPA regulates the actin cytoskeleton through interaction with Filamin and that it controls cytokinesis through association with Filamin and Cortexillin.

Naber, N., A. Malnasi-Csizmadia, et al. (2010). "Combining EPR with fluorescence spectroscopy to monitor conformational changes at the myosin nucleotide pocket." J Mol Biol 396(4): 937-948.
	We used spin-labeled nucleotide analogs and fluorescence spectroscopy to monitor conformational changes at the nucleotide-binding site of wild-type Dictyostelium discoideum (WT) myosin and a construct containing a single tryptophan at position F239 near the switch 1 loop. Electron paramagnetic resonance (EPR) spectroscopy and tryptophan fluorescence have been used previously to investigate changes at the myosin nucleotide site. A limitation of fluorescence spectroscopy is that it must be done on mutated myosins containing only a single tryptophan. A limitation of EPR spectroscopy is that one infers protein conformational changes from alterations in the mobility of an attached probe. These limitations have led to controversies regarding conclusions reached by the two approaches. For the first time, the data presented here allow direct correlations to be made between the results from the two spectroscopic approaches on the same proteins and extend our previous EPR studies to a nonmuscle myosin. EPR probe mobility indicates that the conformation of the nucleotide pocket of the WTSLADP (spin-labeled ADP) complex is similar to that of skeletal myosin. The pocket is closed in the absence of actin for both diphosphate and triphosphate nucleotide states. In the actin myosin diphosphate state, the pocket is in equilibrium between closed and open conformations, with the open conformation slightly more favorable than that seen for fast skeletal actomyosin. The EPR spectra for the mutant show similar conformations to skeletal myosin, with one exception: in the absence of actin, the nucleotide pocket of the mutant displays an open component that was approximately 4-5 kJ/mol more favorable than in skeletal or WT myosin. These observations resolve the controversies between the two techniques. The data from both techniques confirm that binding of myosin to actin alters the conformation of the myosin nucleotide pocket with similar but not identical energetics in both muscle and nonmuscle myosins.

Nagayama, K. and T. Ohmachi (2010). "Mitochondrial processing peptidase activity is controlled by the processing of alpha-MPP during development in Dictyostelium discoideum." Microbiology 156(Pt 4): 978-989.
	We investigated the expression of the alpha subunit of the Dictyostelium mitochondrial processing peptidase (Ddalpha-MPP) during development. Ddalpha-MPP mRNA is expressed at the highest levels in vegetatively growing cells and during early development, and is markedly downregulated after 10 h of development. The Ddalpha-MPP protein is expressed as two forms, designated alpha-MPP(H) and alpha-MPP(L), throughout the Dictyostelium life cycle. The larger form, alpha-MPP(H), is cleaved to produce the functional alpha-MPP(L) form. We were not able to isolate mutants in which the alpha-mpp gene had been disrupted. Instead, an antisense transformant, alphaA2, expressing alpha-MPP at a lower level than the wild-type AX-3 was isolated to examine the function of the alpha-MPP protein. Development of the alphaA2 strain was normal until the slug formation stage, but the slug stage was prolonged to approximately 24 h. In this prolonged slug stage, only alpha-MPP(H) was present, and alpha-MPP(L) protein and MPP activity were not detected. After 28 h, alpha-MPP(L) and MPP activity reappeared, and normal fruiting bodies were formed after a delay of approximately 8 h compared with normal development. These results indicate that MPP activity is controlled by the processing of alpha-MPP(H) to alpha-MPP(L) during development in Dictyostelium.

Neumann, C. S., C. T. Walsh, et al. (2010). "A flavin-dependent halogenase catalyzes the chlorination step in the biosynthesis of Dictyostelium differentiation-inducing factor 1." Proc Natl Acad Sci U S A 107(13): 5798-5803.
	Differentiation-inducing factor 1 (DIF-1) is a polyketide-derived morphogen which drives stalk cell formation in the developmental cycle of Dictyostelium discoideum. Previous experiments demonstrated that the biosynthetic pathway proceeds via dichlorination of the precursor molecule THPH, but the enzyme responsible for this transformation has eluded characterization. Our recent studies on prokaryotic flavin-dependent halogenases and insights from the sequenced Dd genome led us to a candidate gene for this transformation. In this work, we present in vivo and in vitro evidence that chlA from Dd encodes a flavin-dependent halogenase capable of catalyzing both chlorinations in the biosynthesis of DIF-1. The results provide in vitro characterization of a eukaryotic oxygen-dependent halogenase and demonstrate a broad reach in biology for this molecular tailoring strategy, notably its involvement in the differentiation program of a social amoeba.

Nguyen, H. N., B. Raisley, et al. (2010). "MAP kinases have different functions in Dictyostelium G protein-mediated signaling." Cell Signal 22(5): 836-847.
	Extracellular signal regulated kinases (ERKs) are a class of MAP kinases that function in many signaling pathways in eukaryotic cells and in some cases, a single stimulus can activate more than one ERK suggesting functional redundancy or divergence from a common pathway. Dictyostelium discoideum encodes only two MAP kinases, ERK1 and ERK2, that both function during the developmental life cycle. To determine if ERK1 and ERK2 have overlapping functions, chemotactic and developmental phenotypes of erk1(-) and erk2(-) mutants were assessed with respect to G protein-mediated signal transduction pathways. ERK1 was specifically required for Galpha5-mediated tip morphogenesis and inhibition of folate chemotaxis but not for cAMP-stimulated chemotaxis or cGMP accumulation. ERK2 was the primary MAPK phosphorylated in response to folate or cAMP stimulation. Cell growth was not altered in erk1(-), erk2(-) or erk1(-)erk2(-) mutants but each mutant displayed a different pattern of cell sorting in chimeric aggregates. The distribution of GFP-ERK1 or GFP-ERK2 fusion proteins in the cytoplasm and nucleus was not grossly altered in cells stimulated with cAMP or folate. These results suggest ERK1 and ERK2 have different roles in G protein-mediated signaling during growth and development.

Noguchi, T. Q., Y. Gomibuchi, et al. (2010). "Dominant negative mutant actins identified in flightless Drosophila can be classified into three classes." J Biol Chem 285(7): 4337-4347.
	Strongly dominant negative mutant actins, identified by An and Mogami (An, H. S., and Mogami, K. (1996) J. Mol. Biol. 260, 492-505), in the indirect flight muscle of Drosophila impaired its flight, even when three copies of the wild-type gene were present. Understanding how these strongly dominant negative mutant actins disrupt the function of wild-type actin would provide useful information about the molecular mechanism by which actin functions in vivo. Here, we expressed and purified six of these strongly dominant negative mutant actins in Dictyostelium and classified them into three groups based on their biochemical phenotypes. The first group, G156D, G156S, and G268D actins, showed impaired polymerization and a tendency to aggregate under conditions favoring polymerization. G63D actin of the second group was also unable to polymerize but, unlike those in the first group, remained soluble under polymerizing conditions. Kinetic analyses using G63D actin or G63D actin.gelsolin complexes suggested that the pointed end surface is defective, which would alter the polymerization kinetics of wild-type actin when mixed and could affect formation of thin filament structures in indirect flight muscle. The third group, R95C and E226K actins, was normal in terms of polymerization, but their motility on heavy meromyosin surfaces in the presence of tropomyosin-troponin indicated altered sensitivity to Ca(2+). Cofilaments in which R95C or E226K actins were copolymerized with a 3-fold excess of wild-type actin also showed altered Ca(2+) sensitivity in the presence of tropomyosin-troponin.

Odell, L. R., D. Howan, et al. (2010). "The pthaladyns: GTP competitive inhibitors of dynamin I and II GTPase derived from virtual screening." J Med Chem 53(14): 5267-5280.
	We report the development of a homology model for the GTP binding domain of human dynamin I based on the corresponding crystal structure of Dictyostelium discoidum dynamin A. Virtual screening identified 2-[(2-biphenyl-2-yl-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carbonyl)amino]-4-chloro benzoic acid (1) as a approximately 170 microM potent inhibitor. Homology modeling- and focused library-led synthesis resulted in development of a series of active compounds (the "pthaladyns") with 4-chloro-2-(2-(4-(hydroxymethyl)phenyl)-1,3-dioxoisoindoline-5-carboxamido)benzoi c acid (29), a 4.58 +/- 0.06 microM dynamin I GTPase inhibitor. Pthaladyn-29 displays borderline selectivity for dynamin I relative to dynamin II ( approximately 5-10 fold). Only pthaladyn-23 (dynamin I IC(50) 17.4 +/- 5.8 microM) was an effective inhibitor of dynamin I mediated synaptic vesicle endocytosis in brain synaptosomes with an IC(50) of 12.9 +/- 5.9 microM. This compound was also competitive with respect to Mg(2+).GTP. Thus the pthaladyns are the first GTP competitive inhibitors of dynamin I and II GTPase and may be effective new tools for the study of neuronal endocytosis.

Pang, T. L., F. C. Chen, et al. (2010). "Costars, a Dictyostelium protein similar to the C-terminal domain of STARS, regulates the actin cytoskeleton and motility." J Cell Sci 123(Pt 21): 3745-3755.
	Through analysis of a chemotaxis mutant obtained from a genetic screen in Dictyostelium discoideum, we have identified a new gene involved in regulating cell migration and have named it costars (cosA). The 82 amino acid Costars protein sequence appears highly conserved among diverse species, and significantly resembles the C-terminal region of the striated muscle activator of Rho signaling (STARS), a mammalian protein that regulates the serum response factor transcriptional activity through actin binding and Rho GTPase activation. The cosA-null (cosA(-)) cells formed smooth plaques on bacterial lawns, produced abnormally small fruiting bodies when developed on the non-nutrient agar and displayed reduced migration towards the cAMP source in chemotactic assays. Analysis of cell motion in cAMP gradients revealed decreased speed but wild-type-like directional persistence of cosA(-) cells, suggesting a defect in the cellular machinery for motility rather than for chemotactic orientation. Consistent with this notion, cosA(-) cells exhibited changes in the actin cytoskeleton, showing aberrant distribution of F-actin in fluorescence cell staining and an increased amount of cytoskeleton-associated actin. Excessive pseudopod formation was also noted in cosA(-) cells facing chemoattractant gradients. Expressing cosA or its human counterpart mCostars eliminated abnormalities of cosA(-) cells. Together, our results highlight a role for Costars in modulating actin dynamics and cell motility.

Parikh, A., E. Huang, et al. (2010). "New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data." BMC Bioinformatics 11: 163.
	BACKGROUND: Identifying candidate genes in genetic networks is important for understanding regulation and biological function. Large gene expression datasets contain relevant information about genetic networks, but mining the data is not a trivial task. Algorithms that infer Bayesian networks from expression data are powerful tools for learning complex genetic networks, since they can incorporate prior knowledge and uncover higher-order dependencies among genes. However, these algorithms are computationally demanding, so novel techniques that allow targeted exploration for discovering new members of known pathways are essential. RESULTS: Here we describe a Bayesian network approach that addresses a specific network within a large dataset to discover new components. Our algorithm draws individual genes from a large gene-expression repository, and ranks them as potential members of a known pathway. We apply this method to discover new components of the cAMP-dependent protein kinase (PKA) pathway, a central regulator of Dictyostelium discoideum development. The PKA network is well studied in D. discoideum but the transcriptional networks that regulate PKA activity and the transcriptional outcomes of PKA function are largely unknown. Most of the genes highly ranked by our method encode either known components of the PKA pathway or are good candidates. We tested 5 uncharacterized highly ranked genes by creating mutant strains and identified a candidate cAMP-response element-binding protein, yet undiscovered in D. discoideum, and a histidine kinase, a candidate upstream regulator of PKA activity. CONCLUSIONS: The single-gene expansion method is useful in identifying new components of known pathways. The method takes advantage of the Bayesian framework to incorporate prior biological knowledge and discovers higher-order dependencies among genes while greatly reducing the computational resources required to process high-throughput datasets.

Parikh, A., E. R. Miranda, et al. (2010). "Conserved developmental transcriptomes in evolutionarily divergent species." Genome Biol 11(3): R35.
	BACKGROUND: Evolutionarily divergent organisms often share developmental anatomies despite vast differences between their genome sequences. The social amoebae Dictyostelium discoideum and Dictyostelium purpureum have similar developmental morphologies although their genomes are as divergent as those of man and jawed fish. RESULTS: Here we show that the anatomical similarities are accompanied by extensive transcriptome conservation. Using RNA sequencing we compared the abundance and developmental regulation of all the transcripts in the two species. In both species, most genes are developmentally regulated and the greatest expression changes occur during the transition from unicellularity to multicellularity. The developmental regulation of transcription is highly conserved between orthologs in the two species. In addition to timing of expression, the level of mRNA production is also conserved between orthologs and is consistent with the intuitive notion that transcript abundance correlates with the amount of protein required. Furthermore, the conservation of transcriptomes extends to cell-type specific expression. CONCLUSIONS: These findings suggest that developmental programs are remarkably conserved at the transcriptome level, considering the great evolutionary distance between the genomes. Moreover, this transcriptional conservation may be responsible for the similar developmental anatomies of Dictyostelium discoideum and Dictyostelium purpureum.

Peracino, B., A. Balest, et al. (2010). "Phosphoinositides differentially regulate bacterial uptake and Nramp1-induced resistance to Legionella infection in Dictyostelium." J Cell Sci 123(Pt 23): 4039-4051.
	Membrane phosphatidylinositides recruit cytosolic proteins to regulate phagocytosis, macropinocytosis and endolysosomal vesicle maturation. Here, we describe effects of inactivation of PI3K, PTEN or PLC on Escherichia coli and Legionella pneumophila uptake by the professional phagocyte Dictyostelium discoideum. We show that L. pneumophila is engulfed by macropinocytosis, a process that is partially sensitive to PI3K inactivation, unlike phagocytosis of E. coli. Both processes are blocked by PLC inhibition. Whereas E. coli is rapidly digested, Legionella proliferates intracellularly. Proliferation is blocked by constitutively expressing Nramp1, an endolysosomal iron transporter that confers resistance against invasive bacteria. Inactivation of PI3K, but not PTEN or PLC, enhances Legionella infection and suppresses the protective effect of Nramp1 overexpression. PI3K activity is restricted to early infection and is not mediated by effects on the actin cytoskeleton; rather L. pneumophila, in contrast to E. coli, subverts phosphoinositide-sensitive fusion of Legionella-containing macropinosomes with acidic vesicles, without affecting Nramp1 recruitment. A model is presented to explain how Legionella escapes fusion with acidic vesicles and Nramp1-induced resistance to pathogens.

Phillips, J. E. and R. H. Gomer (2010). "The ROCO kinase QkgA is necessary for proliferation inhibition by autocrine signals in Dictyostelium discoideum." Eukaryot Cell 9(10): 1557-1565.
	AprA and CfaD are secreted proteins that function as autocrine signals to inhibit cell proliferation in Dictyostelium discoideum. Cells lacking AprA or CfaD proliferate rapidly, and adding AprA or CfaD to cells slows proliferation. Cells lacking the ROCO kinase QkgA proliferate rapidly, with a doubling time 83% of that of the wild type, and overexpression of a QkgA-green fluorescent protein (GFP) fusion protein slows cell proliferation. We found that qkgA(-) cells accumulate normal levels of extracellular AprA and CfaD. Exogenous AprA or CfaD does not slow the proliferation of cells lacking qkgA, and expression of QkgA-GFP in qkgA(-) cells rescues this insensitivity. Like cells lacking AprA or CfaD, cells lacking QkgA tend to be multinucleate, accumulate nuclei rapidly, and show a mass and protein accumulation per nucleus like those of the wild type, suggesting that QkgA negatively regulates proliferation but not growth. Despite their rapid proliferation, cells lacking AprA, CfaD, or QkgA expand as a colony on bacteria less rapidly than the wild type. Unlike AprA and CfaD, QkgA does not affect spore viability following multicellular development. Together, these results indicate that QkgA is necessary for proliferation inhibition by AprA and CfaD, that QkgA mediates some but not all of the effects of AprA and CfaD, and that QkgA may function downstream of these proteins in a signal transduction pathway regulating proliferation.

Price, C. T., T. Al-Quadan, et al. (2010). "Exploitation of conserved eukaryotic host cell farnesylation machinery by an F-box effector of Legionella pneumophila." J Exp Med 207(8): 1713-1726.
	Farnesylation involves covalent linkage of eukaryotic proteins to a lipid moiety to anchor them into membranes, which is essential for the biological function of Ras and other proteins. A large cadre of bacterial effectors is injected into host cells by intravacuolar pathogens through elaborate type III-VII translocation machineries, and many of these effectors are incorporated into the pathogen-containing vacuolar membrane by unknown mechanisms. The Dot/Icm type IV secretion system of Legionella pneumophila injects into host cells the F-box effector Ankyrin B (AnkB), which functions as platforms for the docking of polyubiquitinated proteins to the Legionella-containing vacuole (LCV) to enable intravacuolar proliferation in macrophages and amoeba. We show that farnesylation of AnkB is indispensable for its anchoring to the cytosolic face of the LCV membrane, for its biological function within macrophages and Dictyostelium discoideum, and for intrapulmonary proliferation in mice. Remarkably, the protein farnesyltransferase, RCE-1 (Ras-converting enzyme-1), and isoprenyl cysteine carboxyl methyltransferase host farnesylation enzymes are recruited to the LCV in a Dot/Icm-dependent manner and are essential for the biological function of AnkB. In conclusion, this study shows novel localized recruitment of the host farnesylation machinery and its anchoring of an F-box effector to the LCV membrane, and this is essential for biological function in vitro and in vivo.

Pruvot, B., V. Laurens, et al. (2010). "Comparative analysis of nonaspanin protein sequences and expression studies in zebrafish." Immunogenetics 62(10): 681-699.
	Nonaspanins constitute a family of proteins, also called TM9SF, characterized by a large non-cytoplasmic domain and nine putative transmembrane domains. This family is highly conserved through evolution and comprises three members in Saccharomyces cerevisiae, Dictyostelium discoideum, and Drosophila melanogaster, and four members are reported in mammals (TM9SF1-TM9SF4). Genetic studies in Dictyostelium and Drosophila have shown that TM9SF members are required for adhesion and phagocytosis in innate immune response, furthermore, human TM9SF1 plays a role in the regulation of autophagy and human TM9SF4 in tumor cannibalism. Here we report that the zebrafish genome encodes five members of this family, TM9SF1-TM9SF5, which show high level of sequence conservation with the previously reported members. Expression analysis in zebrafish showed that all members are maternally expressed and continue to be present throughout embryogenesis to adults. Gene expression could not be regulated by pathogen-associated molecular patterns such as LPS, CpG, or Poly I:C. By bioinformatic analyses of 80 TM9SF protein sequences from yeast, plants, and animals, we confirmed a very conserved protein structure. An evolutionary conserved immunoreceptor tyrosine-based inhibition motif has been detected in the cytoplasmic domain between transmembrane domain (TM) 7 and TM8 in TM9SF1, TM9SF2, TM9SF4 and TM9SF5, and at the extreme C-terminal end of TM9SF4. Finally, a conserved TRAF2 binding domain could also be predicted in the cytoplasmic regions of TM9SF2, TM9SF3, TM9SF4, and TM9SF5. This confirms the hypothesis that TM9SF proteins may play a regulatory role in a specific and ancient cellular mechanism that is involved in innate immunity.

Qian, Y., C. M. West, et al. (2010). "UDP-GlcNAc:Glycoprotein N-acetylglucosamine-1-phosphotransferase mediates the initial step in the formation of the methylphosphomannosyl residues on the high mannose oligosaccharides of Dictyostelium discoideum glycoproteins." Biochem Biophys Res Commun 393(4): 678-681.
	The Dictyostelium discoideum gene gpt1 encodes a protein XP_638036 with sequence similarity to the alpha/beta subunits of mammalian UDP-GlcNAc:Glycoprotein N-acetylglucosamine-1-phosphotransferase. We now demonstrate that extracts of D. discoideum clones with mutations in this gene transfer GlcNAc-P from UDP-GlcNAc to mannose residues at less than 5% the wild type value. Further, the lysosomal hydrolases of these mutant clones fail to bind to a cation-independent mannose 6-phosphate receptor affinity column, indicating a lack of methylphosphomannosyl residues on the high mannose oligosaccharides of these proteins. We conclude that the gpt1 gene product catalyzes the initial step in the formation of methylphosphomannosyl residues on D. discoideum lysosomal hydrolases.

Raisley, B., H. N. Nguyen, et al. (2010). "G{alpha}5 subunit-mediated signalling requires a D-motif and the MAPK ERK1 in Dictyostelium." Microbiology 156(Pt 3): 789-797.
	The Dictyostelium Galpha5 subunit has been shown to reduce cell viability, inhibit folate chemotaxis and accelerate tip morphogenesis and gene expression during multicellular development. Alteration of the D-motif (mitogen-activated protein kinase docking site) at the amino terminus of the Galpha 5 subunit or the loss of extracellular signal-regulated kinase (ERK)1 diminished the lethality associated with the overexpression or constitutive activation of the Galpha5 subunit. The amino-terminal D-motif of the Galpha5 subunit was also found to be necessary for the reduced cell size, small aggregate formation and precocious developmental gene expression associated with Galpha5 subunit overexpression. This D-motif also contributed to the aggregation delay in cells expressing a constitutively active Galpha5 subunit, but the D-motif was not necessary for the inhibition of folate chemotaxis. These results suggest that the amino-terminal D-motif is required for some but not all phenotypes associated with elevated Galpha5 subunit functions during growth and development and that ERK1 can function in Galpha5 subunit-mediated signal transduction.

Reddy, A. K., P. K. Balne, et al. (2010). "Dictyostelium polycephalum infection of human cornea." Emerg Infect Dis 16(10): 1644-1645.
	
Robinson, D. N. (2010). "14-3-3, an integrator of cell mechanics and cytokinesis." Small Gtpases 1(3): 165-169.
	One of the goals of understanding cytokinesis is to uncover the molecular regulation of the cellular mechanical properties that drive cell shape change. Such regulatory pathways are likely to be used at multiple stages of a cell's life, but are highly featured during cell division. Recently, we demonstrated that 14-3-3 (encoded by a single gene in the social amoeba Dictyostelium discoideum) serves to integrate key cytoskeletal components-microtubules, Rac and myosin II-to control cell mechanics and cytokinesis. As 14-3-3 proteins are frequently altered in a variety of human tumors, we extend these observations to suggest possible additional roles for how 14-3-3 proteins may contribute to tumorigenesis.

Rollins, A. W., J. C. Landolt, et al. (2010). "Dictyostelid cellular slime molds associated with grasslands of the central and western United States." Mycologia 102(5): 996-1003.
	Dictyostelid cellular slime molds (dictyostelids) associated with grassland ecosystems of the central and western United States were investigated at nine sites that included examples of the three major ecological types of grasslands (tall grass, mixed grass and short grass) generally recognized for the region. Samples of soil/humus collected from each site were examined with the Cavender method of isolating dictyostelids. For each of those six sites with well developed gallery forests present, an additional set of forest soil/humus samples was collected. A more intensive sampling effort was carried out at one site (Konza LTER) to assess the possible effects of burning and grazing on dictyostelid diversity and density. Twelve species of dictyostelids were recovered from grassland sites, whereas gallery forest sites yielded only nine species. Four cosmopolitan species (Dictyostelium giganteum, D. mucoroides, D. sphaerocephalum and Polysphondylium pallidum) were represented by the greatest densities of clones, with D. sphaerocephalum particularly common. The general pattern across all sites was that both species richness and density of dictyostelids decreased with decreasing precipitation. Samples collected from ungrazed grassland plots yielded higher numbers of both species and clones as compared to grazed plots, and the general pattern was for both values to increase as the interval between fires increased. For numbers of clones this correlation was statistically significant.

Romeralo, M., J. C. Landolt, et al. (2010). "Two new species of dictyostelid cellular slime molds from Alaska." Mycologia 102(3): 588-595.
	In sampling soils to survey dictyostelid cellular slime molds in Alaska we encountered two groups of isolates that have morphologies that differ from any previously described species within their group. We sequenced the nuclear small subunit ribosomal RNA gene (SSU rDNA) of selected isolates from the two groups and found sequences from both groups to be distinct from all previously described dictyostelid sequences. Phylogenetic analyses place one novel species in dictyostelid Group 2 and the other in Group 4 (Schaap et al. 2006). In this paper we formally describe as new these two species of cellular slime molds, Dictyostelium ammophilum sp. nov. and Dictyostelium boreale sp. nov., based on the combination of morphological and molecular characters.

Romeralo, M., F. W. Spiegel, et al. (2010). "A fully resolved phylogeny of the social amoebas (Dictyostelia) based on combined SSU and ITS rDNA sequences." Protist 161(4): 539-548.
	The dictyostelids possess a complex life cycle including aggregative and multicellular stages. They also include one of the most widely studied protistan model organisms, Dictyostelium discoideum. The current molecular phylogeny of dictyostelids is based largely on SSU (18S) rDNA sequences and shows a deep taxon consisting of four major groups, none of which correspond to the three traditional morphologically-defined genera. However, due to the generally slowly evolving nature of SSU rDNA, these data fail to resolve the majority of branches within the four groups. Given the highly morphologically mixed nature of the dictyostelid groups, it is important to resolve relationships within them. We have determined sequences for the internal transcribed spacers (ITS) of rDNA for nearly all species in the original dictyostelid global phylogeny. Phylogenetic analyses of these data, in combination with the previously determined SSU rDNA sequences, confidently resolve nearly all branches in the tree. This now fully resolved phylogeny confirms the utility of ITS for dictyostelid systematics and lays the ground work for further evolutionary study of the group.

Samereier, M., I. Meyer, et al. (2010). "Live cell-imaging techniques for analyses of microtubules in Dictyostelium." Methods Cell Biol 97: 341-357.
	Dictyostelium amoebae provide a popular model system for analyses of cell and cytoskeletal dynamics. Yet, the sensitivity of Dictyostelium cells to phototoxic effects, their rapid cell movement, and the extraordinary motility of their microtubule system are specific challenges for live cell imaging. The protocols outlined in this chapter are optimized to minimize these challenges, using Dictyostelium cells expressing green fluorescent tubulin or microtubule plus-end markers such as TACC. We describe suitable specimen preparations, treatments with microtubule-depolymerizing drugs, and applicable settings on wide-field and confocal microscopy systems for four-dimensional time-lapse and fluorescence recovery after photobleaching analyses of microtubule dynamics.

Sathe, S., S. Kaushik, et al. (2010). "Genetic heterogeneity in wild isolates of cellular slime mold social groups." Microb Ecol 60(1): 137-148.
	This study addresses the issues of spatial distribution, dispersal, and genetic heterogeneity in social groups of the cellular slime molds (CSMs). The CSMs are soil amoebae with an unusual life cycle that consists of alternating solitary and social phases. Because the social phase involves division of labor with what appears to be an extreme form of "altruism", the CSMs raise interesting evolutionary questions regarding the origin and maintenance of sociality. Knowledge of the genetic structure of social groups in the wild is necessary for answering these questions. We confirm that CSMs are widespread in undisturbed forest soil from South India. They are dispersed over long distances via the dung of a variety of large mammals. Consistent with this mode of dispersal, most social groups in the two species examined for detailed study, Dictyostelium giganteum and Dictyostelium purpureum, are multi-clonal.

Saxer, G., D. A. Brock, et al. (2010). "Cheating does not explain selective differences at high and low relatedness in a social amoeba." BMC Evol Biol 10: 76.
	BACKGROUND: Altruism can be favored by high relatedness among interactants. We tested the effect of relatedness in experimental populations of the social amoeba Dictyostelium discoideum, where altruism occurs in a starvation-induced social stage when some amoebae die to form a stalk that lifts the fertile spores above the soil facilitating dispersal. The single cells that aggregate during the social stage can be genetically diverse, which can lead to conflict over spore and stalk allocation. We mixed eight genetically distinct wild isolates and maintained twelve replicated populations at a high and a low relatedness treatment. After one and ten social generations we assessed the strain composition of the populations. We expected that some strains would be out-competed in both treatments. In addition, we expected that low relatedness might allow the persistence of social cheaters as it provides opportunity to exploit other strains. RESULTS: We found that at high relatedness a single clone prevailed in all twelve populations. At low relatedness three clones predominated in all twelve populations. Interestingly, exploitation of some clones by others in the social stage did not explain the results. When we mixed each winner against the pool of five losers, the winner did not prevail in the spores because all contributed fairly to the stalk and spores. Furthermore, the dominant clone at high-relatedness was not cheated by the other two that persisted at low relatedness. A combination of high spore production and short unicellular stage most successfully explained the three successful clones at low relatedness, but not why one of them fared better at high relatedness. Differences in density did not account for the results, as the clones did not differ in vegetative growth rates nor did they change the growth rates over relevant densities. CONCLUSIONS: These results suggest that social competition and something beyond solitary growth differences occurs during the vegetative stage when amoebae eat bacteria and divide by binary fission. The high degree of repeatability of our results indicates that these effects are strong and points to the importance of new approaches to studying interactions in D. discoideum.

Scherer, A., S. Kuhl, et al. (2010). "Ca2+ chemotaxis in Dictyostelium discoideum." J Cell Sci 123(Pt 21): 3756-3767.
	Using a newly developed microfluidic chamber, we have demonstrated in vitro that Ca(2+) functions as a chemoattractant of aggregation-competent Dictyostelium discoideum amoebae, that parallel spatial gradients of cAMP and Ca(2+) are more effective than either alone, and that cAMP functions as a stronger chemoattractant than Ca(2+). Effective Ca(2+) gradients are extremely steep compared with effective cAMP gradients. This presents a paradox because there is no indication to date that steep Ca(2+) gradients are generated in aggregation territories. However, given that Ca(2+) chemotaxis is co-acquired with cAMP chemotaxis during development, we speculate on the role that Ca(2+) chemotaxis might have and the possibility that steep, transient Ca(2+) gradients are generated during natural aggregation in the interstitial regions between cells.

Shimada, N., K. Inouye, et al. (2010). "SunB, a novel Sad1 and UNC-84 domain-containing protein required for development of Dictyostelium discoideum." Dev Growth Differ 52(7): 577-590.
	A gene, sunB, encoding a novel class of Sad1 and UNC-84 (SUN) domain, was isolated from a cDNA screen for suppressors of a mutation in Dd-STATa - a Dictyostelium homologue of metazoan STAT (signal transducers and activators of transcription). The SunB protein localized in the area around the nucleus in growing cells, but in the multicellular stages it was predominantly found in prespore vacuoles (PSVs). A disruptant of sunB was multinucleated in the vegetative phase; during development it formed mounds with multiple tips and failed to culminate. The mutation was cell autonomous, and showed reduced expression of the prespore marker gene pspA and elevated expression of marker genes for prestalk AB cells. Interestingly, the level of SunB was abnormally high in the prestalk cells of Dd-STATa mutants, which are defective in culmination. We conclude that SunB is essential for accurate prestalk/prespore differentiation during Dictyostelium development and that its cell-type dependent localization is regulated by a Dd-STATa-mediated signaling pathway.

Shina, M. C., R. Muller, et al. (2010). "A cytohesin homolog in Dictyostelium amoebae." PLoS One 5(2): e9378.
	BACKGROUND: Dictyostelium, an amoeboid motile cell, harbors several paralogous Sec7 genes that encode members of three distinct subfamilies of the Sec7 superfamily of Guanine nucleotide exchange factors. Among them are proteins of the GBF/BIG family present in all eukaryotes. The third subfamily represented with three members in D. discoideum is the cytohesin family that has been thought to be metazoan specific. Cytohesins are characterized by a Sec7 PH tandem domain and have roles in cell adhesion and migration. PRINCIPAL FINDINGS: Dictyostelium SecG exhibits highest homologies to the cytohesins. It harbors at its amino terminus several ankyrin repeats that are followed by the Sec7 PH tandem domain. Mutants lacking SecG show reduced cell-substratum adhesion whereas cell-cell adhesion that is important for development is not affected. Accordingly, multicellular development proceeds normally in the mutant. During chemotaxis secG(-) cells elongate and migrate in a directed fashion towards cAMP, however speed is moderately reduced. SIGNIFICANCE: The data indicate that SecG is a relevant factor for cell-substrate adhesion and reveal the basic function of a cytohesin in a lower eukaryote.

Shina, M. C., C. Unal, et al. (2010). "A Coronin7 homolog with functions in actin-driven processes." J Biol Chem 285(12): 9249-9261.
	Dictyostelium discoideum Coronin7 (DdCRN7) together with human Coronin7 (CRN7) and Pod-1 of Drosophila melanogaster and Caenorhabditis elegans belong to the coronin family of WD-repeat domain-containing proteins. Coronin7 proteins are characterized by two WD-repeat domains that presumably fold into two beta-propeller structures. DdCRN7 shares highest homology with human CRN7, a protein with roles in membrane trafficking. DdCRN7 is present in the cytosol and accumulates in cell surface projections during movement and phago- and pinocytosis. Cells lacking CRN7 have altered chemotaxis and phagocytosis. Furthermore, loss of CRN7 affects the infection process by the pathogen Legionella pneumophila and allows a more efficient internalization of bacteria. To provide a mechanism for CNR7 action, we studied actin-related aspects. We could show that CRN7 binds directly to F-actin and protects actin filaments from depolymerization. CRN7 also associated with F-actin in vivo. It was present in the Triton X-100-insoluble cytoskeleton, colocalized with F-actin, and its distribution was sensitive to drugs affecting the actin cytoskeleton. We propose that the CRN7 role in chemotaxis and phagocytosis is through its effect on the actin cytoskeleton.

Shu, S., X. Liu, et al. (2010). "Expression of Y53A-actin in Dictyostelium disrupts the cytoskeleton and inhibits intracellular and intercellular chemotactic signaling." J Biol Chem 285(36): 27713-27725.
	We showed previously that phosphorylation of Tyr(53), or its mutation to Ala, inhibits actin polymerization in vitro with formation of aggregates of short filaments, and that expression of Y53A-actin in Dictyostelium blocks differentiation and development at the mound stage (Liu, X., Shu, S., Hong, M. S., Levine, R. L., and Korn, E. D. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 13694-13699; Liu, X., Shu, S., Hong, M. S., Yu, B., and Korn, E. D. (2010) J. Biol. Chem. 285, 9729-9739). We now show that expression of Y53A-actin, which does not affect cell growth, phagocytosis, or pinocytosis, inhibits the formation of head-to-tail cell streams during cAMP-induced aggregation, although individual amoebae chemotax normally. We show that expression of Y53A-actin causes a 50% reduction of cell surface cAMP receptors, and inhibits cAMP-induced increases in adenylyl cyclase A activity, phosphorylation of ERK2, and actin polymerization. Trafficking of vesicles containing adenylyl cyclase A to the rear of the cell and secretion of the ACA vesicles are also inhibited. The actin cytoskeleton of cells expressing Y53A-actin is characterized by numerous short filaments, and bundled and aggregated filaments similar to the structures formed by copolymerization of purified Y53A-actin and wild-type actin in vitro. This disorganized actin cytoskeleton may be responsible for the inhibition of intracellular and intercellular cAMP signaling in cells expressing F-Y53A-actin.

Singh, D., R. Rani, et al. (2010). "Human spleen tyrosine kinase (Syk) recombinant expression systems for high-throughput assays." Biotechnol J 5(2): 201-212.
	Spleen tyrosine kinase (Syk) is an important non-receptor tyrosine kinase and its aberrant regulation is associated with a variety of allergic disorders and autoimmune diseases. To identify small molecule inhibitors of Syk in high-throughput assays, recombinant Syk protein is needed in bulk quantity. We studied the expression of recombinant human Syk in three heterologous systems: E. coli, baculovirus expression vector system (BEVS), and the cellular slime mold Dictyostelium discoideum (Dd). Syk activity was higher in the BEVS as compared to the Dd expression host, whereas in E. coli, no activity was observed under our assay conditions. Purified Syk kinase domain protein from BEVS showed concentration dependent inhibition with OXSI-2, a known Syk inhibitor. Molecular modeling and docking studies were performed to understand the binding mode and critical interactions of the inhibitor with catalytic domain of Syk. The BEVS generated Syk kinase domain showed stability upon multiple freeze-thaw cycles and exhibited significantly higher levels of tyrosine phosphorylation at pTyr(525)/Tyr(526) in the Syk activation loop. Based on our data, we conclude that BEVS is the ideal host to produce an active and stable enzyme, which can be successfully employed for screening of Syk inhibitors in a high-throughput system.

Skoge, M., M. Adler, et al. (2010). "Gradient sensing in defined chemotactic fields." Integr Biol (Camb) 2(11-12): 659-668.
	Cells respond to a variety of secreted molecules by modifying their physiology, growth patterns, and behavior. Motile bacteria and eukaryotic cells can sense extracellular chemoattractants and chemorepellents and alter their movement. In this way fibroblasts and leukocytes can find their way to sites of injury and cancer cells can home in on sites that are releasing growth factors. Social amoebae such as Dictyostelium are chemotactic to cAMP which they secrete several hours after they have initiated development. These eukaryotic cells are known to be able to sense extremely shallow gradients but the processes underlying their exquisite sensitivity are still largely unknown. In this study we determine the responses of developed cells of Dictyostelium discoideum to stable linear gradients of cAMP of varying steepness generated in 2 mum deep gradient chambers of microfluidic devices. The gradients are generated by molecular diffusion between two 80 mum deep flow-through channels, one of which is perfused with a solution of cAMP and the other with buffer, serving as continuously replenished source and sink. These low ceiling gradient chambers constrained the cells in the vertical dimension, facilitating confocal imaging, such that subcellular localization of fluorescently tagged proteins could be followed for up to 30 min without noticeable phototoxicity. Chemotactic cells enter these low ceiling chambers by flattening and elongating and then move almost as rapidly as unconstrained cells. By following the localization of activated Ras (RasGTP) using a Ras Binding Domain fused to Green Fluorescent Protein (RBD-GFP), we observed the rapid appearance of membrane associated patches at the tips of pseudopods. These patches remained associated with pseudopods while they continued to extend but were rapidly disassembled when pseudopods stalled and the cell moved past them. Likewise, fluorescence associated with localized RasGTP rapidly disappeared when the gradient was turned off. Correlation of the size and persistence of RasGTP patches with extension of pseudopods may set the rules for understanding how the signal transduction mechanisms convert a weak external signal to a strong directional bias.

Smith, E. W., W. C. Lima, et al. (2010). "Effect of starvation on the endocytic pathway in Dictyostelium cells." Eukaryot Cell 9(3): 387-392.
	Dictyostelium discoideum amoebae have been used extensively to study the structure and dynamics of the endocytic pathway. Here, we show that while the general structure of the endocytic pathway is maintained in starved cells, its dynamics rapidly slow down. In addition, analysis of apm3 and lvsB mutants reveals that the functional organization of the endocytic pathway is profoundly modified upon starvation. Indeed, in these mutant cells, some of the defects observed in rich medium persist in starved cells, notably an abnormally slow transfer of endocytosed material between endocytic compartments. Other parameters, such as endocytosis of the fluid phase or the rate of fusion of postlysosomes to the cell surface, vary dramatically upon starvation. Studying the endocytic pathway in starved cells can provide a different perspective, allowing the primary (invariant) defects resulting from specific mutations to be distinguished from their secondary (conditional) consequences.

Smith, T. S., J. M. Pineda, et al. (2010). "Copine A plays a role in the differentiation of stalk cells and the initiation of culmination in Dictyostelium development." BMC Dev Biol 10: 59.
	BACKGROUND: Copines are calcium-dependent phospholipid-binding proteins found in diverse eukaryotic organisms. We are studying the function of copines in Dictyostelium discoideum, a single-celled amoeba that undergoes cell differentiation and morphogenesis to form multicellular fruiting bodies when placed in starvation conditions. Previously, we showed that Dictyostelium cells lacking the copine A (cpnA) gene are not able to complete the developmental cycle, arresting at the slug stage. The aim of this study is to further characterize the developmental defect of the cpnA- cells. RESULTS: Time-lapse imaging revealed that cpnA- cells exhibited delayed aggregation and made large mounds that formed one large slug as compared to the smaller slugs of the wild-type cells. While the prespore cell patterning appeared to be normal within the cpnA- slugs, the prestalk cell patterning was different from wild-type. When cpnA- cells were mixed with a small percentage of wild-type cells, chimeric fruiting bodies with short stalks formed. When a small percentage of cpnA- cells was mixed with wild-type cells, the cpnA- cells labeled with GFP were found located throughout the chimeric slug and in both the stalk and sporehead of the fruiting bodies. However, there appeared to be a small bias towards cpnA- cells becoming spore cells. When cpnA- cells were developed in buffer containing EGTA, they were also able to differentiate into either stalk or spore cells to form fruiting bodies with short stalks. CONCLUSIONS: Our results indicate that CpnA is involved in the regulation of aggregation, slug size, and culmination during Dictyostelium development. More specifically, CpnA appears to be involved in the function and differentiation of prestalk cells and plays a role in a calcium-regulated signaling pathway critical to triggering the initiation of culmination.

Socol, M., C. Lefrou, et al. (2010). "Synchronization of Dictyostelium discoideum adhesion and spreading using electrostatic forces." Bioelectrochemistry 79(2): 198-210.
	Synchronization of cell spreading is valuable for the study of molecular events involved in the formation of adhesive contacts with the substrate. At a low ionic concentration (0.17 mM) Dictyostelium discoideum cells levitate over negatively charged surfaces due to electrostatic repulsion. First, a two-chamber device, divided by a porous membrane, allows to quickly increase the ionic concentration around the levitating cells. In this way, a good synchronization was obtained, the onsets of cell spreading being separated by less than 5 s. Secondly applying a high potential pulse (2.5 V/Ref, 0.1s) to an Indium Tin Oxide surface attracts the cells toward the surface where they synchronously spread as monitored by LimE(Deltacoil)-GFP. During spreading, actin polymerizes in series of active spots. On average, the first spot appears 8-11s after the electric pulse and the next ones appear regularly, separated by about 10s. Synchronized actin-polymerization activity continues for 40s. Using an electric pulse to control the exact time point at which cells contact the surface has allowed for the first time to quantify the cellular response time for actin polymerization. Electrochemical synchronization is therefore a valuable tool to study intracellular responses to contact.

Stamatopoulou, V., C. Toumpeki, et al. (2010). "Domain architecture of the DRpp29 protein and its interaction with the RNA subunit of Dictyostelium discoideum RNase P." Biochemistry 49(50): 10714-10727.
	Dictyostelium discoideum nuclear RNase P is a ribonucleoprotein complex that displays similarities with its counterparts from higher eukaryotes such as the human enzyme, but at the same time it retains distinctive characteristics. In the present study, we report the molecular cloning and interaction details of DRpp29 and RNase P RNA, two subunits of the RNase P holoenzyme from D. discoideum. Electrophoretic mobility shift assays exhibited that DRpp29 binds specifically to the RNase P RNA subunit, a feature that was further confirmed by the molecular modeling of the DRpp29 structure. Moreover, deletion mutants of DRpp29 were constructed in order to investigate the domains of DRpp29 that contribute to and/or are responsible for the direct interaction with the D. discoideum RNase P RNA. A eukaryotic specific, lysine- and arginine-rich region was revealed, which seems to facilitate the interaction between these two subunits. Furthermore, we tested the ability of wild-type and mutant DRpp29 to form active RNase P enzymatic particles with the Escherichia coli RNase P RNA.

Sugden, C., S. Ross, et al. (2010). "Two novel Src homology 2 domain proteins interact to regulate dictyostelium gene expression during growth and early development." J Biol Chem 285(30): 22927-22935.
	There are 13 Dictyostelium Src homology 2 (SH2) domain proteins, almost 10-fold fewer than in mammals, and only three are functionally unassigned. One of these, LrrB, contains a novel combination of protein interaction domains: an SH2 domain and a leucine-rich repeat domain. Growth and early development appear normal in the mutant, but expression profiling reveals that three genes active at these stages are greatly underexpressed: the ttdA metallohydrolase, the abcG10 small molecule transporter, and the cinB esterase. In contrast, the multigene family encoding the lectin discoidin 1 is overexpressed in the disruptant strain. LrrB binds to 14-3-3 protein, and the level of binding is highest during growth and decreases during early development. Comparative tandem affinity purification tagging shows that LrrB also interacts, via its SH2 domain and in a tyrosine phosphorylation-dependent manner, with two novel proteins: CldA and CldB. Both of these proteins contain a Clu domain, a &gt;200-amino acid sequence present within highly conserved eukaryotic proteins required for correct mitochondrial dispersal. A functional interaction of LrrB with CldA is supported by the fact that a cldA disruptant mutant also underexpresses ttdA, abcG10, and cinB. Significantly, CldA is itself one of the three functionally unassigned SH2 domain proteins. Thus, just as in metazoa, but on a vastly reduced numerical scale, an interacting network of SH2 domain proteins regulates specific Dictyostelium gene expression.

Sun, S. X., S. Walcott, et al. (2010). "Cytoskeletal cross-linking and bundling in motor-independent contraction." Curr Biol 20(15): R649-654.
	Eukaryotic and prokaryotic cells use cytoskeletal proteins to regulate and modify cell shape. During cytokinesis or eukaryotic cell crawling, contractile forces are generated inside the cell to constrict the division site or to haul the rear of the cell forward, respectively. In many cases, these forces have been attributed to the activity of molecular motors, such as myosin II, which, by pulling on actin filaments, can produce contraction of the actin cytoskeleton. However, prokaryotic division is driven by the tubulin-like protein FtsZ and does not seem to require additional molecular motors to constrict the division site. Likewise, Dictyostelium discoideum and Saccharomyces cerevisiae can perform cytokinesis under motor-free conditions. In addition, many crawling cells can translocate when myosin is inhibited or absent. In this review, we point out another force-generation mechanism that can play a significant role in driving these processes in eukaryotes and prokaryotes. This mechanism is mediated by cross-linking and bundling proteins that form effective interactions between cytoskeletal filaments. Some recent studies in this area are reviewed and the physical underpinnings of this force-generation mechanism are explained.

Surcel, A., Y. S. Kee, et al. (2010). "Cytokinesis through biochemical-mechanical feedback loops." Semin Cell Dev Biol 21(9): 866-873.
	Cytokinesis is emerging as a control system defined by interacting biochemical and mechanical modules, which form a system of feedback loops. This integrated system accounts for the regulation and kinetics of cytokinesis furrowing and demonstrates that cytokinesis is a whole-cell process in which the global and equatorial cortices and cytoplasm are active players in the system. Though originally defined in Dictyostelium, features of the control system are recognizable in other organisms, suggesting a universal mechanism for cytokinesis regulation and contractility.

Swaney, K. F., C. H. Huang, et al. (2010). "Eukaryotic chemotaxis: a network of signaling pathways controls motility, directional sensing, and polarity." Annu Rev Biophys 39: 265-289.
	Chemotaxis, the directed migration of cells in chemical gradients, is a vital process in normal physiology and in the pathogenesis of many diseases. Chemotactic cells display motility, directional sensing, and polarity. Motility refers to the random extension of pseudopodia, which may be driven by spontaneous actin waves that propagate through the cytoskeleton. Directional sensing is mediated by a system that detects temporal and spatial stimuli and biases motility toward the gradient. Polarity gives cells morphologically and functionally distinct leading and lagging edges by relocating proteins or their activities selectively to the poles. By exploiting the genetic advantages of Dictyostelium, investigators are working out the complex network of interactions between the proteins that have been implicated in the chemotactic processes of motility, directional sensing, and polarity.

Tanaka, T., Y. Shima, et al. (2010). "Expression, identification and purification of Dictyostelium acetoacetyl-coa thiolase expressed in Escherichia coli." Int J Biol Sci 7(1): 9-17.
	Acetoacetyl-CoA thiolase (AT) is an enzyme that catalyses the CoA-dependent thiolytic cleavage of acetoacetyl-CoA to yield 2 molecules of acetyl-CoA, or the reverse condensation reaction. A full-length cDNA clone pBSGT-3, which has homology to known thiolases, was isolated from Dictyostelium cDNA library. Expression of the protein encoded in pBSGT-3 in Escherichia coli, its thiolase enzyme activity, and the amino acid sequence homology search revealed that pBSGT-3 encodes an AT. The recombinant AT (r-thiolase) was expressed in an active form in an E. coli expression system, and purified to homogeneity by selective ammonium sulfate fractionation and two steps of column chromatography. The purified enzyme exhibited a specific activity of 4.70 mU/mg protein. Its N-terminal sequence was (NH)-Arg-Met-Tyr-Thr-Thr-Ala-Lys-Asn-Leu-Glu-, which corresponds to the sequence from positions 15 to 24 of the amino acid sequence deduced from pBSGT-3 clone. The r-thiolase in the inclusion body expressed highly in E. coli was the precursor form, which is slightly larger than the purified r-thiolase. When incubated with the cell-free extract of Dictyostelium cells, the precursor was converted to the same size to the purified r-thiolase, suggesting that the presequence at the N-terminus is removed by a Dictyostelium processing peptidase.

Teo, R., K. J. Lewis, et al. (2010). "Glycogen synthase kinase-3 is required for efficient Dictyostelium chemotaxis." Mol Biol Cell 21(15): 2788-2796.
	Glycogen synthase kinase-3 (GSK3) is a highly conserved protein kinase that is involved in several important cell signaling pathways and is associated with a range of medical conditions. Previous studies indicated a major role of the Dictyostelium homologue of GSK3 (gskA) in cell fate determination during morphogenesis of the fruiting body; however, transcriptomic and proteomic studies have suggested that GSK3 regulates gene expression much earlier during Dictyostelium development. To investigate a potential earlier role of GskA, we examined the effects of loss of gskA on cell aggregation. We find that cells lacking gskA exhibit poor chemotaxis toward cAMP and folate. Mutants fail to activate two important regulatory signaling pathways, mediated by phosphatidylinositol 3,4,5-trisphosphate (PIP(3)) and target of rapamycin complex 2 (TORC2), which in combination are required for chemotaxis and cAMP signaling. These results indicate that GskA is required during early stages of Dictyostelium development, in which it is necessary for both chemotaxis and cell signaling.

Tovy, A., B. Hofmann, et al. (2010). "In vitro tRNA methylation assay with the Entamoeba histolytica DNA and tRNA methyltransferase Dnmt2 (Ehmeth) enzyme." J Vis Exp(44).
	Protozoan parasites are among the most devastating infectious agents of humans responsible for a variety of diseases including amebiasis, which is one of the three most common causes of death from parasitic disease. The agent of amebiasis is the amoeba parasite Entamoeba histolytica that exists under two stages: the infective cyst found in food or water and the invasive trophozoite living in the intestine. The clinical manifestations of amebiasis range from being asymptomatic to colitis, dysentery or liver abscesses. E. histolytica is one of the rare unicellular parasite with 5-methylcytosine (5mC) in its genome. It contains a single DNA methyltransferase, Ehmeth, that belongs to the Dnmt2 family. A role for Dnmt2 in the control of repetitive elements has been established in E. histolytica, Dictyostelium discoideum and Drosophila. Our recent work has shown that Ehmeth methylates tRNA(Asp), and this finding indicates that this enzyme has a dual DNA/tRNA(Asp) methyltransferase activity. This observation is in agreement with the dual activity that has been reported for D. discoideum and D. melanogaster. The functional significance of the DNA/tRNA specificity of Dnmt2 enzymes is still unknown. To address this question, a method to determine the tRNA methyltransferase activity of Dnmt2 proteins was established. In this video, we describe a straightforward approach to prepare an adequate tRNA substrate for Dnmt2 and a method to measure its tRNA methyltransferase activity.

Traylor-Knowles, N., U. Hansen, et al. (2010). "The evolutionary diversification of LSF and Grainyhead transcription factors preceded the radiation of basal animal lineages." BMC Evol Biol 10: 101.
	BACKGROUND: The transcription factors of the LSF/Grainyhead (GRH) family are characterized by the possession of a distinctive DNA-binding domain that bears no clear relationship to other known DNA-binding domains, with the possible exception of the p53 core domain. In triploblastic animals, the LSF and GRH subfamilies have diverged extensively with respect to their biological roles, general expression patterns, and mechanism of DNA binding. For example, Grainyhead (GRH) homologs are expressed primarily in the epidermis, and they appear to play an ancient role in maintaining the epidermal barrier. By contrast, LSF homologs are more widely expressed, and they regulate general cellular functions such as cell cycle progression and survival in addition to cell-lineage specific gene expression. RESULTS: To illuminate the early evolution of this family and reconstruct the functional divergence of LSF and GRH, we compared homologs from 18 phylogenetically diverse taxa, including four basal animals (Nematostella vectensis, Vallicula multiformis, Trichoplax adhaerens, and Amphimedon queenslandica), a choanoflagellate (Monosiga brevicollis) and several fungi. Phylogenetic and bioinformatic analyses of these sequences indicate that (1) the LSF/GRH gene family originated prior to the animal-fungal divergence, and (2) the functional diversification of the LSF and GRH subfamilies occurred prior to the divergence between sponges and eumetazoans. Aspects of the domain architecture of LSF/GRH proteins are well conserved between fungi, choanoflagellates, and metazoans, though within the Metazoa, the LSF and GRH families are clearly distinct. We failed to identify a convincing LSF/GRH homolog in the sequenced genomes of the algae Volvox carteri and Chlamydomonas reinhardtii or the amoebozoan Dictyostelium purpureum. Interestingly, the ancestral GRH locus has become split into two separate loci in the sea anemone Nematostella, with one locus encoding a DNA binding domain and the other locus encoding the dimerization domain. CONCLUSIONS: In metazoans, LSF and GRH proteins play a number of roles that are essential to achieving and maintaining multicellularity. It is now clear that this protein family already existed in the unicellular ancestor of animals, choanoflagellates, and fungi. However, the diversification of distinct LSF and GRH subfamilies appears to be a metazoan invention. Given the conserved role of GRH in maintaining epithelial integrity in vertebrates, insects, and nematodes, it is noteworthy that the evolutionary origin of Grh appears roughly coincident with the evolutionary origin of the epithelium.

Tung, S. M., C. Unal, et al. (2010). "Loss of Dictyostelium ATG9 results in a pleiotropic phenotype affecting growth, development, phagocytosis and clearance and replication of Legionella pneumophila." Cell Microbiol 12(6): 765-780.
	Infection of Dictyostelium discoideum with Legionella pneumophila resulted in a large number of differentially regulated genes among them three core autophagy genes, ATG8, ATG9 and ATG16. Macroautophagy contributes to many physiological and pathological processes and might also constitute an important mechanism in cell-autonomous immunity. For further studies we selected the highly conserved ATG9. In colocalization studies with GFP-tagged ATG9 and different organelle marker proteins we neither observed colocalization with mitochondria, the ER nor lysosomes. However, there was partial colocalization with the Golgi apparatus and many ATG9-GFP-containing vesicles localized along microtubules and accumulated around the microtubule organizing centre. ATG9-deficient cells had pleiotropic defects. In addition to growth defects they displayed severe developmental defects, consistent with the known role of autophagy in Dictyostelium development. Unexpectedly, the ATG9 mutant also had a strong phagocytosis defect that was particularly apparent when infecting the cells with L. pneumophila. However, those Legionellae that entered the host could multiply better in mutant than in wild-type cells, because of a less efficient clearance in the early and a more efficient replication in the late phase of infection. We conclude that ATG9 and hence macroautophagy has a protective role during pathogen infection.

Underwood, J., J. Greene, et al. (2010). "Identification of a new mechanism for targeting myosin II heavy chain phosphorylation by Dictyostelium myosin heavy chain kinase B." BMC Res Notes 3: 56.
	BACKGROUND: Heavy chain phosphorylation plays a central role in regulating myosin II bipolar filament assembly in Dictyostelium, as well as in higher eukaryotic nonmuscle cells. Our previous work has demonstrated that the WD-repeat domain of Dictyostelium myosin II heavy chain kinase B (MHCK-B), unlike its counterpart in MHCK-A, is not absolutely required for targeting of the kinase to phosphorylate MHC. Thus, we tested the hypothesis that an asparagine-rich and structurally disordered region that is unique to MHCK-B can by itself function in substrate targeting. FINDINGS: Biochemical assays comparing the activities of full-length MHCK-B, a truncation lacking only the WD-repeat domain (B-Delta-WD), and a truncation lacking both the N-rich region and the WD-repeat domain (B-Delta-N-WD) revealed that the N-rich region targets MHCK-B to phosphorylate MHC in a manner that leads to bipolar filament disassembly. This targeting is physiologically relevant since cellular over-expression of the B-Delta-WD truncation, but not the B-Delta-N-WD truncation, leads to dramatically reduced levels of myosin II filament assembly and associated defects in cytokinesis and multicellular development. CONCLUSIONS: The results presented here demonstrate that an intrinsically unstructured, and asparagine-rich, region of a MHCK-B can mediate specific targeting of the kinase to phosphorylate myosin II heavy chain. This targeting involves a direct binding interaction with myosin II filaments. In terms of regulating myosin bipolar filament assembly, our results suggest that factors affecting the activity of this unique region of MHCK-B could allow for regulation of MHCK-B in a manner that is distinct from the other MHCKs in Dictyostelium.

Urwyler, S., I. Finsel, et al. (2010). "Isolation of Legionella-containing vacuoles by immuno-magnetic separation." Curr Protoc Cell Biol Chapter 3: Unit 3 34.
	The environmental bacterium Legionella pneumophila naturally parasitizes free-living amoebae. L. pneumophila is an opportunistic human pathogen that grows in macrophages, thus causing a life-threatening pneumonia termed Legionnaires' disease. The bacteria replicate intracellularly in environmental and immune phagocytes within a unique compartment, the Legionella-containing vacuole (LCV). Formation of LCVs is a complex and robust process involving &gt;150 secreted bacterial effector proteins, which are believed to subvert host cell signaling and vesicle trafficking pathways. This unit describes a simple approach to purify intact LCVs from Dictyostelium discoideum amoebae. The method comprises a two-step purification protocol that includes immuno-magnetic separation by means of an antibody against an effector protein specifically binding to LCVs, followed by density gradient centrifugation. The use of D. discoideum producing a fluorescent LCV marker and fluorescently labeled L. pneumophila allow tracking the enrichment of LCVs by light microscopy.

Vadell, E. M. (2010). "[Dictyostelium. A social amoeba as a model organism]." Medicina (B Aires) 70(4): 389-392.
	
van Egmond, W. N. and P. J. van Haastert (2010). "Characterization of the Roco protein family in Dictyostelium discoideum." Eukaryot Cell 9(5): 751-761.
	The Roco family consists of multidomain Ras-GTPases that include LRRK2, a protein mutated in familial Parkinson's disease. The genome of the cellular slime mold Dictyostelium discoideum encodes 11 Roco proteins. To study the functions of these proteins, we systematically knocked out the roco genes. Previously described functions for GbpC, Pats1, and QkgA (Roco1 to Roco3) were confirmed, while novel developmental defects were identified in roco4- and roco11-null cells. Cells lacking Roco11 form larger fruiting bodies than wild-type cells, while roco4-null cells show strong developmental defects during the transition from mound to fruiting body; prestalk cells produce reduced levels of cellulose, leading to unstable stalks that are unable to properly lift the spore head. Detailed phylogenetic analysis of four slime mold species reveals that QkgA and Roco11 evolved relatively late by duplication of an ancestor roco4 gene (later than approximately 300 million years ago), contrary to the situation with other roco genes, which were already present before the split of the common ancestor of D. discoideum and Polysphondylium pallidum (before approximately 600 million years ago). Together, our data show that the Dictyostelium Roco proteins serve a surprisingly diverse set of functions and highlight Roco4 as a key protein for proper stalk cell formation.

Van Haastert, P. J. (2010). "A stochastic model for chemotaxis based on the ordered extension of pseudopods." Biophys J 99(10): 3345-3354.
	Many amoeboid cells move by extending pseudopods. Here I present a new stochastic model for chemotaxis that is based on pseudopod extensions by Dictyostelium cells. In the absence of external cues, pseudopod extension is highly ordered with two types of pseudopods: de novo formation of a pseudopod at the cell body in random directions, and alternating right/left splitting of an existing pseudopod that leads to a persistent zig-zag trajectory. We measured the directional probabilities of the extension of splitting and de novo pseudopods in chemoattractant gradients with different steepness. Very shallow cAMP gradients can bias the direction of splitting pseudopods, but the bias is not perfect. Orientation of de novo pseudopods require much steeper cAMP gradients and can be more precise. These measured probabilities of pseudopod directions were used to obtain an analytical model for chemotaxis of cell populations. Measured chemotaxis of wild-type cells and mutants with specific defects in these stochastic pseudopod properties are similar to predictions of the model. These results show that combining splitting and de novo pseudopods is a very effective way for cells to obtain very high sensitivity to stable gradient and still be responsive to changes in the direction of the gradient.

Van Haastert, P. J. (2010). "A model for a correlated random walk based on the ordered extension of pseudopodia." PLoS Comput Biol 6(8).
	Cell migration in the absence of external cues is well described by a correlated random walk. Most single cells move by extending protrusions called pseudopodia. To deduce how cells walk, we have analyzed the formation of pseudopodia by Dictyostelium cells. We have observed that the formation of pseudopodia is highly ordered with two types of pseudopodia: First, de novo formation of pseudopodia at random positions on the cell body, and therefore in random directions. Second, pseudopod splitting near the tip of the current pseudopod in alternating right/left directions, leading to a persistent zig-zag trajectory. Here we analyzed the probability frequency distributions of the angles between pseudopodia and used this information to design a stochastic model for cell movement. Monte Carlo simulations show that the critical elements are the ratio of persistent splitting pseudopodia relative to random de novo pseudopodia, the Left/Right alternation, the angle between pseudopodia and the variance of this angle. Experiments confirm predictions of the model, showing reduced persistence in mutants that are defective in pseudopod splitting and in mutants with an irregular cell surface.

van Hemert, F., M. D. Lazova, et al. (2010). "Mobility of G proteins is heterogeneous and polarized during chemotaxis." J Cell Sci 123(Pt 17): 2922-2930.
	The interaction of G-protein-coupled receptors with G proteins is a key event in transmembrane signal transduction that leads to vital decision-making by the cell. Here, we applied single-molecule epifluorescence microscopy to study the mobility of both the Gbetagamma and the Galpha2 subunits of the G protein heterotrimer in comparison with the cAMP receptor responsible for chemotactic signaling in Dictyostelium discoideum. Our experimental results suggest that approximately 30% of the G protein heterotrimers exist in receptor-precoupled complexes. Upon stimulation in a chemotactic gradient, this complex dissociates, subsequently leading to a linear diffusion and collision amplification of the external signal. We further found that Gbetagamma was partially immobilized and confined in an agonist-, F-actin- and Galpha2-dependent fashion. This led to the hypothesis that functional nanometric domains exist in the plasma membrane, which locally restrict the activation signal, and in turn, lead to faithful and efficient chemotactic signaling.

Veltman, D. M. and R. H. Insall (2010). "WASP family proteins: their evolution and its physiological implications." Mol Biol Cell 21(16): 2880-2893.
	WASP family proteins control actin polymerization by activating the Arp2/3 complex. Several subfamilies exist, but their regulation and physiological roles are not well understood, nor is it even known if all subfamilies have been identified. Our extensive search reveals few novel WASP family proteins. The WASP, WASH, and SCAR/WAVE subfamilies are evolutionarily ancient, with WASH the most universally present, whereas WHAMM/JMY first appears in invertebrates. An unusual Dictyostelium WASP homologue that has lost the WH1 domain has retained its function in clathrin-mediated endocytosis, demonstrating that WASPs can function with a remarkably diverse domain topology. The WASH and SCAR/WAVE regulatory complexes are much more rigidly maintained; their domain topology is highly conserved, and all subunits are present or lost together, showing that the complexes are ancient and functionally interdependent. Finally, each subfamily has a distinctive C motif, indicating that this motif plays a specific role in each subfamily's function, unlike the generic V and A motifs. Our analysis identifies which features are universally conserved, and thus essential, and which are branch-specific modifications. It also shows the WASP family is more widespread and diverse than currently appreciated and unexpectedly biases the physiological role of the Arp2/3 complex toward vesicle traffic.

Wang, H. Y. and J. G. Williams (2010). "Synergy between two transcription factors directs gene expression in Dictyostelium tip-organiser cells." Int J Dev Biol 54(8-9): 1301-1307.
	cotC requires the transcription factor CudA for its expression in the posterior, prespore cells of the slug, while the expL7 gene requires CudA for its expression in the anterior, tip-organiser region. In order to identify additional transcription factors that might mediate tip-organiser specific expression, we performed affinity chromatography on slug nuclear extracts. The affinity matrix bore cap-site distal sequences from region A of the expL7 promoter; an essential region located upstream of the CudA binding domain. One of the proteins purified was G-box binding factor (GBF), a zinc finger transcription factor which binds to G-rich elements, known as G boxes, that are present in the promoters of many developmental genes, including cotC. Previous work identified an essential sequence motif within region A and we show that this element is a G box, that binds recombinant GBF. Moreover, a G box from within the cotC promoter can substitute for region A of expL7 in directing tip-organiser specific expression of expL7. Thus the same two transcription factors, CudA and GBF, seem to co-operate to direct both tip-organiser and prespore gene expression. How then is specificity achieved? Replacing a CudA binding region in the cotC promoter with the CudA binding domain from expL7 strongly represses cotC promoter activity. Hence we suggest that differences in the topology of the multiple CudA half- sites contained within the two different CudA binding regions, coupled with differences in the signalling environment between tip-organiser cells and prespore cells, ensure correct expL7 expression.

Wang, H. Y. and J. G. Williams (2010). "Identification of a target for CudA, the transcription factor which directs formation of the Dictyostelium tip organiser." Int J Dev Biol 54(1): 161-165.
	The tip of the Dictyostelium slug functions much like an embryonic organiser; when grafted onto the flank of a recipient slug, it recruits a mass of prespore cells and leads them away as part of a secondary slug. CudA is a nuclear protein which is expressed in prespore cells where it acts as a specific transcription factor. CudA is also expressed in an anteriorly located group of cells, the tip-organiser, that is believed to constitute the functional tip. We identify an expansin-like gene, expl7, that is expressed within the tip-organiser region and which is not expressed in a cudA null strain. The expl7 promoter contains a region that binds to CudA in vitro and this region is necessary for expression in the tip-organiser. These results provide an end-point for a previously defined signal transduction pathway in which regionalized expression of the ACA adenylyl cyclase within the tip-organiser leads to localised cAMP-induced activation of STATa and consequent binding of STATa to the cudA promoter. STATa then induces expression of cudA and cudA directs the transcription of target genes such as expl7.

West, C. M., Z. A. Wang, et al. (2010). "A cytoplasmic prolyl hydroxylation and glycosylation pathway modifies Skp1 and regulates O2-dependent development in Dictyostelium." Biochim Biophys Acta 1800(2): 160-171.
	The soil amoeba Dictyostelium is an obligate aerobe that monitors O(2) for informational purposes in addition to utilizing it for oxidative metabolism. Whereas low O(2) suffices for proliferation, a higher level is required for slugs to culminate into fruiting bodies, and O(2) influences slug polarity, slug migration, and cell-type proportioning. Dictyostelium expresses a cytoplasmic prolyl 4-hydroxylase (P4H1) known to mediate O(2)-sensing in animals, but lacks HIFalpha, a major hydroxylation target whose accumulation directly induces animal hypoxia-dependent transcriptional changes. The O(2)-requirement for culmination is increased by P4H1-gene disruption and reduced by P4H1 overexpression. A target of Dictyostelium P4H1 is Skp1, a subunit of the SCF-class of E3-ubiquitin ligases related to the VBC-class that mediates hydroxylation-dependent degradation of animal HIFalpha. Skp1 is a target of a novel cytoplasmic O-glycosylation pathway that modifies HyPro143 with a pentasaccharide, and glycosyltransferase mutants reveal that glycosylation intermediates have antagonistic effects toward P4H1 in O(2)-signaling. Current evidence indicates that Skp1 is the only glycosylation target in cells, based on metabolic labeling, biochemical complementation, and enzyme specificity studies. Bioinformatics studies suggest that the HyPro-modification pathway existed in the ancestral eukaryotic lineage and was retained in selected modern day unicellular organisms whose life cycles experience varying degrees of hypoxia. It is proposed that, in Dictyostelium and other protists including the agent for human toxoplasmosis Toxoplasma gondii, prolyl hydroxylation and glycosylation mediate O(2)-signaling in hierarchical fashion via Skp1 to control the proteome, directly via degradation rather than indirectly via transcription as found in animals.

Westendorf, C., A. J. Bae, et al. (2010). "Live cell flattening - traditional and novel approaches." PMC Biophys 3(1): 9.
	Eukaryotic cell flattening is valuable for improving microscopic observations, ranging from bright field (BF) to total internal reflection fluorescence (TIRF) microscopy. Fundamental processes, such as mitosis and in vivo actin polymerization, have been investigated using these techniques. Here, we review the well known agar overlayer protocol and the oil overlay method. In addition, we present more elaborate microfluidics-based techniques that provide us with a greater level of control. We demonstrate these techniques on the social amoebae Dictyostelium discoideum, comparing the advantages and disadvantages of each method.PACS Codes: 87.64.-t, 47.61.-k, 87.80.Ek.

Whitney, T. J., D. G. Gardner, et al. (2010). "Identifying the molecular basis of functions in the transcriptome of the social amoeba Dictyostelium discoideum." Genet Mol Res 9(1): 394-415.
	The unusual life cycle of Dictyostelium discoideum, in which an extra-cellular stressor such as starvation induces the development of a multicellular fruiting body consisting of stalk cells and spores from a culture of identical amoebae, provides an excellent model for investigating the molecular control of differentiation and the transition from single- to multi-cellular life, a key transition in development. We utilized serial analysis of gene expression (SAGE), a molecular method that is unbiased by dependence on previously identified genes, to obtain a transcriptome from a high-density culture of amoebae, in order to examine the transition to multi-cellular development. The SAGE method provides relative expression levels, which allows us to rank order the expressed genes. We found that a large number of ribosomal proteins were expressed at high levels, while various components of the proteosome were expressed at low levels. The only identifiable transmembrane signaling system components expressed in amoebae are related to quorum sensing, and their expression levels were relatively low. The most highly expressed gene in the amoeba transcriptome, dutA untranslated RNA, is a molecule with unknown function that may serve as an inhibitor of translation. These results suggest that high-density amoebae have not initiated development, and they also suggest a mechanism by which the transition into the development program is controlled.

Williams, J. G. (2010). "Dictyostelium finds new roles to model." Genetics 185(3): 717-726.
	Any established or aspiring model organism must justify itself using two criteria: does the model organism offer experimental advantages not offered by competing systems? And will any discoveries made using the model be of wider relevance? This review addresses these issues for the social amoeba Dictyostelium and highlights some of the organisms more recent applications. These cover a remarkably wide gamut, ranging from sociobiological to medical research with much else in between.

Xiong, Y. and P. A. Iglesias (2010). "Tools for analyzing cell shape changes during chemotaxis." Integr Biol (Camb) 2(11-12): 561-567.
	Chemotaxis refers to the ability of cells to sense the direction of external chemical gradients and respond by migrating towards the source. A thorough understanding of the chemotactic response of amoebae and neutrophils requires careful quantification of the cell shape changes observed during cell movement. The stochastic nature of this response calls for a statistical characterization of cellular morphology and this requires the processing of large data sets. For this reason, automatic image analysis algorithms are highly desirable and are becoming increasingly available. These usually include a combination of techniques from image segmentation, morphological transformations, as well as the incorporation of numerical algorithms and physical models. Here we review recent developments in the tracking and understanding of motile chemotaxing cells, with a particular emphasis on the description of pseudopodial activity in chemotactic Dictyostelium cells.

Xiong, Y., C. Kabacoff, et al. (2010). "Automated characterization of cell shape changes during amoeboid motility by skeletonization." BMC Syst Biol 4: 33.
	BACKGROUND: The ability of a cell to change shape is crucial for the proper function of many cellular processes, including cell migration. One type of cell migration, referred to as amoeboid motility, involves alternating cycles of morphological expansion and retraction. Traditionally, this process has been characterized by a number of parameters providing global information about shape changes, which are insufficient to distinguish phenotypes based on local pseudopodial activities that typify amoeboid motility. RESULTS: We developed a method that automatically detects and characterizes pseudopodial behavior of cells. The method uses skeletonization, a technique from morphological image processing to reduce a shape into a series of connected lines. It involves a series of automatic algorithms including image segmentation, boundary smoothing, skeletonization and branch pruning, and takes into account the cell shape changes between successive frames to detect protrusion and retraction activities. In addition, the activities are clustered into different groups, each representing the protruding and retracting history of an individual pseudopod. CONCLUSIONS: We illustrate the algorithms on movies of chemotaxing Dictyostelium cells and show that our method makes it possible to capture the spatial and temporal dynamics as well as the stochastic features of the pseudopodial behavior. Thus, the method provides a powerful tool for investigating amoeboid motility.

Xu, X., T. Meckel, et al. (2010). "Coupling mechanism of a GPCR and a heterotrimeric G protein during chemoattractant gradient sensing in Dictyostelium." Sci Signal 3(141): ra71.
	The coupling of heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) with G proteins is fundamental for GPCR signaling; however, the mechanism of coupling is still debated. Moreover, how the proposed mechanisms affect the dynamics of downstream signaling remains unclear. Here, through experiments involving fluorescence recovery after photobleaching and single-molecule imaging, we directly measured the mobilities of cyclic adenosine monophosphate (cAMP) receptor 1 (cAR1), a chemoattractant receptor, and a G protein betagamma subunit in live cells. We found that cAR1 diffused more slowly in the plasma membrane than did Gbetagamma. Upon binding of ligand to the receptor, the mobility of cAR1 was unchanged, whereas the speed of a fraction of the faster-moving Gbetagamma subunits decreased. Our measurements showed that cAR1 was relatively immobile and Gbetagamma diffused freely, suggesting that chemoattractant-bound cAR1 transiently interacted with G proteins. Using models of possible coupling mechanisms, we computed the temporal kinetics of G protein activation. Our fluorescence resonance energy transfer imaging data showed that fully activated cAR1 induced the sustained dissociation of G protein alpha and betagamma subunits, which indicated that ligand-bound cAR1 activated G proteins continuously. Finally, simulations indicated that a high-affinity coupling of ligand-bound receptors and G proteins was essential for cAR1 to translate extracellular gradient signals into directional cellular responses. We suggest that chemoattractant receptors use a ligand-induced coupling rather than a precoupled mechanism to control the activation of G proteins during chemotaxis.

Yamada, Y., R. R. Kay, et al. (2010). "A new Dictyostelium prestalk cell sub-type." Dev Biol 339(2): 390-397.
	The mature fruiting body of Dictyostelium consists of stalk and spore cells but its construction, and the migration of the preceding slug stage, requires a number of specialized sub-types of prestalk cell whose nature and function are not well understood. The prototypic prestalk-specific gene, ecmA, is inducible by the polyketide DIF-1 in a monolayer assay and requires the DimB and MybE transcription factors for full inducibility. We perform genome-wide microarray analyses, on parental, mybE- and dimB- cells, and identify many additional genes that depend on MybE and DimB for their DIF-1 inducibility. Surprisingly, an even larger number of genes are only DIF inducible in mybE- cells, some genes are only inducible in DimB- cells and some are inducible when either transcription factor is absent. Thus in assay conditions where MybE and DimB function as inducers of ecmA these genes fall under negative control by the same two transcription factors. We have studied in detail rtaA, one of the MybE and DimB repressed genes. One especially enigmatic group of prestalk cells is the anterior-like cells (ALCs), which exist intermingled with prespore cells in the slug. A promoter fusion reporter gene, rtaA:gal(u), is expressed in a subset of the ALCs that is distinct from the ALC population detected by a reporter construct containing ecmA and ecmB promoter fragments. At culmination, when the ALC sort out from the prespore cells and differentiate to form three ancillary stalk cell structures: the upper cup, the lower cup and the outer basal disk, the rtaA:gal(u) expressing cells preferentially populate the upper cup region. This fact, and their virtual absence from the anterior and posterior regions of the slug, identifies them as a new prestalk sub-type: the pstU cells. PstU cell differentiation is, as expected, increased in a dimB- mutant during normal development but, surprisingly, they differentiate normally in a mutant lacking DIF. Thus genetic removal of MybE or DimB reveals an alternate DIF-1 activation pathway, for pstU differentiation, that functions under monolayer assay conditions but that is not essential during multicellular development.

Yamada, Y., H. Minamisawa, et al. (2010). "Prespore cell inducing factor, psi factor, controls both prestalk and prespore gene expression in Dictyostelium development." Dev Growth Differ 52(4): 377-383.
	Prespore cell-inducing (psi, psi) factor (PsiA), encoded by the psiA gene of Dictyostelium, is a secreted signal glycoprotein that induces prespore cell differentiation when added to monolayer cultures. In situ hybridization during normal development showed that the psiA gene is highly expressed in scattered cells at the mound stage and in prespore cells at the onset of culmination. The conventional prespore-cell marker genes, cotC and pspA, were expressed normally in psiA(-) and psiA overexpressing strains. Expressions of rnrB and cudA are repressed in the prestalk cells of a wild type slug to render prespore specific pattern. However, a promoter-reporter fusion gene, rnrB:lacZ, showed an ectopic expression in the prestalk cells of the psiA(-) strain while cudA(psp):lacZ did so in those of the psiA overexpressing strain. Overexpression of psiA delayed expression of the prestalk specific gene, ecmB, during development, while knocking out psiA promoted its expression. In addition, overexpression inhibited DIF-1-induced stalk formation in monolayer cultures. Together with the known prespore inducing activity, the results indicate that PsiA regulates both prespore and prestalk/stalk cell differentiation. These results indicate that PsiA is also involved in prestalk cell differentiation.

Yasukawa, H. and K. Yagita (2010). "Silent information regulator 2 proteins encoded by Cryptosporidium parasites." Parasitol Res 107(3): 707-712.
	Screening in a database has revealed that Cryptosporidium hominis encodes a silent information regulator 2 (Sir2), a nicotinamide adenine dinucleotide (NAD)-dependent protein deacetylase. Cellular localization of the protein, ChSir2, was analyzed by the use of the social amoeba Dictyostelium discoideum as a model system. Fluorescent microscopic analysis showed that ChSir2 fused with green fluorescent protein was localized in the D. discoideum nucleus. D. discoideum expressing ChSir2 grew faster and reached higher cell density than did D. discoideum harboring a control vector. These results suggest that ChSir2 is a nucleus-localizing protein that plays an important role in the growth of C. hominis. We cloned and sequenced the genes for Sir2 orthologs encoded by three isolates of C. hominis, two isolates of Cryptosporidium parvum and one isolate of Cryptosporidium meleagridis. The orthologs conserve critical catalytic or NAD-binding residues but do not have similarity with human Sir2 proteins (SIRTs). Cryptosporidium Sir2 orthologs would therefore be attractive therapeutic targets. The Cryptosporidium orthologs were classified into four variants based on their nucleotide sequences. Each of the four variants produces its own unique restriction fragment length polymorphism pattern by digestion with TfiI.

Ye, Q., S. W. Crawley, et al. (2010). "Crystal structure of the alpha-kinase domain of Dictyostelium myosin heavy chain kinase A." Sci Signal 3(111): ra17.
	Dictyostelium discoideum myosin II heavy chain kinase A (MHCK A) disrupts the assembly and cellular activity of bipolar filaments of myosin II by phosphorylating sites within its alpha-helical, coiled-coil tail. MHCK A is a member of the atypical alpha-kinase family of serine and threonine protein kinases and displays no sequence homology to typical eukaryotic protein kinases. We report the crystal structure of the alpha-kinase domain (A-CAT) of MHCK A. When crystallized in the presence of adenosine triphosphate (ATP), A-CAT contained adenosine monophosphate (AMP) at the active site. However, when crystallized in the presence of ATP and a peptide substrate, which does not appear in the structure, adenosine diphosphate (ADP) was found at the active site and an invariant aspartic acid residue (Asp(766)) at the active site was phosphorylated. The aspartylphosphate group was exposed to the solvent within an active-site pocket that might function as a docking site for substrates. Access to the aspartylphosphate was regulated by a conformational switch in a loop that bound to a magnesium ion (Mg(2+)), providing a mechanism that allows alpha-kinases to sense and respond to local changes in Mg(2+).

Yoshihara, T., F. Takahashi-Yanaga, et al. (2010). "Anti-angiogenic effects of differentiation-inducing factor-1 involving VEGFR-2 expression inhibition independent of the Wnt/beta-catenin signaling pathway." Mol Cancer 9: 245.
	BACKGROUND: Differentiation-inducing factor-1 (DIF-1) is a putative morphogen that induces cell differentiation in Dictyostelium discoideum. DIF-1 inhibits proliferation of various mammalian tumor cells by suppressing the canonical Wnt/beta-catenin signaling pathway. To assess the potential of a novel cancer chemotherapy based on the pharmacological effect of DIF-1, we investigated whether DIF-1 exhibits anti-angiogenic effects in vitro and in vivo. RESULTS: DIF-1 not only inhibited the proliferation of human umbilical vein endothelial cells (HUVECs) by restricting cell cycle in the G0/G1 phase and degrading cyclin D1, but also inhibited the ability of HUVECs to form capillaries and migrate. Moreover, DIF-1 suppressed VEGF- and cancer cell-induced neovascularization in Matrigel plugs injected subcutaneously to murine flank. Subsequently, we attempted to identify the mechanism behind the anti-angiogenic effects of DIF-1. We showed that DIF-1 strongly decreased vascular endothelial growth factor receptor-2 (VEGFR-2) expression in HUVECs by inhibiting the promoter activity of human VEGFR-2 gene, though it was not caused by inhibition of the Wnt/beta-catenin signaling pathway. CONCLUSION: These results suggested that DIF-1 inhibits angiogenesis both in vitro and in vivo, and reduction of VEGFR-2 expression is involved in the mechanism. A novel anti-cancer drug that inhibits neovascularization and tumor growth may be developed by successful elucidation of the target molecules for DIF-1 in the future.

Zanchi, R., G. Howard, et al. (2010). "The exocytic gene secA is required for Dictyostelium cell motility and osmoregulation." J Cell Sci 123(Pt 19): 3226-3234.
	We investigated the link between cell movement and plasma membrane recycling using a fast-acting, temperature-sensitive mutant of the Dictyostelium SecA exocytic protein. Strikingly, most mutant cells become almost paralysed within minutes at the restrictive temperature. However, they can still sense cyclic-AMP (cAMP) gradients and polymerise actin up-gradient, but form only abortive pseudopodia, which cannot expand. They also relay a cAMP signal normally, suggesting that cAMP is released by a non-exocytic mechanism. To investigate why SecA is required for motility, we examined membrane trafficking in the mutant. Plasma membrane circulation is rapidly inhibited at the restrictive temperature and the cells acquire a prominent vesicle. Organelle-specific markers show that this is an undischarged contractile vacuole, and we found the cells are correspondingly osmo-sensitive. Electron microscopy shows that many smaller vesicles, probably originating from the plasma membrane, also accumulate at the restrictive temperature. Consistent with this, the surface area of mutant cells shrinks. We suggest that SecA mutant cells cannot move at the restrictive temperature because their block in exocytosis results in a net uptake of plasma membrane, reducing its area, and so restricting pseudopodial expansion. This demonstrates the importance of proper surface area regulation in cell movement.

Zhang, P., Y. Wang, et al. (2010). "Proteomic identification of phosphatidylinositol (3,4,5) triphosphate-binding proteins in Dictyostelium discoideum." Proc Natl Acad Sci U S A 107(26): 11829-11834.
	Phosphatidylinositol (3,4,5)-triphosphate (PtdInsP(3)) mediates intracellular signaling for directional sensing and pseudopod extension at the leading edge of migrating cells during chemotaxis. How this PtdInsP(3) signal is translated into remodeling of the actin cytoskeleton is poorly understood. Here, using a proteomics approach, we identified multiple PtdInsP(3)-binding proteins in Dictyostelium discoideum, including five pleckstrin homology (PH) domain-containing proteins. Two of these, the serine/threonine kinase Akt/protein kinase B and the PH domain-containing protein PhdA, were previously characterized as PtdInsP(3)-binding proteins. In addition, PhdB, PhdG, and PhdI were identified as previously undescribed PH domain-containing proteins. Specific PtdInsP(3) interactions with PhdB, PhdG, and PhdI were confirmed using an in vitro lipid-binding assay. In cells, PhdI associated with the plasma membrane in a manner dependent on both the PH domain and PtdInsP(3). Consistent with this finding, PhdI located to the leading edge in migrating cells. In contrast, PhdG was found in the cytosol in WT cells. However, when PtdInsP(3) was overproduced in pten(-) cells, PhdG located to the plasma membrane, suggesting its weak affinity for PtdInsP(3). PhdB was found to bind to the plasma membrane via both PtdInsP(3)-dependent and -independent mechanisms. The PtdInsP(3)-independent interaction was mediated by the middle domain, independent of the PH domain. In migrating cells, the majority of PhdB was found at the lagging edge. Finally, we deleted the genes encoding PhdB and PhdG and demonstrated that both proteins are required for efficient chemotaxis. Thus, this study advances our understanding of the PtdInsP(3)-mediated signaling mechanisms that control directed cell migration in chemotaxis.

Zhang, Y. and V. N. Gladyshev (2010). "General trends in trace element utilization revealed by comparative genomic analyses of Co, Cu, Mo, Ni, and Se." J Biol Chem 285(5): 3393-3405.
	Trace elements are used by all organisms and provide proteins with unique coordination and catalytic and electron transfer properties. Although many trace element-containing proteins are well characterized, little is known about the general trends in trace element utilization. We carried out comparative genomic analyses of copper, molybdenum, nickel, cobalt (in the form of vitamin B(12)), and selenium (in the form of selenocysteine) in 747 sequenced organisms at the following levels: (i) transporters and transport-related proteins, (ii) cofactor biosynthesis traits, and (iii) trace element-dependent proteins. Few organisms were found to utilize all five trace elements, whereas many symbionts, parasites, and yeasts used only one or none of these elements. Investigation of metalloproteomes and selenoproteomes revealed examples of increased utilization of proteins that use copper in land plants, cobalt in Dehalococcoides and Dictyostelium, and selenium in fish and algae, whereas nematodes were found to have great diversity of copper transporters. These analyses also characterized trace element metabolism in common model organisms and suggested new model organisms for experimental studies of individual trace elements. Mismatches in the occurrence of user proteins and corresponding transport systems revealed deficiencies in our understanding of trace element biology. Biological interactions among some trace elements were observed; however, such links were limited, and trace elements generally had unique utilization patterns. Finally, environmental factors, such as oxygen requirement and habitat, correlated with the utilization of certain trace elements. These data provide insights into the general features of utilization and evolution of trace elements in the three domains of life.

Zhou, Q., Y. S. Kee, et al. (2010). "14-3-3 coordinates microtubules, Rac, and myosin II to control cell mechanics and cytokinesis." Curr Biol 20(21): 1881-1889.
	BACKGROUND: During cytokinesis, regulatory signals are presumed to emanate from the mitotic spindle. However, what these signals are and how they lead to the spatiotemporal changes in the cortex structure, mechanics, and regional contractility are not well understood in any system. RESULTS: To investigate pathways that link the microtubule network to the cortical changes that promote cytokinesis, we used chemical genetics in Dictyostelium to identify genetic suppressors of nocodazole, a microtubule depolymerizer. We identified 14-3-3 and found that it is enriched in the cortex, helps maintain steady-state microtubule length, contributes to normal cortical tension, modulates actin wave formation, and controls the symmetry and kinetics of cleavage furrow contractility during cytokinesis. Furthermore, 14-3-3 acts downstream of a Rac small GTPase (RacE), associates with myosin II heavy chain, and is needed to promote myosin II bipolar thick filament remodeling. CONCLUSIONS: 14-3-3 connects microtubules, Rac, and myosin II to control several aspects of cortical dynamics, mechanics, and cytokinesis cell shape change. Furthermore, 14-3-3 interacts directly with myosin II heavy chain to promote bipolar thick filament remodeling and distribution. Overall, 14-3-3 appears to integrate several critical cytoskeletal elements that drive two important processes-cytokinesis cell shape change and cell mechanics.

Zhuang, N., K. H. Seo, et al. (2010). "Purification, crystallization and crystallographic analysis of Dictyostelium discoideum phenylalanine hydroxylase in complex with dihydrobiopterin and FeIII." Acta Crystallogr Sect F Struct Biol Cryst Commun 66(Pt 4): 463-466.
	Dictyostelium discoideum phenylalanine hydroxylase (DicPAH; residues 1-415) was expressed in Escherichia coli and purified for structural analysis. Apo DicPAH and DicPAH complexed with dihydrobiopterin (BH(2)) and Fe(III) were crystallized using 0.06 M PIPES pH 7.0, 26%(w/v) PEG 2000 by the hanging-drop vapour-diffusion method. Crystals of apo DicPAH and the DicPAH-BH(2)-Fe(III) complex diffracted to 2.6 and 2.07 A resolution, respectively, and belonged to space group P2(1), with unit-cell parameters a = 70.02, b = 85.43, c = 74.86 A, beta = 110.12 degrees and a = 70.97, b = 85.33, c = 74.89 A, beta = 110.23 degrees , respectively. There were two molecules in the asymmetric unit. The structure of DicPAH has been solved by molecular replacement.

Abad, M. G., Y. Long, et al. (2011). "A role for tRNA(His) guanylyltransferase (Thg1)-like proteins from Dictyostelium discoideum in mitochondrial 5'-tRNA editing." RNA 17(4): 613-623.
	Genes with sequence similarity to the yeast tRNA(His) guanylyltransferase (Thg1) gene have been identified in all three domains of life, and Thg1 family enzymes are implicated in diverse processes, ranging from tRNA(His) maturation to 5'-end repair of tRNAs. All of these activities take advantage of the ability of Thg1 family enzymes to catalyze 3'-5' nucleotide addition reactions. Although many Thg1-containing organisms have a single Thg1-related gene, certain eukaryotic microbes possess multiple genes with sequence similarity to Thg1. Here we investigate the activities of four Thg1-like proteins (TLPs) encoded by the genome of the slime mold, Dictyostelium discoideum (a member of the eukaryotic supergroup Amoebozoa). We show that one of the four TLPs is a bona fide Thg1 ortholog, a cytoplasmic G(-1) addition enzyme likely to be responsible for tRNA(His) maturation in D. discoideum. Two other D. discoideum TLPs exhibit biochemical activities consistent with a role for these enzymes in mitochondrial 5'-tRNA editing, based on their ability to efficiently repair the 5' ends of mitochondrial tRNA editing substrates. Although 5'-tRNA editing was discovered nearly two decades ago, the identity of the protein(s) that catalyze this activity has remained elusive. This article provides the first identification of any purified protein that appears to play a role in the 5'-tRNA editing reaction. Moreover, the presence of multiple Thg1 family members in D. discoideum suggests that gene duplication and divergence during evolution has resulted in paralogous proteins that use 3'-5' nucleotide addition reactions for diverse biological functions in the same organism.

Adamek, M., J. Overhage, et al. (2011). "Genotyping of environmental and clinical Stenotrophomonas maltophilia isolates and their pathogenic potential." PLoS One 6(11): e27615.
	Stenotrophomonas maltophilia is a highly versatile species with useful biotechnological potential but also with pathogenic properties. In light of possible differences in virulence characteristics, knowledge about genomic subgroups is therefore desirable. Two different genotyping methods, rep-PCR fingerprinting and partial gyrB gene sequencing were used to elucidate S. maltophilia intraspecies diversity. Rep-PCR fingerprinting revealed the presence of 12 large subgroups, while gyrB gene sequencing distinguished 10 subgroups. For 8 of them, the same strain composition was shown with both typing methods. A subset of 59 isolates representative for the gyrB groups was further investigated with regards to their pathogenic properties in a virulence model using Dictyostelium discoideum and Acanthamoeba castellanii as host organisms. A clear tendency towards accumulation of virulent strains could be observed for one group with A. castellanii and for two groups with D. discoideum. Several virulent strains did not cluster in any of the genetic groups, while other groups displayed no virulence properties at all. The amoeba pathogenicity model proved suitable in showing differences in S. maltophilia virulence. However, the model is still not sufficient to completely elucidate virulence as critical for a human host, since several strains involved in human infections did not show any virulence against amoeba.

Afonso, P. V. and C. A. Parent (2011). "PI3K and chemotaxis: a priming issue?" Sci Signal 4(170): pe22.
	Although the spatiotemporal activation of phosphoinositide 3-kinases (PI3Ks) at the leading edge of chemotaxing cells represents a key marker of polarity, both Dictyostelium discoideum and neutrophils lacking measurable PI3K activity can still migrate directionally under certain conditions. Evidence from various papers suggests that the differentiation state of cells or their priming status can consolidate otherwise contradictory findings.

Aggarwal, R. K., J. Allainguillaume, et al. (2011). "Permanent genetic resources added to Molecular Ecology Resources Database 1 August 2010-30 September 2010." Mol Ecol Resour 11(1): 219-222.
	This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis x Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

Al-Quadan, T. and Y. A. Kwaik (2011). "Molecular Characterization of Exploitation of the Polyubiquitination and Farnesylation Machineries of Dictyostelium Discoideum by the AnkB F-Box Effector of Legionella Pneumophila." Front Microbiol 2: 23.
	The Dot/Icm-translocated Ankyrin B (AnkB) F-box effector of Legionella pneumophila is essential for intra-vacuolar proliferation and functions as a platform for the docking of polyubiquitinated proteins to the Legionella-containing vacuole (LCV) within macrophages and ameba. Here we show that ectopically expressed AnkB in Dictyostelium discoideum is targeted to the plasma membrane where it recruits polyubiquitinated proteins and it trans-rescues the intracellular growth defect of the ankB null mutant, which has never been demonstrated for any effector in ameba. Using co-immunoprecipitation and bimolecular fluorescence complementation we show specific interaction of Skp1 of D. discoideum with the F-box domain of AnkB, which has never been demonstrated in ameba. We show that anchoring of AnkB to the cytosolic face of the LCV membrane in D. discoideum is mediated by the host farnesylation of the C-terminal eukaryotic CaaX motif of AnkB and is independent of the F-box and the two ANK domains, which has never been demonstrated in ameba. Importantly, the three host farnesylation enzymes farnesyl transferase, RCE-1, and isoprenyl cysteine carboxyl methyl transferase of D. discoideum are recruited to the LCV in a Dot/Icm-dependent manner, which has never been demonstrated in ameba. We conclude that the polyubiquitination and farnesylation enzymatic machineries of D. discoideum are recruited to the LCV in a Dot/Icm-dependent manner and the AnkB effector exploits the two evolutionarily conserved eukaryotic machineries to proliferate within ameba, similar to mammalian cells. We propose that L. pneumophila has acquired ankB through inter-kingdom horizontal gene transfer from primitive eukaryotes, which facilitated proliferation of L. pneumophila within human cells and the emergence of Legionnaires' disease.

Alexander, S. and H. Alexander (2011). "Lead genetic studies in Dictyostelium discoideum and translational studies in human cells demonstrate that sphingolipids are key regulators of sensitivity to cisplatin and other anticancer drugs." Semin Cell Dev Biol 22(1): 97-104.
	A Dictyostelium discoideum mutant with a disruption in the sphingosine-1-phosphate (S-1-P) lyase gene was obtained in an unbiased genetic analysis, using random insertional mutagenesis, for mutants with increased resistance to the widely used cancer chemotherapeutic drug cisplatin. This finding opened the way to extensive studies in both D. discoideum and human cells on the role and mechanism of action of the bioactive sphingolipids S-1-P and ceramide in regulating the response to chemotherapeutic drugs. These studies showed that the levels of activities of the sphingolipid metabolizing enzymes S-1-P lyase, sphingosine kinase and ceramide synthase, affect whether a cell dies or lives in the presence of specific drugs. The demonstration that multiple enzymes of this biochemical pathway were involved in regulating drug sensitivity provided new opportunities to test whether pharmacological intervention might increase sensitivity. Thus it is of considerable clinical significance that pharmacological inhibition of sphingosine kinase synergistically sensitizes cells to cisplatin, both in D. discoideum and human cells. Linkage to the p38 MAP kinase and protein kinase C (PKC) signaling pathways has been demonstrated. This work demonstrates the utility of D. discoideum as a lead genetic system to interrogate molecular mechanisms controlling the sensitivity of tumor cells to chemotherapeutic agents and for determining novel ways of increasing efficacy. The D. discoideum system could be easily adapted to a high throughput screen for novel chemotherapeutic agents.

Alibaud, L., Y. Rombouts, et al. (2011). "A Mycobacterium marinum TesA mutant defective for major cell wall-associated lipids is highly attenuated in Dictyostelium discoideum and zebrafish embryos." Mol Microbiol 80(4): 919-934.
	Infection of the zebrafish with Mycobacterium marinum is regarded as a well-established experimental model to study the pathogenicity of Mycobacterium tuberculosis. Herein, a M. marinum transposon mutant library was screened for attenuated M. marinum phenotypes using a Dictyostelium discoideum assay. In one attenuated mutant, the transposon was located within tesA, encoding a putative type II thioesterase. Thin-layer chromatography analyses indicated that the tesA::Tn mutant failed to produce two major cell wall-associated lipids. Mass spectrometry and nuclear magnetic resonance clearly established the nature of missing lipids as phthioglycol diphthioceranates and phenolic glycolipids, respectively, indicating that TesA is required for the synthesis of both lipids. When injected into the zebrafish embryo bloodstream, the mutant was found to be highly attenuated, thus validating the performance and relevance of the Dictyostelium screen. Consistent with these in vivo findings, tesA::Tn exhibited increased permeability defects in vitro, which may explain its failure to survive in host macrophages. Unexpectedly, virulence was retained when bacteria were injected into the notochord. Histological and ultrastructural studies of the infected notochord revealed the presence of actively proliferating mycobacteria, leading to larval death. This work presents for the first time the notochord as a compartment highly susceptible to mycobacterial infection.

Amagai, A. (2011). "Ethylene as a potent inducer of sexual development." Dev Growth Differ 53(4): 617-623.
	A novel and critical function of ethylene, a potent plant hormone, has been well documented in Dictyostelium, because it leads cells to the sexual development (macrocyst formation) by inducing zygote formation. Zygote formation (sexual cell fusion) and the subsequent nuclear fusion are the characteristic events occurring during macrocyst formation. A novel gene, zyg1 was found to be predominantly expressed during the sexual development, and its enforced expression actually induces zygote formation. As expected, the zygote inducer, ethylene enhances the expression of zyg1. Thus the function of ethylene has been verified at all of individual (macrocyst formation), cellular (zygote formation), and molecular levels (zyg1 expression). Based on our recent studies concerning the behavior and function of the zyg1 product (ZYG1 protein), the signal transduction pathways involved in zygote formation are proposed in this review.

Andersson, J. O. (2011). "Evolution of patchily distributed proteins shared between eukaryotes and prokaryotes: Dictyostelium as a case study." J Mol Microbiol Biotechnol 20(2): 83-95.
	Protein families are often patchily distributed in the tree of life; they are present in distantly related organisms, but absent in more closely related lineages. This could either be the result of lateral gene transfer between ancestors of organisms that encode them, or losses in the lineages that lack them. Here a novel approach is developed to study the evolution of patchily distributed proteins shared between prokaryotes and eukaryotes. Proteins encoded in the genome of cellular slime mold Dictyostelium discoideum and a restricted number of other lineages, including at least one prokaryote, were identified. Analyses of the phylogenetic distribution of 49 such patchily distributed protein families showed conflicts with organismal phylogenies; 25 are shared with the distantly related amoeboflagellate Naegleria (Excavata), whereas only two are present in the more closely related Entamoeba. Most protein families show unexpected topologies in phylogenetic analyses; eukaryotes are polyphyletic in 85% of the trees. These observations suggest that gene transfers have been an important mechanism for the distribution of patchily distributed proteins across all domains of life. Further studies of this exchangeable gene fraction are needed for a better understanding of the origin and evolution of eukaryotic genes and the diversification process of eukaryotes.

Anjard, C., Y. Su, et al. (2011). "The polyketide MPBD initiates the SDF-1 signaling cascade that coordinates terminal differentiation in Dictyostelium." Eukaryot Cell 10(7): 956-963.
	Dictyostelium uses a wide array of chemical signals to coordinate differentiation as it switches from a unicellular to a multicellular organism. MPBD, the product of the polyketide synthase encoded by stlA, regulates stalk and spore differentiation by rapidly stimulating the release of the phosphopeptide SDF-1. By analyzing specific mutants affected in MPBD or SDF-1 production, we delineated a signal transduction cascade through the membrane receptor CrlA coupled to Galpha1, leading to the inhibition of GskA so that the precursor of SDF-1 is released. It is then processed by the extracellular protease of TagB on prestalk cells. SDF-1 apparently acts through the adenylyl cyclase ACG to activate the cyclic AMP (cAMP)-dependent protein kinase A (PKA) and trigger the production of more SDF-1. This signaling cascade shows similarities to the SDF-2 signaling pathway, which acts later to induce rapid spore encapsulation.

Annesley, S. J., R. Bago, et al. (2011). "Dictyostelium discoideum nucleoside diphosphate kinase C plays a negative regulatory role in phagocytosis, macropinocytosis and exocytosis." PLoS One 6(10): e26024.
	Nucleoside diphosphate kinases (NDPKs) are ubiquitous phosphotransfer enzymes responsible for producing most of the nucleoside triphosphates except for ATP. This role is important for the synthesis of nucleic acids and proteins and the metabolism of sugars and lipids. Apart from this housekeeping role NDPKs have been shown to have many regulatory functions in diverse cellular processes including proliferation and endocytosis. Although the protein has been shown to have a positive regulatory role in clathrin- and dynamin-mediated micropinocytosis, its roles in macropinocytosis and phagocytosis have not been studied. The additional non-housekeeping roles of NDPK are often independent of enzyme activity but dependent on the expression level of the protein. In this study we altered the expression level of NDPK in the model eukaryotic organism Dictyostelium discoideum through antisense inhibition and overexpression. We demonstrate that NDPK levels affect growth, endocytosis and exocytosis. In particular we find that Dictyostelium NDPK negatively regulates endocytosis in contrast to the positive regulatory role identified in higher eukaryotes. This can be explained by the differences in types of endocytosis that have been studied in the different systems - phagocytosis and macropinocytosis in Dictyostelium compared with micropinocytosis in mammalian cells. This is the first report of a role for NDPK in regulating macropinocytosis and phagocytosis, the former being the major fluid phase uptake mechanism for macrophages, dendritic cells and other (non dendritic) cells exposed to growth factors.

Annesley, S. J., R. Bago, et al. (2011). "A genetic interaction between NDPK and AMPK in Dictyostelium discoideum that affects motility, growth and development." Naunyn Schmiedebergs Arch Pharmacol 384(4-5): 341-349.
	Many of the expanding roles of nucleoside diphosphate kinase have been attributed to its ability to interact with other proteins. One proposal is an interaction with the cellular energy sensor AMP-activated protein kinase, and here, we apply the simple eukaryotic organism, Dictyostelium discoideum as a test model. Stable cotransformants were created in which NDPK expression was knocked down by antisense inhibition, and AMPK activity was chronically elevated either by constitutive overexpression of its active, catalytic domain (AMPKalphaT) or as a result of mitochondrial dysfunction (created by antisense inhibition of expression of a mitochondrial chaperone protein, chaperonin 60). To investigate a biochemical interaction, transformants were created which contained constructs expressing FLAG-NDPK and hexahistidine-tagged full-length AMPK or AMPKalphaT. The protein extract from these transformants was used in coimmunoprecipitations. Knock down of NDPK expression suppressed the phenotypic defects that are caused by AMPK hyperactivity resulting either from overexpression of AMPKalphaT or from mitochondrial dysfunction. These included rescue of defects in slug phototaxis, fruiting body morphology and growth in a liquid medium. Coimmunoprecipitation experiments failed to demonstrate a biochemical interaction between the two proteins. The results demonstrate a genetic interaction between NDPK and AMPK in Dictyostelium in that NDPK is required for the phenotypic effects of activated AMPK. Coimmunoprecipitations suggest that this interaction is not mediated by a direct interaction between the two proteins.

Artemenko, Y., K. F. Swaney, et al. (2011). "Assessment of development and chemotaxis in Dictyostelium discoideum mutants." Methods Mol Biol 769: 287-309.
	Studies using the social amoeba Dictyostelium discoideum have greatly contributed to the current understanding of the signaling network that underlies chemotaxis. Since directed migration is essential for normal D. discoideum multicellular development, mutants with chemotactic impairments are likely to have abnormal developmental morphologies. We have used multicellular development as a readout in a screen of mutants to identify new potential regulators of chemotaxis. In this chapter, we describe how mutants generated by restriction enzyme-mediated integration (REMI) are analyzed, from assessment of development to detailed characterization of 3',5'-cyclic adenosine monophosphate (cAMP)-induced responses. Two complementary approaches, plating cells either clonally on a bacterial lawn or as a population on non-nutrient agar, are used to evaluate multicellular development. Once mutants with aberrant developmental phenotypes are identified, their chemotaxis toward cAMP is assessed by both small population and micropipette assays. Furthermore, mutants are tested for defects in both general and specific signaling pathways by examining the recruitment of actin-binding LimE(Deltacoil) or PIP3-binding PH domains to the plasma membrane in response to cAMP stimulation.

Avesson, L., H. T. Schumacher, et al. (2011). "Abundant class of non-coding RNA regulates development in the social amoeba dictyostelium discoideum." RNA Biol 8(6).
	Non-coding (nc)RNAs are important players in most biological processes. Although small RNAs such as microRNAs and small interfering RNAs have emerged as exceptionally important regulators of gene expression, great numbers of larger ncRNAs have also been identified. Many of these are abundant and differentially expressed but their functions have in most cases not been elucidated. The social amoeba Dictyostelium discoideum contain the ncRNAs commonly found in eukaryotes. In addition, we previously reported the identification of two novel classes of 42-65 nt long stem-loop forming RNAs, Class I and Class II RNAs, with unknown function. In this study we have further characterized these abundant ncRNAs, which are down regulated during development. We have confirmed expression of 29 Class I RNAs and experimentally verified the formation of the computationally predicted short conserved stem structure. Furthermore, we have for the first time created knockout strains for several small ncRNA genes in D. discoideum and found that deletion of one of the Class I RNAs, DdR-21, results in aberrant development. In addition we have shown that this Class I RNA forms a complex with one or several proteins but do not appear to be associated with ribosomes or polysomes. In a pull down assay, several proteins interacting with DdR-21 were identified, one of these has two RNA recognition motifs (RRMs). The purified RRM containing protein was demonstrated to bind directly and specifically to DdR-21.

Balest, A., B. Peracino, et al. (2011). "Legionella pneumophila infection is enhanced in a RacH-null mutant of Dictyostelium." Commun Integr Biol 4(2): 194-197.
	Recently we reported that Dictyostelium cells ingest Legionella pneumophila by macropinocytosis, whereas other bacteria, such as Escherichia coli, Mycobacterium avium, Neisseria meningitidis or Salmonella typhimurium, are taken up by phagocytosis.1 In contrast to phagocytosis, macropinocytosis is partially inhibited by PI3K or PTEN inactivation, whereas both processes are sensitive to PLC inhibition. Independently from reduced uptake, L. pneumophila proliferates more efficiently in PI3K-null than in wild-type cells. PI3K inactivation also neutralizes resistance to infection conferred by constitutively expressing the endo-lysosomal iron transporter Nramp1. We have shown this to be due to altered recruitment of the V-H(+) ATPase, but not Nramp1, in the Legionella-containing vacuole (LCV) early during infection.1 As further evidence for impaired LCV acidification we examine here the effects of disrupting the small G protein RacH on Legionella infection.

Bastounis, E., R. Meili, et al. (2011). "The SCAR/WAVE complex is necessary for proper regulation of traction stresses during amoeboid motility." Mol Biol Cell 22(21): 3995-4003.
	Cell migration requires a tightly regulated, spatiotemporal coordination of underlying biochemical pathways. Crucial to cell migration is SCAR/WAVE-mediated dendritic F-actin polymerization at the cell's leading edge. Our goal is to understand the role the SCAR/WAVE complex plays in the mechanics of amoeboid migration. To this aim, we measured and compared the traction stresses exerted by Dictyostelium cells lacking the SCAR/WAVE complex proteins PIR121 (pirA(-)) and SCAR (scrA(-)) with those of wild-type cells while they were migrating on flat, elastic substrates. We found that, compared to wild type, both mutant strains exert traction stresses of different strengths that correlate with their F-actin levels. In agreement with previous studies, we found that wild-type cells migrate by repeating a motility cycle in which the cell length and strain energy exerted by the cells on their substrate vary periodically. Our analysis also revealed that scrA(-) cells display an altered motility cycle with a longer period and a lower migration velocity, whereas pirA(-) cells migrate in a random manner without implementing a periodic cycle. We present detailed characterization of the traction-stress phenotypes of the various cell lines, providing new insights into the role of F-actin polymerization in regulating cell-substratum interactions and stresses required for motility.

Bilzer, A., H. Dolz, et al. (2011). "The C-module-binding factor supports amplification of TRE5-A retrotransposons in the Dictyostelium discoideum genome." Eukaryot Cell 10(1): 81-86.
	Retrotransposable elements are molecular parasites that have invaded the genomes of virtually all organisms. Although retrotransposons encode essential proteins to mediate their amplification, they also require assistance by host cell-encoded machineries that perform functions such as DNA transcription and repair. The retrotransposon TRE5-A of the social amoeba Dictyostelium discoideum generates a notable amount of both sense and antisense RNAs, which are generated from element-internal promoters, located in the A module and the C module, respectively. We observed that TRE5-A retrotransposons depend on the C-module-binding factor (CbfA) to maintain high steady-state levels of TRE5-A transcripts and that CbfA supports the retrotransposition activity of TRE5-A elements. The carboxy-terminal domain of CbfA was found to be required and sufficient to mediate the accumulation of TRE5-A transcripts, but it did not support productive retrotransposition of TRE5-A. This result suggests different roles for CbfA protein domains in the regulation of TRE5-A retrotransposition frequency in D. discoideum cells. Although CbfA binds to the C module in vitro, the factor regulates neither C-module nor A-module promoter activity in vivo. We speculate that CbfA supports the amplification of TRE5-A retrotransposons by suppressing the expression of an as yet unidentified component of the cellular posttranscriptional gene silencing machinery.

Blagg, S. L., S. E. Battom, et al. (2011). "Cell type-specific filamin complex regulation by a novel class of HECT ubiquitin ligase is required for normal cell motility and patterning." Development 138(8): 1583-1593.
	Differential cell motility, which plays a key role in many developmental processes, is perhaps most evident in examples of pattern formation in which the different cell types arise intermingled before sorting out into discrete tissues. This is thought to require heterogeneities in responsiveness to differentiation-inducing signals that result in the activation of cell type-specific genes and 'salt and pepper' patterning. How differential gene expression results in cell sorting is poorly defined. Here we describe a novel gene (hfnA) that provides the first mechanistic link between cell signalling, differential gene expression and cell type-specific sorting in Dictyostelium. HfnA defines a novel group of evolutionarily conserved HECT ubiquitin ligases with an N-terminal filamin domain (HFNs). HfnA expression is induced by the stalk differentiation-inducing factor DIF-1 and is restricted to a subset of prestalk cells (pstO). hfnA(-) pstO cells differentiate but their sorting out is delayed. Genetic interactions suggest that this is due to misregulation of filamin complex activity. Overexpression of filamin complex members phenocopies the hfnA(-) pstO cell sorting defect, whereas disruption of filamin complex function in a wild-type background results in pstO cells sorting more strongly. Filamin disruption in an hfnA(-) background rescues pstO cell localisation. hfnA(-) cells exhibit altered slug phototaxis phenotypes consistent with filamin complex hyperactivity. We propose that HfnA regulates filamin complex activity and cell type-specific motility through the breakdown of filamin complexes. These findings provide a novel mechanism for filamin regulation and demonstrate that filamin is a crucial mechanistic link between responses to differentiation signals and cell movement in patterning based on 'salt and pepper' differentiation and sorting out.

Bloomfield, G. (2011). "Genetics of sex determination in the social amoebae." Dev Growth Differ 53(4): 608-616.
	The social amoebae possess a sexual cycle that involves transient mutlicellularity: first a zygote attracts surrounding haploid amoebae to form a walled aggregate around it, and then cannibalizes these peripheral cells, eventually forming a dormant single-celled macrocyst. Self-fertile homothallic isolates occur as well as breeding groups of self-infertile heterothallic cells, which commonly have more than two mating types. The mating-type locus of the widely studied model organism Dictyostelium discoideum, which has three mating types, has recently been identified. Two of the three mating types are determined by single putative regulatory genes bearing no mutual similarity, while the third is specified by homologues of both of these genes. This is the first sex-determining locus of an Amoebozoan to be described and, since none of the key regulators show homology to known proteins, may be a first glimpse of a novel mode of regulation used in these organisms. The sexual cycle of dictyostelids has been relatively neglected, but continues to yield much interesting biology as well as having the potential to add to the genetic tools available for the study of these organisms.

Boesler, C., J. Kruse, et al. (2011). "Sequence and generation of mature ribosomal RNA transcripts in Dictyostelium discoideum." J Biol Chem 286(20): 17693-17703.
	The amoeba Dictyostelium discoideum is a well established model organism for studying numerous aspects of cellular and developmental functions. Its ribosomal RNA (rRNA) is encoded in an extrachromosomal palindrome that exists in approximately 100 copies in the cell. In this study, we have set out to investigate the sequence of the expressed rRNA. For this, we have ligated the rRNA ends and performed RT-PCR on these circular RNAs. Sequencing revealed that the mature 26 S, 17 S, 5.8 S, and 5 S rRNAs have sizes of 3741, 1871, 162, and 112 nucleotides, respectively. Unlike the published data, all mature rRNAs of the same type uniformly display the same start and end nucleotides in the analyzed AX2 strain. We show the existence of a short lived primary transcript covering the rRNA transcription unit of 17 S, 5.8 S, and 26 S rRNA. Northern blots and RT-PCR reveal that from this primary transcript two precursor molecules of the 17 S and two precursors of the 26 S rRNA are generated. We have also determined the sequences of these precursor molecules, and based on these data, we propose a model for the maturation of the rRNAs in Dictyostelium discoideum that we compare with the processing of the rRNA transcription unit of Saccharomyces cerevisiae.

Bonifait, L., S. J. Charette, et al. (2011). "Amoeba host model for evaluation of Streptococcus suis virulence." Appl Environ Microbiol 77(17): 6271-6273.
	The Gram-positive bacterium Streptococcus suis is a major swine pathogen worldwide that causes meningitis, septicemia, and endocarditis. In this study, we demonstrate that the amoeba Dictyostelium discoideum can be a relevant alternative system to study the virulence of S. suis.

Bowman, R. L., Y. Xiong, et al. (2011). "eIF2alpha kinases control chalone production in Dictyostelium discoideum." Eukaryot Cell 10(4): 494-501.
	Growing Dictyostelium cells secrete CfaD and AprA, two proteins that have been characterized as chalones. They exist within a high-molecular-weight complex that reversibly inhibits cell proliferation, but not growth, via cell surface receptors and a signaling pathway that includes G proteins. How the production of these two proteins is regulated is unknown. Dictyostelium cells possess three GCN2-type eukaryotic initiation factor 2 alpha subunit (eIF2alpha) kinases, proteins that phosphorylate the translational initiation factor eIF2alpha and possess a tRNA binding domain involved in their regulation. The Dictyostelium kinases have been shown to function during development in regulating several processes. We show here that expression of an unregulated, activated kinase domain greatly inhibits cell proliferation. The inhibitory effect on proliferation is not due to a general inhibition of translation. Instead, it is due to enhanced production of a secreted factor(s). Indeed, extracellular CfaD and AprA proteins, but not their mRNAs, are overproduced in cells expressing the activated kinase domain. The inhibition of proliferation is not seen when the activated kinase domain is expressed in cells lacking CfaD or AprA or in cells that contain a nonphosphorylatable eIF2alpha. We conclude that production of the chalones CfaD and AprA is translationally regulated by eIF2alpha phosphorylation. Both proteins are upregulated at the culmination of development, and this enhanced production is lacking in a strain that possesses a nonphosphorylatable eIF2alpha.

Bozzaro, S. and L. Eichinger (2011). "The professional phagocyte Dictyostelium discoideum as a model host for bacterial pathogens." Curr Drug Targets 12(7): 942-954.
	The use of simple hosts such as Dictyostelium discoideum in the study of host pathogen interactions offers a number of advantages and has steadily increased in recent years. Infection-specific genes can often only be studied in a very limited way in man and even in the mouse model their analysis is usually expensive, time consuming and technically challenging or sometimes even impossible. In contrast, their functional analysis in D. discoideum and other simple model organisms is often easier, faster and cheaper. Because host-pathogen interactions necessarily involve two organisms, it is desirable to be able to genetically manipulate both the pathogen and its host. Particularly suited are those hosts, like D. discoideum, whose genome sequence is known and annotated and for which excellent genetic and cell biological tools are available in order to dissect the complex crosstalk between host and pathogen. The review focusses on host-pathogen interactions of D. discoideum with Legionella pneumophila, mycobacteria, and Salmonella typhimurium which replicate intracellularly.

Bradbury, R. S., D. W. Reid, et al. (2011). "Decreased virulence of cystic fibrosis Pseudomonas aeruginosa in Dictyostelium discoideum." Microbiol Immunol 55(4): 224-230.
	The characteristics of clinical and environmental isolates of Pseudomonas aeruginosa from both hospital and community settings were analyzed in a eukaryotic virulence model employing the AX2 and X22 mutants of Dictyostelium discoideum. Thirty-one strains, including two Australian epidemic strains, of P. aeruginosa were analyzed, five from environmental sources, six from clinical sources other than cystic fibrosis (CF) patients and nineteen from CF patients' respiratory secretions. The majority of CF isolates almost uniquely supported the growth of D. discoideum. CF isolates of P. aeruginosa were found to be less virulent than isolates from other sources. Varying degrees of inhibition of the developmental cycle of D. discoideum when growing on CF isolates were also noted. This is the first description of P. aeruginosa isolates from clinical and environmental sources supporting the growth of D. discoideum.

Brock, D. A., T. E. Douglas, et al. (2011). "Primitive agriculture in a social amoeba." Nature 469(7330): 393-396.
	Agriculture has been a large part of the ecological success of humans. A handful of animals, notably the fungus-growing ants, termites and ambrosia beetles, have advanced agriculture that involves dispersal and seeding of food propagules, cultivation of the crop and sustainable harvesting. More primitive examples, which could be called husbandry because they involve fewer adaptations, include marine snails farming intertidal fungi and damselfish farming algae. Recent work has shown that microorganisms are surprisingly like animals in having sophisticated behaviours such as cooperation, communication and recognition, as well as many kinds of symbiosis. Here we show that the social amoeba Dictyostelium discoideum has a primitive farming symbiosis that includes dispersal and prudent harvesting of the crop. About one-third of wild-collected clones engage in husbandry of bacteria. Instead of consuming all bacteria in their patch, they stop feeding early and incorporate bacteria into their fruiting bodies. They then carry bacteria during spore dispersal and can seed a new food crop, which is a major advantage if edible bacteria are lacking at the new site. However, if they arrive at sites already containing appropriate bacteria, the costs of early feeding cessation are not compensated for, which may account for the dichotomous nature of this farming symbiosis. The striking convergent evolution between bacterial husbandry in social amoebas and fungus farming in social insects makes sense because multigenerational benefits of farming go to already established kin groups.

Budniak, A. and D. H. O'Day (2011). "Tyrosine phosphorylation of actin during microcyst formation and germination in Polysphondylium pallidum." Protist 162(3): 490-502.
	High osmolarity causes amoebae of the cellular slime mould Polysphondylium pallidum to individually encyst, forming microcysts. During microcyst differentiation, actin is tyrosine phosphorylated. Tyrosine phosphorylation of actin is independent of encystment conditions and occurs during the final stages of microcyst formation. During microcyst germination, actin undergoes dephosphorylation prior to amoebal emergence. Renewed phosphorylation of actin in germinating microcysts can be triggered by increasing the osmolarity of the medium which inhibits emergence. Immunofluorescence reveals that actin is dispersed throughout the cytoplasm in dormant microcysts. Following the onset of germination, actin is observed around vesicles where it co-localizes with phosphotyrosine. Prior to emergence, actin localizes to patches near the cell surface. Increasing osmolarity disrupts this localization and causes actin to redistribute throughout the cytoplasm, a situation similar to that observed in dormant microcysts. The tyrosine phosphorylation state of actin does not appear to influence the long-term viability of dormant microcysts. Together, these results indicate an association between actin tyrosine phosphorylation, organization of the actin cytoskeleton, and microcyst dormancy.

Cai, H. and P. N. Devreotes (2011). "Moving in the right direction: how eukaryotic cells migrate along chemical gradients." Semin Cell Dev Biol 22(8): 834-841.
	Many cells have the ability to grow or migrate towards chemical cues. Oriented growth and movement require detection of the external chemical gradient, transduction of signals, and reorganization of the cytoskeleton. Recent studies in Dictyostelium discoideum and mammalian neutrophils have revealed a complex signaling network that enables cells to migrate in chemical gradients.

Calvo-Garrido, J., S. Carilla-Latorre, et al. (2011). "A proteolytic cleavage assay to monitor autophagy in Dictyostelium discoideum." Autophagy 7(9): 1063-1068.
	Dictyostelium discoideum is a good model of autophagy. However, the lack of autophagic flux techniques hinders the assessment of new mutants or drugs. One of these techniques, which has been used successfully in yeast and mammalian cells, but has not yet been described in Dictyostelium, is based on the presence of proteolytic fragments derived from autophagic degradation of expressed fusion proteins. Lysosomotropic agents such as NH 4Cl penetrate acidic compartments and raise their pH, thus allowing the accumulation and measurement of these cleaved fragments, which otherwise would be rapidly degraded. We have used this property to detect the presence of free GFP fragments derived from the fusion protein GFP-Tkt-1, a cytosolic marker. We demonstrate that this proteolytic event is dependent on autophagy and can be used to detect differences in the level of autophagic flux among different mutant strains. Moreover, treatment with NH4Cl also facilitates the assessment of autophagic flux by confocal microscopy using the marker RFP-GFP-Atg8.

Carnell, M., T. Zech, et al. (2011). "Actin polymerization driven by WASH causes V-ATPase retrieval and vesicle neutralization before exocytosis." J Cell Biol 193(5): 831-839.
	WASP and SCAR homologue (WASH) is a recently identified and evolutionarily conserved regulator of actin polymerization. In this paper, we show that WASH coats mature Dictyostelium discoideum lysosomes and is essential for exocytosis of indigestible material. A related process, the expulsion of the lethal endosomal pathogen Cryptococcus neoformans from mammalian macrophages, also uses WASH-coated vesicles, and cells expressing dominant negative WASH mutants inefficiently expel C. neoformans. D. discoideum WASH causes filamentous actin (F-actin) patches to form on lysosomes, leading to the removal of vacuolar adenosine triphosphatase (V-ATPase) and the neutralization of lysosomes to form postlysosomes. Without WASH, no patches or coats are formed, neutral postlysosomes are not seen, and indigestible material such as dextran is not exocytosed. Similar results occur when actin polymerization is blocked with latrunculin. V-ATPases are known to bind avidly to F-actin. Our data imply a new mechanism, actin-mediated sorting, in which WASH and the Arp2/3 complex polymerize actin on vesicles to drive the separation and recycling of proteins such as the V-ATPase.

Carnell, M. J. and R. H. Insall (2011). "Actin on disease--studying the pathobiology of cell motility using Dictyostelium discoideum." Semin Cell Dev Biol 22(1): 82-88.
	The actin cytoskeleton in eukaryotic cells provides cell structure and organisation, and allows cells to generate forces against membranes. As such it is a central component of a variety of cellular structures involved in cell motility, cytokinesis and vesicle trafficking. In multicellular organisms these processes contribute towards embryonic development and effective functioning of cells of all types, most obviously rapidly moving cells like lymphocytes. Actin also defines and maintains the architecture of complex structures such as neuronal synapses and stereocillia, and is required for basic housekeeping tasks within the cell. It is therefore not surprising that misregulation of the actin cytoskeleton can cause a variety of disease pathologies, including compromised immunity, neurodegeneration, and cancer spread. Dictyostelium discoideum has long been used as a tool for dissecting the mechanisms by which eukaryotic cells migrate and chemotax, and recently it has gained precedence as a model organism for studying the roles of conserved pathways in disease processes. Dictyostelium's unusual lifestyle, positioned between unicellular and multicellular organisms, combined with ease of handling and strong conservation of actin regulatory machinery with higher animals, make it ideally suited for studying actin-related diseases. Here we address how research in Dictyostelium has contributed to our understanding of immune deficiencies and neurological defects in humans, and briefly discuss its future prospects for furthering our understanding of neurodegenerative disorders.

Catalano, A. and D. H. O'Day (2011). "Nucleolar localization and identification of nuclear/nucleolar localization signals of the calmodulin-binding protein nucleomorphin during growth and mitosis in Dictyostelium." Histochem Cell Biol 135(3): 239-249.
	The calmodulin-binding protein nucleomorphin isoform NumA1 is a nuclear number regulator in Dictyostelium that localizes to intra-nuclear patches adjacent to the nuclear envelope and to a lesser extent the nucleoplasm. Earlier studies have shown similar patches to be nucleoli but only three nucleolar proteins have been identified in Dictyostelium. Here, actinomycin-D treatment caused the loss of NumA1 localization, while calcium and calmodulin antagonists had no effect. In keeping with a nucleolar function, NumA1 moved out of the presumptive nucleoli during mitosis redistributing to areas within the nucleus, the spindle fibers, and centrosomal region before re-accumulating in the presumptive nucleoli at telophase. Together, these data verify NumA1 as a true nucleolar protein. Prior to this study, the dynamics of specific nucleolar proteins had not been determined during mitosis in Dictyostelium. FITC-conjugated peptides equivalent to presumptive nuclear localization signals within NumA1 localized to nucleoli indicating that they also act as nucleolar localization signals. To our knowledge, these represent the first precisely defined nucleolar localization signals as well as the first nuclear/nucleolar localization signals identified in Dictyostelium. Together, these results reveal that NumA1 is a true nucleolar protein and the only nucleolar calmodulin-binding protein identified in Dictyostelium. The possible use of nuclear/nucleolar localization signal-mediated drug targeting to nucleoli is discussed.

Catalano, A., Y. Poloz, et al. (2011). "Dictyostelium puromycin-sensitive aminopeptidase A is a nucleoplasmic nucleomorphin-binding protein that relocates to the cytoplasm during mitosis." Histochem Cell Biol 136(6): 677-688.
	Nucleomorphin (NumA1) is a nucleolar/nucleoplasmic protein linked to cell cycle in Dictyostelium. It interacts with puromycin-sensitive aminopeptidase A (PsaA) which in other organisms is a Zn(2+)-metallopeptidase thought to be involved in cell cycle progression and is involved in several human diseases. Here, we have shown that Dictyostelium PsaA contains domains characteristic of the M1 family of Zn(2+)-metallopeptidases: a GAMEN motif and a Zn(2+)-binding domain. PsaA colocalized with NumA1 in the nucleoplasm in vegetative cells and was also present to a lesser extent in the cytoplasm. The same localization pattern was observed in cells from slugs, however, in fruiting bodies PsaA was only detected in spore nuclei. During mitosis PsaA redistributed mainly throughout the cytoplasm. It possesses a functional nuclear localization signal ((680)RKRF(683)) necessary for nuclear entry. To our knowledge, this is the first nuclear localization signal identified in a Psa from any organism. Treatment with Ca(2+) chelators or calmodulin antagonists indicated that neither Ca(2+) nor calmodulin is involved in PsaA localization. These results are interpreted in terms of the inter-relationship between NumA1 and PsaA in cell function in Dictyostelium.

Cha, I. and T. J. Jeon (2011). "Dynamic localization of the actin-bundling protein cortexillin I during cell migration." Mol Cells 32(3): 281-287.
	Cortexillins are actin-bundling proteins that play a critical role in regulating cell morphology and actin cytoskeleton reorganization in Dictyostelium. Here, we investigated dynamic subcellular localization of cortexillin I in chemotaxing Dictyostelium cells. Most of the cortexillin I was enriched on the lateral sides of moving cells. Upon chemoattractant stimulation, cortexillin I was rapidly released from the cortex followed by a transient translocation to the cell cortex with a peak at ~5 s and a subsequent decrease to basal levels, indicating that localization of cor-texillin I at the cortex in chemotaxing cells is controlled by two more signaling components, one for the initial delocalization from the cortex and another for the translocation to the cortex ~5 s after chemoattractant stimulation. Loss of cortexillins leads to reduced cell polarity and an increased number of lateral pseudopodia during chemotaxis, suggesting that cortexillins play an inhibitory role in producing pseudopodia along the lateral sides of the cell. Cells lacking cortexillins displayed extended chemoattrac-tant-mediated Arp2/3 complex translocation kinetics to the cortex. Our present study provides a new insight into the function of cortexillins during reorganization of the actin cytoskeleton and cell migration.

Chakraborty, A., S. Kim, et al. (2011). "Inositol pyrophosphates as mammalian cell signals." Sci Signal 4(188): re1.
	Inositol pyrophosphates are highly energetic inositol polyphosphate molecules present in organisms from slime molds and yeast to mammals. Distinct classes of enzymes generate different forms of inositol pyrophosphates. The biosynthesis of these substances principally involves phosphorylation of inositol hexakisphosphate (IP) to generate the pyrophosphate IP. Initial insights into functions of these substances derived primarily from yeast, which contain a single isoform of IP kinase (yIPK), as well as from the slime mold Dictyostelium. Mammalian functions for inositol pyrophosphates have been investigated by using cell lines to establish roles in various processes, including insulin secretion and apoptosis. More recently, mice with targeted deletion of IPK isoforms as well as the related inositol polyphosphate multikinase (IPMK) have substantially enhanced our understanding of inositol polyphosphate physiology. Phenotypic alterations in mice lacking inositol hexakisphosphate kinase 1 (IPK1) reveal signaling roles for these molecules in insulin homeostasis, obesity, and immunological functions. Inositol pyrophosphates regulate these processes at least in part by inhibiting activation of the serine-threonine kinase Akt. Similar studies of IPK2 establish this enzyme as a cell death inducer acting by stimulating the proapoptotic protein p53. IPMK is responsible for generating the inositol phosphate IP but also has phosphatidylinositol 3-kinase activity--that participates in activation of Akt. Here, we discuss recent advances in understanding the physiological functions of the inositol pyrophosphates based in substantial part on studies in mice with deletion of IPK isoforms. These findings highlight the interplay of IPMK and IPK in regulating growth factor and nutrient-mediated cell signaling.

Chattwood, A. and C. R. Thompson (2011). "Non-genetic heterogeneity and cell fate choice in Dictyostelium discoideum." Dev Growth Differ 53(4): 558-566.
	From microbes to metazoans, it is now clear that fluctuations in the abundance of mRNA transcripts and protein molecules enable genetically identical cells to oscillate between several distinct states (Kaern et al. 2005). Since this cell-cell variability does not derive from physical differences in the genetic code it is termed non-genetic heterogeneity. Non-genetic heterogeneity endows cell populations with useful capabilities they could never achieve if each cell were the same as its neighbors (Raj &amp; van Oudenaarden 2008; Eldar &amp; Elowitz 2010). One such example is seen during multicellular development and "salt and pepper" cell type differentiation. In this review, we will first examine the importance of non-genetic heterogeneity in initiating "salt and pepper" pattern formation during Dictyostelium discoideum development. Second, we will discuss the various ways in which non-genetic heterogeneity might be generated, as well as recent advances in understanding the molecular basis of heterogeneity in this system.

Chen, C., H. L. Kim, et al. (2011). "Structural insights into the dual substrate specificities of mammalian and Dictyostelium dihydropteridine reductases toward two stereoisomers of quinonoid dihydrobiopterin." FEBS Lett 585(17): 2640-2646.
	Up to now, d-threo-tetrahydrobiopterin (DH(4), dictyopterin) was detected only in Dictyostelium discoideum, while the isomer L-erythro-tetrahydrobioterin (BH(4)) is common in mammals. To elucidate the mechanism of DH(4) regeneration by D. discoideum dihydropteridine reductase (DicDHPR), we have determined the crystal structure of DicDHPR complexed with NAD(+) at 2.16 A resolution. Significant structural differences from mammalian DHPRs are found around the coenzyme binding site, resulting in a higher K(m) value for NADH (K(m)=46.51+/-0.4 muM) than mammals. In addition, we have found that rat DHPR as well as DicDHPR could bind to both substrates quinonoid-BH(2) and quinonoid-DH(2) by docking calculations and have confirmed their catalytic activity by in vitro assay.

Couto, C. A., H. Y. Wang, et al. (2011). "PARP regulates nonhomologous end joining through retention of Ku at double-strand breaks." J Cell Biol 194(3): 367-375.
	Poly adenosine diphosphate (ADP)-ribosylation (PARylation) by poly ADP-ribose (PAR) polymerases (PARPs) is an early response to DNA double-strand breaks (DSBs). In this paper, we exploit Dictyostelium discoideum to uncover a novel role for PARylation in regulating nonhomologous end joining (NHEJ). PARylation occurred at single-strand breaks, and two PARPs, Adprt1b and Adprt2, were required for resistance to this kind of DNA damage. In contrast, although Adprt1b was dispensable for PARylation at DSBs, Adprt1a and, to a lesser extent, Adprt2 were required for this event. Disruption of adprt2 had a subtle impact on the ability of cells to perform NHEJ. However, disruption of adprt1a decreased the ability of cells to perform end joining with a concomitant increase in homologous recombination. PAR-dependent regulation of NHEJ was achieved through promoting recruitment and/or retention of Ku at DSBs. Furthermore, a PAR interaction motif in Ku70 was required for this regulation and efficient NHEJ. These data illustrate that PARylation at DSBs promotes NHEJ through recruitment or retention of repair factors at sites of DNA damage.

Cox, A. D., F. St Michael, et al. (2011). "Investigating the potential of conserved inner core oligosaccharide regions of Moraxella catarrhalis lipopolysaccharide as vaccine antigens: accessibility and functional activity of monoclonal antibodies and glycoconjugate derived sera." Glycoconj J 28(3-4): 165-182.
	We investigated the conservation and antibody accessibility of inner core epitopes of Moraxella catarrhalis lipopolysaccharide (LPS) in order to assess their potential as vaccine candidates. Two LPS mutants, a single mutant designated lgt2 and a double mutant termed lgt2/lgt4, elaborating truncated inner core structures were generated in order to preclude expression of host-like outer core structures and to create an inner core structure that was shared by all three serotypes A, B and C of M. catarrhalis. Murine monoclonal antibodies (mAbs), designated MC2-1 and MC2-10 were obtained by immunising mice with the lgt2 mutant of M. catarrhalis serotype A strain. We showed that mAb MC2-1 can bind to the core LPS of wild-type (wt) serotype A, B and C organisms and concluded that mAb MC2-1 defines an immunogenic inner core epitope of M. catarrhalis LPS. We were unsuccessful in obtaining mAbs to the lgt2/lgt4 mutant. MAb MC2-10 only recognised the lgt2 mutant and the wt serotype A strain, and exhibited a strong requirement for the terminal N-acetyl-glucosamine residue of the lgt2 mutant core oligosaccharide, suggesting that this residue was immunodominant. Subsequently, we showed that both mAbs MC2-1 and MC2-10 could facilitate bactericidal killing of the lgt2 mutant, however neither mAb could facilitate bactericidal killing of the wt serotype A strain. We then confirmed and extended the candidacy of the inner core LPS by demonstrating that it is possible to elicit functional antibodies against M. catarrhalis wt strains following immunisation of rabbits with glycoconjugates elaborating the conserved inner core LPS antigen. The present study describes three conjugation strategies that either uses amidases produced by Dictyostelium discoideum, targeting the amino functionality created by the amidase activity as the attachment point on the LPS molecule, or a strong base treatment to remove all fatty acids from the LPS, thus creating amino functionalities in the lipid A region to conjugate via maleimide-thiol linker strategies targeting the carboxyl residues of the carrier protein and the free amino functionalities of the derived lipid A region of the carbohydrate resulted in a high loading of carbohydrates per carrier protein from these carbohydrate preparations. Immunisation derived antisera from rabbits recognised fully extended M. catarrhalis LPS and whole cells. Moreover, bactericidal activity was demonstrated to both the immunising carbohydrate antigen and importantly to wt cells, thus further supporting the consideration of inner core LPS as a potential vaccine antigen to combat disease caused by M. catarrhalis.

Crawley, S. W., M. S. Gharaei, et al. (2011). "Autophosphorylation activates Dictyostelium myosin II heavy chain kinase A by providing a ligand for an allosteric binding site in the alpha-kinase domain." J Biol Chem 286(4): 2607-2616.
	Dictyostelium discoideum myosin II heavy chain kinase A (MHCK A), a member of the atypical alpha-kinase family, phosphorylates sites in the myosin II tail that block filament assembly. Here we show that the catalytic activity of A-CAT, the alpha-kinase domain of MHCK A (residues 552-841), is severely inhibited by the removal of a disordered C-terminal tail sequence (C-tail; residues 806-841). The key residue in the C-tail was identified as Thr(825), which was found to be constitutively autophosphorylated. Dephosphorylation of Thr(825) using shrimp alkaline phosphatase decreased A-CAT activity. The activity of a truncated A-CAT lacking Thr(825) could be rescued by P(i), phosphothreonine, and a phosphorylated peptide, but not by threonine, glutamic acid, aspartic acid, or an unphosphorylated peptide. These results focused attention on a P(i)-binding pocket located in the C-terminal lobe of A-CAT. Mutational analysis demonstrated that the P(i)-pocket was essential for A-CAT activity. Based on these results, it is proposed that autophosphorylation of Thr(825) activates ACAT by providing a covalently tethered ligand for the P(i)-pocket. Ab initio modeling studies using the Rosetta FloppyTail and FlexPepDock protocols showed that it is feasible for the phosphorylated Thr(825) to dock intramolecularly into the P(i)-pocket. Allosteric activation is predicted to involve a conformational change in Arg(734), which bridges the bound P(i) to Asp(762) in a key active site loop. Sequence alignments indicate that a comparable regulatory mechanism is likely to be conserved in Dictyostelium MHCK B-D and metazoan eukaryotic elongation factor-2 kinases.

Crawley, S. W., J. Liburd, et al. (2011). "Identification of calmodulin and MlcC as light chains for Dictyostelium myosin-I isozymes." Biochemistry 50(30): 6579-6588.
	Dictyostelium discoideum express seven single-headed myosin-I isozymes (MyoA-MyoE and MyoK) that drive motile processes at the cell membrane. The light chains for MyoA and MyoE were identified by expressing Flag-tagged constructs consisting of the motor domain and the two IQ motifs in the neck region in Dictyostelium. The MyoA and MyoE constructs both copurified with calmodulin. Isothermal titration calorimetry (ITC) showed that apo-calmodulin bound to peptides corresponding to the MyoA and MyoE IQ motifs with micromolar affinity. In the presence of calcium, calmodulin cross-linked two IQ motif peptides, with one domain binding with nanomolar affinity and the other with micromolar affinity. The IQ motifs were required for the actin-activated MgATPase activity of MyoA but not MyoE; however, neither myosin exhibited calcium-dependent activity. A Flag-tagged construct consisting of the MyoC motor domain and the three IQ motifs in the adjacent neck region bound a novel 8.6 kDa two EF-hand protein named MlcC, for myosin light chain for MyoC. MlcC is most similar to the C-terminal domain of calmodulin but does not bind calcium. ITC studies showed that MlcC binds IQ1 and IQ2 but not IQ3 of MyoC. IQ3 contains a proline residue that may render it nonfunctional. Each long-tailed Dictyostelium myosin-I has now been shown to have a unique light chain (MyoB-MlcB, MyoC-MlcC, and MyoD-MlcD), whereas the short-tailed myosins-I, MyoA and MyoE, have the multifunctional calmodulin as a light chain. The diversity in light chain composition is likely to contribute to the distinct cellular functions of each myosin-I isozyme.

Daher, R. K., G. Filion, et al. (2011). "Alteration of virulence factors and rearrangement of pAsa5 plasmid caused by the growth of Aeromonas salmonicida in stressful conditions." Vet Microbiol 152(3-4): 353-360.
	Aeromonas salmonicida, a fish pathogen, is the causative agent of furunculosis. It was already shown that growing this bacterium in stressful conditions such as temperature above 22 degrees C might lead to virulence attenuation. Unfortunately, many veterinary microbiology services and reference centers still routinely cultivate A. salmonicida at 25 degrees C. Here we tested the presence of virulence factors by growth on specific medium as well as the integrity of the pAsa5 plasmid, which bears an important virulence factor, the type III secretion system (TTSS), by PCR analysis in twenty strains, most of which were grown at 25 degrees C in their laboratory of origin. The analysis revealed that strains, which encountered the more stressful growth conditions displayed the most frequent absence of A-layer protein and secreted proteolytic activity. Moreover, many strains had lost parts of the pAsa5 plasmid in which the TTSS region was almost always affected. To confirm the effect of stressful growth conditions on the plasmid, three strains with an intact pAsa5 were cultured at 25 degrees C for two weeks. A low but significant fraction of the tested colonies displayed pAsa5 rearrangements. The rearrangement always affected the TTSS region and led to a loss of virulence in the Dictyostelium discoideum co-culture assay. These results demonstrate that the instability of pAsa5 did not lead to its complete loss as previously proposed but to a more complex rearrangement phenomenon and emphasizes the necessity to grow A. salmonicida in appropriate conditions to preserve the complete virulence of the bacterium.

Dallon, J. C., B. Dalton, et al. (2011). "Understanding streaming in Dictyostelium discoideum: theory versus experiments." Bull Math Biol 73(7): 1603-1626.
	Recent experimental work involving Dictyostelium discoideum seems to contradict several theoretical models. Experiments suggest that localization of the release of the chemoattractant cyclic adenosine monophosphate to the uropod of the cell is important for stream formation during aggregation. Yet several mathematical models are able to reproduce streaming as the cells aggregate without taking into account localization of the chemoattractant. A careful analysis of the experiments and the theory suggests the two major features of the system which are important to stream formation are random cell motion and chemotaxis to regions of higher cell density. Random cell motion acts to reduce streaming, whereas chemotaxis to regions of higher cell density reinforces streaming. With this understanding, the experimental results can be explained in a manner consistent with the theoretical results. In all the experiments, alterations in the two main factors of random motion and chemotaxis to regions of higher cell density, not the localization of the release of the chemoattractant, can explain the results as they relate to streaming. Additionally, a comparison of results from a mathematical model that simulates cells which localize the chemoattractant and cells which do not shows little difference in the streaming patterns.

Dames, S. A., A. Junemann, et al. (2011). "Structure, dynamics, lipid binding, and physiological relevance of the putative GTPase-binding domain of Dictyostelium formin C." J Biol Chem 286(42): 36907-36920.
	Dictyostelium Formin C (ForC) is involved in the regulation of local actin cytoskeleton reorganization (e.g. during cellular adhesion or migration). ForC contains formin homology 2 and 3 (FH2 and -3) domains and an N-terminal putative GTPase-binding domain (GBD) but lacks a canonical FH1 region. To better understand the role of the GBD, its structure, dynamics, lipid-binding properties, and cellular functions were analyzed by NMR and CD spectroscopy and by in vivo fluorescence microscopy. Moreover, the program CS-Rosetta was tested for the structure prediction based on chemical shift data only. The ForC GBD adopts an ubiquitin-like alpha/beta-roll fold with an unusually long loop between beta-strands 1 and 2. Based on the lipid-binding data, the presence of DPC micelles induces the formation of alpha-helical secondary structure and a rearrangement of the tertiary structure. Lipid-binding studies with a mutant protein and a peptide suggest that the beta1-beta2 loop is not relevant for these conformational changes. Whereas small amounts of negatively charged phosphoinositides (1,2-dioctanoyl-sn-glycero-3-(phosphoinositol 4,5-bisphosphate) and 1,2-dihexanoyl-sn-glycero-3-(phosphoinositol 3,4,5-trisphosphate)) lower the micelle concentration necessary to induce the observed spectral changes, other negatively charged phospholipids (1,2-dihexanoyl-sn-glycero-3-(phospho-L-serine) and 1,2-dihexanoyl-sn-glycero-3-phospho-(1'-rac-glycerol)) had no such effect. Interestingly, bicelles and micelles composed of diacylphosphocholines had no effect on the GBD structure. Our data suggest a model in which part of the large positively charged surface area of the GBD mediates localization to specific membrane patches, thereby regulating interactions with signaling proteins. Our cellular localization studies show that both the GBD and the FH3 domain are required for ForC targeting to cell-cell contacts and early phagocytic cups and macropinosomes.

Dames, S. A., A. Schonichen, et al. (2011). "1H, 15N, and 13C assignments of the N-terminal activation domain of Dictyostelium discoideum Formin C." Biomol NMR Assign 5(1): 47-49.
	Dictyostelium discoideum Formin C (ForC) plays an important role in the fruiting body formation during the multicellular stages of the slime mold. Formins are multidomain proteins that are known to regulate the actin cytoskeleton. Here, we report the assignments of the (1)H, (15)N, and (13)C nuclei of the N-terminal activation domain (residues 1-100) of ForC. Chemical shifts have been deposited at the BioMagResBank under the BMRB accession number 17,029. The N-terminal region of the 131 kDa ForC protein is supposed to form a GTPase-binding domain required for activation of the formin.

Das, S., E. C. Rericha, et al. (2011). "Direct biochemical measurements of signal relay during Dictyostelium development." J Biol Chem 286(44): 38649-38658.
	Upon starvation, individual Dictyostelium discoideum cells enter a developmental program that leads to collective migration and the formation of a multicellular organism. The process is mediated by extracellular cAMP binding to the G protein-coupled cAMP receptor 1, which initiates a signaling cascade leading to the activation of adenylyl cyclase A (ACA), the synthesis and secretion of additional cAMP, and an autocrine and paracrine activation loop. The release of cAMP allows neighboring cells to polarize and migrate directionally and form characteristic chains of cells called streams. We now report that cAMP relay can be measured biochemically by assessing ACA, ERK2, and TORC2 activities at successive time points in development after stimulating cells with subsaturating concentrations of cAMP. We also find that the activation profiles of ACA, ERK2, and TORC2 change in the course of development, with later developed cells showing a loss of sensitivity to the relayed signal. We examined mutants in PKA activity that have been associated with precocious development and find that this loss in responsiveness occurs earlier in these mutants. Remarkably, we show that this loss in sensitivity correlates with a switch in migration patterns as cells transition from streams to aggregates. We propose that as cells proceed through development, the cAMP-induced desensitization and down-regulation of cAMP receptor 1 impacts the sensitivities of chemotactic signaling cascades leading to changes in migration patterns.

de Keijzer, S., J. Galloway, et al. (2011). "Disrupting microtubule network immobilizes amoeboid chemotactic receptor in the plasma membrane." Biochim Biophys Acta 1808(6): 1701-1708.
	Signaling cascades are initiated in the plasma membrane via activation of one molecule by another. The interaction depends on the mutual availability of the molecules to each other and this is determined by their localization and lateral diffusion in the cell membrane. The cytoskeleton plays a very important role in this process by enhancing or restricting the possibility of the signaling partners to meet in the plasma membrane. In this study we explored the mode of diffusion of the cAMP receptor, cAR1, in the plasma membrane of Dictyostelium discoideum cells and how this is regulated by the cytoskeleton. Single-particle tracking of fluorescently labeled cAR1 using Total Internal Reflection Microscopy showed that 70% of the cAR1 molecules were mobile. These receptors showed directed motion and we demonstrate that this is not because of tracking along the actin cytoskeleton. Instead, destabilization of the microtubules abolished cAR1 mobility in the plasma membrane and this was confirmed by Fluorescence Recovery after Photobleaching. As a result of microtubule stabilization, one of the first downstream signaling events, the jump of the PH domain of CRAC, was decreased. These results suggest a role for microtubules in cAR1 dynamics and in the ability of cAR1 molecules to interact with their signaling partners.

Dickinson, D. J., W. J. Nelson, et al. (2011). "A polarized epithelium organized by beta- and alpha-catenin predates cadherin and metazoan origins." Science 331(6022): 1336-1339.
	A fundamental characteristic of metazoans is the formation of a simple, polarized epithelium. In higher animals, the structural integrity and functional polarization of simple epithelia require a cell-cell adhesion complex that contains a classical cadherin, the Wnt-signaling protein beta-catenin and the actin-binding protein alpha-catenin. We show that the non-metazoan Dictyostelium discoideum forms a polarized epithelium that is essential for multicellular development. Although D. discoideum lacks a cadherin homolog, we identify an alpha-catenin ortholog that binds a beta-catenin-related protein. Both proteins are essential for formation of the epithelium, polarized protein secretion, and proper multicellular morphogenesis. Thus, the organizational principles of metazoan multicellularity may be more ancient than previously recognized, and the role of the catenins in cell polarity predates the evolution of Wnt signaling and classical cadherins.

Diensthuber, R. P., M. Muller, et al. (2011). "Phalloidin perturbs the interaction of human non-muscle myosin isoforms 2A and 2C1 with F-actin." FEBS Lett 585(5): 767-771.
	Phalloidin and fluorescently labeled phalloidin analogs are established reagents to stabilize and mark actin filaments for the investigation of acto-myosin interactions. In the present study, we employed transient and steady-state kinetic measurements as well as in vitro motility assays to show that phalloidin perturbs the productive interaction of human non-muscle myosin-2A and -2C1 with filamentous actin. Phalloidin binding to F-actin results in faster dissociation of the complex formed with non-muscle myosin-2A and -2C1, reduced actin-activated ATP turnover, and slower velocity of actin filaments in the in vitro motility assay. In contrast, phalloidin binding to F-actin does not affect the interaction with human non-muscle myosin isoform 2B and Dictyostelium myosin-2 and myosin-5b.

Douglas, T. E., M. R. Kronforst, et al. (2011). "Genetic diversity in the social amoeba Dictyostelium discoideum: population differentiation and cryptic species." Mol Phylogenet Evol 60(3): 455-462.
	The social amoeba Dictyostelium discoideum is a commonly used model organism for the study of social evolution, multicellularity, and cell biology. But the boundaries and structure of the species have not been explored. The lack of morphological traits to distinguish D. discoideum makes even knowing whether a given clone is D. discoideum a challenge. We address this with a phylogeny of a widespread collection of clones from a range of locations and including clones identified previously as potential cryptic species. We sequenced portions of nuclear ribosomal DNA and mitochondrial DNA, analyzing approximately 5500 and 2500 base pairs from the two regions respectively. We compared these sequences to known reference sequences for both D. discoideum and other closely related Dictyostelium species to create Bayesian and neighbor-joining phylogenetic trees representing the evolutionary relationships among the clones. We identified 51 unique D. discoideum concatenated sequences based on the combined mitochondrial and ribosomal sequence data. We also identified four unique D. citrinum concatenated sequences, three of which were previously classified as D. discoideum clones. Our analysis of the data revealed that all D. discoideum clones form a monophyletic group, but there are several well-supported subclades and pronounced genetic differentiation among locations (F(ST)=0.242, P=0.011), suggesting the presence of geographic or other barriers between populations. Our results reveal the need for further investigation into potential tropical cryptic species.

Driscoll, M. K., J. T. Fourkas, et al. (2011). "Local and global measures of shape dynamics." Phys Biol 8(5): 055001.
	The shape and motion of cells can yield significant insights into the internal operation of a cell. We present a simple, yet versatile, framework that provides multiple metrics of cell shape and cell shape dynamics. Analysis of migrating Dictyostelium discoideum cells shows that global and local metrics highlight distinct cellular processes. For example, a global measure of shape shows rhythmic oscillations suggestive of contractions, whereas a local measure of shape shows wave-like dynamics indicative of protrusions. From a local measure of dynamic shape, or boundary motion, we extract the times and locations of protrusions and retractions. We find that protrusions zigzag, while retractions remain roughly stationary along the boundary. We do not observe any temporal relationship between protrusions and retractions. Our analysis framework also provides metrics of the boundary as whole. For example, as the cell speed increases, we find that the cell shape becomes more elongated. We also observe that while extensions and retractions have similar areas, their shapes differ.

Dubin, M. J., S. Kasten, et al. (2011). "Characterization of the Dictyostelium homolog of chromatin binding protein DET1 suggests a conserved pathway regulating cell type specification and developmental plasticity." Eukaryot Cell 10(3): 352-362.
	DET1 (De-etiolated 1) is a chromatin binding protein involved in developmental regulation in both plants and animals. DET1 is largely restricted to multicellular eukaryotes, and here we report the characterization of a DET1 homolog from the social amoeba Dictyostelium discoideum. As in other species, Dictyostelium DET1 is nuclear localized. In contrast to other species, where it is an essential protein, loss of DET1 is nonlethal in Dictyostelium, although viability is significantly reduced. The phenotype of the det1(-) mutant is highly pleiotropic and results in a large degree of heterogeneity in developmental parameters. Loss of DET1 results in delayed and abnormal development with enlarged aggregation territories. Mutant slugs displayed cell type patterning with a bias toward the prestalk pathway. A number of DET1-interacting proteins are conserved in Dictyostelium, and the apparently conserved role of DET1 in regulatory pathways involving the bZIP transcription factors DimB, c-Jun, and HY5 suggests a highly conserved mechanism regulating development in multicellular eukaryotes. While the mechanism by which DET1 functions is unclear, it appears that it has a key role in regulation of developmental plasticity and integration of information on environmental conditions into the developmental program of an organism.

Elphick, L. M., N. Pawolleck, et al. (2011). "Conserved valproic-acid-induced lipid droplet formation in Dictyostelium and human hepatocytes identifies structurally active compounds." Dis Model Mech.
	Lipid droplet formation and subsequent steatosis (the abnormal retention of lipids within a cell) has been reported to contribute to hepatotoxicity and is an adverse effect of many pharmacological agents including the antiepileptic drug valproic acid (VPA). In this study, we have developed a simple model system (Dictyostelium discoideum) to investigate the effects of VPA and related compounds in lipid droplet formation. In mammalian hepatocytes, VPA increases lipid droplet accumulation over a 24-hour period, giving rise to liver cell damage, and we show a similar effect in Dictyostelium following 30 minutes of VPA treatment. Using (3)H-labelled polyunsaturated (arachidonic) or saturated (palmitic) fatty acids, we shown that VPA treatment of Dictyostelium gives rise to an increased accumulation of both types of fatty acids in phosphatidylcholine, phosphatidylethanolamine and non-polar lipids in this time period, with a similar trend observed in human hepatocytes (Huh7 cells) labelled with [(3)H]arachidonic acid. In addition, pharmacological inhibition of beta-oxidation in Dictyostelium phenocopies fatty acid accumulation, in agreement with data reported in mammalian systems. Using Dictyostelium, we then screened a range of VPA-related compounds to identify those with high and low lipid-accumulation potential, and validated these activities for effects on lipid droplet formation by using human hepatocytes. Structure-activity relationships for these VPA-related compounds suggest that lipid accumulation is independent of VPA-catalysed teratogenicity and inositol depletion. These results suggest that Dictyostelium could provide both a novel model system for the analysis of lipid droplet formation in human hepatocytes and a rapid method for identifying VPA-related compounds that show liver toxicology.

Escalante, R. (2011). "Dictyostelium as a model for human disease." Semin Cell Dev Biol 22(1): 69.
	
Flegel, K. A., J. M. Pineda, et al. (2011). "Copine A is expressed in prestalk cells and regulates slug phototaxis and thermotaxis in developing Dictyostelium." Dev Growth Differ 53(8): 948-959.
	Copines are calcium-dependent membrane-binding proteins found in many eukaryotic organisms. We are studying the function of copines using the model organism, Dictyostelium discoideum. When under starvation conditions, Dictyostelium cells aggregate into mounds that become migrating slugs, which can move toward light and heat before culminating into a fruiting body. Previously, we showed that Dictyostelium cells lacking the copine A (cpnA) gene are not able to form fruiting bodies and instead arrest at the slug stage. In this study, we compared the slug behavior of cells lacking the cpnA gene to the slug behavior of wild-type cells. The slugs formed by cpnA- cells were much larger than wild-type slugs and exhibited no phototaxis and negative thermotaxis in the same conditions that wild-type slugs exhibited positive phototaxis and thermotaxis. Mixing as little as 5% wild-type cells with cpnA- cells rescued the phototaxis and thermotaxis defects, suggesting that CpnA plays a specific role in the regulation of the production and/or release of a signaling molecule. Reducing extracellular levels of ammonia also partially rescued the phototaxis and thermotaxis defects of cpnA- slugs, suggesting that CpnA may have a specific role in regulating ammonia signaling. Expressing the lacZ gene under the cpnA promoter in wild-type cells indicated cpnA is preferentially expressed in the prestalk cells found in the anterior part of the slug, which include the cells at the tip of the slug that regulate phototaxis, thermotaxis, and the initiation of culmination into fruiting bodies. Our results suggest that CpnA plays a role in the regulation of the signaling pathways, including ammonia signaling, necessary for sensing and/or orienting toward light and heat in the prestalk cells of the Dictyostelium slug.

Francione, L. M., S. J. Annesley, et al. (2011). "The Dictyostelium model for mitochondrial disease." Semin Cell Dev Biol 22(1): 120-130.
	Mitochondrial diseases are a diverse family of genetic disorders caused by mutations affecting mitochondrial proteins encoded in either the nuclear or the mitochondrial genome. By impairing mitochondrial oxidative phosphorylation, they compromise cellular energy production and the downstream consequences in humans are a bewilderingly complex array of signs and symptoms that can affect any of the major organ systems in unpredictable combinations. This complexity and unpredictability has limited our understanding of the cytopathological consequences of mitochondrial dysfunction. By contrast, in Dictyostelium the mitochondrial disease phenotypes are consistent, measurable "readouts" of dysregulated intracellular signalling pathways. When the underlying genetic defects would produce coordinate, generalized deficiencies in multiple mitochondrial respiratory complexes, the disease phenotypes are mediated by chronic activation of an energy-sensing protein kinase, AMP-activated protein kinase (AMPK). This chronic AMPK hyperactivity maintains mitochondrial mass and cellular ATP concentrations at normal levels, but chronically impairs growth, cell cycle progression, multicellular development, photosensory and thermosensory signal transduction. It also causes the cells to support greater proliferation of the intracellular bacterial pathogen, Legionella pneumophila. Notably however, phagocytic and macropinocytic nutrient uptake are impervious both to AMPK signalling and to these types of mitochondrial dysfunction. Surprisingly, a Complex I-specific deficiency (midA knockout) not only causes the foregoing AMPK-mediated defects, but also produces a dramatic deficit in endocytic nutrient uptake accompanied by an additional secondary defect in growth. More restricted and specific phenotypic outcomes are produced by knocking out genes for nuclear-encoded mitochondrial proteins that are not required for respiration. The Dictyostelium model for mitochondrial disease has thus revealed consistent patterns of sublethal dysregulation of intracellular signalling pathways that are produced by different types of underlying mitochondrial dysfunction.

Francione, L. M. and P. R. Fisher (2011). "Heteroplasmic mitochondrial disease in Dictyostelium discoideum." Biochem Pharmacol 82(10): 1510-1520.
	The bewildering complexity of the relationship between genotype and phenotype in human mitochondrial diseases has delayed an understanding of the related cytopathological mechanisms. To explore the relationship between mitochondrial dysfunction in Dictyostelium discoideum and the related cytopathologies, we determined whether the phenotypic outcomes were similar regardless of which D. discoideum mitochondrial gene was targeted for disruption. The disruption of the mitochondrial genes resulted in a similar pattern of phenotypes to those caused by other mitochondrial defects. These include impairment of phototaxis, multicellular development and growth on plates and in liquid medium. As the reduced growth rates could have been due to defective phagocytic or macropinocytic nutrient uptake, these processes were tested but found to be unaffected. Since mitochondria have been associated with Legionella pathogenesis of human macrophages, it was also determined if mitochondrially diseased Dictyostelium strains were better or worse than healthy cells at supporting the growth of Legionella pneumophila. The results revealed that the mitochondrially diseased strains supported greater L. pneumophila growth than the wild type Dictyostelium strain (AX2). Quantitative Northern blotting showed a significant reduction in the level of expression of the entire mitochondrial genome, regardless of which mitochondrial gene was targeted for disruption, suggesting a generalized deficiency in mitochondrial gene expression and function. The phenotypic outcomes were the same as those shown previously to result from chronic hyperactivity of the energy-sensing protein kinase, AMPK, after knockdown of mitochondrial chaperonin 60.

Friedberg, F. (2011). "Single and multiple CH (calponin homology) domain containing multidomain proteins in Arabidopsis and Saccharomyces: an inventory." Mol Biol Rep 38(1): 213-218.
	Genes for individual domains such as CH, lim, ankyrin, PH and RhoGAP, IQ motif, Ig_FLMN, spectrin, and EF hand probably existed in early evolution before there were plants, fungi or animals so that when we examine multidomain proteins in Arabidopsis, Saccharomyces, Dictyostelium or Homo Sapiens we encounter various combinations of such domains. While all of these four species express Fimbrin and EB1, the lists of CH containing multidomain proteins, however, differ in number and in type for each of them. There was no further great increase in the number of new single domain proteins. Still many new multidomain genes evolved--but far more so in metazoans--than in plants or fungi. In both plants and fungi only singlet CH domains but no doublets (other than those forming the Fimbrin quadruplet) were incorporated. That is in these two branches one finds no alpha actinin, dystrophin or filamin even though the individual building blocks (i.e. domains such as spectrin or IG-FLMN) were available in Arabidopsis. Possibly transposons create new chimeric multidomain genes by mixing and matching genes or gene fragments.

Friedrich, M., R. Nozadze, et al. (2011). "Detection of Single Quantum Dots in Model Systems with Sheet Illumination Microscopy." J Fluoresc.
	Single molecule detection and tracking provides at times the only possible method to observe the interactions of low numbers of biomolecules, inlcuding DNA, receptors and signal mediating proteins in living systems. However, most existing imaging methods do not enable both high sensitivity and non-invasive imaging of large specimens. In this study we report a new setup for selective plane illumination microscopy (SPIM), which enables fast imaging and single molecule tracking with the resolution of confocal microscopy and the optical penetration beyond 300 mum. We detect and report our instrumental figures of merit, control values of fluorescence properties of single nano crystals in comparison to both standard widefield configurations, and also values of nanocrystals in multicellular "fruiting bodies" of Dictyostelium, an excellent control as a model developmental system. In the Dictyostelium , we also report some of our first tracking of single nanocrystals with SPIM. The new SPIM setup represents a new technique, which enables fast single molecule imaging and tracking in living systems.

Fukuzawa, M. (2011). "Control of prestalk-cell differentiation by transcription factors." Dev Growth Differ 53(4): 538-547.
	Transcriptional control of developmental genes is important for cell differentiation and pattern formation. Developing Dictyostelium discoideum cells form a multicellular structure in which individual cells differentiate into either stalk cells or spores. This simplicity makes the organism an attractive model for studying fundamental problems in developmental biology. However, the morphogenetic process of forming a stalked fruiting body conceals a certain degree of complexity. This is reflected in the presence of multiple prestalk subtypes that have individual roles to generate the fruiting body. This review describes recent advances in understanding the molecular mechanisms, mediated by transcription factors that generate prestalk-cell heterogeneity.

Fumanelli, L., M. Iannelli, et al. (2011). "Mathematical modeling of bacterial virulence and host-pathogen interactions in the Dictyostelium/Pseudomonas system." J Theor Biol 270(1): 19-24.
	We present some studies on the mechanisms of pathogenesis based on experimental work and on its interpretation through a mathematical model. Using a collection of clinical strains of the opportunistic human pathogen Pseudomonas aeruginosa, we performed co-culture experiments with Dictyostelium amoebae, to investigate the two organisms' interaction, characterized by a cross action between amoeba, feeding on bacteria, and bacteria exerting their pathogenic action against amoeba. In order to classify bacteria virulence, independently of this cross interaction, we have also performed killing experiments of bacteria against the nematode Caenorhabditis elegans. A mathematical model was developed to infer how the populations of the amoeba-bacteria system evolve according to a number of parameters, taking into account the specific features underlying the interaction. The model does not fall within the class of traditional prey-predator models because not only does an amoeba feed on bacteria, but also it is in turn attacked by them; thus the model must include a feedback term modeling this further interaction aspect. The model shows the existence of multiple steady states and the resulting behavior of the solutions, showing bi-stability of the system, gives a qualitative explanation of the co-culture experiments.

Gao, R. C., X. D. Zhang, et al. (2011). "Different roles of membrane potentials in electrotaxis and chemotaxis of dictyostelium cells." Eukaryot Cell 10(9): 1251-1256.
	Many types of cells migrate directionally in direct current (DC) electric fields (EFs), a phenomenon termed galvanotaxis or electrotaxis. The directional sensing mechanisms responsible for this response to EFs, however, remain unknown. Exposing cells to an EF causes changes in plasma membrane potentials (V(m)). Exploiting the ability of Dictyostelium cells to tolerate drastic V(m) changes, we investigated the role of V(m) in electrotaxis and, in parallel, in chemotaxis. We used three independent factors to control V(m): extracellular pH, extracellular [K(+)], and electroporation. Changes in V(m) were monitored with microelectrode recording techniques. Depolarized V(m) was observed under acidic (pH 5.0) and alkaline (pH 9.0) conditions as well as under higher extracellular [K(+)] conditions. Electroporation permeabilized the cell membrane and significantly reduced the V(m), which gradually recovered over 40 min. We then recorded the electrotactic behaviors of Dictyostelium cells with a defined V(m) using these three techniques. The directionality (directedness of electrotaxis) was quantified and compared to that of chemotaxis (chemotactic index). We found that a reduced V(m) significantly impaired electrotaxis without significantly affecting random motility or chemotaxis. We conclude that extracellular pH, [K(+)], and electroporation all significantly affected electrotaxis, which appeared to be mediated by the changes in V(m). The initial directional sensing mechanisms for electrotaxis therefore differ from those of chemotaxis and may be mediated by changes in resting V(m).

Gaudet, P., P. Fey, et al. (2011). "dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa." Nucleic Acids Res 39(Database issue): D620-624.
	dictyBase (http://www.dictybase.org), the model organism database for Dictyostelium, aims to provide the broad biomedical research community with well integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a 'reference genome' in the Amoebozoa clade. We highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase.

Gerisch, G., M. Ecke, et al. (2011). "Different modes of state transitions determine pattern in the Phosphatidylinositide-Actin system." BMC Cell Biol 12: 42.
	BACKGROUND: In a motile polarized cell the actin system is differentiated to allow protrusion at the front and retraction at the tail. This differentiation is linked to the phosphoinositide pattern in the plasma membrane. In the highly motile Dictyostelium cells studied here, the front is dominated by PI3-kinases producing PI(3,4,5)tris-phosphate (PIP3), the tail by the PI3-phosphatase PTEN that hydrolyses PIP3 to PI(4,5)bis-phosphate. To study de-novo cell polarization, we first depolymerized actin and subsequently recorded the spontaneous reorganization of actin patterns in relation to PTEN. RESULTS: In a transient stage of recovery from depolymerization, symmetric actin patterns alternate periodically with asymmetric ones. The switches to asymmetry coincide with the unilateral membrane-binding of PTEN. The modes of state transitions in the actin and PTEN systems differ. Transitions in the actin system propagate as waves that are initiated at single sites by the amplification of spontaneous fluctuations. In PTEN-null cells, these waves still propagate with normal speed but loose their regular periodicity. Membrane-binding of PTEN is induced at the border of a coherent PTEN-rich area in the form of expanding and regressing gradients. CONCLUSIONS: The state transitions in actin organization and the reversible transition from cytoplasmic to membrane-bound PTEN are synchronized but their patterns differ. The transitions in actin organization are independent of PTEN, but when PTEN is present, they are coupled to periodic changes in the membrane-binding of this PIP3-degrading phosphatase. The PTEN oscillations are related to motility patterns of chemotaxing cells.

Gole, L., C. Riviere, et al. (2011). "A quorum-sensing factor in vegetative Dictyostelium discoideum cells revealed by quantitative migration analysis." PLoS One 6(11): e26901.
	BACKGROUND: Many cells communicate through the production of diffusible signaling molecules that accumulate and once a critical concentration has been reached, can activate or repress a number of target genes in a process termed quorum sensing (QS). In the social amoeba Dictyostelium discoideum, QS plays an important role during development. However little is known about its effect on cell migration especially in the growth phase. METHODS AND FINDINGS: To investigate the role of cell density on cell migration in the growth phase, we use multisite timelapse microscopy and automated cell tracking. This analysis reveals a high heterogeneity within a given cell population, and the necessity to use large data sets to draw reliable conclusions on cell motion. In average, motion is persistent for short periods of time (t &lt;/= 5 min), but normal diffusive behavior is recovered over longer time periods. The persistence times are positively correlated with the migrated distances. Interestingly, the migrated distance decreases as well with cell density. The adaptation of cell migration to cell density highlights the role of a secreted quorum sensing factor (QSF) on cell migration. Using a simple model describing the balance between the rate of QSF generation and the rate of QSF dilution, we were able to gather all experimental results into a single master curve, showing a sharp cell transition between high and low motile behaviors with increasing QSF. CONCLUSION: This study unambiguously demonstrates the central role played by QSF on amoeboid motion in the growth phase.

Gomer, R. H., W. Jang, et al. (2011). "Cell density sensing and size determination." Dev Growth Differ 53(4): 482-494.
	The social amoeba Dictyostelium discoideum is one of the leading model systems used to study how cells count themselves to determine the number and/or density of cells. In this review, we describe work on three different cell-density sensing systems used by Dictyostelium. The first involves a negative feedback loop in which two secreted signals inhibit cell proliferation during the growth phase. As the cell density increases, the concentrations of the secreted factors concomitantly increase, allowing the cells to sense their density. The two signals act as message authenticators for each other, and the existence of two different signals that require each other for activity may explain why previous efforts to identify autocrine proliferation-inhibiting signals in higher eukaryotes have generally failed. The second system involves a signal made by growing cells that is secreted only when they starve. This then allows cells to sense the density of just the starving cells, and is an example of a mechanism that allows cells in a tissue to sense the density of one specific cell type. The third cell density counting system involves cells in aggregation streams secreting a signal that limits the size of fruiting bodies. Computer simulations predicted, and experiments then showed, that the factor increases random cell motility and decreases cell-cell adhesion to cause streams to break up if there are too many cells in the stream. Together, studies on Dictyostelium cell density counting systems will help elucidate how higher eukaryotes regulate the size and composition of tissues.

Greene, D. M., G. Bloomfield, et al. (2011). "Targets downstream of Cdk8 in Dictyostelium development." BMC Dev Biol 11: 2.
	BACKGROUND: Cdk8 is a component of the mediator complex which facilitates transcription by RNA polymerase II and has been shown to play an important role in development of Dictyostelium discoideum. This eukaryote feeds as single cells but starvation triggers the formation of a multicellular organism in response to extracellular pulses of cAMP and the eventual generation of spores. Strains in which the gene encoding Cdk8 have been disrupted fail to form multicellular aggregates unless supplied with exogenous pulses of cAMP and later in development, cdk8- cells show a defect in spore production. RESULTS: Microarray analysis revealed that the cdk8- strain previously described (cdk8-HL) contained genome duplications. Regeneration of the strain in a background lacking detectable gene duplication generated strains (cdk8-2) with identical defects in growth and early development, but a milder defect in spore generation, suggesting that the severity of this defect depends on the genetic background. The failure of cdk8- cells to aggregate unless rescued by exogenous pulses of cAMP is consistent with a failure to express the catalytic subunit of protein kinase A. However, overexpression of the gene encoding this protein was not sufficient to rescue the defect, suggesting that this is not the only important target for Cdk8 at this stage of development. Proteomic analysis revealed two potential targets for Cdk8 regulation, one regulated post-transcriptionally (4-hydroxyphenylpyruvate dioxygenase (HPD)) and one transcriptionally (short chain dehydrogenase/reductase (SDR1)). CONCLUSIONS: This analysis has confirmed the importance of Cdk8 at multiple stages of Dictyostelium development, although the severity of the defect in spore production depends on the genetic background. Potential targets of Cdk8-mediated gene regulation have been identified in Dictyostelium which will allow the mechanism of Cdk8 action and its role in development to be determined.

Hadwiger, J. A. and H. N. Nguyen (2011). "MAPKs in development: insights from Dictyostelium signaling pathways." Biomol Concepts 2(1-2): 39-46.
	Mitogen activated protein kinases (MAPKs) play important roles in the development of eukaryotic organisms through the regulation of signal transduction pathways stimulated by external signals. MAPK signaling pathways have been associated with the regulation of cell growth, differentiation, and chemotaxis, indicating MAPKs contribute to a diverse set of developmental processes. In most eukaryotes, the diversity of external signals is likely to far exceed the diversity of MAPKs, suggesting that multiple signaling pathways might share MAPKs. Do different signaling pathways converge before MAPK function or can MAPKs maintain signaling specificity through interactions with specific proteins? The genetic and biochemical analysis of MAPK pathways in simple eukaryotes such as Dictyostelium offers opportunities to investigate functional specificity of MAPKs in G protein-mediated signal transduction pathways. This review considers the regulation and specificity of MAPK function in pathways that control Dictyostelium growth and development.

Harwood, A. J. (2011). "Prolyl oligopeptidase, inositol phosphate signalling and lithium sensitivity." CNS Neurol Disord Drug Targets 10(3): 333-339.
	Inhibition of prolyl oligopeptidase (PO) elevates inositol phosphate (IP) signalling and reduces cell sensitivity to lithium (Li+). This review discusses recent evidence that shows PO acts via the multiple inositol polyphosphate phosphatase (MIPP) to regulate gene expression. As a consequence, PO inhibition causes both a transient, rapid increase in I(1,4,5)P(3) and a long-term elevation of IP signalling. This pathway is evolutionary conserved, being present in both the social amoeba Dictyostelium and human cell systems, and has potential implications for mental health.

Hasselbring, B. M., M. K. Patel, et al. (2011). "Dictyostelium discoideum as a model system for identification of Burkholderia pseudomallei virulence factors." Infect Immun 79(5): 2079-2088.
	Burkholderia pseudomallei is an emerging bacterial pathogen and category B biothreat. Human infections with B. pseudomallei (called melioidosis) present as a range of manifestations, including acute septicemia and pneumonia. Although melioidosis can be fatal, little is known about the molecular basis of B. pseudomallei pathogenicity, in part because of the lack of simple, genetically tractable eukaryotic models to facilitate en masse identification of virulence determinants or explore host-pathogen interactions. Two assays, one high-throughput and one quantitative, were developed to monitor levels of resistance of B. pseudomallei and the closely related nearly avirulent species Burkholderia thailandensis to predation by the phagocytic amoeba Dictyostelium discoideum. The quantitative assay showed that levels of resistance to, and survival within, amoeba by these bacteria and their known virulence mutants correlate well with their published levels of virulence in animals. Using the high-throughput assay, we screened a 1,500-member B. thailandensis transposon mutant library and identified 13 genes involved in resistance to predation by D. discoideum. Orthologs of these genes were disrupted in B. pseudomallei, and nearly all mutants had similarly decreased resistance to predation by D. discoideum. For some mutants, decreased resistance also correlated with reduced survival in and cytotoxicity toward macrophages, as well as attenuated virulence in mice. These observations suggest that some factors required by B. pseudomallei for resistance to environmental phagocytes also aid in resistance to phagocytic immune cells and contribute to disease in animals. Thus, D. discoideum provides a novel, high-throughput model system for facilitating inquiry into B. pseudomallei virulence.

Hecht, I., M. L. Skoge, et al. (2011). "Activated membrane patches guide chemotactic cell motility." PLoS Comput Biol 7(6): e1002044.
	Many eukaryotic cells are able to crawl on surfaces and guide their motility based on environmental cues. These cues are interpreted by signaling systems which couple to cell mechanics; indeed membrane protrusions in crawling cells are often accompanied by activated membrane patches, which are localized areas of increased concentration of one or more signaling components. To determine how these patches are related to cell motion, we examine the spatial localization of RasGTP in chemotaxing Dictyostelium discoideum cells under conditions where the vertical extent of the cell was restricted. Quantitative analyses of the data reveal a high degree of spatial correlation between patches of activated Ras and membrane protrusions. Based on these findings, we formulate a model for amoeboid cell motion that consists of two coupled modules. The first module utilizes a recently developed two-component reaction diffusion model that generates transient and localized areas of elevated concentration of one of the components along the membrane. The activated patches determine the location of membrane protrusions (and overall cell motion) that are computed in the second module, which also takes into account the cortical tension and the availability of protrusion resources. We show that our model is able to produce realistic amoeboid-like motion and that our numerical results are consistent with experimentally observed pseudopod dynamics. Specifically, we show that the commonly observed splitting of pseudopods can result directly from the dynamics of the signaling patches.

Heidel, A. J., H. M. Lawal, et al. (2011). "Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication." Genome Res 21(11): 1882-1891.
	Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced the genomes of Dictyostelium fasciculatum (DF) and Polysphondylium pallidum (PP), which represent the early diverging groups 1 and 2, respectively. In contrast to DD, PP and DF have conventional telomere organization and strongly reduced numbers of transposable elements. The number of protein-coding genes is similar between species, but only half of them comprise an identifiable set of orthologous genes. In general, genes involved in primary metabolism, cytoskeletal functions and signal transduction are conserved, while genes involved in secondary metabolism, export, and signal perception underwent large differential gene family expansions. This most likely signifies involvement of the conserved set in core cell and developmental mechanisms, and of the diverged set in niche- and species-specific adaptations for defense and food, mate, and kin selection. Phylogenetic dating using a concatenated data set and extensive loss of synteny indicate that DF, PP, and DD split from their last common ancestor at least 0.6 billion years ago.

Hilbi, H., S. Weber, et al. (2011). "Anchors for effectors: subversion of phosphoinositide lipids by legionella." Front Microbiol 2: 91.
	The facultative intracellular pathogen Legionella pneumophila replicates in free-living amoebae and macrophages within a distinct compartment, the "Legionella-containing vacuole" (LCV). LCV formation involves phosphoinositide (PI) glycerolipids, which are key factors controlling vesicle trafficking pathways and membrane dynamics of eukaryotic cells. To govern the interactions with host cells, L. pneumophila employs the Icm/Dot type IV secretion system and more than 250 translocated "effector proteins" that presumably subvert host signaling and vesicle trafficking pathways. Some of the effector proteins anchor through distinct PIs to the cytosolic face of LCVs and promote the interaction with host vesicles and organelles, catalyze guanine nucleotide exchange of small GTPases, or bind to PI-metabolizing enzymes, such as OCRL1. The PI 5-phosphatase OCRL1 and its Dictyostelium homologue Dd5P4 restrict intracellular growth of L. pneumophila. Moreover, OCRL1/Dd5P4, PI 3-kinases (PI3Ks), and PI4KIIIbeta regulate LCV formation and localization of the effector protein SidC, which selectively decorates the LCV membrane. SidC and its 20-kDa "P4C" fragment are robust and specific probes for phosphatidylinositol-4-phosphate, and SidC can be targeted to purify intact LCVs by immuno-magnetic separation. Taken together, bacterial PI-binding effectors as well as host PIs and PI-modulating enzymes play a pivotal role for intracellular replication of L. pneumophila, and the PI-binding effectors are valuable tools for the analysis of eukaryotic PI lipids.

Hirose, S., R. Benabentos, et al. (2011). "Self-recognition in social amoebae is mediated by allelic pairs of tiger genes." Science 333(6041): 467-470.
	Free-living cells of the social amoebae Dictyostelium discoideum can aggregate and develop into multicellular fruiting bodies in which many die altruistically as they become stalk cells that support the surviving spores. Dictyostelium cells exhibit kin discrimination--a potential defense against cheaters, which sporulate without contributing to the stalk. Kin discrimination depends on strain relatedness, and the polymorphic genes tgrB1 and tgrC1 are potential components of that mechanism. Here, we demonstrate a direct role for these genes in kin discrimination. We show that a matching pair of tgrB1 and tgrC1 alleles is necessary and sufficient for attractive self-recognition, which is mediated by differential cell-cell adhesion. We propose that TgrB1 and TgrC1 proteins mediate this adhesion through direct binding. This system is a genetically tractable ancient model of eukaryotic self-recognition.

Hofer, B., B. Povaz ay, et al. (2011). "Artefact reduction for cell migration visualization using spectral domain optical coherence tomography." J Biophotonics.
	Visualization of cell migration during chemotaxis using spectral domain optical coherence tomography (OCT) requires non-standard processing techniques. Stripe artefacts and camera noise floor present in OCT data prevent detailed computer-assisted reconstruction and quantification of cell locomotion. Furthermore, imaging artefacts lead to unreliable results in automated texture based cell analysis.Here we characterize three pronounced artefacts that become visible when imaging sample structures with high dynamic range, e.g. cultured cells: (i) time-varying fixed-pattern noise; (ii) stripe artefacts generated by background estimation using tomogram averaging; (iii) image modulations due to spectral shaping. We evaluate techniques to minimize the above mentioned artefacts using an 800 nm optical coherence microscope. Effect of artefact reduction is shown exemplarily on two cell cultures, i.e. Dictyostelium on nitrocellulose substrate, and retinal ganglion cells (RGC-5) cultured on a glass coverslip. Retinal imaging also profits from the proposed processing techniques. ((c) 2011 WILEY-VCH Verlag GmbH &amp; Co. KGaA, Weinheim).

Hofer, B., B. Povazay, et al. (2011). "Artefact reduction for cell migration visualization using spectral domain optical coherence tomography." J Biophotonics 4(5): 355-367.
	Visualization of cell migration during chemotaxis using spectral domain optical coherence tomography (OCT) requires non-standard processing techniques. Stripe artefacts and camera noise floor present in OCT data prevent detailed computer-assisted reconstruction and quantification of cell locomotion. Furthermore, imaging artefacts lead to unreliable results in automated texture based cell analysis. Here we characterize three pronounced artefacts that become visible when imaging sample structures with high dynamic range, e.g. cultured cells: (i) time-varying fixed-pattern noise; (ii) stripe artefacts generated by background estimation using tomogram averaging; (iii) image modulations due to spectral shaping. We evaluate techniques to minimize the above mentioned artefacts using an 800 nm optical coherence microscope. Effect of artefact reduction is shown exemplarily on two cell cultures, i.e. Dictyostelium on nitrocellulose substrate, and retinal ganglion cells (RGC-5) cultured on a glass coverslip. Retinal imaging also profits from the proposed processing techniques.

Hsu, D. W., R. Kiely, et al. (2011). "DNA double-strand break repair pathway choice in Dictyostelium." J Cell Sci 124(Pt 10): 1655-1663.
	DNA double-strand breaks (DSBs) can be repaired by homologous recombination (HR) or non-homologous end joining (NHEJ). The mechanisms that govern whether a DSB is repaired by NHEJ or HR remain unclear. Here, we characterise DSB repair in the amoeba Dictyostelium. HR is the principal pathway responsible for resistance to DSBs during vegetative cell growth, a stage of the life cycle when cells are predominantly in G2. However, we illustrate that restriction-enzyme-mediated integration of DNA into the Dictyostelium genome is possible during this stage of the life cycle and that this is mediated by an active NHEJ pathway. We illustrate that Dclre1, a protein with similarity to the vertebrate NHEJ factor Artemis, is required for NHEJ independently of DNA termini complexity. Although vegetative dclre1(-) cells are not radiosensitive, they exhibit delayed DSB repair, further supporting a role for NHEJ during this stage of the life cycle. By contrast, cells lacking the Ku80 component of the Ku heterodimer that binds DNA ends to facilitate NHEJ exhibit no such defect and deletion of ku80 suppresses the DSB repair defect of dclre1(-) cells through increasing HR efficiency. These data illustrate a functional NHEJ pathway in vegetative Dictyostelium and the importance of Ku in regulating DSB repair choice during this phase of the life cycle.

Huang, E., S. Talukder, et al. (2011). "BzpF is a CREB-like transcription factor that regulates spore maturation and stability in Dictyostelium." Dev Biol 358(1): 137-146.
	The cAMP response element-binding protein (CREB) is a highly conserved transcription factor that integrates signaling through the cAMP-dependent protein kinase A (PKA) in many eukaryotes. PKA plays a critical role in Dictyostelium development but no CREB homologue has been identified in this system. Here we show that Dictyostelium utilizes a CREB-like protein, BzpF, to integrate PKA signaling during late development. bzpF(-) mutants produce compromised spores, which are extremely unstable and germination defective. Previously, we have found that BzpF binds the canonical CRE motif in vitro. In this paper, we determined the DNA binding specificity of BzpF using protein binding microarray (PBM) and showed that the motif with the highest specificity is a CRE-like sequence. BzpF is necessary to activate the transcription of at least 15 PKA-regulated, late-developmental target genes whose promoters contain BzpF binding motifs. BzpF is sufficient to activate two of these genes. The comparison of RNA sequencing data between wild type and bzpF(-) mutant revealed that the mutant fails to express 205 genes, many of which encode cellulose-binding and sugar-binding proteins. We propose that BzpF is a CREB-like transcription factor that regulates spore maturation and stability in a PKA-related manner.

Huber, R. and D. H. O'Day (2011). "EGF-like peptide-enhanced cell motility in Dictyostelium functions independently of the cAMP-mediated pathway and requires active Ca2+/calmodulin signaling." Cell Signal 23(4): 731-738.
	Current knowledge suggests that cell movement in the eukaryotic slime mold Dictyostelium discoideum is mediated by different signaling pathways involving a number of redundant components. Our previous research has identified a specific motility-enhancing function for epidermal growth factor-like (EGFL) repeats in Dictyostelium, specifically for the EGFL repeats of cyrA, a matricellular, calmodulin (CaM)-binding protein in Dictyostelium. Using mutants of cAMP signaling (carA(-), carC(-), gpaB(-), gpbA(-)), the endogenous calcium (Ca(2+)) release inhibitor TMB-8, the CaM antagonist W-7, and a radial motility bioassay, we show that DdEGFL1, a synthetic peptide whose sequence is obtained from the first EGFL repeat of cyrA, functions independently of the cAMP-mediated signaling pathways to enhance cell motility through a mechanism involving Ca(2+) signaling, CaM, and RasG. We show that DdEGFL1 increases the amounts of polymeric myosin II heavy chain and actin in the cytoskeleton by 24.1+/-10.7% and 25.9+/-2.1% respectively and demonstrate a link between Ca(2+)/CaM signaling and cytoskeletal dynamics. Finally, our findings suggest that carA and carC mediate a brake mechanism during chemotaxis since DdEGFL1 enhanced the movement of carA(-)/carC(-) cells by 844+/-136% compared to only 106+/-6% for parental DH1 cells. Based on our data, this signaling pathway also appears to involve the G-protein beta subunit, RasC, RasGEFA, and protein kinase B. Together, our research provides insight into the functionality of EGFL repeats in Dictyostelium and the signaling pathways regulating cell movement in this model organism. It also identifies several mechanistic components of DdEGFL1-enhanced cell movement, which may ultimately provide a model system for understanding EGFL repeat function in higher organisms.

Huber, R. J. and D. H. O'Day (2011). "Nucleocytoplasmic transfer of cyclin dependent kinase 5 and its binding to puromycin-sensitive aminopeptidase in Dictyostelium discoideum." Histochem Cell Biol 136(2): 177-189.
	The Dictyostelium discoideum homolog of mammalian cyclin dependent kinase 5 (Cdk5) has previously been shown to be required for optimal growth and differentiation in this model organism, however, the subcellular localization of the protein has not previously been studied. In this study, immunolocalizations and a GFP fusion construct localized Cdk5 predominantly to the nucleus of vegetative cells. Western blots showed that Cdk5 was present in both nuclear and non-nuclear fractions, suggesting a functional role in both cellular locales. During the early stages of mitosis, Cdk5 gradually moved from a punctate nucleoplasmic distribution to localize adjacent to the inner nuclear envelope. During anaphase and telophase, Cdk5 localized to the cytoplasm and was not detected in the nucleoplasm. Cdk5 returned to the nucleus during cytokinesis. Proteolytic activity has been shown to be a critical regulator of the cell cycle. Immunoprecipitations coupled with immunolocalizations identified puromycin-sensitive aminopeptidase A (PsaA) as a potential Cdk5 binding partner in Dictyostelium. Immunoprecipitations also identified two phosphotyrosine proteins (35 and 18 kDa) that may interact with Cdk5 in vivo. Together, this work provides new insight into the localization of Cdk5, its function during cell division, and its binding to a proteolytic enzyme in Dictyostelium.

Jang, W. and R. H. Gomer (2011). "Initial cell type choice in Dictyostelium." Eukaryot Cell 10(2): 150-155.
	Much remains to be understood about how a group of cells break symmetry and differentiate into distinct cell types. The simple eukaryote Dictyostelium discoideum is an excellent model system for studying questions such as cell type differentiation. Dictyostelium cells grow as single cells. When the cells starve, they aggregate to develop into a multicellular structure with only two main cell types: spore and stalk. There has been a longstanding controversy as to how a cell makes the initial choice of becoming a spore or stalk cell. In this review, we describe how the controversy arose and how a consensus developed around a model in which initial cell type choice in Dictyostelium is dependent on the cell cycle phase that a cell happens to be in at the time that it starves.

Jin, T. (2011). "GPCR-controlled chemotaxis in Dictyostelium discoideum." Wiley Interdiscip Rev Syst Biol Med 3(6): 717-727.
	Dictyostelium discoideum has been chosen as the key model organism for the study of eukaryotic chemotaxis. Studies in this lower eukaryotic organism have allowed us to discover eukaryotic chemotaxis behavior and to gradually understand the mechanism of chemotaxis. Investigations in this simple organism often guide the direction of chemotaxis studies in areas such as forming concepts, discovering molecular components, revealing pathways and networks. The cooperation between experimental approaches and computational modeling has helped us to comprehend the signaling network as a system. To further reveal the relationships among the molecular mechanisms of individual signaling steps, a continuous interplay between model development and refinement and experimental testing and verification will be useful. This article focuses on a chemoattractant G-protein-coupled receptor (GPCR)/G-protein gradient sensing machinery, which is monitored by PIP(3) responses and investigated by the interplay between live cell imaging experiments and computational modeling. We believe that such an approach will lead to a much better understanding of GPCR-controlled chemotaxis of all eukaryotic cells.

Kalla, S. E., D. C. Queller, et al. (2011). "Kin discrimination and possible cryptic species in the social amoeba Polysphondylium violaceum." BMC Evol Biol 11: 31.
	BACKGROUND: The genetic diversity of many protists is unknown. The differences that result from this diversity can be important in interactions among individuals. The social amoeba Polysphondylium violaceum, which is a member of the Dictyostelia, has a social stage where individual amoebae aggregate together to form a multicellular fruiting body with dead stalk cells and live spores. Individuals can either cooperate with amoebae from the same clone, or sort to form clonal fruiting bodies. In this study we look at genetic diversity in P. violaceum and at how this diversity impacts social behavior. RESULTS: The phylogeny of the ribosomal DNA sequence (17S to 5.8S region) shows that P. violaceum is made up of at least two groups. Mating compatibility is more common between clones from the same phylogenetic group, though matings between clones from different phylogenetic groups sometimes occurred. P. violaceum clones are more likely to form clonal fruiting bodies when they are mixed with clones from a different group than when they are mixed with a clone of the same group. CONCLUSION: Both the phylogenetic and mating analyses suggest the possibility of cryptic species in P. violaceum. The level of divergence found within P. violaceum is comparable to the divergence between sibling species in other dictyostelids. Both major groups A/B and C/D/E/F show kin discrimination, which elevates relatedness within fruiting bodies but not to the level of clonality. The diminished cooperation in mixes between groups suggests that the level of genetic variation between individuals influences the extent of their cooperation.

Kamino, K., K. Fujimoto, et al. (2011). "Collective oscillations in developing cells: insights from simple systems." Dev Growth Differ 53(4): 503-517.
	From hormonal secretion to gene expression, multicellular dynamics are rich in oscillatory regulation. When organized in space and time, periodic cell-cell signaling can give rise to long-range coordination of gene expression and cell movement in tissues. Lack of synchrony of the oscillations on the other hand can serve as a source of initial divergence of cell fate in stem cells. How properties of individual cells can account for collective rhythmic behaviors at the tissue level remains elusive in most cases. Recently, studies in chemical reactions, synthetic gene circuits, yeast and social amoeba Dictyostelium have greatly enhanced our view of collective oscillations in cell populations. From these relatively simple systems, a unified view of how excitable and oscillatory regulations could be tuned and coupled to give rise to tissue-level oscillations is emerging. The review focuses on recent progress in cyclic adenosine monophosphate oscillations in Dictyostelium and highlights similarities and differences with other systems. We will see that the autonomy of single-cell level oscillations and different ways in which cells are coupled influence how group-level information can be encoded in collective oscillations.

Kastner, P. M., M. Schleicher, et al. (2011). "The NDR family kinase NdrA of Dictyostelium localizes to the centrosome and is required for efficient phagocytosis." Traffic 12(3): 301-312.
	Dictyostelium discoideum cells are professional phagocytes that provide an easily accessible system to gain insights into the mechanisms and the regulatory machinery controlling phagocytosis. Here, we describe a novel function for nuclear Dbf2-related (NDR) family kinases in phagocytosis of D. discoideum. Deletion of one of the four NDR kinases of D. discoideum, NdrA, resulted in impaired cell growth caused by reduced phagocytosis rates. Detailed analysis of NdrA-null cells revealed that the formation of phagocytic cups was delayed. Microscopic investigations showed that NdrA localizes to centrosomes, and NdrA was also identified in isolated centrosome preparations. The localization of NdrA is regulated during the cell cycle. In prophase, NdrA disappears from the centrosome and forms a cloud-like structure around the spindle, which is totally absent during later stages until completion of mitosis. Our results suggest that a signal which originates from the NdrA kinase at the centrosome affects the efficiency of phagocytosis. We assume that in NdrA-null cells the defects in phagocytosis may be caused by an impairment of vesicle trafficking, which is involved in providing new membrane at the sites of particle uptake.

Kawata, T. (2011). "STAT signaling in Dictyostelium development." Dev Growth Differ 53(4): 548-557.
	Signal transducers and activators of transcription (STAT) proteins are one of the important mediators of phosphotyrosine-regulated signaling in metazoan cells. These proteins are components of JAK/STAT signal transduction pathways, which regulate immune responses, cell fate, proliferation, cell migration, and programmed cell death in multicellular organisms. The cellular slime mould, Dictyostelium discoideum, is the simplest multicellular organism using molecules homologous to STATs, Dd-STATa-d. The Dd-STATa null mutant displays delayed aggregation, no phototaxis and fails culmination. Here, the functions of Dictyostelium STATs during development and their associated signaling molecules are discussed.

Kawata, T., T. Hirano, et al. (2011). "Evidence for a functional link between Dd-STATa and Dd-PIAS, a Dictyostelium PIAS homologue." Dev Growth Differ 53(7): 897-909.
	Several mammalian protein families inhibit the activity of signal transducer and activator of transcription (STAT) proteins. The protein inhibitor of activated STAT (PIAS) was initially identified through its ability to interact with human STAT proteins. We isolated a gene (pisA) encoding a Dictyostelium orthologue of PIAS, Dd-PIAS, which possesses almost all the representative motifs and domains of mammalian PIAS proteins. A Dd-PIAS null mutant strain displays a normal terminal morphology but with accelerated development once cells are aggregated. In contrast, Dd-PIAS overexpressor strains demonstrate delayed aggregation, almost no slug phototaxis, impaired slug motility, and a prolonged slug migration period. This strain is a near phenocopy of the Dd-STATa null mutant, although it eventually forms a fruiting body, albeit inefficiently. The expression of several Dd-STATa-activated genes is upregulated in the Dd-PIAS null mutant and there is ectopic expression of pstAB makers. The concentration of a PIAS-green fluorescent protein (GFP) fusion protein, expressed under the PIAS promoter, is greatest in the pstO cells and gradually decreases with proximity to the tip of the slug and culminant: a pattern diametrically opposite to that of Dd-STATa. Our results suggest a functional interrelationship between Dd-PIAS and Dd-STATa that influences gene expression and development.

Kihara, K., K. Mori, et al. (2011). "Probabilistic transition from unstable predator-prey interaction to stable coexistence of Dictyostelium discoideum and Escherichia coli." Biosystems 103(3): 342-347.
	Predator-prey interactions have been found at all levels within ecosystems. Despite their ecological ubiquity and importance, the process of transition to a stable coexistent state has been poorly verified experimentally. To investigate the stabilization process of predator-prey interactions, we previously constructed a reproducible experimental predator-prey system between Dictyostelium discoideum and Escherichia coli, and showed that the phenotypically changed E. coli contributed to stabilization of the system. In the present study, we focused on the transition to stable coexistence of both species after the phenotypic change in E. coli. Analysis of E. coli cells isolated from co-culture plates as single colony enabled us to readily identify the appearance of phenotypically changed E. coli that differed in colony morphology and growth rate. It was also demonstrated that two types of viscous colony, i.e., the dense-type and sparse-type, differing in spatial distribution of both species emerged probabilistically and all of the viscous colonies maintained stably were of the sparse-type. These results suggest that the phenotypically changed E. coli may produce two types of viscous colonies probabilistically. The difference in spatial distribution would affect localized interactions between both species and then cause probabilistic stabilization of predator-prey interactions.

Kim, D. N., C. T. Nguyen, et al. (2011). "Conformational dynamics of supramolecular protein assemblies." J Struct Biol 173(2): 261-270.
	Supramolecular protein assemblies including molecular motors, cytoskeletal filaments, chaperones, and ribosomes play a central role in a broad array of cellular functions ranging from cell division and motility to RNA and protein synthesis and folding. Single-particle reconstructions of such assemblies have been growing rapidly in recent years, providing increasingly high resolution structural information under native conditions. While the static structure of these assemblies provides essential insight into their mechanism of biological function, their dynamical motions provide additional important information that cannot be inferred from structure alone. Here we present an unsupervised computational framework for the analysis of high molecular weight protein assemblies and use it to analyze the conformational dynamics of structures deposited in the Electron Microscopy Data Bank. Protein assemblies are modeled using a recently introduced coarse-grained modeling framework based on the finite element method, which is used to compute equilibrium thermal fluctuations, elastic strain energy distributions associated with specific conformational transitions, and dynamical correlations in distant molecular domains. Results are presented in detail for the ribosome-bound termination factor RF2 from Escherichia coli, the nuclear pore complex from Dictyostelium discoideum, and the chaperonin GroEL from E. coli. Elastic strain energy distributions reveal hinge-regions associated with specific conformational change pathways, and correlations in collective molecular motions reveal dynamical coupling between distant molecular domains that suggest new, as well as confirm existing, allosteric mechanisms. Results are publically available for use in further investigation and interpretation of biological function including cooperative transitions, allosteric communication, and molecular mechanics, as well as in further classification and refinement of electron microscopy based structures.

Kim, H. L., M. B. Park, et al. (2011). "Tetrahydrobiopterin is functionally distinguishable from tetrahydrodictyopterin in Dictyostelium discoideum Ax2." FEBS Lett 585(19): 3047-3051.
	Dictyostelium discoideum Ax2 produces both L-erythro-tetrahydrobiopterin (BH4) and its stereoisomer D-threo-BH4 (DH4). The putative cofactor function of them for phenylalanine hydroxylase (PAH) was investigated through genetic manipulation and quantitative determination of pteridines. In addition to establishing that dihydropteridine reductase (DHPR) and dihydrofolate reductase (DHFR) constitute the regeneration pathway of both BH4 and DH4, the results suggested that BH4 is a preferential cofactor for PAH in vivo, not a secondary product of DH4, which functions mainly as an antioxidant. Our result also demonstrated that PAH may be essential for Dictyostelium growth in nature, and thus it appears that the organism has evolved a strategy to maintain BH4 level via regeneration pathway at the expense of DH4 under oxidative stress conditions.

Kim, J. S., J. H. Seo, et al. (2011). "Homeoprotein Hbx4 represses the expression of the adhesion molecule DdCAD-1 governing cytokinesis and development." FEBS Lett 585(12): 1864-1872.
	We investigated the function of homeodomain-containing protein Hbx4 in Dictyostelium discoideum. Hbx4-overexpressing cells (Hbx4(OE)) displayed defects in growth rate and cytokinesis and showed differences in slug motility and cell-type proportioning from KAx3. Furthermore, the overexpression of Hbx4 inhibited the induction of cadA, which encoded the Ca(2+)-dependent cell adhesion molecule DdCAD-1, despite expression of csaA and gpaB. The electrophoretic mobility shift assay showed that the promoter of cadA contained the Hbx4-binding site. Moreover, constitutively expressed DdCAD-1 in Hbx4(OE) rescued the defects in cytokinesis and development. These results suggest that Hbx4 modulates DdCAD-1-mediated cytokinesis and cell-type proportioning.

Kim, L., J. Brzostowski, et al. (2011). "Combinatorial cell-specific regulation of GSK3 directs cell differentiation and polarity in Dictyostelium." Development 138(3): 421-430.
	In Dictyostelium, the interaction of secreted cAMP with specific cell surface receptors regulates the activation/de-activation of GSK3, which mediates developmental cell patterning. In addition, Dictyostelium cells polarize in response to extracellular cAMP, although a potential role for GSK3 in this pathway has not been investigated. Previously, we had shown that ZAK1 was an activating tyrosine kinase for GSK3 function in Dictyostelium and we now identify ZAK2 as the other tyrosine kinase in the cAMP-activation pathway for GSK3; no additional family members exist. We also now show that tyrosine phosphorylation/activation of GSK3 by ZAK2 and ZAK1 separately regulate GSK3 in distinct differentiated cell populations, and that ZAK2 acts in both autonomous and non-autonomous pathways to regulate these cell-type differentiations. Finally, we demonstrate that efficient polarization of Dictyostelium towards cAMP depends on ZAK1-mediated tyrosine phosphorylation of GSK3. Combinatorial regulation of GSK3 by ZAK kinases in Dictyostelium guides cell polarity, directional cell migration and cell differentiation, pathways that extend the complexity of GSK3 signaling throughout the development of Dictyostelium.

Kim, M. K., H. S. Yim, et al. (2011). "Crystallization and preliminary X-ray crystallographic analysis of the NmrA-like DDB_G0286605 protein from the social amoeba Dictyostelium discoideum." Acta Crystallogr Sect F Struct Biol Cryst Commun 67(Pt 1): 94-97.
	The DDB_G0286605 gene product from Dictyostelium discoideum, an NmrA-like protein that belongs to the short-chain dehydrogenase/reductase family, has been crystallized by the hanging-drop vapour-diffusion method at 295 K. A 1.64 A resolution data set was collected using synchrotron radiation. The DDB_G0286605 protein crystals belonged to space group P2(1), with unit-cell parameters a=67.598, b=54.935, c=84.219 A, beta = 109.620 degrees . Assuming the presence of two molecules in the asymmetric unit, the solvent content was estimated to be about 43.25% with 99% probability. Molecular-replacement trials were attempted with three NmrA-like proteins, NmrA, HSCARG and QOR2, as search models, but failed. This may be a consequence of the low sequence identity between the DDB_G0286605 protein and the search models (DDB_G0286605 has a primary-sequence identity of 28, 32 and 19% to NmrA, HCARG and QOR2, respectively).

Kim, M. K., H. S. Yim, et al. (2011). "Crystallization and preliminary X-ray crystallographic analysis of the short-chain dehydrogenase/reductase-type DDB_G0291732 protein from Dictyostelium discoideum." Acta Crystallogr Sect F Struct Biol Cryst Commun 67(Pt 1): 98-100.
	The DDB_G0291732 gene product from Dictyostelium discoideum, which is a NmrA-like protein that belongs to the short-chain dehydrogenase/reductase superfamily but shows deviations in conserved sequence regions, has been crystallized by the hanging-drop vapour-diffusion method at 295 K. A 1.65 A resolution data set was collected using synchrotron radiation. The crystals of DDB_G0291732 protein belonged to space group P2(1), with unit-cell parameters a=38.5, b=63.7, c=56.0 A, beta=91.7 degrees . Assuming the presence of one molecule in the asymmetric unit, the solvent content was estimated to be about 38.1%.

King, J. S., D. M. Veltman, et al. (2011). "The induction of autophagy by mechanical stress." Autophagy 7(12).
	The ability to respond and adapt to changes in the physical environment is a universal and essential cellular property. Here we demonstrate that cells respond to mechanical compressive stress by rapidly inducing autophagosome formation. We measure this response in both Dictyostelium and mammalian cells, indicating that this is an evolutionarily conserved, general response to mechanical stress. In Dictyostelium, the number of autophagosomes increases 20 fold within 10 minutes of 1kPa pressure being applied and a similar response is seen in mammalian cells after 30 minutes. We show in both cell types that autophagy is highly sensitive to changes in mechanical pressure and the response is graduated, with a half-maximal responses at ~0.2kPa, similar to other mechano-sensitive responses. We further show that the mechanical induction of autophagy is TOR-independent and transient, lasting until the cells adapt to their new environment and recover their shape. The autophagic response is therefore part of an integrated response to mechanical challenge, allowing cells to cope with a continuously changing physical environment.

Klein, J. C., R. J. Moen, et al. (2011). "Structural and functional impact of site-directed methionine oxidation in myosin." Biochemistry 50(47): 10318-10327.
	We have examined the structural and functional effects of site-directed methionine oxidation in Dictyostelium (Dicty) myosin II using mutagenesis, in vitro oxidation, and site-directed spin-labeling for electron paramagnetic resonance (EPR). Protein oxidation by reactive oxygen and nitrogen species is critical for normal cellular function, but oxidative stress has been implicated in disease progression and biological aging. Our goal is to bridge understanding of protein oxidation and muscle dysfunction with molecular-level insights into actomyosin interaction. In order to focus on methionine oxidation and to facilitate site-directed spectroscopy, we started with a Cys-lite version of Dicty myosin II. For Dicty myosin containing native methionines, peroxide treatment decreased actin-activated myosin ATPase activity, consistent with the decline in actomyosin function previously observed in biologically aged or peroxide-treated muscle. Methionine-to-leucine mutations, used to protect specific sites from oxidation, identified a single methionine that is functionally sensitive to oxidation: M394, near the myosin cardiomyopathy loop in the actin-binding interface. Previously characterized myosin labeling sites for spectroscopy in the force-producing region and actin-binding cleft were examined; spin-label mobility and distance measurements in the actin-binding cleft were sensitive to oxidation, but particularly in the presence of actin. Overall secondary structure and thermal stability were unaffected by oxidation. We conclude that the oxidation-induced structural change in myosin includes a redistribution of existing structural states of the actin-binding cleft. These results will be applicable to the many biological and therapeutic contexts in which a detailed understanding of protein oxidation as well as function and structure relationships is sought.

Kon, T., K. Sutoh, et al. (2011). "X-ray structure of a functional full-length dynein motor domain." Nat Struct Mol Biol 18(6): 638-642.
	Dyneins are large microtubule-based motors that power a wide variety of cellular processes. Here we report a 4.5-A X-ray crystallographic analysis of the entire functional motor domain of cytoplasmic dynein with ADP from Dictyostelium discoideum, which has revealed the detailed architecture of the functional units required for motor activity, including the ATP-hydrolyzing ring, the long coiled-coil microtubule-binding stalk and the force-generating rod-like linker. We discovered a Y-shaped protrusion composed of two long coiled coils-the stalk and the newly identified 'strut'. This structure supports our model in which the strut coiled coil actively contributes to communication between the primary ATPase site in the ring and the microtubule-binding site at the tip of the stalk coiled coil. Our work also provides insight into how the two motor domains are arranged and how they interact with each other in a functional dimer form of cytoplasmic dynein.

Korohoda, W., M. Kucia, et al. (2011). "Solute-dependent activation of cell motility in strongly hypertonic solutions in Dictyostelium discoideum, human melanoma HTB-140 cells and walker 256 carcinosarcoma cells." Cell Mol Biol Lett 16(3): 412-430.
	Published data concerning the effects of hypertonicity on cell motility have often been controversial. The interpretation of results often rests on the premise that cell responses result from cell dehydration, i.e. osmotic effects. The results of induced hypertonicity on cell movement of Dictyostelium discoideum amoebae and human melanoma HTB-140 cells reported here show that: i) hypertonic solutions of identical osmolarity will either inhibit or stimulate cell movement depending on specific solutes (Na(+) or K(+), sorbitol or saccharose); ii) inhibition of cell motility by hypertonic solutions containing Na(+) ions or carbohydrates can be reversed by the addition of calcium ions; iii) various cell types react differently to the same solutions, and iv) cells can adapt to hypertonic solutions. Various hypertonic solutions are now broadly used in medicine and to study modulation of gene expression. The observations reported suggest the need to examine whether the other responses of cells to hypertonicity can also be based on the solute-dependent cell responses besides cell dehydration due to the osmotic effects.

Kortholt, A., R. Kataria, et al. (2011). "Dictyostelium chemotaxis: essential Ras activation and accessory signalling pathways for amplification." EMBO Rep 12(12): 1273-1279.
	Central to chemotaxis is the molecular mechanism by which cells exhibit directed movement in shallow gradients of a chemoattractant. We used Dictyostelium mutants to investigate the minimal requirements for chemotaxis, and identified a basal signalling module providing activation of Ras at the leading edge, which is sufficient for chemotaxis. The signalling enzymes PI3K, TorC2, PLA2 and sGC are not required for Ras activation and chemotaxis to folate or to steep gradients of cAMP, but they provide a memory of direction and improved orientation of the cell, which together increase the sensitivity about 150-fold for chemotaxis in shallow cAMP gradients.

Kowal, A. S. and R. L. Chisholm (2011). "Uncovering a role for the tail of the Dictyostelium discoideum SadA protein in cell-substrate adhesion." Eukaryot Cell 10(5): 662-671.
	Previous work from our laboratory showed that the Dictyostelium discoideum SadA protein plays a central role in cell-substrate adhesion. SadA null cells exhibit a loss of adhesion, a disrupted actin cytoskeleton, and a cytokinesis defect. How SadA mediates these phenotypes is unknown. This work addresses the mechanism of SadA function, demonstrating an important role for the C-terminal cytoplasmic tail in SadA function. We found that a SadA tailless mutant was unable to rescue the sadA adhesion deficiency, and overexpression of the SadA tail domain reduced adhesion in wild-type cells. We also show that SadA is closely associated with the actin cytoskeleton. Mutagenesis studies suggested that four serine residues in the tail, S924/S925 and S940/S941, may regulate association of SadA with the actin cytoskeleton. Glutathione S-transferase pull-down assays identified at least one likely interaction partner of the SadA tail, cortexillin I, a known actin bundling protein. Thus, our data demonstrate an important role for the carboxy-terminal cytoplasmic tail in SadA function and strongly suggest that a phosphorylation event in this tail regulates an interaction with cortexillin I. Based on our data, we propose a model for the function of SadA.

Krauss, V. and G. Reuter (2011). "DNA methylation in Drosophila--a critical evaluation." Prog Mol Biol Transl Sci 101: 177-191.
	Drosophila belongs to the so-called "Dnmt2 only" organisms, and does not contain any of the canonical DNA methyltransferases (Dnmt1 and Dnmt3). Furthermore, no functional homologs of known 5-methylcytosine reader proteins are found. Nevertheless, there is strong evidence for DNA methylation in this organism. It has been suggested that DNA methylation in Drosophila is simply a byproduct of Dnmt2, which is a DNA methyltransferase (Dnmt) according to structure and type of catalysis but functions in vivo as a tRNA methyltransferase. However, concerning the very specific timing of cytosine methylation in Drosophila, their suggested functions in control of retrotransposon silencing and genome stability, and the obvious DNA methylation activity of Dnmt2 enzymes in the protozoans Dictyostelium discoideum and Entamoeba histolytica, we tend to disagree with this notation. Dnmt2 probably serves, and not only in Drosophila, as a methyltransferase of both specific DNA and tRNA targets.

Kuwayama, H., H. Kikuchi, et al. (2011). "Artificial compounds differentially control Dictyostelium chemotaxis and cell differentiation." Cell Struct Funct 36(1): 21-26.
	Differentiation-inducing factor-1 and -2 (DIF-1 and DIF-2) are small lipophilic signal molecules that control both cell differentiation and chemotaxis in the cellular slime mold Dictyostelium discoideum. In this study, we examined the effects of four amide derivatives of DIF-1 on stalk cell differentiation and chemotaxis. The DIF derivatives differentially affected cell differentiation and chemotaxis, suggesting the possible existence of at least three receptors for DIFs: one receptor responsible for stalk cell induction, and two receptors responsible for chemotaxis modulation. Furthermore, our results indicate that DIF derivatives can be utilized to analyze the DIF-signaling pathways.

Kuzdzal-Fick, J. J., S. A. Fox, et al. (2011). "High relatedness is necessary and sufficient to maintain multicellularity in Dictyostelium." Science 334(6062): 1548-1551.
	Most complex multicellular organisms develop clonally from a single cell. This should limit conflicts between cell lineages that could threaten the extensive cooperation of cells within multicellular bodies. Cellular composition can be manipulated in the social amoeba Dictyostelium discoideum, which allows us to test and confirm the two key predictions of this theory. Experimental evolution at low relatedness favored cheating mutants that could destroy multicellular development. However, under high relatedness, the forces of mutation and within-individual selection are too small for these destructive cheaters to spread, as shown by a mutation accumulation experiment. Thus, we conclude that the single-cell bottleneck is a powerful stabilizer of cellular cooperation in multicellular organisms.

Lahr, D. J., T. B. Nguyen, et al. (2011). "Evolution of the actin gene family in testate lobose amoebae (Arcellinida) is characterized by two distinct clades of paralogs and recent independent expansions." Mol Biol Evol 28(1): 223-236.
	The evolution of actin gene families is characterized by independent expansions and contractions across the eukaryotic tree of life. Here, we assess diversity of actin gene sequences within three lineages of the genus Arcella, a free-living testate (shelled) amoeba in the Arcellinida. We established four clonal lines of two morphospecies, Arcella hemisphaerica and A. vulgaris, and assessed their phylogenetic relationship within the "Amoebozoa" using small subunit ribosomal DNA (SSU-rDNA) genealogy. We determined that the two lines of A. hemisphaerica are identical in SSU-rDNA, while the two A. vulgaris are independent genetic lineages. Furthermore, we characterized multiple actin gene copies from all lineages. Analyses of the resulting sequences reveal numerous diverse actin genes, which differ mostly by synonymous substitutions. We estimate that the actin gene family contains 40-50 paralogous members in each lineage. None of the three independent lineages share the same paralog with another, and divergence between actins reaches 29% in contrast to just 2% in SSU-rDNA. Analyses of effective number of codons (ENC), compositional bias, recombination signatures, and genetic diversity in the context of a gene tree indicate that there are two groups of actins evolving with distinct patterns of molecular evolution. Within these groups, there have been multiple independent expansions of actin genes within each lineage. Together, these data suggest that the two groups are located in different regions of the Arcella genome. Furthermore, we compare the Arcella actin gene family with the relatively well-described gene family in the slime mold Dictyostelium discoideum and other members of the Amoebozoa clade. Overall patterns of molecular evolution are similar in Arcella and Dictyostelium. However, the separation of genes in two distinct groups coupled with recent expansion is characteristic of Arcella and might reflect an unusual pattern of gene family evolution in the lobose testate amoebae. We provide a model to account for both the existence of two distinct groups and the pattern of recent independent expansion leading to a large number of actins in each lineage.

Lelong, E., A. Marchetti, et al. (2011). "Role of magnesium and a phagosomal P-type ATPase in intracellular bacterial killing." Cell Microbiol 13(2): 246-258.
	Bacterial ingestion and killing by phagocytic cells are essential processes to protect the human body from infectious microorganisms. However, only few proteins implicated in intracellular bacterial killing have been identified to date. We used Dictyostelium discoideum, a phagocytic bacterial predator, to study intracellular killing. In a random genetic screen we identified Kil2, a type V P-ATPase as an essential element for efficient intracellular killing of Klebsiella pneumoniae bacteria. Interestingly, kil2 knockout cells still killed efficiently several other species of bacteria, and did not show enhanced susceptibility to Mycobacterium marinum intracellular replication. Kil2 is present in the phagosomal membrane, and its structure suggests that it pumps cations into the phagosomal lumen. The killing defect of kil2 knockout cells was rescued by the addition of magnesium ions, suggesting that Kil2 may function as a magnesium pump. In agreement with this, kil2 mutant cells exhibited a specific defect for growth at high concentrations of magnesium. Phagosomal protease activity was lower in kil2 mutant cells than in wild-type cells, a phenotype reversed by the addition of magnesium to the medium. Kil2 may act as a magnesium pump maintaining magnesium concentration in phagosomes, thus ensuring optimal activity of phagosomal proteases and efficient killing of bacteria.

Lelong, E., A. Marchetti, et al. (2011). "Evolution of Pseudomonas aeruginosa virulence in infected patients revealed in a Dictyostelium discoideum host model." Clin Microbiol Infect 17(9): 1415-1420.
	Pseudomonas aeruginosa can cause acute lung infections in intubated patients or chronic infections in patients with cystic fibrosis (CF). In both situations, P. aeruginosa accumulates specific mutations, in particular in the lasR quorum-sensing regulator gene. Using a Dictyostelium discoideum amoeba model, we assessed whether these mutations affect bacterial virulence. Among a collection of clinical isolates from 16 CF patients, initial isolates were fully virulent in 15 patients, but for late isolates collected several years later, virulence was decreased in eight patients. No significant correlation between genetic inactivation of lasR and decreased virulence was observed. Among strains isolated from ten colonized intubated patients, all initial isolates were fully virulent. Despite the accumulation of lasR-inactivating mutations in strains collected over a 3-week period, no decrease in virulence was observed in eight of 10 patients. In one intubated patient, the virulent initial strain was replaced a few days later with a different, less virulent, strain. We observed a gradual decrease in bacterial virulence in only one intubated patient. We conclude that adaptation of P. aeruginosa to chronically infected CF patients can lead to a slow and gradual loss of virulence, as measured in a Dictyostelium model system. However, loss of virulence is not caused predominantly by mutations in lasR. During short-term colonization of intubated patients for up to 20 days, a decrease in virulence was exceptional, despite the accumulation of lasR mutations.

Li, L., E. C. Cox, et al. (2011). "'Dicty dynamics': Dictyostelium motility as persistent random motion." Phys Biol 8(4): 046006.
	We model the motility of Dictyostelium cells in a systematic data-driven manner. We deduce a minimal dynamical model that reproduces the statistical features of experimental trajectories. These are trajectories of the centroid of the cell perimeter, which is more sensitive to pseudopod activity than the usual tracking by centroid or nucleus. Our data account for cell individuality and dictate a model that extends the cell-type specific models recently derived for mammalian cells. Two generalized Langevin equations model stochastic periodic pseudopod motion parallel and orthogonal to the amoeba's direction of motion. This motion propels the amoeba with a random periodic left-right waddle in a direction that has a long persistence time. The model fully accounts for the statistics of the experimental trajectories, including velocity power spectra and auto-correlations, non-Gaussian velocity distributions, and multiplicative noise. Thus, we find neither need nor place in our data for an interpretation in terms of anomalous diffusion. The model faithfully captures cell individuality as different parameter values in the model, and serves as a basis for integrating the local mechanics of cell motion with our observed long-term behavior.

Li, S. I. and M. D. Purugganan (2011). "The cooperative amoeba: Dictyostelium as a model for social evolution." Trends Genet 27(2): 48-54.
	Social interactions, including cooperation and altruism, are characteristic of numerous species, but many aspects of the evolution, ecology and genetics of social behavior remain unclear. The microbial soil amoeba Dictyostelium discoideum is a model system for the study of social evolution and provides insights into the nature of social cooperation and its genetic basis. This species exhibits altruism during both asexual and sexual cycles of its life history, and recent studies have uncovered several possible genetic mechanisms associated with kin discrimination and cheating behavior during asexual fruiting-body formation. By contrast, the molecular and evolutionary mechanisms that underlie sexual macrocyst formation remain largely enigmatic. D. discoideum, given its utility in molecular genetic studies, should continue to help us address these and other relevant questions in sociobiology, and thereby contribute to a coherent theoretical framework for the nature of social cooperation.

Lienard, J., A. Croxatto, et al. (2011). "Estrella lausannensis, a new star in the Chlamydiales order." Microbes Infect 13(14-15): 1232-1241.
	Originally, the Chlamydiales order was represented by a single family, the Chlamydiaceae, composed of several pathogens, such as Chlamydia trachomatis, Chlamydia pneumoniae, Chlamydia psittaci and Chlamydia abortus. Recently, 6 new families of Chlamydia-related bacteria have been added to the Chlamydiales order. Most of these obligate intracellular bacteria are able to replicate in free-living amoebae. Amoebal co-culture may be used to selectively isolate amoeba-resisting bacteria. This method allowed in a previous work to discover strain CRIB 30, from an environmental water sample. Based on its 16S rRNA gene sequence similarity with Criblamydia sequanensis, strain CRIB 30 was considered as a new member of the Criblamydiaceae family. In the present work, phylogenetic analyses of the genes gyrA, gyrB, rpoA, rpoB, secY, topA and 23S rRNA as well as MALDI-TOF MS confirmed the taxonomic classification of strain CRIB 30. Morphological examination revealed peculiar star-shaped elementary bodies (EBs) similar to those of C. sequanensis. Therefore, this new strain was called "Estrella lausannensis". Finally, E. lausannensis showed a large amoebal host range and a very efficient replication rate in Acanthamoeba species. Furthermore, E. lausannensis is the first member of the Chlamydiales order to grow successfully in the genetically tractable Dictyostelium discoideum, which opens new perspectives in the study of chlamydial biology.

Lima, W. C., E. Lelong, et al. (2011). "What can Dictyostelium bring to the study of Pseudomonas infections?" Semin Cell Dev Biol 22(1): 77-81.
	Bacterial infections are complex events. They are studied in a variety of simple model systems, using mammalian or non-mammalian hosts, all of which fail to reproduce fully the situation in infected patients. Each model presents a combination of conceptual, practical, and ethical advantages and disadvantages. In this review, we detail the use of Dictyostelium discoideum amoebae as a model to study Pseudomonas aeruginosa. More specifically, our aim is to explore what this additional model system can bring to our understanding of Pseudomonas infections. The study of interactions between Dictyostelium amoebae and Pseudomonas provides a view of the selection pressures exerted by environmental predators on Pseudomonas. It also represents a unique system to assess the virulence of very large numbers of Pseudomonas strains.

Linkner, J., G. Witte, et al. (2011). "High-resolution X-ray structure of the trimeric Scar/WAVE-complex precursor Brk1." PLoS One 6(6): e21327.
	The Scar/WAVE-complex links upstream Rho-GTPase signaling to the activation of the conserved Arp2/3-complex. Scar/WAVE-induced and Arp2/3-complex-mediated actin nucleation is crucial for actin assembly in protruding lamellipodia to drive cell migration. The heteropentameric Scar/WAVE-complex is composed of Scar/WAVE, Abi, Nap, Pir and a small polypeptide Brk1/HSPC300, and recent work suggested that free Brk1 serves as a homooligomeric precursor in the assembly of this complex. Here we characterized the Brk1 trimer from Dictyostelium by analytical ultracentrifugation and gelfiltration. We show for the first time its dissociation at concentrations in the nanomolar range as well as an exchange of subunits within different DdBrk1 containing complexes. Moreover, we determined the three-dimensional structure of DdBrk1 at 1.5 A resolution by X-ray crystallography. Three chains of DdBrk1 are associated with each other forming a parallel triple coiled-coil bundle. Notably, this structure is highly similar to the heterotrimeric alpha-helical bundle of HSPC300/WAVE1/Abi2 within the human Scar/WAVE-complex. This finding, together with the fact that Brk1 is collectively sandwiched by the remaining subunits and also constitutes the main subunit connecting the triple-coil domain of the HSPC300/WAVE1/Abi2/ heterotrimer to Sra1(Pir1), implies a critical function of this subunit in the assembly process of the entire Scar/WAVE-complex.

Liu, P. and Y. Li (2011). "New species and new records of dictyostelids from Ukraine." Mycologia 103(3): 641-645.
	Three species of dictyostelid cellular slime molds were isolated from forest soil, meadow soil and leaf litter collected from Yalta, Crimea, Ukraine. Dictyostelium globisporum is new to science; D. crassicaule and D. sphaerocephalum are new records from Ukraine. Descriptions and illustrations are given based on the Ukraine specimens.

Loomis, W. F. and G. Shaulsky (2011). "Developmental changes in transcriptional profiles." Dev Growth Differ 53(4): 567-575.
	Recent advances in quantitation of mRNA by hybridization to microarrayed gene sequences or by deep sequencing of cDNA (RNA-seq) have provided global views of the abundance of each transcript. Analyses of RNA samples taken at 2 or 4 h intervals throughout development of Dictyostelium discoideum have defined the developmental changes in transcriptional profiles. Comparisons of the transcriptome of wild-type cells to that of mutant strains lacking a gene critical to progression through the developmental stages have defined key steps in the progression. The transcriptional response to cAMP pulses depends on the expression of pulse-independent genes that have been identified by transcriptional profiling with microarrays. Similar techniques were used to discover that the DNA binding protein GBF functions in a feed-forward loop to regulate post-aggregation genes and that expression of a set of late genes during culmination is dependent on the DNA binding protein SrfA. RNA-seq is able to reliably measure individual mRNAs present as a single copy per cell as well as mRNAs present at a thousand fold higher abundance. Using this technique it was found that 65% of the genes in Dictyostelium change twofold or more during development. Many decrease during the first 8 h of development, while the rest increase at specific stages and this pattern is evolutionarily conserved as found by comparing the transcriptomes of D. discoideum and Dictyostelium purpureum. The transcriptional profile of each gene is readily available at dictyBase and more sophisticated analyses are available on DictyExpress.

Luciani, M. F., C. Giusti, et al. (2011). "Atg1 allows second-signaled autophagic cell death in Dictyostelium." Autophagy 7(5): 501-508.
	We investigated the role of Atg1 in autophagic cell death (ACD) in a Dictyostelium monolayer model. The model is especially propitious, not only because of genetic tractability and absence of apoptosis machinery, but also because induction of ACD requires two successive exogenous signals, first the combination of starvation and cAMP, second the differentiation factor DIF-1. This enables one to analyze separately first-signal-induced autophagy and subsequent second-signal-induced ACD. We used mutants of atg1, a gene that plays an essential role in the initiation of autophagy. Upon starvation/cAMP, in contrast to parental cells, atg1 mutant cells showed irreversible lesions, clearly establishing a protective role for Atg1. Upon subsequent exposure to DIF-1 or to more ACD-specific second signals, starved parental cells progressed to ACD, but starved atg1 mutant cells did not, showing that Atg1 was required for ACD. Thus, in the same cells Atg1 was required in two apparently opposite ways, upon first-signaling for cell survival and upon second-signaling for ACD. Our findings strongly suggest that Atg1, thus presumably autophagy, protects the cells from starvation-induced cell death, allowing subsequent induction of ACD by the second signal. ACD is therefore not only "with" autophagy (since it showed signs of autophagy throughout), but is also "allowed by" autophagy. This does not exclude a role for autophagy also after second signaling. These results may account for discrepancies reported in the literature, encourage searches for second signals in different developmental models of ACD, and incite caution in autophagy-related therapeutic attempts.

Ludtmann, M. H., K. Boeckeler, et al. (2011). "Molecular pharmacology in a simple model system: implicating MAP kinase and phosphoinositide signalling in bipolar disorder." Semin Cell Dev Biol 22(1): 105-113.
	Understanding the mechanisms of drug action has been the primary focus for pharmacological researchers, traditionally using rodent models. However, non-sentient model systems are now increasingly being used as an alternative approach to better understand drug action or targets. One of these model systems, the social amoeba Dictyostelium, enables the rapid ablation or over-expression of genes, and the subsequent use of isogenic cell culture for the analysis of cell signalling pathways in pharmacological research. The model also supports an increasingly important ethical view of research, involving the reduction, replacement and refinement of animals in biomedical research. This review outlines the use of Dictyostelium in understanding the pharmacological action of two commonly used bipolar disorder treatments (valproic acid and lithium). Both of these compounds regulate mitogen activated protein (MAP) kinase and inositol phospholipid-based signalling by unknown means. Analysis of the molecular pathways targeted by these drugs in Dictyostelium and translation of discoveries to animal systems has helped to further understand the molecular mechanisms of these bipolar disorder treatments.

Lusche, D. F., D. Wessels, et al. (2011). "Nhe1 is essential for potassium but not calcium facilitation of cell motility and the monovalent cation requirement for chemotactic orientation in Dictyostelium discoideum." Eukaryot Cell 10(3): 320-331.
	In Dictyostelium discoideum, extracellular K+ or Ca2+ at a concentration of 40 or 20 mM, respectively, facilitates motility in the absence or presence of a spatial gradient of chemoattractant. Facilitation results in maximum velocity, cellular elongation, persistent translocation, suppression of lateral pseudopod formation, and myosin II localization in the posterior cortex. A lower threshold concentration of 15 mM K+ or Na or 5 mM Ca2+ is required for chemotactic orientation. Although the common buffer solutions used by D. discoideum researchers to study chemotaxis contain sufficient concentrations of cations for chemotactic orientation, the majority contain insufficient levels to facilitate motility. Here it has been demonstrated that Nhe1, a plasma membrane protein, is required for K+ but not Ca2+ facilitation of cell motility and for the lower K+ but not Ca2+ requirement for chemotactic orientation.

Maeda, Y. (2011). "Cell-cycle checkpoint for transition from cell division to differentiation." Dev Growth Differ 53(4): 463-481.
	In general, growth and differentiation are mutually exclusive, but they are cooperatively regulated during the course of development. Thus, the process of a cell's transition from growth to differentiation is of general importance for the development of organisms, and terminally differentiated cells such as nerve cells never divide. Meanwhile, the growth rate speeds up when cells turn malignant. The cellular slime mold Dictyostelium discoideum grows and multiplies as long as nutrients are supplied, and its differentiation is triggered by starvation. A critical checkpoint (growth/differentiation transition or GDT point), from which cells start differentiating in response to starvation, has been precisely specified in the cell cycle of D. discoideum Ax-2 cells. Accordingly, integration of GDT point-specific events with starvation-induced events is needed to understand the mechanism regulating GDTs. A variety of intercellular and intracellular signals are involved positively or negatively in the initiation of differentiation, making a series of cross-talks. As was expected from the presence of the GDT point, the cell's positioning in cell masses and subsequent cell-type choices occur depending on the cell's phase in the cell cycle at the onset of starvation. Since novel and multiple functions of mitochondria in various respects of development including the initiation of differentiation have been directly realized in Dictyostelium cells, they are also reviewed in this article.

Maniak, M. (2011). "Dictyostelium as a model for human lysosomal and trafficking diseases." Semin Cell Dev Biol 22(1): 114-119.
	Dictyostelium cells are genetically haploid and therefore easily analyzed for mutant phenotypes. In the past, many tools and molecular markers have been developed for a quantitative and qualitative analysis of the endocytic pathway in these amoebae. This review outlines parallels and discrepancies between mutants in Dictyostelium, the corresponding mammalian cells and the symptoms of human patients affected by lysosomal and trafficking defects. Situations where knowledge from Dictyostelium may potentially help understand human disease and vice versa are also addressed.

Meier, B., A. Zielinski, et al. (2011). "Chemotactic cell trapping in controlled alternating gradient fields." Proc Natl Acad Sci U S A 108(28): 11417-11422.
	Directed cell migration toward spatio-temporally varying chemotactic stimuli requires rapid cytoskeletal reorganization. Numerous studies provide evidence that actin reorganization is controlled by intracellular redistribution of signaling molecules, such as the PI4,5P2/PI3,4,5P3 gradient. However, exploring underlying mechanisms is difficult and requires careful spatio-temporal control of external chemotactic stimuli. We designed a microfluidic setup to generate alternating chemotactic gradient fields for simultaneous multicell exposure, greatly facilitating statistical analysis. For a quantitative description of intracellular response dynamics, we apply alternating time sequences of spatially homogeneous concentration gradients across 300 mum, reorienting on timescales down to a few seconds. Dictyostelium discoideum amoebae respond to gradient switching rates below 0.02 Hz by readapting their migration direction. For faster switching, cellular repolarization ceases and is completely stalled at 0.1 Hz. In this "chemotactically trapped" cell state, external stimuli alternate faster than intracellular feedback is capable to respond by onset of directed migration. To investigate intracellular actin cortex rearrangement during gradient switching, we correlate migratory cell response with actin repolymerization dynamics, quantified by a fluorescence distribution moment of the GFP fusion protein LimEDeltacc. We find two fundamentally different cell polarization types and we could reveal the role of PI3-Kinase for cellular repolarization. In the early aggregation phase, PI3-Kinase enhances the capability of D. discoideum cells to readjust their polarity in response to spatially alternating gradient fields, whereas in aggregation competent cells the effect of PI3-Kinase perturbation becomes less relevant.

Meyer, I., O. Kuhnert, et al. (2011). "Functional analyses of lissencephaly-related proteins in Dictyostelium." Semin Cell Dev Biol 22(1): 89-96.
	Lissencephaly is a severe brain developmental disease in human infants, which is usually caused by mutations in either of two genes, LIS1 and DCX. These genes encode proteins interacting with both the microtubule and the actin systems. Here, we review the implications of data on Dictyostelium LIS1 for the elucidation of LIS1 function in higher cells and emphasize the role of LIS1 and nuclear envelope proteins in nuclear positioning, which is also important for coordinated cell migration during neocortical development. Furthermore, for the first time we characterize Dictyostelium DCX, the only bona fide orthologue of human DCX outside the animal kingdom. We show that DCX functionally interacts with LIS1 and that both proteins have a cytoskeleton-independent function in chemotactic signaling during development. Dictyostelium LIS1 is also required for proper attachment of the centrosome to the nucleus and, thus, nuclear positioning, where the association of these two organelles has turned out to be crucial. It involves not only dynein and dynein-associated proteins such as LIS1 but also SUN proteins of the nuclear envelope. Analyses of Dictyostelium SUN1 mutants have underscored the importance of these proteins for the linkage of centrosomes and nuclei and for the maintenance of chromatin integrity. Taken together, we show that Dictyostelium amoebae, which provide a well-established model to study the basic aspects of chemotaxis, cell migration and development, are well suited for the investigation of the molecular and cell biological basis of developmental diseases such as lissencephaly.

Milanesio, P., A. Arce-Rodriguez, et al. (2011). "Regulatory exaptation of the catabolite repression protein (Crp)-cAMP system in Pseudomonas putida." Environ Microbiol 13(2): 324-339.
	The genome of the soil bacterium Pseudomonas putida KT2440 encodes singular orthologues of genes crp (encoding the catabolite repression protein, Crp) and cyaA (adenylate cyclase) of Escherichia coli. The levels of cAMP formed by P. putida cells were below detection with a Dictyostelium biosensor in vivo. The cyaA(P. putida) gene was transcribed in vivo but failed to complement the lack of maltose consumption of a cyaA mutant of E. coli, thereby indicating that cyaA(P. putida) was poorly translated or rendered non-functional in the heterologous host. Yet, generation of cAMP by CyaA(P. putida) could be verified by expressing the cyaA(P. putida) gene in a hypersensitive E. coli strain. On the other hand, the crp(P. putida) gene restored the metabolic capacities of an equivalent crp mutant of E. coli, but not in a double crp/cyaA strain, suggesting that the ability to regulate such functions required cAMP. In order to clarify the breadth of the Crp/cAMP system in P. putida, crp and cyaA mutants were generated and passed through a battery of phenotypic tests for recognition of gross metabolic properties and stress-endurance abilities. These assays revealed that the loss of each gene led in most (but not all) cases to the same phenotypic behaviour, indicating a concerted functionality. Unexpectedly, none of the mutations affected the panel of carbon compounds that can be used by P. putida as growth substrates, the mutants being impaired only in the use of various dipeptides as N sources. Furthermore, the lack of crp or cyaA had little influence on the gross growth fingerprinting of the cells. The poor physiological profile of the Crp-cAMP system of P. putida when compared with E. coli exposes a case of regulatory exaptation, i.e. the process through which a property evolved for a particular function is co-opted for a new use.

Miyata, S. T., M. Kitaoka, et al. (2011). "Vibrio cholerae requires the type VI secretion system virulence factor VasX to kill Dictyostelium discoideum." Infect Immun 79(7): 2941-2949.
	The type VI secretion system (T6SS) is recognized as an important virulence mechanism in several Gram-negative pathogens. In Vibrio cholerae, the causative agent of the diarrheal disease cholera, a minimum of three gene clusters--one main cluster and two auxiliary clusters--are required to form a functional T6SS apparatus capable of conferring virulence toward eukaryotic and prokaryotic hosts. Despite an increasing understanding of the components that make up the T6SS apparatus, little is known about the regulation of these genes and the gene products delivered by this nanomachine. VasH is an important regulator of the V. cholerae T6SS. Here, we present evidence that VasH regulates the production of a newly identified protein, VasX, which in turn requires a functional T6SS for secretion. Deletion of vasX does not affect export or enzymatic function of the structural T6SS proteins Hcp and VgrG-1, suggesting that VasX is dispensable for the assembly of the physical translocon complex. VasX localizes to the bacterial membrane and interacts with membrane lipids. We present VasX as a novel virulence factor of the T6SS, as a V. cholerae mutant lacking vasX exhibits a phenotype of attenuated virulence toward Dictyostelium discoideum.

Moen, R. J., D. O. Johnsrud, et al. (2011). "Characterization of a myosin VII MyTH/FERM domain." J Mol Biol 413(1): 17-23.
	A group of closely related myosins is characterized by the presence of at least one MyTH/FERM (myosin tail homology; band 4.1, ezrin, radixin, moesin) domain in their C-terminal tails. This domain interacts with a variety of binding partners, and mutations in either the MyTH4 or the FERM domain of myosin VII and myosin XV result in deafness, highlighting the functional importance of each domain. The N-terminal MyTH/FERM region of Dictyostelium myosin VII (M7) has been isolated as a first step toward gaining insight into the function of this domain and its interaction with binding partners. The M7 MyTH4/FERM domain (MF1) binds to both actin and microtubules in vitro, with dissociation constants of 13.7 and 1.7 muM, respectively. Gel filtration and UV spectroscopy reveal that MF1 exists as a monomer in solution and forms a well-folded, compact conformation with a high degree of secondary structure. These results indicate that MF1 forms an integrated structural domain that serves to couple actin filaments and microtubules in specific regions of the cytoskeleton.

Moncho-Amor, V., M. Galardi-Castilla, et al. (2011). "The dual-specificity protein phosphatase MkpB, homologous to mammalian MKP phosphatases, is required for D. discoideum post-aggregative development and cisplatin response." Differentiation 81(3): 199-207.
	Dual-specificity protein phosphatases participate in signal transduction pathways inactivating mitogen-activated protein kinases (MAP kinases). These signaling pathways are of critical importance in the regulation of numerous biological processes, including cell proliferation, differentiation and development. The social ameba Dictyostelium discoideum harbors 14 genes coding for proteins containing regions very similar to the dual-specificity protein phosphatase domain. One of these genes, mkpB, additionally codes for a region similar to the Rhodanase domain, characteristic of animal MAP kinase-phosphatases, in its N-terminal region. Cells that over-express this gene show increased protein phosphatase activity. mkpB is expressed in D. discoideum ameba at growth but it is greatly induced at 12h of multicellular development. Although it is expressed in all the cells of developmental structures, mkpB mRNA is enriched in cells with a distribution typical of anterior-like cells. Cells that express a catalytically inactive mutant of MkpB grow and aggregate like wild-type cells but show a greatly impaired post-aggregative development. In addition, the expression of cell-type specific genes is very delayed, indicating that this protein plays an important role in cell differentiation and development. Cells expressing the MkpB catalytically inactive mutant show increased sensitivity to cisplatin, while cells over-expressing wild type MkpB, or MkpA, proteins or mutated in the MAP kinase erkB gene are more resistant to this chemotherapeutic drug, as also shown in human tumor cells.

Mujumdar, N., A. K. Dubey, et al. (2011). "Autonomous and non-autonomous traits mediate social cooperation in Dictyostelium discoideum." J Biosci 36(3): 505-516.
	In the trishanku (triA-) mutant of the social amoeba Dictyostelium discoideum, aggregates are smaller than usual and the spore mass is located mid-way up the stalk, not at the apex. We have monitored aggregate territory size, spore allocation and fruiting body morphology in chimaeric groups of (quasi-wild-type) Ax2 and triA- cells. Developmental canalisation breaks down in chimaeras and leads to an increase in phenotypic variation. A minority of triA- cells causes largely Ax2 aggregation streams to break up; the effect is not due to the counting factor. Most chimaeric fruiting bodies resemble those of Ax2 or triA-. Others are double-deckers with a single stalk and two spore masses, one each at the terminus and midway along the stalk. The relative number of spores belonging to the two genotypes depends both on the mixing ratio and on the fruiting body morphology. In double-deckers formed from 1:1 chimaeras, the upper spore mass has more Ax2 spores, and the lower spore mass more triA- spores, than expected. Thus, the traits under study depend partly on the cells' own genotype and partly on the phenotypes, and so genotypes, of other cells: they are both autonomous and non-autonomous. These findings strengthen the parallels between multicellular development and behaviour in social groups. Besides that, they reinforce the point that a trait can be associated with a genotype only in a specified context.

Muller-Taubenberger, A., C. Bonisch, et al. (2011). "The histone methyltransferase Dot1 is required for DNA damage repair and proper development in Dictyostelium." Biochem Biophys Res Commun 404(4): 1016-1022.
	Posttranslational histone modifications play an important role in modulating gene expression and chromatin structure. Here we report the identification of histone H3K79 dimethylation in the simple eukaryote Dictyostelium discoideum. We have deleted the D. discoideum Dot1/KMT4 homologue and demonstrate that it is the sole enzyme responsible for histone H3K79me2. Cells lacking Dot1 are reduced in growth and delayed in development, but do not show apparent changes in cell cycle regulation. Furthermore, our results indicate that Dot1 contributes to UV damage resistance and DNA repair in D. discoideum. In summary, the data support the view that the machinery controlling the setting of histone marks is evolutionary highly conserved and provide evidence that D. discoideum is a suitable model system to analyze these modifications and their functions during development and differentiation.

Myre, M. A., A. L. Lumsden, et al. (2011). "Deficiency of huntingtin has pleiotropic effects in the social amoeba Dictyostelium discoideum." PLoS Genet 7(4): e1002052.
	Huntingtin is a large HEAT repeat protein first identified in humans, where a polyglutamine tract expansion near the amino terminus causes a gain-of-function mechanism that leads to selective neuronal loss in Huntington's disease (HD). Genetic evidence in humans and knock-in mouse models suggests that this gain-of-function involves an increase or deregulation of some aspect of huntingtin's normal function(s), which remains poorly understood. As huntingtin shows evolutionary conservation, a powerful approach to discovering its normal biochemical role(s) is to study the effects caused by its deficiency in a model organism with a short life-cycle that comprises both cellular and multicellular developmental stages. To facilitate studies aimed at detailed knowledge of huntingtin's normal function(s), we generated a null mutant of hd, the HD ortholog in Dictyostelium discoideum. Dictyostelium cells lacking endogenous huntingtin were viable but during development did not exhibit the typical polarized morphology of Dictyostelium cells, streamed poorly to form aggregates by accretion rather than chemotaxis, showed disorganized F-actin staining, exhibited extreme sensitivity to hypoosmotic stress, and failed to form EDTA-resistant cell-cell contacts. Surprisingly, chemotactic streaming could be rescued in the presence of the bivalent cations Ca(2+) or Mg(2+) but not pulses of cAMP. Although hd(-) cells completed development, it was delayed and proceeded asynchronously, producing small fruiting bodies with round, defective spores that germinated spontaneously within a glassy sorus. When developed as chimeras with wild-type cells, hd(-) cells failed to populate the pre-spore region of the slug. In Dictyostelium, huntingtin deficiency is compatible with survival of the organism but renders cells sensitive to low osmolarity, which produces pleiotropic cell autonomous defects that affect cAMP signaling and as a consequence development. Thus, Dictyostelium provides a novel haploid organism model for genetic, cell biological, and biochemical studies to delineate the functions of the HD protein.

Nageshan, R. K., N. Roy, et al. (2011). "Post-transcriptional repair of a split heat shock protein 90 gene by mRNA trans-splicing." J Biol Chem 286(9): 7116-7122.
	Heat shock protein 90 participates in diverse biological processes ranging from protein folding, cell cycle, signal transduction and development to evolution in all eukaryotes. It is also critically involved in regulating growth of protozoa such as Dictyostelium discoideum, Leishmania donovani, Plasmodium falciparum, Trypanosoma cruzi, and Trypanosoma evansi. Selective inhibition of Hsp90 has also been explored as an intervention strategy against important human diseases such as cancer, malaria, or trypanosomiasis. Giardia lamblia, a simple protozoan parasite of humans and animals, is an important cause of diarrheal disease with significant morbidity and some mortality in tropical countries. Here we show that the G. lamblia cytosolic hsp90 (glhsp90) is split in two similar sized fragments located 777 kb apart on the same scaffold. Intrigued by this unique arrangement, which appears to be specific for the Giardiinae, we have investigated the biosynthesis of GlHsp90. We used genome sequencing to confirm the split nature of the giardial hsp90. However, a specific antibody raised against the peptide detected a product with a mass of about 80 kDa, suggesting a post-transcriptional rescue of the genomic defect. We show evidence for the joining of the two independent Hsp90 transcripts in-trans to one long mature mRNA presumably by RNA splicing. The splicing junction carries hallmarks of classical cis-spliced introns, suggesting that the regular cis-splicing machinery may be sufficient for repair of the open reading frame. A complementary 26-nt sequence in the "intron" regions adjacent to the splice sites may assist in positioning the two pre-mRNAs for processing. This is the first example of post-transcriptional rescue of a split gene by trans-splicing.

Nair, D. R., R. Ghosh, et al. (2011). "Two functionally distinctive phosphopantetheinyl transferases from amoeba Dictyostelium discoideum." PLoS One 6(9): e24262.
	The life cycle of Dictyostelium discoideum is proposed to be regulated by expression of small metabolites. Genome sequencing studies have revealed a remarkable array of genes homologous to polyketide synthases (PKSs) that are known to synthesize secondary metabolites in bacteria and fungi. A crucial step in functional activation of PKSs involves their post-translational modification catalyzed by phosphopantetheinyl transferases (PPTases). PPTases have been recently characterized from several bacteria; however, their relevance in complex life cycle of protozoa remains largely unexplored. Here we have identified and characterized two phosphopantetheinyl transferases from D. discoideum that exhibit distinct functional specificity. DiAcpS specifically modifies a stand-alone acyl carrier protein (ACP) that possesses a mitochondrial import signal. DiSfp in contrast is specific to Type I multifunctional PKS/fatty acid synthase proteins and cannot modify the stand-alone ACP. The mRNA of two PPTases can be detected during the vegetative as well as starvation-induced developmental pathway and the disruption of either of these genes results in non-viable amoebae. Our studies show that both PPTases play an important role in Dictyostelium biology and provide insight into the importance of PPTases in lower eukaryotes.

Nakagawa, M., H. Tojo, et al. (2011). "A glycan of Psi-factor from Dictyostelium discoideum contains a bisecting-GlcNAc, an intersecting-GlcNAc, and a core alpha-1,6-fucose." Biosci Biotechnol Biochem 75(10): 1964-1970.
	A secretory glycoprotein named Psi-factor that we have purified and cloned from Dictyostelium discoideum is prespore cell-inducing factor. To address its functional significance, it is necessary to examine the attached sites and structures of its glycans as well as its protein structure. Here we identified and isolated a tryptic glycosylated peptide with the 71st to 89th amino acids of Psi-factor that contained the consensus amino acid sequence for an N-linked glycan (N-T-T). MALDI-TOF mass spectrometry indicated that the major protonated molecular ions, [M+H](+), of the glycopeptide were present at m/z 3,806, the minor m/z 3,603 and 3,400 ions corresponding to the loss of one and two N-acetylhexosamines respectively. Digestion of it with N-glycosidase F gave a molecular mass of 1,766.9 for the whole glycan moiety, which accounts for its composition of five hexoses, four N-acetylhexosamines, and a deoxyhexose. Further digestion experiments on the basis of the substrate specificity of alpha-mannosidase and beta-N-acetylhexosaminidase allowed us to elucidate the unique structure of the glycan, which contains a bisecting and an intersecting GlcNAc and a core alpha1,6-fucosyl moiety.

Nanjundiah, V. and S. Sathe (2011). "Social selection and the evolution of cooperative groups: the example of the cellular slime moulds." Integr Biol (Camb) 3(4): 329-342.
	In social selection the phenotype of an individual depends on its own genotype as well as on the phenotypes, and so genotypes, of other individuals. This makes it impossible to associate an invariant phenotype with a genotype: the social context is crucial. Descriptions of metazoan development, which often is viewed as the acme of cooperative social behaviour, ignore or downplay this fact. The implicit justification for doing so is based on a group-selectionist point of view. Namely, embryos are clones, therefore all cells have the same evolutionary interest, and the visible differences between cells result from a common strategy. The reasoning is flawed, because phenotypic heterogeneity within groups can result from contingent choices made by cells from a flexible repertoire as in multicellular development. What makes that possible is phenotypic plasticity, namely the ability of a genotype to exhibit different phenotypes. However, co-operative social behaviour with division of labour requires that different phenotypes interact appropriately, not that they belong to the same genotype, or have overlapping genetic interests. We sketch a possible route to the evolution of social groups that involves many steps: (a) individuals that happen to be in spatial proximity benefit simply by virtue of their number; (b) traits that are already present act as preadaptations and improve the efficiency of the group; and (c) new adaptations evolve under selection in the social context--that is, via interactions between individuals--and further strengthen group behaviour. The Dictyostelid or cellular slime mould amoebae (CSMs) become multicellular in an unusual way, by the aggregation of free-living cells. In nature the resulting group can be genetically homogeneous (clonal) or heterogeneous (polyclonal); in either case its development, which displays strong cooperation between cells (to the extent of so-called altruism) is not affected. This makes the CSMs exemplars for the study of social behaviour.

Narita, T. B., K. Koide, et al. (2011). "Dictyostelium hybrid polyketide synthase, SteelyA, produces 4-methyl-5-pentylbenzene-1,3-diol and induces spore maturation." FEMS Microbiol Lett 319(1): 82-87.
	The genome of Dictyostelium contains two novel hybrid-type polyketide synthases (PKSs) known as 'Steely'; the Steely enzyme is formed by the fusion of type I and type III PKSs. One of these enzymes, SteelyB, is known to be responsible for the production of the stalk cell-inducing factor DIF-1 in vivo. On the other hand, the product(s) and expression pattern of SteelyA are not clearly understood, because there are two different reports associated with the in vitro products of SteelyA and its expression pattern. To solve this problem, we first examined the expression pattern using two different primer sets and found that it was quite similar to that shown in the dictyExpress database. stlA expression peaked at approximately 3 h and declined, but showed a small peak around the end of development. Next, we examined the in vivo product of SteelyA using a stlA null mutant and found that the mutant lacked 4-methyl-5-pentylbenzene-1,3-diol (MPBD). This null mutant showed aberrant, glassy sori, and most of the cells in the sori remained amoeba-like without a cell wall. This defect was restored by adding 200 nM of MPBD to the agar. These results indicate that SteelyA produces MPBD in vivo and induces spore maturation.

Neilson, M. P., D. M. Veltman, et al. (2011). "Chemotaxis: a feedback-based computational model robustly predicts multiple aspects of real cell behaviour." PLoS Biol 9(5): e1000618.
	The mechanism of eukaryotic chemotaxis remains unclear despite intensive study. The most frequently described mechanism acts through attractants causing actin polymerization, in turn leading to pseudopod formation and cell movement. We recently proposed an alternative mechanism, supported by several lines of data, in which pseudopods are made by a self-generated cycle. If chemoattractants are present, they modulate the cycle rather than directly causing actin polymerization. The aim of this work is to test the explanatory and predictive powers of such pseudopod-based models to predict the complex behaviour of cells in chemotaxis. We have now tested the effectiveness of this mechanism using a computational model of cell movement and chemotaxis based on pseudopod autocatalysis. The model reproduces a surprisingly wide range of existing data about cell movement and chemotaxis. It simulates cell polarization and persistence without stimuli and selection of accurate pseudopods when chemoattractant gradients are present. It predicts both bias of pseudopod position in low chemoattractant gradients and--unexpectedly--lateral pseudopod initiation in high gradients. To test the predictive ability of the model, we looked for untested and novel predictions. One prediction from the model is that the angle between successive pseudopods at the front of the cell will increase in proportion to the difference between the cell's direction and the direction of the gradient. We measured the angles between pseudopods in chemotaxing Dictyostelium cells under different conditions and found the results agreed with the model extremely well. Our model and data together suggest that in rapidly moving cells like Dictyostelium and neutrophils an intrinsic pseudopod cycle lies at the heart of cell motility. This implies that the mechanism behind chemotaxis relies on modification of intrinsic pseudopod behaviour, more than generation of new pseudopods or actin polymerization by chemoattractants.

Numata, N., T. Shima, et al. (2011). "C-sequence of the Dictyostelium cytoplasmic dynein participates in processivity modulation." FEBS Lett 585(8): 1185-1190.
	We examined the functional roles of C-sequence, a 47-kDa non-AAA+ module at the C-terminal end of the 380-kDa Dictyostelium dynein motor domain. When the distal segment of the C-sequence was deleted from the motor domain, the single-molecule processivity of the dimerized motor domain was selectively impaired without its ensemble motile ability and ATPase activity being severely affected. When the hinge-like sequence between the distal and proximal C-sequence segments was made more or less flexible, the dimeric motor showed lower or higher processivity, respectively. These results suggest a potential function of the distal C-sequence segment as a modulator of processivity.

Nunez-Corcuera, B., J. Birch, et al. (2011). "A SET/MYND chromatin re-modelling protein regulates Dictyostelium prespore patterning." Int J Dev Biol 55(2): 205-208.
	SmdA is a Dictyostelium orthologue of the SET/MYND chromatin re-modelling proteins. In developing structures derived from a null mutant for smdA (a smdA- strain), prestalk patterning is normal, but using a prespore lacZ reporter fusion, there is ectopic accumulation of beta-galactosidase in the prestalk region. As wild type slugs migrate, there is continual forward movement and re-differentiation of prespore cells into prestalk cells. Thus, a potential explanation for the ectopic reporter localization in smdA null prestalk cells is an increased rate of re-differentiation and anterior movement of prespore cells. In support of this notion, analysis of an unstable lacZ reporter, driven by the prespore promoter, reveals a normal staining pattern in the smdA- strain. We suggest that one or more genes regulated by SmdA acts to repress prespore re-specification.

O'Day, D. H. and A. Keszei (2011). "Signalling and sex in the social amoebozoans." Biol Rev Camb Philos Soc.
	The social amoebozoans have a life tricycle consisting of asexual multicellular development leading to fruiting bodies, sexual multicellular development resulting in macrocysts, and unicellular development generating microcysts. This review covers the events of sexual development in the best-studied heterothallic (Dictyostelium discoideum) and homothallic (D. mucoroides) mating systems. Sexual development begins with pheromonal interactions that produce fusion-competent cells (gametes) which undergo cell and pronuclear fusion. Calcium- and calmodulin-mediated signalling mediates these early events. As they initiate chemotactic signalling, each zygote increases in size becoming a zygote giant cell. Using cyclic AMP (cAMP), the zygote chemotactically lures in amoebae and engulfs them in an act of cannibalistic phagocytosis. Chemotaxis proceeds more quickly than endocytosis because the breakdown products of cAMP (5-AMP, adenosine) bind to a presumptive adenosine receptor to inhibit sexual phagocytosis. This slowing of phagocytosis allows amoebae to accumulate around the zygote to form a precyst aggregate. Zygote giant cells also produce several other signalling molecules that feed back to regulate early events. The amoebae surrounding the zygote seal their fate as zygotic foodstuff by secreting a primary cellulose wall, the extracellular sheath, around the zygote and aggregated amoebae, which prevents their escape. Phagocytosis within this precyst continues until all peripheral amoebae are internalized as endocytes and the final macrocyst wall is formed. Endocyte digestion results in a mature macrocyst with a uniform cytoplasm containing a diploid nucleus. After detailing the morphological events of heterothallic and homothallic mating, we review the various intercellular signalling events and other mechanisms involved in each stage. This complete and comprehensive review sets the stage for future research on the unique events that characterize sex in the social amoebozoans.

Ochiai, H., K. Takeda, et al. (2011). "Protein kinase B gene homologue pkbR1 performs one of its roles at first finger stage of Dictyostelium." Eukaryot Cell 10(4): 512-520.
	Dictyostelium discoideum has protein kinases AKT/PKBA and PKBR1 that belong to the AGC family of kinases. The protein kinase B-related kinase (PKBR1) has been studied with emphasis on its role in chemotaxis, but its roles in late development remained obscure. The pkbR1 null mutant stays in the first finger stage for about 16 h or longer. Only a few aggregates continue to the migrating slug stage; however, the slugs immediately go back probably to the previous first finger stage and stay there for approximately 37 h. Finally, the mutant fingers diversify into various multicellular bodies. The expression of the pkbR1 finger protein probably is required for development to the slug stage and to express ecmB, which is first observed in migrating slugs. The mutant also showed no ST-lacZ expression, which is of the earliest step in differentiation to one of the stalk cell subtypes. The pkbR1 null mutant forms a small number of aberrant fruiting bodies, but in the presence of 10% of wild-type amoebae the mutant preferentially forms viable spores, driving the wild type to form nonviable stalk cells. These results suggest that the mutant has defects in a system that changes the physiological dynamics in the prestalk cell region of a finger. We suggest that the arrest of its development is due to the loss of the second wave of expression of a protein kinase A catalytic subunit gene (pkaC) only in the prestalk region of the pkbR1 null mutant.

Pakes, N. K., S. N. Jayasinghe, et al. (2011). "Bio-electrospraying and aerodynamically assisted bio-jetting the model eukaryotic Dictyostelium discoideum: assessing stress and developmental competency post treatment." J R Soc Interface 8(61): 1185-1191.
	Bio-electrospraying (BES) and aerodynamically assisted bio-jetting (AABJ) have recently been established as important novel biospray technologies for directly manipulating living cells. To elucidate their potential in medical and clinical sciences, these bio-aerosol techniques have been subjected to increasingly rigorous investigations. In parallel to these studies, we wish to introduce these unique biotechnologies for use in the basic biological sciences, for handling a wide range of cell types and systems, thus increasing the range and the scope of these techniques for modern research. Here, the authors present the analysis of the new use of these biospray techniques for the direct handling of the simple eukaryotic biomedical model organism Dictyostelium discoideum. These cells are widely used as a model for immune cell chemotaxis and as a simple model for development. We demonstrate that AABJ of these cells did not cause cell stress, as defined by the stress-gene induction, nor affect cell development. Furthermore, although BES induced the increased expression of one stress-related gene (gapA), this was not a generalized stress response nor did it affect cell development. These data suggest that these biospray techniques can be used to directly manipulate single cells of this biomedical model without inducing a generalized stress response or perturbing later development.

Pan, Y. J., T. L. Lin, et al. (2011). "Use of a Dictyostelium model for isolation of genetic loci associated with phagocytosis and virulence in Klebsiella pneumoniae." Infect Immun 79(3): 997-1006.
	Phagocytosis resistance is an important virulence factor in Klebsiella pneumoniae. Dictyostelium has been used to study the interaction between phagocytes and bacteria because of its similarity to mammalian macrophages. In this study, we used a Dictyostelium model to investigate genes for resistance to phagocytosis in NTUH-K2044, a strain of K. pneumoniae causing pyogenic liver abscess that is highly resistant to phagocytosis. A total of 2,500 transposon mutants were screened by plaque assay, and 29 of them permitted phagocytosis by Dictyostelium. In the 29 mutants, six loci were identified; three were capsular synthesis genes. Of the other three, one was related to carnitine metabolism, one encoded a subunit of protease (clpX), and one encoded a lipopolysaccharide O-antigen transporter (wzm). Deletion and complementation of these genes showed that only DeltaclpX and Deltawzm mutants became susceptible to Dictyostelium phagocytosis, and their complementation restored the phagocytosis resistance phenotype. These two mutants were also susceptible to phagocytosis by human neutrophils and revealed attenuated virulence in a mouse model, implying that they play important roles in the pathogenesis of K. pneumoniae. Furthermore, we demonstrated that clpP, which exists in an operon with clpX, was also involved in resistance to phagocytosis. The transcriptional profile of DeltaclpX was examined by microarray analysis and revealed a 3-fold lower level of expression of capsular synthesis genes. Therefore, we have identified genes involved in resistance to phagocytosis in K. pneumoniae using Dictyostelium, and this model is useful to explore genes associated with resistance to phagocytosis in heavily encapsulated bacteria.

Parkinson, K., N. J. Buttery, et al. (2011). "A simple mechanism for complex social behavior." PLoS Biol 9(3): e1001039.
	The evolution of cooperation is a paradox because natural selection should favor exploitative individuals that avoid paying their fair share of any costs. Such conflict between the self-interests of cooperating individuals often results in the evolution of complex, opponent-specific, social strategies and counterstrategies. However, the genetic and biological mechanisms underlying complex social strategies, and therefore the evolution of cooperative behavior, are largely unknown. To address this dearth of empirical data, we combine mathematical modeling, molecular genetic, and developmental approaches to test whether variation in the production of and response to social signals is sufficient to generate the complex partner-specific social success seen in the social amoeba Dictyostelium discoideum. Firstly, we find that the simple model of production of and response to social signals can generate the sort of apparent complex changes in social behavior seen in this system, without the need for partner recognition. Secondly, measurements of signal production and response in a mutant with a change in a single gene that leads to a shift in social behavior provide support for this model. Finally, these simple measurements of social signaling can also explain complex patterns of variation in social behavior generated by the natural genetic diversity found in isolates collected from the wild. Our studies therefore demonstrate a novel and elegantly simple underlying mechanistic basis for natural variation in complex social strategies in D. discoideum. More generally, they suggest that simple rules governing interactions between individuals can be sufficient to generate a diverse array of outcomes that appear complex and unpredictable when those rules are unknown.

Phillips, J. E., E. Huang, et al. (2011). "The putative bZIP transcription factor BzpN slows proliferation and functions in the regulation of cell density by autocrine signals in Dictyostelium." PLoS One 6(7): e21765.
	The secreted proteins AprA and CfaD function as autocrine signals that inhibit cell proliferation in Dictyostelium discoideum, thereby regulating cell numbers by a negative feedback mechanism. We report here that the putative basic leucine zipper transcription factor BzpN plays a role in the inhibition of proliferation by AprA and CfaD. Cells lacking BzpN proliferate more rapidly than wild-type cells but do not reach a higher stationary density. Recombinant AprA inhibits wild-type cell proliferation but does not inhibit the proliferation of cells lacking BzpN. Recombinant CfaD also inhibits wild-type cell proliferation, but promotes the proliferation of cells lacking BzpN. Overexpression of BzpN results in a reduced cell density at stationary phase, and this phenotype requires AprA, CfaD, and the kinase QkgA. Conditioned media from high-density cells stops the proliferation of wild-type but not bzpN(-) cells and induces a nuclear localization of a BzpN-GFP fusion protein, though this localization does not require AprA or CfaD. Together, the data suggest that BzpN is necessary for some but not all of the effects of AprA and CfaD, and that BzpN may function downstream of AprA and CfaD in a signal transduction pathway that inhibits proliferation.

Preller, M., S. Bauer, et al. (2011). "Structural basis for the allosteric interference of myosin function by reactive thiol region mutations G680A and G680V." J Biol Chem 286(40): 35051-35060.
	The cold-sensitive single-residue mutation of glycine 680 in the reactive thiol region of Dictyostelium discoideum myosin-2 or the corresponding conserved glycine in other myosin isoforms has been reported to interfere with motor function. Here we present the x-ray structures of myosin motor domain mutants G680A in the absence and presence of nucleotide as well as the apo structure of mutant G680V. Our results show that the Gly-680 mutations lead to uncoupling of the reactive thiol region from the surrounding structural elements. Structural and functional data indicate that the mutations induce the preferential population of a state that resembles the ADP-bound state. Moreover, the Gly-680 mutants display greatly reduced dynamic properties, which appear to be related to the recovery of myosin motor function at elevated temperatures.

Preller, M., K. Chinthalapudi, et al. (2011). "Inhibition of Myosin ATPase activity by halogenated pseudilins: a structure-activity study." J Med Chem 54(11): 3675-3685.
	Myosin activity is crucial for many biological functions. Strong links have been established between changes in the activity of specific myosin isoforms and diseases such as cancer, cardiovascular failure, and disorders of sensory organs and the central nervous system. The modulation of specific myosin isoforms therefore holds a strong therapeutic potential. In recent work, we identified members of the marine alkaloid family of pseudilins as potent inhibitors of myosin-dependent processes. Here, we report the crystal structure of the complex between the Dictyostelium myosin 2 motor domain and 2,4-dichloro-6-(3,4,5-tribromo-1H-pyrrole-2-yl)phenol (3). Detailed comparison with previously solved structures of the myosin 2 complex with bound pentabromopseudilin (2a) or pentachloropseudilin (4a) provides insights into the molecular basis of the allosteric communication between the catalytic and the allosteric sites. Moreover, we describe the inhibitory potency for a congeneric series of halogenated pseudilins. Insight into their mode of action is gained by applying a combination of experimental and computational approaches.

Pribic, J., R. Garcia, et al. (2011). "Paxillin and phospholipase D interact to regulate actin-based processes in Dictyostelium discoideum." Eukaryot Cell 10(7): 977-984.
	The actin cytoskeleton forms a membrane-associated network whose proper regulation is essential for numerous processes, including cell differentiation, proliferation, adhesion, chemotaxis, endocytosis, exocytosis, and multicellular development. In this report, we show that in Dictyostelium discoideum, paxillin (PaxB) and phospholipase D (PldB) colocalize and coimmunoprecipitate, suggesting that they interact physically. Additionally, the phenotypes observed during development, cell sorting, and several actin-required processes, including cyclic AMP (cAMP) chemotaxis, cell-substrate adhesion, actin polymerization, phagocytosis, and exocytosis, reveal a genetic interaction between paxB and pldB, suggesting a functional interaction between their gene products. Taken together, our data point to PldB being a required binding partner of PaxB during processes involving actin reorganization.

Rai, A., H. Nothe, et al. (2011). "Dictyostelium dynamin B modulates cytoskeletal structures and membranous organelles." Cell Mol Life Sci 68(16): 2751-2767.
	Dictyostelium discoideum cells produce five dynamin family proteins. Here, we show that dynamin B is the only member of this group of proteins that is initially produced as a preprotein and requires processing by mitochondrial proteases for formation of the mature protein. Our results show that dynamin B-depletion affects many aspects of cell motility, cell-cell and cell-surface adhesion, resistance to osmotic shock, and fatty acid metabolism. The mature form of dynamin B mediates a wide range and unique combination of functions. Dynamin B affects events at the plasma membrane, peroxisomes, the contractile vacuole system, components of the actin-based cytoskeleton, and cell adhesion sites. The modulating effect of dynamin B on the activity of the contractile vacuole system is unique for the Dictyostelium system. Other functions displayed by dynamin B are commonly associated with either classical dynamins or dynamin-related proteins.

Rai, V. and T. T. Egelhoff (2011). "Role of B regulatory subunits of protein phosphatase type 2A in myosin II assembly control in Dictyostelium discoideum." Eukaryot Cell 10(4): 604-610.
	In Dictyostelium discoideum, myosin II resides predominantly in a soluble pool as the result of phosphorylation of the myosin heavy chain (MHC), and dephosphorylation of the MHC is required for myosin II filament assembly, recruitment to the cytoskeleton, and force production. Protein phosphatase type 2A (PP2A) was identified in earlier studies in Dictyostelium as a key biochemical activity that can drive MHC dephosphorylation. We report here gene targeting and cell biological studies addressing the roles of candidate PP2A B regulatory subunits (phr2aBalpha and phr2aBbeta) in myosin II assembly control in vivo. Dictyostelium phr2aBalpha- and phr2aBbeta-null cells show delayed development, reduction in the assembly of myosin II in cytoskeletal ghost assays, and defects in cytokinesis when grown in suspension compared to parental cell lines. These results demonstrate that the PP2A B subunits phr2aBalpha and phr2aBbeta contribute to myosin II assembly control in vivo, with phr2aBalpha having the predominant role facilitating MHC dephosphorylation to facilitate filament assembly.

Rajawat, J., H. Mir, et al. (2011). "Differential role of poly(ADP-ribose) polymerase in D. discoideum growth and development." BMC Dev Biol 11: 14.
	BACKGROUND: Poly(ADP-ribose) polymerase is evolutionarily conserved as a responder to various forms of stress. Though PARP's role in cell death is well addressed, its role in development and multicellularity is still an enigma. We have previously reported the role of PARP in oxidative stress induced delayed development of D. discoideum. RESULTS: In the current study we highlight the involvement of PARP during D. discoideum development. Oxidative stress affects expression of aca and cAR1 thus affecting aggregation. Although parp expression is not affected during oxidative stress but it is involved during normal development as confirmed by our PARP down-regulation studies. Constitutive PARP down-regulation resulted in blocked development while no effect was observed on D. discoideum growth. Interestingly, stage specific PARP down-regulation arrested development at the slug stage. CONCLUSION: These results emphasize that PARP is essential for complex differentiation and its function may be linked to multicellularity. This is the first report where the involvement of PARP during normal multicellular development in D. discoideum, an ancient eukaryote, is established which could be of evolutionary significance. Thus our study adds one more role to the multitasking function of PARP.

Ray, S., Y. Chen, et al. (2011). "Phospholipase D controls Dictyostelium development by regulating G protein signaling." Cell Signal 23(2): 335-343.
	Dictyostelium discoideum cells normally exist as individual amoebae, but will enter a period of multicellular development upon starvation. The initial stages of development involve the aggregation of individual cells, using cAMP as a chemoattractant. Chemotaxis is initiated when cAMP binds to its receptor, cAR1, and activates the associated G protein, Galpha2betagamma. However, chemotaxis will not occur unless there is a high density of starving cells present, as measured by high levels of the secreted quorum sensing molecule, CMF. We previously demonstrated that cells lacking PldB bypass the need for CMF and can aggregate at low cell density, whereas cells overexpressing pldB do not aggregate even at high cell density. Here, we found that PldB controlled both cAMP chemotaxis and cell sorting. PldB was also required by CMF to regulate G protein signaling. Specifically, CMF used PldB, to regulate the dissociation of Galpha2 from Gbetagamma. Using fluorescence resonance energy transfer (FRET), we found that along with cAMP, CMF increased the dissociation of the G protein. In fact, CMF augmented the dissociation induced by cAMP. This augmentation was lost in cells lacking PldB. PldB appears to mediate the CMF signal through the production of phosphatidic acid, as exogenously added phosphatidic acid phenocopies overexpression of pldB. These results suggest that phospholipase D activity is required for CMF to alter the kinetics of cAMP-induced G protein signaling.

Riyahi, T. Y., F. Frese, et al. (2011). "RpkA, a highly conserved GPCR with a lipid kinase domain, has a role in phagocytosis and anti-bacterial defense." PLoS One 6(11): e27311.
	RpkA (Receptor phosphatidylinositol kinase A) is an unusual seven-helix transmembrane protein of Dictyostelium discoideum with a G protein coupled receptor (GPCR) signature and a C-terminal lipid kinase domain (GPCR-PIPK) predicted as a phosphatidylinositol-4-phosphate 5-kinase. RpkA-homologs are present in all so far sequenced Dictyostelidae as well as in several other lower eukaryotes like the oomycete Phytophthora, and in the Legionella host Acanthamoeba castellani. Here we show by immunofluorescence that RpkA localizes to endosomal membranes and is specifically recruited to phagosomes. RpkA interacts with the phagosomal protein complex V-ATPase as proteins of this complex co-precipitate with RpkA-GFP as well as with the GST-tagged PIPK domain of RpkA. Loss of RpkA leads to a defect in phagocytosis as measured by yeast particle uptake. The uptake of the pathogenic bacterium Legionella pneumophila was however unaltered whereas its intra-cellular replication was significantly enhanced in rpkA(-). The difference between wild type and rpkA(-) was even more prominent when L. hackeliae was used. When we investigated the reason for the enhanced susceptibility for L. pneumophila of rpkA(-) we could not detect a difference in endosomal pH but rpkA(-) showed depletion of phosphoinositides (PIP and PIP(2)) when we compared metabolically labeled phosphoinositides from wild type and rpkA(-). Furthermore rpkA(-) exhibited reduced nitrogen starvation tolerance, an indicator for a reduced autophagy rate. Our results indicate that RpkA is a component of the defense system of D. discoideum as well as other lower eukaryotes.

Roberge-White, E. and M. Katoh-Kurasawa (2011). "Plasticity in the development and dedifferentiation of Dictyostelium discoideum." Dev Growth Differ 53(4): 587-596.
	Dictyostelium discoideum has served as a model for development and differentiation for over 70 years. Also regulated in Dictyostelium is the process of dedifferentiation, which consists of multiple cellular events that are separately regulated, providing an excellent model system for studying the return of partially differentiated cells to a more pluripotent state. An interesting aspect of Dictyostelium development is the plasticity between growth and development. Reversibility of the processes of differentiation and dedifferentiation exist, allowing Dictyostelium to adjust to changing conditions by reverting to the growth phase during differentiation or reinitiating development during dedifferentiation. This ability of cells to respond to environmental cues is mediated by the checkpoint-like events "commitment" and "erasure," which occur during differentiation and dedifferentiation, respectively. Our review will discuss the current state of knowledge regarding dedifferentiation and the plasticity of the developmental process in both the forward and reverse directions.

Robery, S., J. Mukanowa, et al. (2011). "Investigating the effect of emetic compounds on chemotaxis in Dictyostelium identifies a non-sentient model for bitter and hot tastant research." PLoS One 6(9): e24439.
	Novel chemical entities (NCEs) may be investigated for emetic liability in a range of unpleasant experiments involving retching, vomiting or conditioned taste aversion/food avoidance in sentient animals. We have used a range of compounds with known emetic /aversive properties to examine the possibility of using the social amoeba, Dictyostelium discoideum, for research into identifying and understanding emetic liability, and hence reduce adverse animal experimentation in this area. Twenty eight emetic or taste aversive compounds were employed to investigate the acute (10 min) effect of compounds on Dictyostelium cell behaviour (shape, speed and direction of movement) in a shallow chemotaxic gradient (Dunn chamber). Compound concentrations were chosen based on those previously reported to be emetic or aversive in in vivo studies and results were recorded and quantified by automated image analysis. Dictyostelium cell motility was rapidly and strongly inhibited by four structurally distinct tastants (three bitter tasting compounds--denatonium benzoate, quinine hydrochloride, phenylthiourea, and the pungent constituent of chilli peppers--capsaicin). In addition, stomach irritants (copper chloride and copper sulphate), and a phosphodiesterase IV inhibitor also rapidly blocked movement. A concentration-dependant relationship was established for five of these compounds, showing potency of inhibition as capsaicin (IC(50) = 11.9 +/- 4.0 microM) &gt; quinine hydrochloride (IC(50) = 44.3 +/- 6.8 microM) &gt; denatonium benzoate (IC(50) = 129 +/- 4 microM) &gt; phenylthiourea (IC(50) = 366 +/- 5 microM) &gt; copper sulphate (IC(50) = 1433 +/- 3 microM). In contrast, 21 compounds within the cytotoxic and receptor agonist/antagonist classes did not affect cell behaviour. Further analysis of bitter and pungent compounds showed that the effect on cell behaviour was reversible and not cytotoxic, suggesting an uncharacterised molecular mechanism of action for these compounds. These results therefore demonstrate that Dictyostelium has potential as a non-sentient model in the analysis of the molecular effects of tastants, although it has limited utility in identification of emetic agents in general.

Romeralo, M., J. C. Cavender, et al. (2011). "An expanded phylogeny of social amoebas (Dictyostelia) shows increasing diversity and new morphological patterns." BMC Evol Biol 11: 84.
	BACKGROUND: Social Amoebae or Dictyostelia are eukaryotic microbes with a unique life cycle consisting of both uni- and multicellular stages. They have long fascinated molecular, developmental and evolutionary biologists, and Dictyostelium discoideum is now one of the most widely studied eukaryotic microbial models. The first molecular phylogeny of Dictyostelia included most of the species known at the time and suggested an extremely deep taxon with a molecular depth roughly equivalent to Metazoa. The group was also shown to consist of four major clades, none of which correspond to traditional genera. Potential morphological justification was identified for three of the four major groups, on the basis of which tentative names were assigned. RESULTS: Over the past four years, the Mycetozoan Global Biodiversity Survey has identified many new isolates that appear to be new species of Dictyostelia, along with numerous isolates of previously described species. We have determined 18S ribosomal RNA gene sequences for all of these new isolates. Phylogenetic analyses of these data show at least 50 new species, and these arise from throughout the dictyostelid tree breaking up many previously isolated long branches. The resulting tree now shows eight well-supported major groups instead of the original four. The new species also expand the known morphological diversity of the previously established four major groups, violating nearly all previously suggested deep morphological patterns. CONCLUSIONS: A greatly expanded phylogeny of Dictyostelia now shows even greater morphological plasticity at deep taxonomic levels. In fact, there now seem to be no obvious deep evolutionary trends across the group. However at a finer level, patterns in morphological character evolution are beginning to emerge. These results also suggest that there is a far greater diversity of Dictyostelia yet to be discovered, including novel morphologies.

Romeralo, M., R. Escalante, et al. (2011). "Evolution and Diversity of Dictyostelid Social Amoebae." Protist.
	Dictyostelid social amoebae are a large and ancient group of soil microbes with an unusual multicellular stage in their life cycle. Taxonomically, they belong to the eukaryotic supergroup Amoebozoa, the sister group to Opisthokonta (animals + fungi). Roughly half of the approximately 150 known dictyostelid species were discovered during the last five years and probably many more remain to be found. The traditional classification system of Dictyostelia was completely overturned by cladistic analyses and molecular phylogenies of the past six years. As a result, it now appears that, instead of three major divisions there are eight, none of which correspond to traditional higher-level taxa. In addition to the widely studied Dictyostelium discoideum, there are now efforts to develop model organisms and complete genome sequences for each major group. Thus Dictyostelia is becoming an excellent model for both practical, medically related research and for studying basic principles in cell-cell communication and developmental evolution. In this review we summarize the latest information about their life cycle, taxonomy, evolutionary history, genome projects and practical importance.

Romeralo, M., J. Moya-Larano, et al. (2011). "Social amoebae: environmental factors influencing their distribution and diversity across south-western Europe." Microb Ecol 61(1): 154-165.
	The social amoebae (dictyostelids) are the only truly multicellular lineage within the superkingdom Amoebozoa, the sister group to Ophistokonts (Metazoa+Fungi). Despite the exceptional phylogenetic and evolutionary value of this taxon, the environmental factors that determine their distribution and diversity are largely unknown. We have applied statistical modeling to a set of data obtained from an extensive and detailed survey in the south-western of Europe (The Iberian Peninsula including Spain and Portugal) in order to estimate some of the main environmental factors influencing the distribution and diversity of dictyostelid in temperate climates. It is the first time that this methodology is applied to the study of this unique group of soil microorganisms. Our results show that a combination of climatic (temperature, water availability), physical (pH) and vegetation (species richness) factors favor dictyostelid species richness. In the Iberian Peninsula, dictyostelid diversity is highest in colder and wet environments, indicating that this group has likely diversified in relatively cold places with high levels of water availability.

Rump, A., T. Scholz, et al. (2011). "Myosin-1C associates with microtubules and stabilizes the mitotic spindle during cell division." J Cell Sci 124(Pt 15): 2521-2528.
	The mitotic spindle in eukaryotic cells is composed of a bipolar array of microtubules (MTs) and associated proteins that are required during mitosis for the correct partitioning of the two sets of chromosomes to the daughter cells. In addition to the well-established functions of MT-associated proteins (MAPs) and MT-based motors in cell division, there is increasing evidence that the F-actin-based myosin motors are important mediators of F-actin-MT interactions during mitosis. Here, we report the functional characterization of the long-tailed class-1 myosin myosin-1C from Dictyostelium discoideum during mitosis. Our data reveal that myosin-1C binds to MTs and has a role in maintenance of spindle stability for accurate chromosome separation. Both myosin-1C motor function and tail-domain-mediated MT-F-actin interactions are required for the cell-cycle-dependent relocalization of the protein from the cell periphery to the spindle. We show that the association of myosin-1C with MTs is mediated through the tail domain. The myosin-1C tail can inhibit kinesin motor activity, increase the stability of MTs, and form crosslinks between MTs and F-actin. These data illustrate that myosin-1C is involved in the regulation of MT function during mitosis in D. discoideum.

Samereier, M., O. Baumann, et al. (2011). "Analysis of Dictyostelium TACC reveals differential interactions with CP224 and unusual dynamics of Dictyostelium microtubules." Cell Mol Life Sci 68(2): 275-287.
	We have localized TACC to the microtubule-nucleating centrosomal corona and to microtubule plus ends. Using RNAi we proved that Dictyostelium TACC promotes microtubule growth during interphase and mitosis. For the first time we show in vivo that both TACC and XMAP215 family proteins can be differentially localized to microtubule plus ends during interphase and mitosis and that TACC is mainly required for recruitment of an XMAP215-family protein to interphase microtubule plus ends but not for recruitment to centrosomes and kinetochores. Moreover, we have now a marker to study dynamics and behavior of microtubule plus ends in living Dictyostelium cells. In a combination of live cell imaging of microtubule plus ends and fluorescence recovery after photobleaching (FRAP) experiments of GFP-alpha-tubulin cells we show that Dictyostelium microtubules are dynamic only in the cell periphery, while they remain stable at the centrosome, which also appears to harbor a dynamic pool of tubulin dimers.

Sanchez, C. (2011). "Microbial genetics: social amoebae get ready for sex." Nat Rev Microbiol 9(2): 79.
	
Schaap, P. (2011). "Evolution of developmental cyclic adenosine monophosphate signaling in the Dictyostelia from an amoebozoan stress response." Dev Growth Differ 53(4): 452-462.
	The Dictyostelid social amoebas represent one of nature's several inventions of multicellularity. Though normally feeding as single cells, nutrient stress triggers the collection of amoebas into colonies that form delicately shaped fruiting structures in which the cells differentiate into spores and up to three cell types to support the spore mass. Cyclic adenosine monophosphate (cAMP) plays a very dominant role in controlling morphogenesis and cell differentiation in the model species Dictyostelium discoideum. As a secreted chemoattractant cAMP coordinates cell movement during aggregation and fruiting body morphogenesis. Secreted cAMP also controls gene expression at different developmental stages, while intracellular cAMP is extensively used to transduce the effect of other stimuli that control the developmental program. In this review, I present an overview of the different roles of cAMP in the model D. discoideum and I summarize studies aimed to resolve how these roles emerged during Dictyostelid evolution.

Schaap, P. (2011). "Evolutionary crossroads in developmental biology: Dictyostelium discoideum." Development 138(3): 387-396.
	Dictyostelium discoideum belongs to a group of multicellular life forms that can also exist for long periods as single cells. This ability to shift between uni- and multicellularity makes the group ideal for studying the genetic changes that occurred at the crossroads between uni- and multicellular life. In this Primer, I discuss the mechanisms that control multicellular development in Dictyostelium discoideum and reconstruct how some of these mechanisms evolved from a stress response in the unicellular ancestor.

Schafer, E., C. Westendorf, et al. (2011). "Shape oscillations of Dictyostelium discoideum cells on ultramicroelectrodes monitored by impedance analysis." Small 7(6): 723-726.
	
Schonitzer, V., N. Eichner, et al. (2011). "Transmembrane myosin chitin synthase involved in mollusc shell formation produced in Dictyostelium is active." Biochem Biophys Res Commun 415(4): 586-590.
	Several mollusc shells contain chitin, which is formed by a transmembrane myosin motor enzyme. This protein could be involved in sensing mechanical and structural changes of the forming, mineralizing extracellular matrix. Here we report the heterologous expression of the transmembrane myosin chitin synthase Ar-CS1 of the bivalve mollusc Atrina rigida (2286 amino acid residues, M.W. 264 kDa/monomer) in Dictyostelium discoideum, a model organism for myosin motor proteins. Confocal laser scanning immunofluorescence microscopy (CLSM), chitin binding GFP detection of chitin on cells and released to the cell culture medium, and a radiochemical activity assay of membrane extracts revealed expression and enzymatic activity of the mollusc chitin synthase in transgenic slime mold cells. First high-resolution atomic force microscopy (AFM) images of Ar-CS1 transformed cellulose synthase deficient D. discoideumdcsA(-) cell lines are shown.

Serfontein, J., R. E. Nisbet, et al. (2011). "Conservation of structural and functional elements of TSC1 and TSC2: a bioinformatic comparison across animal models." Behav Genet 41(3): 349-356.
	The tuberous sclerosis complex 1/2-mammalian target of rapamycin (TSC1/2-mTOR) proteins act as integrators of a range of intracellular signalling pathways. Various genetic disorders associated with learning and behavioural deficits, including TSC, Fragile X, Neurofibromatosis Type 1, Noonan and Leopard syndromes, are associated with abnormalities in TSC-mTOR signalling. Based on the assumption that signalling proteins and their structural and functional components are widely conserved, a number of animal models are used to study aspects of the physical and behavioural phenotypes of these human disorders. Model organisms include rat (Rattus norvegicus), mouse (Mus musculus), zebrafish (Danio rerio), fruitfly (Drosophila melanogaster) and fission yeast (Schizosaccharomyces pombe). Here we used a bioinformatic approach to examine the presence of structural and functional elements of TSC1 and TSC2 across these organisms, together with Strongylocentrotus purpuratus and Dictyostelium discoideum. Results suggest that while Rattus norvegicus and Mus musculus TSC1 and TSC2 showed very high similarity to the human sequences, this was not the case for Danio rerio, Drosophila melanogaster, Strongylocentrotus purpuratus, Schizosaccharomyces pombe or Disctyostelium discoideum. Findings indicate that caution should be exercised in detailed interpretation of results from some model organisms.

Serge, A., S. de Keijzer, et al. (2011). "Quantification of GPCR internalization by single-molecule microscopy in living cells." Integr Biol (Camb) 3(6): 675-683.
	Receptor internalization upon ligand stimulation is a key component of a cell's response and allows a cell to correctly sense its environment. Novel fluorescent methods have enabled the direct visualization of the agonist-stimulated G-protein-coupled receptors (GPCR) trafficking in living cells. However, it is difficult to observe internalization of GPCRs in vivo due to intrinsic autofluorescence and cytosolic signals of fluorescently labeled GPCRs. This study uses the superior positional accuracy of single-molecule fluorescence microscopy to visualize in real time the internalization of Dictyostelium discoideum cAMP receptors, cAR1, genetically encoded with eYFP. This technique made it possible to follow the number of receptors in time revealing that the fraction of cytosolic receptors increases after persistent agonist stimulation and that the majority of the receptors were degraded after internalization. The observed internalization process was phosphorylation dependent, as shown with the use of a phosphorylation deficient cAR1 mutant, cm1234-eYFP, or stimulation with an antagonist, Rp-cAMPS that does not induce receptor phosphorylation. Furthermore, experiments done in mound-stage cells suggest that intrinsic, phosphorylation-induced internalization of cAR1 is necessary for Dictyostelium wild type cells to progress properly through multicellular development. To our knowledge, this observation illustrates for the first time phosphorylation-dependent internalization of single cAR1 molecules in living cells and its involvement in multicellular development. This very sensitive imaging of receptor internalization can be a useful and universal approach for pharmacological characterization of GPCRs in other cell types.

Shen, B., Y. Fang, et al. (2011). "Biogenesis of the posterior pole is mediated by the exosome/microvesicle protein-sorting pathway." J Biol Chem 286(51): 44162-44176.
	Biogenesis of the posterior pole is critical to directed cell migration and other polarity-dependent processes. We show here that proteins are targeted to the posterior pole on the basis of higher order oligomerization and plasma membrane binding, the same elements that target proteins to exosomes/microvesicles (EMVs), HIV, and other retrovirus particles. We also demonstrate that the polarization of the EMV protein-sorting pathway can occur in morphologically non-polarized cells, defines the site of uropod formation, is induced by increased expression of EMV cargo proteins, and is evolutionarily conserved between humans and the protozoan Dictyostelium discoideum. Based on these results, we propose a mechanism of posterior pole biogenesis in which elevated levels of EMV cargoes (i) polarize the EMV protein-sorting pathway, (ii) generate a nascent posterior pole, and (iii) prime cells for signal-induced biogenesis of a uropod. This model also offers a mechanistic explanation for the polarized budding of EMVs and retroviruses, including HIV.

Shen, H. M. and P. Codogno (2011). "Autophagic cell death: Loch Ness monster or endangered species?" Autophagy 7(5): 457-465.
	The concept of autophagic cell death was first established based on observations of increased autophagic markers in dying cells. The major limitation of such a morphology-based definition of autophagic cell death is that it fails to establish the functional role of autophagy in the cell death process, and thus contributes to the confusion in the literature regarding the role of autophagy in cell death and cell survival. Here we propose to define autophagic cell death as a modality of non-apoptotic or necrotic programmed cell death in which autophagy serves as a cell death mechanism, upon meeting the following set of criteria: (i) cell death occurs without the involvement of apoptosis; (ii) there is an increase of autophagic flux, and not just an increase of the autophagic markers, in the dying cells; and (iii) suppression of autophagy via both pharmacological inhibitors and genetic approaches is able to rescue or prevent cell death. In light of this new definition, we will discuss some of the common problems and difficulties in the study of autophagic cell death and also revisit some well-reported cases of autophagic cell death, aiming to achieve a better understanding of whether autophagy is a real killer, an accomplice or just an innocent bystander in the course of cell death. At present, the physiological relevance of autophagic cell death is mainly observed in lower eukaryotes and invertebrates such as Dictyostelium discoideum and Drosophila melanogaster. We believe that such a clear definition of autophagic cell death will help us study and understand the physiological or pathological relevance of autophagic cell death in mammals.

Shina, M. C., A. Muller-Taubenberger, et al. (2011). "Redundant and unique roles of coronin proteins in Dictyostelium." Cell Mol Life Sci 68(2): 303-313.
	Dictyostelium discoideum harbors a short (CRN12) and a long coronin (CRN7) composed of one and two beta-propellers, respectively. They are primarily present in the cell cortex and cells lacking CRN12 (corA) or CRN7 (corB) have defects in actin driven processes. We compared the characteristics of a mutant cell line (corA/corB) lacking CRN12 and CRN7 with the single mutants focusing on cytokinesis, phagocytosis, chemotaxis and development. Cytokinesis, uptake of small particles, and developmental defects were not enhanced in the corA/corB strain as compared to the single mutants, whereas motility and phagocytosis of yeast particles were more severely impaired. It appears that although both proteins affect the same processes they do not act in a redundant manner. Rather, they often act antagonistically, which is in accordance with their proposed roles in the actin cytoskeleton where CRN12 acts in actin disassembly whereas CRN7 stabilizes actin filaments and protects them from disassembly.

Sillo, A., J. Matthias, et al. (2011). "Salmonella typhimurium is pathogenic for Dictyostelium cells and subverts the starvation response." Cell Microbiol 13(11): 1793-1811.
	In unicellular amoebae, such as Dictyostelium discoideum, bacterial phagocytosis is a food hunting device, while in higher organisms it is the first defence barrier against microbial infection. In both cases, pathogenic bacteria exploit phagocytosis to enter the cell and multiply intracellularly. Salmonella typhimurium, the agent of food-borne gastroenteritis, is phagocytosed by both macrophages and Dictyostelium cells. By using cell biological assays and global transcriptional analysis with DNA microarrays covering the Dictyostelium genome, we show here that S. typhimurium is pathogenic for Dictyostelium cells. Depending on the degree of virulence, which in turn depended on bacterial growth conditions, Salmonella could kill Dictyostelium cells or inhibit their growth and development. In the early phase of infection in non-nutrient buffer, the ingested bacteria escaped degradation, induced a starvation-like transcriptional response but inhibited selectively genes required for chemotaxis and aggregation. This way differentiation of the host cells into spore and stalk cells was blocked or delayed, which in turn is likely to be favourable for the establishment of a replicative niche for Salmonella. Inhibition of the aggregation competence and chemotactic streaming of aggregation-competent cells in the presence of Salmonella suggests interference with cAMP signalling.

Siol, O., T. Spaller, et al. (2011). "Genetically tagged TRE5-A retrotransposons reveal high amplification rates and authentic target site preference in the Dictyostelium discoideum genome." Nucleic Acids Res 39(15): 6608-6619.
	Retrotransposons contribute significantly to the evolution of eukaryotic genomes. They replicate by producing DNA copies of their own RNA, which are integrated at new locations in the host cell genome. In the gene-dense genome of the social amoeba Dictyostelium discoideum, retrotransposon TRE5-A avoids insertional mutagenesis by targeting the transcription factor (TF) IIIC/IIIB complex and integrating approximately 50 bp upstream of tRNA genes. We generated synthetic TRE5-A retrotransposons (TRE5-A(bsr)) that were tagged with a selection marker that conferred resistance to blasticidin after a complete retrotransposition cycle. We found that the TRE5-A(bsr) elements were efficiently mobilized in trans by proteins expressed from the endogenous TRE5-A population found in D. discoideum cells. ORF1 protein translated from TRE5-A(bsr) elements significantly enhanced retrotransposition. We observed that the 5' untranslated region of TRE5-A could be replaced by an unrelated promoter, whereas the 3' untranslated region of TRE5-A was essential for retrotransposition. A predicted secondary structure in the RNA of the 3' untranslated region of TRE5-A may be involved in the retrotransposition process. The TRE5-A(bsr) elements were capable of identifying authentic integration targets in vivo, including formerly unnoticed, putative binding sites for TFIIIC on the extrachromosomal DNA element that carries the ribosomal RNA genes.

Siu, C. H., S. Sriskanthadevan, et al. (2011). "Regulation of spatiotemporal expression of cell-cell adhesion molecules during development of Dictyostelium discoideum." Dev Growth Differ 53(4): 518-527.
	The social amoeba Dictyostelium discoideum is a simple but powerful model organism for the study of cell-cell adhesion molecules and their role in morphogenesis during development. Three adhesive systems have been characterized and studied in detail. The spatiotemporal expression of these adhesion proteins is stringently regulated, often coinciding with major shifts in the morphological complexity of development. At the onset of development, amoeboid cells express the Ca(2+) -dependent cell-cell adhesion molecule DdCAD-1, which initiates weak homophilic interactions between cells and assists in the recruitment of individuals into cell streams. DdCAD-1 is unique because it is synthesized as a soluble protein in the cytoplasm. It is targeted for presentation on the cell surface by an unconventional protein transport mechanism via the contractile vacuole. Concomitant with the aggregation stage is the expression of the contact sites A glycoprotein csA/gp80 and TgrC1, both of which mediate Ca(2+) /Mg(2+) -independent cell-cell adhesion. Whereas csA/gp80 is a homophilic binding protein, TgrC1 binds to a heterophilic receptor on the cell. During cell aggregation, csA/gp80 associates preferentially with lipid rafts, which facilitate the rapid assembly of adhesion complexes. TgrC1 is synthesized at low levels during aggregation and rapid accumulation occurs initially in the peripheral cells of loose mounds. The extracellular portion of TgrC1 is shed and becomes part of the extracellular matrix. Additionally, analyses of knockout mutants have revealed important biological roles played by these adhesion proteins, including size regulation, cell sorting and cell-type proportioning.

Sprio, A. E., F. Di Scipio, et al. (2011). "Differentiation-inducing factor-1 enhances 5-fluorouracil action on oral cancer cells inhibiting E2F1 and thymidylate synthase mRNAs accumulation." Cancer Chemother Pharmacol.
	PURPOSE: Differentiation-inducing factor-1 (DIF-1) is a morphogen originally identified in the amoebozoan Dictyostelium discoideum. In mammalian cells, it has been shown to activate GSK3beta, which in turn is expected to reduce levels of beta-catenin and cyclin D1, thus mediating DIF-1 antiproliferative properties. Since this could alter the expression and activity of E2F1 transcription factor and consequently those of the prognostic marker/chemotherapy target thymidylate synthase (TS), we evaluated (1) whether DIF-1 could effectively regulate these genes, (2) whether it could interfere with cell viability, and (3) whether DIF-1 activity could enhance the efficacy of the TS inhibitor 5-fluorouracil (5-FU). METHODS: We investigated the effects of DIF-1 in continuous human cell lines derived from two oral tumor histotypes (corresponding to an adenosquamous and a squamous carcinoma) and a gingival epithelium. We evaluated mRNA accumulation by means of quantitative real-time PCR and efficacy of drugs on cell viability by means of MTT assay. RESULTS: DIF-1 inhibited the accumulation of E2F1 mRNA and reduces TS mRNA levels in tumor cell lines, but did not alter mRNA levels in the gingival counterpart. As a result, it inhibited proliferation preferentially of tumor cell in time- and concentration-dependent manner. Moreover, it enhanced cytotoxic effects of 5-FU only in tumor cell, whereas reduced them in the gingival counterpart. CONCLUSIONS: These findings suggest a tumor-specific action of DIF-1 on oral carcinoma cells. Thus, interfering with E2F1 and TS transcription, DIF-1 potentiates TS enzymatic inhibitors.

Sriskanthadevan, S., Y. Zhu, et al. (2011). "The cell adhesion molecule DdCAD-1 regulates morphogenesis through differential spatiotemporal expression in Dictyostelium discoideum." Development 138(12): 2487-2497.
	During development of Dictyostelium, multiple cell types are formed and undergo a coordinated series of morphogenetic movements guided by their adhesive properties and other cellular factors. DdCAD-1 is a unique homophilic cell adhesion molecule encoded by the cadA gene. It is synthesized in the cytoplasm and transported to the plasma membrane by contractile vacuoles. In chimeras developed on soil plates, DdCAD-1-expressing cells showed greater propensity to develop into spores than did cadA-null cells. When development was performed on non-nutrient agar, wild-type cells sorted from the cadA-null cells and moved to the anterior zone. They differentiated mostly into stalk cells and eventually died, whereas the cadA-null cells survived as spores. To assess the role of DdCAD-1 in this novel behavior of wild-type and mutant cells, cadA-null cells were rescued by the ectopic expression of DdCAD-1-GFP. Morphological studies have revealed major spatiotemporal changes in the subcellular distribution of DdCAD-1 during development. Whereas DdCAD-1 became internalized in most cells in the post-aggregation stages, it was prominent in the contact regions of anterior cells. Cell sorting was also restored in cadA(-) slugs by exogenous recombinant DdCAD-1. Remarkably, DdCAD-1 remained on the surface of anterior cells, whereas it was internalized in the posterior cells. Additionally, DdCAD-1-expressing cells migrated slower than cadA(-) cells and sorted to the anterior region of chimeric slugs. These results show that DdCAD-1 influences the sorting behavior of cells in slugs by its differential distribution on the prestalk and prespore cells.

St Michael, F., C. Cairns, et al. (2011). "Investigating the candidacy of lipopolysaccharide-based glycoconjugates as vaccines to combat Mannheimia haemolytica." Glycoconj J 28(6): 397-410.
	Inner core lipopolysaccharide (LPS) has been shown to be conserved in the majority of veterinary strains from the species Mannheimia haemolytica, Actinobacillus pleuropneumoniae and Pasteurella multocida and as such is being considered as a possible vaccine antigen. The proof-in-principle that a LPS-based antigen could be considered as a vaccine candidate has been demonstrated from studies with monoclonal antibodies raised to the inner core LPS of Mannheimia haemolytica, which were shown to be both bactericidal and protective in a mouse model of disease. In this study we confirm and extend the candidacy of the inner core LPS by demonstrating that it is possible to elicit functional antibodies against Mannheimia haemolytica wild-type strains following immunisation of rabbits with glycoconjugates elaborating the conserved inner core LPS antigen. The present study describes a conjugation strategy that uses amidases produced by Dictyostelium discoideum, targeting the amino functionality created by the amidase activity as the attachment point on the LPS molecule. To protect the amino functionality on the phosphoethanolamine (PEtn) residue of the inner core, we developed a novel blocking and unblocking strategy with t-butyl oxycarbonyl. A maleimide-thiol linker strategy with the thiol linker on the carboxyl residues of the carrier protein and the maleimide linker on the carbohydrate resulted in a high loading of carbohydrates per carrier protein. Immunisation derived antisera from rabbits recognised fully extended Mannheimia haemolytica LPS and whole cells from serotypes 1 and 2, despite a somewhat immunodominant response to the linkers also being observed. Moreover, bactericidal activity was demonstrated to a strain elaborating the immunising carbohydrate antigen and crucially to wild-type cells of serotypes 1 and 2, thus further supporting the consideration of inner core LPS as a potential vaccine antigen to combat disease caused by Mannheimia haemolytica.

Steinert, M. (2011). "Pathogen-host interactions in Dictyostelium, Legionella, Mycobacterium and other pathogens." Semin Cell Dev Biol 22(1): 70-76.
	Dictyostelium discoideum is a haploid social soil amoeba that is an established host model for several human pathogens. The research areas presently pursued include the use of D. discoideum to identify genetic host factors determining the outcome of infections and the use as screening system for identifying bacterial virulence factors. Here we report about the Legionella pneumophila directed phagosome biogenesis and the cell-to-cell spread of Mycobacterium species. Moreover, we highlight recent insights from the host-pathogen cross-talk between D. discoideum and the pathogens Salmonella typhimurium, Klebsiella pneumoniae, Yersinia pseudotuberculosis, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Burkholderia cenocepacia, Vibrio cholerae and Neisseria meningitidis.

Stevense, M., J. R. Chubb, et al. (2011). "Nuclear organization and transcriptional dynamics in Dictyostelium." Dev Growth Differ 53(4): 576-586.
	The Dictyostelium model has a set of features uniquely well-suited to developing our understanding of transcriptional control. The complete Dictyostelium discoideum genome sequence has revealed that many of the molecular components regulating transcription in larger eukaryotes are conserved in Dictyostelium, from transcription factors and chromatin components to the enzymes and signals that regulate them. In addition, the system permits visualization of single gene firing events in living cells, which provides a more detailed view of transcription and its relationships to cell and developmental processes. This review will bring together the available knowledge of the structure and dynamics of the Dictyostelium nucleus and discuss recent transcription imaging studies and their implications for stability and accuracy of cell decisions.

Strassmann, J. E. and D. C. Queller (2011). "Evolution of cooperation and control of cheating in a social microbe." Proc Natl Acad Sci U S A 108 Suppl 2: 10855-10862.
	Much of what we know about the evolution of altruism comes from animals. Here, we show that studying a microbe has yielded unique insights, particularly in understanding how social cheaters are controlled. The social stage of Dictylostelium discoideum occurs when the amoebae run out of their bacterial prey and aggregate into a multicellular, motile slug. This slug forms a fruiting body in which about a fifth of cells die to form a stalk that supports the remaining cells as they form hardy dispersal-ready spores. Because this social stage forms from aggregation, it is analogous to a social group, or a chimeric multicellular organism, and is vulnerable to internal conflict. Advances in cell labeling, microscopy, single-gene knockouts, and genomics, as well as the results of decades of study of D. discoideum as a model for development, allow us to explore the genetic basis of social contests and control of cheaters in unprecedented detail. Cheaters are limited from exploiting other clones by high relatedness, kin discrimination, pleiotropy, noble resistance, and lottery-like role assignment. The active nature of these limits is reflected in the elevated rates of change in social genes compared with nonsocial genes. Despite control of cheaters, some conflict is still expressed in chimeras, with slower movement of slugs, slightly decreased investment in stalk compared with spore cells, and differential contributions to stalk and spores. D. discoideum is rapidly becoming a model system of choice for molecular studies of social evolution.

Strassmann, J. E. and D. C. Queller (2011). "How social evolution theory impacts our understanding of development in the social amoeba Dictyostelium." Dev Growth Differ 53(4): 597-607.
	Dictyostelium discoideum has been very useful for elucidating principles of development over the last 50 years, but a key attribute means there is a lot to be learned from a very different intellectual tradition: social evolution. Because Dictyostelium arrives at multicellularity by aggregation instead of through a single-cell bottleneck, the multicellular body could be made up of genetically distinct cells. If they are genetically distinct, natural selection will result in conflict over which cells become fertile spores and which become dead stalk cells. Evidence for this conflict includes unequal representation of two genetically different clones in spores of a chimera, the poison-like differentiation inducing factor (DIF) system that appears to involve some cells forcing others to become stalk, and reduced functionality in migrating chimeras. Understanding how selection operates on chimeras of genetically distinct clones is crucial for a comprehensive view of Dictyostelium multicellularity. In nature, Dictyostelium fruiting bodies are often clonal, or nearly so, meaning development will often be very cooperative. Relatedness levels tell us what benefits must be present for sociality to evolve. Therefore it is important to measure relatedness in nature, show that it has an impact on cooperation in the laboratory, and investigate genes that Dictyostelium uses to discriminate between relatives and non-relatives. Clearly, there is a promising future for research at the interface of development and social evolution in this fascinating group.

Suarez, A., R. J. Huber, et al. (2011). "An extracellular matrix, calmodulin-binding protein from Dictyostelium with EGF-like repeats that enhance cell motility." Cell Signal 23(7): 1197-1206.
	CyrA is a novel cysteine-rich protein with four EGFL repeats that was isolated using the calmodulin (CaM) binding overlay technique (CaMBOT), suggesting it is a CaM-binding protein (CaMBP). The full-length 63kDa cyrA is cleaved into two major C-terminal fragments, cyrA-C45 and cyrA-C40. A putative CaM-binding domain was detected and both CaM-agarose binding and CaM immunoprecipitation verified that cyrA-C45 and cyrA-C40 each bind to CaM in both a Ca(2+)-dependent and -independent manner. cyrA-C45 was present continuously throughout growth and development but was secreted at high levels during the multicellular slug stage of Dictyostelium development. At this time, cyrA localizes to the extracellular matrix (ECM). ECM purification verified the presence of cyrA-C45. An 18 amino acid peptide (DdEGFL1) from the first EGFL repeat sequence of cyrA (EGFL1) that is present in both cyrA-C45 and -C40 enhances both random cell motility and cAMP-mediated chemotaxis. Here we reveal that the dose-dependent enhancement of motility by DdEGFL1 is related to the time of cell starvation. Addition of DdEGFL1 also inhibits cyrA proteolysis. The status of cyrA as an extracellular CaMBP was further clarified by the demonstration that CaM is secreted during development. Antagonism of CaM with W7 resulted in enhanced cyrA proteolysis suggesting a functional role for extracellular CaM in protecting CaMBPs from proteolysis. cyrA is the first extracellular CaMBP identified in Dictyostelium and since it is an ECM protein with EGF-like repeats that enhance cell motility and it likely also represents the first matricellular protein identified in a lower eukaryote.

Sucgang, R., A. Kuo, et al. (2011). "Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum." Genome Biol 12(2): R20.
	BACKGROUND: The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. RESULTS: We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 x coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict. CONCLUSIONS: The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.

Sugden, C., S. Ross, et al. (2011). "A Dictyostelium SH2 adaptor protein required for correct DIF-1 signaling and pattern formation." Dev Biol 353(2): 290-301.
	Dictyostelium is the only non-metazoan with functionally analyzed SH2 domains and studying them can give insights into their evolution and wider potential. LrrB has a novel domain configuration with leucine-rich repeat, 14-3-3 and SH2 protein-protein interaction modules. It is required for the correct expression of several specific genes in early development and here we characterize its role in later, multicellular development. During development in the light, slug formation in LrrB null (lrrB-) mutants is delayed relative to the parental strain, and the slugs are highly defective in phototaxis and thermotaxis. In the dark the mutant arrests development as an elongated mound, in a hitherto unreported process we term dark stalling. The developmental and phototaxis defects are cell autonomous and marker analysis shows that the pstO prestalk sub-region of the slug is aberrant in the lrrB- mutant. Expression profiling, by parallel micro-array and deep RNA sequence analyses, reveals many other alterations in prestalk-specific gene expression in lrrB- slugs, including reduced expression of the ecmB gene and elevated expression of ampA. During culmination ampA is ectopically expressed in the stalk, there is no expression of ampA and ecmB in the lower cup and the mutant fruiting bodies lack a basal disc. The basal disc cup derives from the pstB cells and this population is greatly reduced in the lrrB- mutant. This anatomical feature is a hallmark of mutants aberrant in signaling by DIF-1, the polyketide that induces prestalk and stalk cell differentiation. In a DIF-1 induction assay the lrrB- mutant is profoundly defective in ecmB activation but only marginally defective in ecmA induction. Thus the mutation partially uncouples these two inductive events. In early development LrrB interacts physically and functionally with CldA, another SH2 domain containing protein. However, the CldA null mutant does not phenocopy the lrrB- in its aberrant multicellular development or phototaxis defect, implying that the early and late functions of LrrB are affected in different ways. These observations, coupled with its domain structure, suggest that LrrB is an SH2 adaptor protein active in diverse developmental signaling pathways.

Sun, T. and L. Kim (2011). "Tyrosine phosphorylation-mediated signaling pathways in dictyostelium." J Signal Transduct 2011: 894351.
	While studies on metazoan cell proliferation, cell differentiation, and cytokine signaling laid the foundation of the current paradigms of tyrosine kinase signaling, similar studies using lower eukaryotes have provided invaluable insight for the understanding of mammalian pathways, such as Wnt and STAT pathways. Dictyostelium is one of the leading lower eukaryotic model systems where stress-induced cellular responses, Wnt-like pathways, and STAT-mediated pathways are well investigated. These Dictyostelium pathways will be reviewed together with their mammalian counterparts to facilitate the comparative understanding of these variant and noncanonical pathways.

Sunderland, M. E. (2011). "Morphogenesis, Dictyostelium, and the search for shared developmental processes." Stud Hist Philos Biol Biomed Sci 42(4): 508-517.
	In the 1930s John Tyler Bonner began studying the slime mold, Dictyostelium discoideum, as a way to investigate how organisms develop. With a life cycle that includes periods of unicellularity and multicellularity, Dictyostelium raises questions fundamental to development and evolution. In Morphogenesis: An Essay on Development (1952), Bonner built on his work with Dictyostelium to inform developmental theory and practice. By exploring how Bonner's early work with Dictyostelium motivated his synthetic approach in Morphogenesis, this paper presents an example of how those who studied development sought ways to gain traction in the rapidly changing life sciences. While a biochemical viewpoint of development became dominant, morphogenesis provided a way to reintroduce and emphasize biological organization at the organismal level. Bonner's early work offers a window to mid-twentieth century studies of development, an understudied area in the history of science, and shows that it was a time when growing experimental evidence enabled new ways of thinking about the relationship between ontogeny and evolution, and more broadly, about how the parts of nature might fit together.

Takahashi, K., M. Murakami, et al. (2011). "Derivatives of Dictyostelium differentiation-inducing factors promote mitogen-activated IL-2 production via AP-1 in Jurkat cells." Life Sci 88(11-12): 480-485.
	AIMS: Differentiation-inducing factors (DIFs) are chlorinated alkylphenones found in the cellular slime mold Dictyostelium discoideum. DIF derivatives exhibit antiproliferative activities and promote glucose consumption in mammalian cells in vitro. Here, we assessed the ability of DIFs to regulate the immune system in a mammalian cell-line and investigated their mechanisms of action. MAIN METHODS: We examined the effects of 30 DIF derivatives on concanavalin A-induced interleukin-2 (IL-2) production (CIIP) in Jurkat T-cells. We also examined the effects of these DIF derivatives on the activity of three transcription factors required for CIIP: namely, activator protein-1 (AP-1), nuclear factor of activated T-cells (NFAT), and nuclear factor kappa B (NFkappaB). KEY FINDINGS: A reporter gene assay suggested that 2 DIF derivatives, termed DIF-1(+1) and DIF-3(3M), significantly promoted CIIP in Jurkat cells, at least in part, by enhancing the activity of AP-1. These 2 DIF derivatives had no significant effect on concanavalin A-induced interferon-gamma production. SIGNIFICANCE: The results suggest that DIF derivatives could be developed as novel drugs for the activation of IL-2 production and resultant stimulation of the immune system.

Tang, M., M. Iijima, et al. (2011). "Disruption of PKB signaling restores polarity to cells lacking tumor suppressor PTEN." Mol Biol Cell 22(4): 437-447.
	By limiting phosphotidylinositol 3,4,5-triphosphate (PIP(3)) levels, tumor suppressor PTEN not only controls cell growth but also maintains cell polarity required for cytokinesis and chemotaxis. To identify the critical targets of PIP(3) that link it to the cytoskeleton, we deleted secondary genes to reverse the deficiencies of pten- cells in Dictyostelium. The polarity defects in pten- cells correlate with elevated phosphorylations of PKB substrates. Deletion of AKT orthologue, PkbA, or a subunit of its activator TORC2, reduced the phosphorylations and suppressed the cytokinesis and chemotaxis defects in pten- cells. In these double mutants, the excessive PIP(3) levels and, presumably, activation of other PIP(3)-binding proteins had little or no effect on the cytoskeleton. In bands with increased phosphorylation in pten- cells, we found PKB substrates, PI5K, GefS, GacG, and PakA. Disruption of PakA in pten- cells restored a large fraction of the cells to normal behavior. Consistently, expression of phosphomimetic PakA in pten- cells exacerbated the defects but nonphosphorylatable PakA had no effect. Thus, among many putative PTEN- and PIP(3)-dependent events, phosphorylation of PKB substrates is the key downstream regulator of cell polarity.

Terbach, N., R. Shah, et al. (2011). "Identifying an uptake mechanism for the antiepileptic and bipolar disorder treatment valproic acid using the simple biomedical model Dictyostelium." J Cell Sci 124(Pt 13): 2267-2276.
	Valproic acid (VPA) is the most highly prescribed epilepsy treatment worldwide and is also used to prevent bipolar disorder and migraine. Surprisingly, very little is known about its mechanisms of cellular uptake. Here, we employ a range of cellular, molecular and genetic approaches to characterize VPA uptake using a simple biomedical model, Dictyostelium discoideum. We show that VPA is taken up against an electrochemical gradient in a dose-dependent manner. Transport is protein-mediated, dependent on pH and the proton gradient and shows strong substrate structure specificity. Using a genetic screen, we identified a protein homologous to a mammalian solute carrier family 4 (SLC4) bicarbonate transporter that we show is involved in VPA uptake. Pharmacological and genetic ablation of this protein reduces the uptake of VPA and partially protects against VPA-dependent developmental effects, and extracellular bicarbonate competes for VPA uptake in Dictyostelium. We further show that this uptake mechanism is likely to be conserved in both zebrafish (Danio rerio) and Xenopus laevis model systems. These results implicate, for the first time, an uptake mechanism for VPA through SLC4-catalysed activity.

Thomas, A., M. Rey, et al. (2011). "A hybrid model to study pathological mutations of the human ADP/ATP carriers." Biochimie 93(9): 1415-1423.
	The adenine nucleotide carrier (Ancp) plays an essential role in the metabolism of cellular energy by catalyzing the transport of ADP and ATP across the inner mitochondrial membrane. Previous reports have indicated that mutations in the HANC1 gene, encoding the muscle isoform of human Ancp (HAnc1p), are directly involved in several diseases, including autosomal dominant progressive external ophthalmoplegia and cardiomyopathies. In this work, we studied three pathogenic HANC1 mutations at the biochemical level. To do so, we expressed the DdANCA gene, encoding the unique Ancp carrier of Dictyostelium discoideum (DdAncAp), in a yeast strain lacking all endogenous ANC genes. Our results indicate that DdAncAp is a good model for the human protein. It allows the carrier to be studied in yeast, and provides information on how the HANC1 mutations impair ADP/ATP transport in humans. A94D, A126D and V291M mutations, corresponding to A90D, A123D and V289M in HAnc1p, respectively, did not affect levels of DdAncAp in yeast mitochondria. However, while the wild-type DdAncAp fully restored growth of the ANC-null yeast strain on a non-fermentable carbon source, the carriers encompassing either the A94D or the A126D mutation failed to complement the null strain. The effect of the V291M mutation was not as pronounced, but led to impairment mainly of the nucleotide translocation process per se. These findings provide new insights into the mechanisms responsible for the diseases induced by HAnc1p mutations.

Tsujioka, M. (2011). "Cell migration in multicellular environments." Dev Growth Differ 53(4): 528-537.
	Most experiments observing cell migration use planar plastic or glass surfaces despite these conditions being considerably different from physiological ones. On such planar surfaces, cells take a dorsal-ventral polarity to move two-dimensionally. Cells in tissues, however, interact with surrounding cells and the extracellular matrix such that they transverse three-dimensionally. For this reason, three-dimensional matrices have become more and more popular for cell migration experiments. In addition, recent developments in imaging techniques have enabled high resolution observations of in vivo cell migration. The combination of three-dimensional matrices and such imaging techniques has revealed motile mechanisms in tissues not observable in studies using planar surfaces. Regarding models for such cell migration studies, the cellular slime mould Dictyostelium discoideum is ideal. Single amoeboid cells aggregate into hemispherical mound structures upon starvation to begin a multicellular morphogenesis. These tiny and simple multicellular bodies are suitable for observing the behaviors of individual cells in multicellular structures. Furthermore, the unique life cycle can be exploited to identify which genes are involved in cell migration in multicellular environments. Since mutants lacking such genes are expected to fail to undergo morphogenesis, easy and systematic gene screening is possible by isolating mutants whose developments arrest around the mound stage, which is the case for several mutants lacking specific cytoskeletal proteins. In this article, I discuss the basic elements required for cell migration in multicellular environments and how Dictyostelium can be used to elucidate them.

Uchikawa, T., A. Yamamoto, et al. (2011). "Origin and function of the stalk-cell vacuole in Dictyostelium." Dev Biol 352(1): 48-57.
	Large vacuoles are characteristic of plant and fungal cells, and their origin has long attracted interest. The cellular slime mould provides a unique opportunity to study the de novo formation of vacuoles because, in its life cycle, a subset of the highly motile animal-like cells (prestalk cells) rapidly develops a single large vacuole and cellulosic cell wall to become plant-like cells (stalk cells). Here we describe the origin and process of vacuole formation using live-imaging of Dictyostelium cells expressing GFP-tagged ammonium transporter A (AmtA-GFP), which was found to reside on the membrane of stalk-cell vacuoles. We show that stalk-cell vacuoles originate from acidic vesicles and autophagosomes, which fuse to form autolysosomes. Their repeated fusion and expansion accompanied by concomitant cell wall formation enable the stalk cells to rapidly develop turgor pressure necessary to make the rigid stalk to hold the spores aloft. Contractile vacuoles, which are rich in H(+)-ATPase as in plant vacuoles, remained separate from these vacuoles. We further argue that AmtA may play an important role in the control of stalk-cell differentiation by modulating the pH of autolysosomes.

Urushihara, H. (2011). "Social amoeba and the origin of multicellularity." Dev Growth Differ 53(4): 451.
	
Uyeda, T. Q., Y. Iwadate, et al. (2011). "Stretching actin filaments within cells enhances their affinity for the myosin II motor domain." PLoS One 6(10): e26200.
	To test the hypothesis that the myosin II motor domain (S1) preferentially binds to specific subsets of actin filaments in vivo, we expressed GFP-fused S1 with mutations that enhanced its affinity for actin in Dictyostelium cells. Consistent with the hypothesis, the GFP-S1 mutants were localized along specific portions of the cell cortex. Comparison with rhodamine-phalloidin staining in fixed cells demonstrated that the GFP-S1 probes preferentially bound to actin filaments in the rear cortex and cleavage furrows, where actin filaments are stretched by interaction with endogenous myosin II filaments. The GFP-S1 probes were similarly enriched in the cortex stretched passively by traction forces in the absence of myosin II or by external forces using a microcapillary. The preferential binding of GFP-S1 mutants to stretched actin filaments did not depend on cortexillin I or PTEN, two proteins previously implicated in the recruitment of myosin II filaments to stretched cortex. These results suggested that it is the stretching of the actin filaments itself that increases their affinity for the myosin II motor domain. In contrast, the GFP-fused myosin I motor domain did not localize to stretched actin filaments, which suggests different preferences of the motor domains for different structures of actin filaments play a role in distinct intracellular localizations of myosin I and II. We propose a scheme in which the stretching of actin filaments, the preferential binding of myosin II filaments to stretched actin filaments, and myosin II-dependent contraction form a positive feedback loop that contributes to the stabilization of cell polarity and to the responsiveness of the cells to external mechanical stimuli.

Vadell, E. M., J. C. Cavender, et al. (2011). "New species of dictyostelids from Patagonia and Tierra del Fuego, Argentina." Mycologia 103(1): 101-117.
	In late Jan and early Feb 2005 samples for isolation of dictyostelid cellular slime molds (dictyostelids) were collected in five different provinces and from six national parks (all located 39-55 degrees S) in Patagonia and Tierra del Fuego, Argentina. Southern beech (Nothofagus) forests represented the primary vegetation type investigated, but some samples were obtained from Patagonian steppe, alpine meadows, Valdivian temperate rainforests and coniferous forests dominated by Araucaria, Austrocedrus and Fitzroya. Among the dictyostelids isolated from the samples we collected were seven species new to science. These species (Dictyostelium austroandinum, D. chordatum, D. fasciculoideum, D. gargantuum, D. leptosomopsis, D. valdivianum and Polysphondylium patagonicum) are described herein on the basis of both morphology and molecular (SSU rDNA) data. One of the new species, D. gargantuum, is one of the largest representatives of the group reported to date. Another unusual species, D. chordatum, produces long interwoven sorocarps that do not appear to respond to a spacing gas similar to the condition first noted in D. implicatum.

Valente, M., S. J. Watterson, et al. (2011). "Expression, purification, electron microscopy, N-glycosylation mutagenesis and molecular modeling of human P2X4 and Dictyostelium discoideum P2XA." Biochim Biophys Acta 1808(12): 2859-2866.
	The recent publication of the apo-, closed-state 3D crystal structure of zebrafish (zf) P2X4.1 has not only revolutionized the P2X research field, but also highlighted the need for further crystal structures, of receptors in different activation states, so that we can gain a complete molecular understanding of ion channel function. zfP2X4.1 was selected as a 3D-crystallization candidate because of its ability to form stable trimers in detergent solution, and purified from over-expression in baculovirus-infected Spodoptera frugiperda (Sf9) insect cells. In this work, we have used a similar approach to express both human P2X4 (hP2X4) and Dictyostelium discoideum P2XA (DdP2XA) in Sf9 cells. Although hP2X4 did not form stable trimers in detergent solution, both receptors bound to ATP-coupled resins, indicating that their extracellular domains were folded correctly. DdP2XA formed strong trimers in detergent solution, and we were able to selectively purify trimers using preparative electrophoresis, and build a 21A-resolution 3D structure using transmission electron microscopy and single particle analysis. Although the structure of DdP2XA possessed similar dimensions to those of the previously determined low-resolution hP2X4 structure and the zfP2X4.1 crystal structure, N-glycosylation mutagenesis and molecular modeling indicated differences between N-glycan usage and predicted accessibility in models of DdP2XA based on the zfP2X4.1 crystal structure. Our data demonstrate that DdP2XA expressed in insect cells retains ATP-binding capacity after detergent solubilization, is an ideal candidate for structural study, and possesses a significantly different 3D structure to that of both hP2X4 and zfP2X4.1.

van der Wel, H., J. M. Johnson, et al. (2011). "Requirements for Skp1 processing by cytosolic prolyl 4(trans)-hydroxylase and alpha-N-acetylglucosaminyltransferase enzymes involved in O signaling in dictyostelium." Biochemistry 50(10): 1700-1713.
	The social amoeba Dictyostelium expresses a hypoxia inducible factor-alpha (HIFalpha) type prolyl 4-hydroxylase (P4H1) and an alpha-N-acetylglucosaminyltransferase (Gnt1) that sequentially modify proline-143 of Skp1, a subunit of the SCF (Skp1/Cullin/F-box protein) class of E3 ubiquitin ligases. Prior genetic studies have implicated Skp1 and its modification by these enzymes in O(2) regulation of development, suggesting the existence of an ancient O(2)-sensing mechanism related to modification of the transcription factor HIFalpha by animal prolyl 4-hydroxylases (PHDs). To better understand the role of Skp1 in P4H1-dependent O(2) signaling, biochemical and biophysical studies were conducted to characterize the reaction product and the basis of Skp1 substrate selection by P4H1 and Gnt1. (1)H NMR demonstrated formation of 4(trans)-hydroxyproline as previously found for HIFalpha, and highly purified P4H1 was inhibited by Krebs cycle intermediates and other compounds that affect animal P4Hs. However, in contrast to hydroxylation of HIFalpha by PHDs, P4H1 depended on features of full-length Skp1, based on truncation, mutagenesis, and competitive inhibition studies. These features are conserved during animal evolution, as even mammalian Skp1, which lacks the target proline, became a good substrate upon its restoration. P4H1 recognition may depend on features conserved for SCF complex formation as heterodimerization with an F-box protein blocked Skp1 hydroxylation. The hydroxyproline-capping enzyme Gnt1 exhibited similar requirements for Skp1 as a substrate. These and other findings support a model in which the protist P4H1 conditionally hydroxylates Skp1 of E3(SCF)ubiquitin ligases to control half-lives of multiple targets, rather than the mechanism of animal PHDs where individual proteins are hydroxylated leading to ubiquitination by the evolutionarily related E3(VBC)ubiquitin ligases.

Veeranki, S., S. H. Hwang, et al. (2011). "LKB1 regulates development and the stress response in Dictyostelium." Dev Biol 360(2): 351-357.
	The serine/threonine kinase LKB1 is a master kinase that regulates a number of critical events such as cell transformation, polarization, development, stress response, and energy metabolism in metazoa. After multiple unsuccessful attempts of generating Dictyostelium lkb1-null cells, an RNAi-based knockdown approach proved effective. Depletion of lkb1 with a knockdown construct displayed severe reduction in prespore cell differentiation and precocious induction of prestalk cells, which were reminiscent of cells lacking GSK3. Similar to gsk3(-) cells, lkb1 depleted cells displayed lower GSK3 activity than wild type cells during development and compromised cAMP-mediated inhibition of the DIF-1 mediated ecmB induction. In response to stress insult, the kinase activity of LKB1, but not that of GSK3, increased. Therefore, LKB1 positively functions at the upstream of GSK3 during development and responds to stress insults independently from GSK3.

Velazquez, F., S. Y. Peak-Chew, et al. (2011). "Identification of a eukaryotic reductive dechlorinase and characterization of its mechanism of action on its natural substrate." Chem Biol 18(10): 1252-1260.
	Chlorinated compounds are important environmental pollutants whose biodegradation may be limited by inefficient dechlorinating enzymes. Dictyostelium amoebae produce a chlorinated alkyl phenone called DIF which induces stalk cell differentiation during their multicellular development. Here we describe the identification of DIF dechlorinase. DIF dechlorinase is active when expressed in bacteria, and activity is lost from Dictyostelium cells when its gene, drcA, is knocked out. It has a K(m) for DIF of 88 nM and K(cat) of 6.7 s(-1). DrcA is related to glutathione S-transferases, but with a key asparagine-to-cysteine substitution in the catalytic pocket. When this change is reversed, the enzyme reverts to a glutathione S-transferase, thus suggesting a catalytic mechanism. DrcA offers new possibilities for the rational design of bioremediation strategies.

Veltman, D. M., G. Auciello, et al. (2011). "Functional analysis of Dictyostelium IBARa reveals a conserved role of the I-BAR domain in endocytosis." Biochem J 436(1): 45-52.
	I-BAR (inverse-Bin/amphiphysin/Rvs)-domain-containing proteins such as IRSp53 (insulin receptor substrate of 53 kDa) associate with outwardly curved membranes and connect them to proteins involved in actin dynamics. Research on I-BAR proteins has focussed on possible roles in filopod and lamellipod formation, but their full physiological function remains unclear. The social amoeba Dictyostelium encodes a single I-BAR/SH3 (where SH3 is Src homology 3) protein, called IBARa, along with homologues of proteins that interact with IRSp53 family proteins in mammalian cells, providing an excellent model to study its cellular function. Disruption of the gene encoding IBARa leads to a mild defect in development, but filopod and pseudopod dynamics are unaffected. Furthermore, ectopically expressed IBARa does not induce filopod formation and does not localize to filopods. Instead, IBARa associates with clathrin puncta immediately before they are endocytosed. This role is conserved: human BAIAP2L2 (brain-specific angiogenesis inhibitor 1-associated protein 2-like 2) also tightly co-localizes with clathrin plaques, although its homologues IRSp53 and IRTKS (insulin receptor tyrosine kinase substrate) associate with other punctate structures. The results from the present study suggest that I-BAR-containing proteins help generate the membrane curvature required for endocytosis and implies an unexpected role for IRSp53 family proteins in vesicle trafficking.

Vinke, F. P., A. G. Grieve, et al. (2011). "The multiple facets of the Golgi reassembly stacking proteins." Biochem J 433(3): 423-433.
	The mammalian GRASPs (Golgi reassembly stacking proteins) GRASP65 and GRASP55 were first discovered more than a decade ago as factors involved in the stacking of Golgi cisternae. Since then, orthologues have been identified in many different organisms and GRASPs have been assigned new roles that may seem disconnected. In vitro, GRASPs have been shown to have the biochemical properties of Golgi stacking factors, but the jury is still out as to whether they act as such in vivo. In mammalian cells, GRASP65 and GRASP55 are required for formation of the Golgi ribbon, a structure which is fragmented in mitosis owing to the phosphorylation of a number of serine and threonine residues situated in its C-terminus. Golgi ribbon unlinking is in turn shown to be part of a mitotic checkpoint. GRASP65 also seems to be the key target of signalling events leading to re-orientation of the Golgi during cell migration and its breakdown during apoptosis. Interestingly, the Golgi ribbon is not a feature of lower eukaryotes, yet a GRASP homologue is present in the genome of Encephalitozoon cuniculi, suggesting they have other roles. GRASPs have no identified function in bulk anterograde protein transport along the secretory pathway, but some cargo-specific trafficking roles for GRASPs have been discovered. Furthermore, GRASP orthologues have recently been shown to mediate the unconventional secretion of the cytoplasmic proteins AcbA/Acb1, in both Dictyostelium discoideum and yeast, and the Golgi bypass of a number of transmembrane proteins during Drosophila development. In the present paper, we review the multiple roles of GRASPs.

Vlahou, G., M. Elias, et al. (2011). "The Ras related GTPase Miro is not required for mitochondrial transport in Dictyostelium discoideum." Eur J Cell Biol 90(4): 342-355.
	Ras-related GTPases of the Miro family have been implicated in mitochondrial homeostasis and microtubule-dependent transport. They consist of two GTP-binding domains separated by calcium-binding motifs and of a C-terminal transmembrane domain that targets the protein to the outer mitochondrial membrane. We disrupted the single Miro-encoding gene in Dictyostelium discoideum and observed a substantial growth defect that we attribute to a decreased mitochondrial mass and cellular ATP content. However, mutant cells even showed an increased rate of oxygen consumption, while glucose consumption, mitochondrial transmembrane potential and production of reactive oxygen species were unaltered. Processes characteristic of the multicellular stage of the D. discoideum life cycle were also unaltered. Although mitochondria occasionally use microtubules for transport in D. discoideum, their size and distribution were not visibly affected. We found Miro in all branches of the eukaryotic tree with the exception of a few protist lineages (mainly those lacking typical mitochondria). Trypanosomatids and ciliates possess structurally unique homologs lacking the N-terminal or the C-terminal GTPase domain, respectively. We propose that in D. discoideum, as in yeasts and plants, Miro plays roles in mitochondrial homeostasis, but the ability to build a complex that regulates its association to kinesin for microtubule-dependent transport probably arose in metazoans.

Walk, A., J. Callahan, et al. (2011). "Lipopolysaccharide enhances bactericidal activity in Dictyostelium discoideum cells." Dev Comp Immunol 35(8): 850-856.
	Innate immune cells respond to invading microbes upon detection of pathogen-associated molecular patterns (PAMPS). PAMP-recognition machinery is evolutionarily conserved, allowing for characterization in model organisms. The model organism Dictyostelium discoideum can exist as single-celled amoebae, which phagocytize bacteria for nutrients. Although D. discoideum is used extensively to study phagocytosis, it has not been determined if D. discoideum detects bacterial PAMPs using pattern-recognition machinery. Here we show that D. discoideum mounts responses against the bacterial cell wall PAMP, lipopolysaccharide (LPS). Upon treatment with LPS or its active component Lipid A, D. discoideum cells more efficiently clear phagocytized bacteria. LPS-enhanced bactericidal activity appears dependent both on MAPK signaling pathways as well as on the D. discoideum toll/interleukin-1 receptor domain-containing protein, TirA. These findings indicate that pattern-recognition machinery required to detect and respond to bacterial PAMPs may be conserved in D. discoideum.

Wang, Y., C. L. Chen, et al. (2011). "Signaling mechanisms for chemotaxis." Dev Growth Differ 53(4): 495-502.
	Cells recognize external chemical gradients and translate these environmental cues into amplified intracellular signaling that results in elongated cell shape, actin polymerization toward the leading edge, and movement along the gradient. Mechanisms underlying chemotaxis are conserved evolutionarily from Dictyostelium amoeba to mammalian neutrophils. Recent studies have uncovered several parallel intracellular signaling pathways that crosstalk in chemotaxing cells. Here, we review these signaling mechanisms in Dictyostelium discoideum.

Wang, Y., P. A. Steimle, et al. (2011). "Dictyostelium huntingtin controls chemotaxis and cytokinesis through the regulation of myosin II phosphorylation." Mol Biol Cell 22(13): 2270-2281.
	Abnormalities in the huntingtin protein (Htt) are associated with Huntington's disease. Despite its importance, the function of Htt is largely unknown. We show that Htt is required for normal chemotaxis and cytokinesis in Dictyostelium discoideum. Cells lacking Htt showed slower migration toward the chemoattractant cAMP and contained lower levels of cortical myosin II, which is likely due to defects in dephosphorylation of myosin II mediated by protein phosphatase 2A (PP2A). htt(-) cells also failed to maintain myosin II in the cortex of the cleavage furrow, generating unseparated daughter cells connected through a thin cytoplasmic bridge. Furthermore, similar to Dictyostelium htt(-) cells, siRNA-mediated knockdown of human HTT also decreased the PP2A activity in HeLa cells. Our data indicate that Htt regulates the phosphorylation status of myosin II during chemotaxis and cytokinesis through PP2A.

Wang, Z. A., D. Singh, et al. (2011). "Prolyl hydroxylation- and glycosylation-dependent functions of Skp1 in O2-regulated development of Dictyostelium." Dev Biol 349(2): 283-295.
	O(2) regulates multicellular development of the social amoeba Dictyostelium, suggesting it may serve as an important cue in its native soil environment. Dictyostelium expresses an HIFalpha-type prolyl 4-hydroxylase (P4H1) whose levels affect the O(2)-threshold for culmination implicating it as a direct O(2)-sensor, as in animals. But Dictyostelium lacks HIFalpha, a mediator of animal prolyl 4-hydroxylase signaling, and P4H1 can hydroxylate Pro143 of Skp1, a subunit of E3(SCF)ubiquitin-ligases. Skp1 hydroxyproline then becomes the target of five sequential glycosyltransferase reactions that modulate the O(2)-signal. Here we show that genetically induced changes in Skp1 levels also affect the O(2)-threshold, in opposite direction to that of the modification enzymes suggesting that the latter reduce Skp1 activity. Consistent with this, overexpressed Skp1 is poorly hydroxylated and Skp1 is the only P4H1 substrate detectable in extracts. Effects of Pro143 mutations, and of combinations of Skp1 and enzyme level perturbations, are consistent with pathway modulation of Skp1 activity. However, some effects were not mirrored by changes in modification of the bulk Skp1 pool, implicating a Skp1 subpopulation and possibly additional unknown factors. Altered Skp1 levels also affected other developmental transitions in a modification-dependent fashion. Whereas hydroxylation of animal HIFalpha results in its polyubiquitination and proteasomal degradation, Dictyostelium Skp1 levels were little affected by its modification status. These data indicate that Skp1 and possibly E3(SCF)ubiquitin-ligase activity modulate O(2)-dependent culmination and other developmental processes, and at least partially mediate the action of the hydroxylation/glycosylation pathway in O(2)-sensing.

Weizenmann, M., A. P. Frasson, et al. (2011). "Kinetic characterization and gene expression of adenosine deaminase in intact trophozoites of Trichomonas vaginalis." FEMS Microbiol Lett 319(2): 115-124.
	Trichomonas vaginalis is a parasite that resides in the human urogenital tract and causes trichomonosis, the most prevalent nonviral sexually transmitted disease. Nucleoside triphosphate diphosphohydrolase (NTPDase), which hydrolyzes extracellular di- and triphosphate nucleotides, and ecto-5'-nucleotidase, which hydrolyzes AMP, have been characterized in T. vaginalis. The aim of this study was to characterize the adenosine deaminase (ADA) activity in intact trophozoites of T. vaginalis. A strong inhibition in adenosine deamination was observed in the presence of calcium and magnesium, which was prevented by EDTA. The apparent K(M) value for adenosine was 1.13 +/- 0.07mM. The calculated V(max) was 2.61 +/- 0.054 nmol NH(3) min(-1) mg(-1) protein. Adenosine deamination was inhibited in the presence of erythro-9-(2-hydroxy-3-nonyl)adenine. Semi-quantitative reverse transcriptase-PCR experiments were performed and both ADA-related genes ada(125) and ada(231) mRNA were expressed, although ada(231) in higher quantity when compared with the ada(125) : alpha-tubulin ratio. Furthermore, a phylogenetic analysis showed that the T. vaginalis sequences formed a clade with Entamoeba histolytica and Dictyostelium discoideum sequences, and it strongly suggests homologous functions in the T. vaginalis genome. The presence of ADA activity in T. vaginalis may be important to modulate the adenosine/inosine levels during infection and, consequently, to maintain the anti-inflammatory properties through different nucleoside-signalling mechanisms.

Wiegand, S., J. Kruse, et al. (2011). "Efficient generation of gene knockout plasmids for Dictyostelium discoideum using one-step cloning." Genomics 97(5): 321-325.
	The amoeba Dictyostelium discoideum is a well-established model organism for studying numerous aspects of cellular and developmental functions. Its rather small (~34Mb) chromosomal genome and the high efficiency of gene disruption by homologous recombination have enabled researchers to dissect various specific gene functions. We describe here the use of one-step cloning for the fast and efficient generation of deletion vectors that are produced in a one-step reaction by inserting two PCR products into an organism-specific, generic acceptor system. This worked efficiently for all 16 tested constructs directed against genes in the amoeba Dictyostelium discoideum. Saving cost and time, the used protocol represents a significant advancement in the generation of such plasmids compared to the conventionally applied restriction enzyme/ligation approach. Using appropriate selection markers, similar systems could also be useful in other organisms, where genes can be knocked out by homologous recombination.

Winckler, T., J. Schiefner, et al. (2011). "Dictyostelium transfer RNA gene-targeting retrotransposons: Studying mobile element-host interactions in a compact genome." Mob Genet Elements 1(2): 145-150.
	The model species of social amoebae, Dictyostelium discoideum, has a compact genome consisting of about two thirds protein-coding regions, with intergenic regions that are rarely larger than 1,000 bp. We hypothesize that the haploid state of D. discoideum cells provides defense against the amplification of mobile elements whose transposition activities would otherwise lead to the accumulation of heterozygous, potentially lethal mutations in diploid populations. We further speculate that complex transposon clusters found on D. discoideum chromosomes do not a priori result from integration preferences of these transposons, but that the clusters instead result from negative selection against cells harboring insertional mutations in genes. D. discoideum cells contain a fraction of retrotransposons that are found in the close vicinity of tRNA genes. Growing evidence suggests that these retrotransposons use active recognition mechanisms to determine suitable integration sites. However, the question remains whether these retrotransposons also cause insertional mutagenesis of genes, resulting in their enrichment at tRNA genes, which are relatively safe sites in euchromatic regions. Recently developed in vivo retrotransposition assays will allow a detailed, genome-wide analysis of de novo integration events in the D. discoideum genome.

Wojtkowska, M., M. Jakalski, et al. (2011). "Phylogenetic Analysis of Mitochondrial Outer Membrane ss-barrel Channels." Genome Biol Evol.
	Transport of molecules across mitochondrial outer membrane is pivotal for a proper function of mitochondria. The transport pathways across the membrane are formed by ion channels that participate in metabolite exchange between mitochondria and cytoplasm (VDAC) as well as in import of proteins encoded by nuclear genes (Tom40, Sam50/Tob55). VDAC, Tom40, and Sam50/Tob55 are present in all eukaryotic organisms, encoded in the nuclear genome and have ss-barrel topology. We have compiled datasets of these protein sequences and studied their phylogenetic relationships with a special focus on the position of Amoebozoa. Additionally, we identified these protein-coding genes in Acanthamoeba castellanii and Dictyostelium discoideum to complement our dataset and verify the phylogenetic position of these model organisms. Our analysis show that mitochondrial beta-barrel channels from Archaeplastida (plants) and Opisthokonta (animals and fungi) experienced many duplication events that resulted in multiple paralogous isoforms and form well-defined monophyletic clades that match the current model of eukaryotic evolution. However, in representatives of Amoebozoa, Chromalveolata, and Excavata (former Protista) they do not form clearly distinguishable clades, although they locate basally to the plant and algae branches. In most cases they do not posses paralogs and their sequences appear to have evolved quickly or degenerated. Consequently, the obtained phylogenies of mitochondrial outer membrane ss-channels do not entirely reflect the recent eukaryotic classification system involving the six supergroups: Chromalveolata, Excavata, Archaeplastida, Rhizaria, Amoebozoa, and Opisthokonta.

Wong, C. C., D. Traynor, et al. (2011). "Defective ribosome assembly in Shwachman-Diamond syndrome." Blood 118(16): 4305-4312.
	Shwachman-Diamond syndrome (SDS), a recessive leukemia predisposition disorder characterized by bone marrow failure, exocrine pancreatic insufficiency, skeletal abnormalities and poor growth, is caused by mutations in the highly conserved SBDS gene. Here, we test the hypothesis that defective ribosome biogenesis underlies the pathogenesis of SDS. We create conditional mutants in the essential SBDS ortholog of the ancient eukaryote Dictyostelium discoideum using temperature-sensitive, self-splicing inteins, showing that mutant cells fail to grow at the restrictive temperature because ribosomal subunit joining is markedly impaired. Remarkably, wild type human SBDS complements the growth and ribosome assembly defects in mutant Dictyostelium cells, but disease-associated human SBDS variants are defective. SBDS directly interacts with the GTPase elongation factor-like 1 (EFL1) on nascent 60S subunits in vivo and together they catalyze eviction of the ribosome antiassociation factor eukaryotic initiation factor 6 (eIF6), a prerequisite for the translational activation of ribosomes. Importantly, lymphoblasts from SDS patients harbor a striking defect in ribosomal subunit joining whose magnitude is inversely proportional to the level of SBDS protein. These findings in Dictyostelium and SDS patient cells provide compelling support for the hypothesis that SDS is a ribosomopathy caused by corruption of an essential cytoplasmic step in 60S subunit maturation.

Xu, X. and T. Jin (2011). "Imaging G-protein coupled receptor (GPCR)-mediated signaling events that control chemotaxis of Dictyostelium discoideum." J Vis Exp(55).
	Many eukaryotic cells can detect gradients of chemical signals in their environments and migrate accordingly (1). This guided cell migration is referred as chemotaxis, which is essential for various cells to carry out their functions such as trafficking of immune cells and patterning of neuronal cells (2, 3). A large family of G-protein coupled receptors (GPCRs) detects variable small peptides, known as chemokines, to direct cell migration in vivo (4). The final goal of chemotaxis research is to understand how a GPCR machinery senses chemokine gradients and controls signaling events leading to chemotaxis. To this end, we use imaging techniques to monitor, in real time, spatiotemporal concentrations of chemoattractants, cell movement in a gradient of chemoattractant, GPCR mediated activation of heterotrimeric G-protein, and intracellular signaling events involved in chemotaxis of eukaryotic cells (5-8). The simple eukaryotic organism, Dictyostelium discoideum, displays chemotaxic behaviors that are similar to those of leukocytes, and D. discoideum is a key model system for studying eukaryotic chemotaxis. As free-living amoebae, D. discoideum cells divide in rich medium. Upon starvation, cells enter a developmental program in which they aggregate through cAMP-mediated chemotaxis to form multicullular structures. Many components involved in chemotaxis to cAMP have been identified in D. discoideum. The binding of cAMP to a GPCR (cAR1) induces dissociation of heterotrimeric G-proteins into Ggamma and Gbetagamma subunits (7, 9, 10). Gbetagamma subunits activate Ras, which in turn activates PI3K, converting PIP(2;) into PIP(3;) on the cell membrane (11-13). PIP(3;) serve as binding sites for proteins with pleckstrin Homology (PH) domains, thus recruiting these proteins to the membrane (14, 15). Activation of cAR1 receptors also controls the membrane associations of PTEN, which dephosphorylates PIP(3;) to PIP(2;)(16, 17). The molecular mechanisms are evolutionarily conserved in chemokine GPCR-mediated chemotaxis of human cells such as neutrophils (18). We present following methods for studying chemotaxis of D. discoideum cells. 1. Preparation of chemotactic component cells. 2. Imaging chemotaxis of cells in a cAMP gradient. 3. Monitoring a GPCR induced activation of heterotrimeric G-protein in single live cells. 4. Imaging chemoattractant-triggered dynamic PIP(3;) responses in single live cells in real time. Our developed imaging methods can be applied to study chemotaxis of human leukocytes.

Yamada, Y., B. Nunez-Corcuera, et al. (2011). "DIF-1 regulates Dictyostelium basal disc differentiation by inducing the nuclear accumulation of a bZIP transcription factor." Dev Biol 354(1): 77-86.
	Exposure of monolayer Dictyostelium cells to the signalling polyketide DIF-1 causes DimB, a bZIPtranscription factor, to accumulate in the nucleus where it induces prestalk gene expression. Here we analyse DimB signalling during normal development. In slugs DimB is specifically nuclear enriched in the pstB cells; a cluster of vital dye-staining cells located on the ventral surface of the posterior, prespore region. PstB cells move at culmination, to form the lower cup and the outer basal disc of the fruiting body, and DimB retains a high nuclear concentration in both these tissues. In a dimB null (dimB-) strain there are very few pstB or lower cup cells, as detected by neutral red staining, and it is known that the outer basal disc is absent or much reduced. In the dimB- strain ecmB, a marker of pstB differentiation, is not DIF inducible. Furthermore, ChIP analysis shows that DimB binds to the ecmB promoter in DIF-induced cells. These results suggest that the differentiation of pstB cells is caused by a high perceived level of DIF-1 signalling, leading to nuclear localization of DimB and direct activation of cell type-specific gene expression.

Yang, L., Y. Liu, et al. (2011). "Pattern differentiation in co-culture biofilms formed by Staphylococcus aureus and Pseudomonas aeruginosa." FEMS Immunol Med Microbiol 62(3): 339-347.
	Biofilm infections may not simply be the result of colonization by one bacterium, but rather the consequence of pathogenic contributions from several bacteria. Interspecies interactions of different organisms in mixed-species biofilms remain largely unexplained, but knowledge of these is very important for understanding of biofilm physiology and the treatment of biofilm-related infectious diseases. Here, we have investigated interactions of two of the major bacterial species of cystic fibrosis lung microbial communities -Pseudomonas aeruginosa and Staphylococcus aureus- when grown in co-culture biofilms. By growing co-culture biofilms of S. aureus with P. aeruginosa mutants in a flow-chamber system and observing them using confocal laser scanning microscopy, we show that wild-type P. aeruginosa PAO1 facilitates S. aureus microcolony formation. In contrast, P. aeruginosa mucA and rpoN mutants do not facilitate S. aureus microcolony formation and tend to outcompete S. aureus in co-culture biofilms. Further investigations reveal that extracellular DNA (eDNA) plays an important role in S. aureus microcolony formation and that P. aeruginosa type IV pili are required for this process, probably through their ability to bind to eDNA. Furthermore, P. aeruginosa is able to protect S. aureus against Dictyostelium discoideum phagocytosis in co-culture biofilms.

Yde, P., B. Mengel, et al. (2011). "Modeling the NF-kappaB mediated inflammatory response predicts cytokine waves in tissue." BMC Syst Biol 5: 115.
	BACKGROUND: Waves propagating in "excitable media" is a reliable way to transmit signals in space. A fascinating example where living cells comprise such a medium is Dictyostelium D. which propagates waves of chemoattractant to attract distant cells. While neutrophils chemotax in a similar fashion as Dictyostelium D., it is unclear if chemoattractant waves exist in mammalian tissues and what mechanisms could propagate them. RESULTS: We propose that chemoattractant cytokine waves may naturally develop as a result of NF-kappaB response. Using a heuristic mathematical model of NF-kappaB-like circuits coupled in space we show that the known characteristics of NF-kappaB response favor cytokine waves. CONCLUSIONS: While the propagating wave of cytokines is generally beneficial for inflammation resolution, our model predicts that there exist special conditions that can cause chronic inflammation and re-occurrence of acute inflammatory response.

Yu, B., P. Fey, et al. (2011). "Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae." Protein Cell 2(5): 395-409.
	Little is known about pre-mRNA splicing in Dictyostelium discoideum although its genome has been completely sequenced. Our analysis suggests that pre-mRNA splicing plays an important role in D. discoideum gene expression as two thirds of its genes contain at least one intron. Ongoing curation of the genome to date has revealed 40 genes in D. discoideum with clear evidence of alternative splicing, supporting the existence of alternative splicing in this unicellular organism. We identified 160 candidate U2-type spliceosomal proteins and related factors in D. discoideum based on 264 known human genes involved in splicing. Spliceosomal small ribonucleoproteins (snRNPs), PRP19 complex proteins and late-acting proteins are highly conserved in D. discoideum and throughout the metazoa. In non-snRNP and hnRNP families, D. discoideum orthologs are closer to those in A. thaliana, D. melanogaster and H. sapiens than to their counterparts in S. cerevisiae. Several splicing regulators, including SR proteins and CUG-binding proteins, were found in D. discoideum, but not in yeast. Our comprehensive catalog of spliceosomal proteins provides useful information for future studies of splicing in D. discoideum where the efficient genetic and biochemical manipulation will also further our general understanding of pre-mRNA splicing.

Zantl, R. and E. Horn (2011). "Chemotaxis of slow migrating mammalian cells analysed by video microscopy." Methods Mol Biol 769: 191-203.
	We present a microfabricated chamber designed for visualising and quantifying the chemotaxis of slow-migrating adherent mammalian cells such as cancer and endothelial cells. Most of the existing solutions for the investigation of chemotaxis are limited to fast migrating cells such as leukocytes or Dictyostelium discoideum. Here, we describe the details of an assay using the mu-Slide Chemotaxis to investigate the chemotactic response of human umbilical vein endothelial cells to a gradient of human vascular endothelial growth factor 165. In combination with phase contrast video microscopy and cell tracking, the trajectories of all single cells migrating in temporally stable gradients are derived. The resulting migration data are displayed and analysed in detail by several different parameters for quantifying chemotaxis. We found that with this tool the potential of chemoattractants to migration of mammalian cells as well as the impact of inhibitors to chemotaxis and migration can be evaluated.

Zheng, J., B. Ho, et al. (2011). "Genetic analysis of anti-amoebae and anti-bacterial activities of the type VI secretion system in Vibrio cholerae." PLoS One 6(8): e23876.
	A type VI secretion system (T6SS) was recently shown to be required for full virulence of Vibrio cholerae O37 serogroup strain V52. In this study, we systematically mutagenized each individual gene in T6SS locus and characterized their functions based on expression and secretion of the hemolysin co-regulated protein (Hcp), virulence towards amoebae of Dictyostelium discoideum and killing of Escherichia coli bacterial cells. We group the 17 proteins characterized in the T6SS locus into four categories: twelve (VipA, VipB, VCA0109-VCA0115, ClpV, VCA0119, and VasK) are essential for Hcp secretion and bacterial virulence, and thus likely function as structural components of the apparatus; two (VasH and VCA0122) are regulators that are required for T6SS gene expression and virulence; another two, VCA0121 and valine-glycine repeat protein G 3 (VgrG-3), are not essential for Hcp expression, secretion or bacterial virulence, and their functions are unknown; the last group is represented by VCA0118, which is not required for Hcp expression or secretion but still plays a role in both amoebae and bacterial killing and may therefore be an effector protein. We also showed that the clpV gene product is required for Dictyostelium virulence but is less important for killing E. coli. In addition, one vgrG gene (vgrG-2) outside of the T6SS gene cluster was required for bacterial killing but another (vgrG-1) was not. However, a bacterial killing defect was observed when vgrG-1 and vgrG-3 were both deleted. Several genes encoded in the same putative operon as vgrG-1 and vgrG-2 also contribute to virulence toward Dictyostelium but have a smaller effect on bacterial killing. Our results provide new insights into the functional requirements of V. cholerae's T6SS in the context of secretion as well as killing of bacterial and eukaryotic phagocytic cells.

Asghar, A., M. Groth, et al. (2012). "Developmental gene regulation by an ancient intercellular communication system in social amoebae." Protist 163(1): 25-37.
	The social amoebae (Dictyostelia) use quorum sensing-like communication systems to coordinate the periodic transition from uni- to multicellularity. The monophyletic descent of the Dictyostelia provides a unique opportunity to study the origin and adaptive evolution of such intercellular communication systems. We determined that the ability of aggregation-competent cells to respond to the intercellular messenger glorin occurred in the most ancient taxa of the Dictyostelia. We show using Illumina sequencing technology that glorin mediates rapid changes in gene expression at the transition from vegetative growth to aggregation. We conclude that peptide-based communication is the most ancient form of intercellular signaling in the evolution of multicellularity in the social amoebae, but has been repeatedly replaced by other communication systems during the monophyletic evolution of the social amoebae. Glorin communication has parallels with quorum sensing in that the molecule diffuses into the field, stimulates gene expression in receptive cells and coordinates a population-wide response.

Cai, H., C. H. Huang, et al. (2012). "Analysis of chemotaxis in Dictyostelium." Methods Mol Biol 757: 451-468.
	Dictyostelium discoideum is an excellent model organism for the study of directed cell migration, since Dictyostelium cells show robust chemotactic responses to the chemoattractant cAMP. Many powerful experimental tools are applicable, including forward and reverse genetics, biochemistry, microscopy, and proteomics. Recent studies have demonstrated that many components involved in chemotaxis are functionally conserved between human neutrophils and Dictyostelium amoebae. In this chapter, we describe how to define the functions of proteins that mediate and regulate cell motility, cell polarity, and directional sensing during chemotaxis in Dictyostelium.

Chang, P., B. Orabi, et al. (2012). "The antiepileptic drug valproic acid and other medium-chain fatty acids acutely reduce phosphoinositide levels independently of inositol in Dictyostelium." Dis Model Mech 5(1): 115-124.
	Valproic acid (VPA) is the most widely prescribed epilepsy treatment worldwide, but its mechanism of action remains unclear. Our previous work identified a previously unknown effect of VPA in reducing phosphoinositide production in the simple model Dictyostelium followed by the transfer of data to a mammalian synaptic release model. In our current study, we show that the reduction in phosphoinositide [PtdInsP (also known as PIP) and PtdInsP(2) (also known as PIP(2))] production caused by VPA is acute and dose dependent, and that this effect occurs independently of phosphatidylinositol 3-kinase (PI3K) activity, inositol recycling and inositol synthesis. In characterising the structural requirements for this effect, we also identify a family of medium-chain fatty acids that show increased efficacy compared with VPA. Within the group of active compounds is a little-studied group previously associated with seizure control, and analysis of two of these compounds (nonanoic acid and 4-methyloctanoic acid) shows around a threefold enhanced potency compared with VPA for protection in an in vitro acute rat seizure model. Together, our data show that VPA and a newly identified group of medium-chain fatty acids reduce phosphoinositide levels independently of inositol regulation, and suggest the reinvestigation of these compounds as treatments for epilepsy.

Chen, C. L., Y. Wang, et al. (2012). "Myosin I Links PIP3 Signaling to Remodeling of the Actin Cytoskeleton in Chemotaxis." Sci Signal 5(209): ra10.
	Class I myosins participate in various interactions between the cell membrane and the cytoskeleton. Several class I myosins preferentially bind to acidic phospholipids, such as phosphatidylserine and phosphatidylinositol 4,5-bisphosphate [PI(4,5)P(2)], through a tail homology 1 (TH1) domain. Here, we show that the second messenger lipid phosphatidylinositol 3,4,5-trisphosphate (PIP(3)) binds to the TH1 domain of a subset of Dictyostelium class I myosins (ID, IE, and IF) and recruits them to the plasma membrane. The PIP(3)-regulated membrane recruitment of myosin I promoted chemotaxis and induced chemoattractant-stimulated actin polymerization. Similarly, PIP(3) recruited human myosin IF to the plasma membrane upon chemotactic stimulation in a neutrophil cell line. These data suggest a mechanism through which the PIP(3) signal is transmitted through myosin I to the actin cytoskeleton.

El-Ajouz, S., D. Ray, et al. (2012). "Molecular basis of selective antagonism of the P2X1 receptor for ATP by NF449 and suramin: contribution of basic amino acids in the cysteine-rich loop." Br J Pharmacol 165(2): 390-400.
	BACKGROUND AND PURPOSE: The cysteine-rich head region, which is adjacent to the proposed ATP-binding pocket in the extracellular ligand-binding loop of P2X receptors for ATP, is absent in the antagonist-insensitive Dictyostelium receptors. In this study we have determined the contribution of the head region to the antagonist action of NF449 and suramin at the human P2X1 receptor. EXPERIMENTAL APPROACH: Chimeras and point mutations in the cysteine-rich head region were made between human P2X1 and P2X2 receptors. Mutant receptors were expressed in Xenopus oocytes and P2X receptor currents characterized using two-electrode voltage clamp. KEY RESULTS: The chimera replacing the region between the third and fourth conserved cysteine residues of the P2X1 receptor with the corresponding part of P2X2 reduced NF449 sensitivity a thousand fold from an IC(50) of approximately 1 nM at the P2X1 receptor to that of the P2X2 receptor (IC(50) approximately 1 microM). A similar decrease in sensitivity resulted from mutation of four positively charged P2X1 receptor residues in this region that are absent from the P2X2 receptor. These chimeras and mutations were also involved in determining sensitivity to the antagonist suramin. Reciprocal chimeras and mutations in the P2X2 receptor produced modest increases in antagonist sensitivity. CONCLUSIONS AND IMPLICATIONS: These data indicate that a cluster of positively charged residues at the base of the cysteine-rich head region can account for the highly selective antagonism of the P2X1 receptor by the suramin derivative NF449.

Filic, V., M. Marinovic, et al. (2012). "A dual role for Rac1 GTPases in the regulation of cell motility." J Cell Sci.
	Rac proteins are the only canonical Rho family GTPases in Dictyostelium, where they act as key regulators of the actin cytoskeleton. To monitor the dynamics of activated Rac1 in Dictyostelium cells, a fluorescent probe was developed that specifically binds to the GTP-bound form of Rac1. The probe is based on the GTPase-binding domain (GBD) from PAK1 kinase, and was selected on the basis of yeast two-hybrid, GST pull-down and fluorescence resonance energy transfer assays. The PAK1 GBD localizes to leading edges of migrating cells and to endocytotic cups. Similarly to its role in vertebrates, activated Rac1 therefore appears to control de novo actin polymerization at protruding regions of the Dictyostelium cell. Additionally, we found that the IQGAP-related protein DGAP1, which sequesters active Rac1 into a quaternary complex with actin-binding proteins cortexillin I and cortexillin II, localizes to the trailing regions of migrating cells. Notably, PAK1 GBD and DGAP1, which both bind to Rac1-GTP, display mutually exclusive localizations in cell migration, phagocytosis and cytokinesis, and opposite dynamics of recruitment to the cell cortex upon stimulation with chemoattractants. Moreover, cortical localization of the PAK1 GBD depends on the integrity of the actin cytoskeleton, whereas cortical localization of DGAP1 does not. Taken together, these results imply that Rac1 GTPases play a dual role in regulation of cell motility and polarity in Dictyostelium.

Froquet, R., M. le Coadic, et al. (2012). "TM9/Phg1 and SadA proteins control surface expression and stability of SibA adhesion molecules in Dictyostelium." Mol Biol Cell.
	TM9 proteins form a family of conserved proteins with nine transmembrane domains essential for cellular adhesion in many biological systems, but their exact role in this process remains unknown. Here we found that in Dictyostelium amoebae, genetic inactivation of the TM9 protein Phg1A dramatically decreases the surface levels of the SibA adhesion molecule. This is due to a decrease in sibA mRNA levels, in SibA protein stability, and in SibA targeting to the cell surface. A similar phenotype was observed in cells devoid of SadA, a protein that does not belong to the TM9 family but also exhibits 9 transmembrane domains and is essential for cellular adhesion. A csA-SibA chimeric protein comprising only the transmembrane and cytosolic domains of SibA and the extracellular domain of csA, a Dictyostelium surface protein, also showed reduced stability and relocalization to endocytic compartments in phg1A knockout cells. These results indicate that TM9 proteins participate in cell adhesion by controlling the levels of adhesion proteins present at the cell surface.

Gopaldass, N., D. Patel, et al. (2012). "Dynamin A, Myosin IB and Abp1 couple phagosome maturation to F-actin binding." Traffic 13(1): 120-130.
	The role of actin, class I myosins and dynamin in endocytic uptake processes is well characterized, but their role during endo-phagosomal membrane trafficking and maturation is less clear. In Dictyostelium, knockout of myosin IB (myoB) leads to a defect in membrane protein recycling from endosomes back to the plasma membrane. Here, we show that actin plays a central role in the morphology and function of the endocytic pathway. Indeed, latrunculin B (LatB) induces endosome tubulation, a phenotype also observed in dynamin A (dymA)-null cells. Knockout of dymA impairs phagosome acidification, whereas knockout of myoB delays reneutralization, a phenotype mimicked by a low dose of LatB. As a read out for actin-dependent processes during maturation, we monitored the capacity of purified phagosomes to bind F-actin in vitro, and correlated this with the presence of actin-binding and membrane-trafficking proteins. Phagosomes isolated from myoB-null cells showed an increased binding to F-actin, especially late phagosomes. In contrast, early phagosomes from dymA-null cells showed reduced binding to F-actin while late phagosomes were unaffected. We provide evidence that Abp1 is the main F-actin-binding protein in this assay and is central for the interplay between DymA and MyoB during phagosome maturation.

Goury-Sistla, P., V. Nanjundiah, et al. (2012). "Bimodal distribution of motility and cell fate in Dictyostelium discoideum." Int J Dev Biol.
	Pre-starvation amoebae of Dictyostelium discoideum exhibit random movements. Starved cells aggregate by directed movements (chemotaxis) towards cyclic AMP and differentiate into live spores or dead stalk cells. Many differences between presumptive spore and stalk cells precede differentiation. We have examined whether cell motility-related factors are also among them. Cell speeds and localisation of motility-related signalling molecules were monitored by live cell imaging and immunostaining (a) in nutrient medium during growth, (b) immediately following transfer to starvation medium and (c) in nutrient medium that was re-introduced after a brief period of starvation. Cells moved randomly under all three conditions but mean speeds increased following transfer from nutrient medium to starvation medium; the transition occurred within 15 min. The distribution of speeds in starvation medium was bimodal: about 20% of the cells moved significantly faster than the remaining 80%. The motility-related molecules F-actin, PTEN and PI3 kinase were distributed differently in slow and fast cells. Among starved cells, the calcium content of slower cells was lower than that of the faster cells. All differences reverted within 15 min after restoration of the nutrient medium. The slow/fast distinction was missing in Polysphondylium pallidum, a cellular slime mould that lacks the presumptive stalk and spore cell classes, and in the trishanku (triA(-)) mutant of D. discoideum, in which the classes exist but are unstable. The transition from growth to starvation triggers a spontaneous and reversible switch in the distribution of D. discoideum cell speeds. Cells whose calcium content is relatively low (known to be presumptive spore cells) move slower than those whose calcium levels are higher (known to be presumptive stalk cells). Slow and fast cells show different distributions of motility-related proteins. The switch is indicative of a bistable mechanism underlying cell motility.

Huber, R. J. and D. H. O'Day (2012). "The cyclin-dependent kinase inhibitor roscovitine inhibits kinase activity, cell proliferation, multicellular development, and Cdk5 nuclear translocation in Dictyostelium discoideum." J Cell Biochem 113(3): 868-876.
	Roscovitine, a cyclin-dependent kinase (Cdk) inhibitor, inhibited kinase activity and the axenic growth of Dictyostelium discoideum at micromolar concentrations. Growth was almost fully rescued in 50 microM and approximately 50% rescued in 100 microM roscovitine-treated cultures by the over-expression of Cdk5-GFP. This supports the importance of Cdk5 function during cell proliferation in Dictyostelium and indicates that Cdk5 is a primary target of the drug. Roscovitine did not affect the expression of Cdk5 protein during axenic growth but did inhibit its nuclear translocation. This novel result suggests that the effects of roscovitine could be due in part to altering Cdk5 translocation in other systems as well. Kinase activity was inhibited by roscovitine in assays using AX3 whole cell lysates, but not in assays using lysates from Cdk5-GFP over-expressing cells. At higher concentrations, roscovitine impaired slug and fruiting body formation. Fruiting bodies that did form were small and produced relatively fewer spores many of which were round. However, roscovitine did not affect stalk cell differentiation. Together with previous findings, these data reveal that roscovitine inhibits Cdk5 during growth and as yet undefined Cdks during mid-late development. J. Cell. Biochem. 113: 868-876, 2012. (c) 2011 Wiley Periodicals, Inc.

Ishihara, D., A. Dovas, et al. (2012). "The chemotactic defect in wiskott-Aldrich syndrome macrophages is due to the reduced persistence of directional protrusions." PLoS One 7(1): e30033.
	Wiskott-Aldrich syndrome protein (WASp) is an actin nucleation promoting factor that is required for macrophages to directionally migrate towards various chemoattractants. The chemotaxis defect of WASp-deficient cells and its activation by Cdc42 in vivo suggest that WASp plays a role in directional sensing, however, its precise role in macrophage chemotaxis is still unclear. Using shRNA-mediated downregulation of WASp in the murine monocyte/macrophage cell line RAW/LR5 (shWASp), we found that WASp was responsible for the initial wave of actin polymerization in response to global stimulation with CSF-1, which in Dictyostelium discoideum amoebae and carcinoma cells has been correlated with the ability to migrate towards chemoattractants. Real-time monitoring of shWASp cells, as well as WASp(-/-) bone marrow-derived macrophages (BMMs), in response to a CSF-1 gradient revealed that the protrusions from WASp-deficient cells were directional, showing intact directional sensing. However, the protrusions from WASp-deficient cells demonstrated reduced persistence compared to their respective control shRNA and wild-type cells. Further examination showed that tyrosine phosphorylation of WASp was required for both the first wave of actin polymerization following global CSF-1 stimulation and proper directional responses towards CSF-1. Importantly, the PI3K, Rac1 and WAVE2 proteins were incorporated normally in CSF-1 - elicited protrusions in the absence of WASp, suggesting that membrane protrusion driven by the WAVE2 complex signaling is intact. Collectively, these results suggest that WASp and its phosphorylation play critical roles in coordinating the actin cytoskeleton rearrangements necessary for the persistence of protrusions required for directional migration of macrophages towards CSF-1.

Jaiswal, P., T. Soldati, et al. (2012). "Regulation of aggregate size and pattern by adenosine and caffeine in cellular slime molds." BMC Dev Biol 12(1): 5.
	ABSTRACT: BACKGROUND: Multicellularity in cellular slime molds is achieved by aggregation of several hundreds to thousands of cells. In the model slime mold Dictyostelium discoideum, adenosine is known to increase the aggregate size and its antagonist caffeine reduces the aggregate size. However, it is not clear if the actions of adenosine and caffeine are evolutionarily conserved among other slime molds known to use structurally unrelated chemoattractants. We have examined how the known factors affecting aggregate size are modulated by adenosine and caffeine. Result: Adenosine and caffeine induced the formation of large and small aggregates respectively, in evolutionarily distinct slime molds known to use diverse chemoattractants for their aggregation. Due to its genetic tractability, we chose D. discoideum to further investigate the factors affecting aggregate size. The changes in aggregate size are caused by the effect of the compounds on several parameters such as cell number and size, cell-cell adhesion, cAMP signal relay and cell counting mechanisms. While some of the effects of these two compounds are opposite to each other, interestingly, both compounds increase the intracellular glucose level and strengthen cell-cell adhesion. These compounds also inhibit the synthesis of cAMP phosphodiesterase (PdsA), weakening the relay of extracellular cAMP signal. Adenosine as well as caffeine rescue mutants impaired in stream formation (pde4- and pdiA-) and colony size (smlA- and ctnA-) and restore their parental aggregate size. CONCLUSION: Adenosine increased the cell division timings thereby making large number of cells available for aggregation and also it marginally increased the cell size contributing to large aggregate size. Reduced cell division rates and decreased cell size in the presence of caffeine makes the aggregates smaller than controls. Both the compounds altered the speed of the chemotactic amoebae causing a variation in aggregate size. Our data strongly suggests that cytosolic glucose and extracellular cAMP levels are the other major determinants regulating aggregate size and pattern. Importantly, the aggregation process is conserved among different lineages of cellular slime molds despite using unrelated signalling molecules for aggregation.

Jingushi, K., F. Takahashi-Yanaga, et al. (2012). "DIF-1 inhibits the Wnt/beta-catenin signaling pathway by inhibiting TCF7L2 expression in colon cancer cell lines." Biochem Pharmacol 83(1): 47-56.
	We previously reported that differentiation-inducing factor-1 (DIF-1), a morphogen in Dictyostelium discoideum, inhibits the proliferation of human cancer cell lines by inducing beta-catenin degradation and suppressing the Wnt/beta-catenin signaling pathway. To determine whether beta-catenin degradation is essential for the effect of DIF-1, we examined the effect of DIF-1 on human colon cancer cell lines (HCT-116, SW-620 and DLD-1), in which the Wnt/beta-catenin signaling pathway is constitutively active. DIF-1 strongly inhibited cell proliferation and arrested the cell cycle in the G(0)/G(1) phase via the suppression of cyclin D1 expression at mRNA and protein levels without reducing beta-catenin protein. TCF-dependent transcriptional activity and cyclin D1 promoter activity were revealed to be inhibited via suppression of transcription factor 7-like 2 (TCF7L2) expression. Luciferase reporter assays and EMSAs using the TCF7L2 promoter fragments indicated that the binding site for the transcription factor early growth response-1 (Egr-1), which is located in the -609 to -601 bp region relative to the start codon in the TCF7L2 promoter, was involved in DIF-1 activity. Moreover, RNAi-mediated depletion of endogenous TCF7L2 resulted in reduced cyclin D1 promoter activity and protein expression, and the overexpression of TCF7L2 overrode the inhibition of the TCF-dependent transcriptional activity and cyclin D1 promoter activity induced by DIF-1. Therefore, DIF-1 seemed to inhibit the Wnt/beta-catenin signaling pathway by suppressing TCF7L2 expression via reduced Egr-1-dependent transcriptional activity in these colon cancer cell lines. Our results provide a novel insight into the mechanisms by which DIF-1 inhibits the Wnt/beta-catenin signaling pathway.

Journet, A., G. Klein, et al. (2012). "Investigating the macropinocytic proteome of Dictyostelium amoebae by high-resolution mass spectrometry." Proteomics 12(2): 241-245.
	The cellular slime mold Dictyostelium discoideum is a soil-living eukaryote, which feeds on microorganisms engulfed by phagocytosis. Axenic laboratory strains have been produced that are able to use liquid growth medium internalized by macropinocytosis as the source of food. To better define the macropinocytosis process, we established the inventory of proteins associated with this pathway using mass spectrometry-based proteomics. Using a magnetic purification procedure and high-performance LC-MS/MS proteome analysis, a list of 2108 non-redundant proteins was established, of which 24% featured membrane-spanning domains. Bioinformatics analyses indicated that the most abundant proteins were linked to signaling, vesicular trafficking and the cytoskeleton. The present repertoire validates our purification method and paves the way for a future proteomics approach to study the dynamics of macropinocytosis.

Kortholt, A., W. N. van Egmond, et al. (2012). "Multiple Regulatory Mechanisms for the Dictyostelium Roco Protein GbpC." J Biol Chem 287(4): 2749-2758.
	GbpC is a multidomain Roco protein in Dictyostelium, involved in transduction of intracellular cGMP that is produced by chemotactic signals. We have shown previously that cGMP binding to GbpC induces an intramolecular signaling cascade by activating subsequently the GEF, Ras, and kinase domains. In this study, we report on the cellular localization of GbpC. In resting cells, the protein is present in the cytoplasm, but GbpC rapidly translocates to the cell boundary upon stimulation with the chemoattractant cAMP. Also, during the formation of cell-cell streams and osmotic shock, the protein localizes toward the plasma membrane and actin cytoskeleton. The translocation upon cAMP stimulation occurs downstream of heterotrimeric G proteins but is independent of guanylyl cyclases and the previously identified cGMP-induced intramolecular signaling cascade in GbpC. Mutations in the GRAM domain of GbpC lead to disturbed membrane association and inactivation of GbpC function during chemotaxis in vivo. Furthermore, we show that the GRAM domain itself associates with cellular membranes and binds various phospholipids in vitro. Together, the results show that GbpC receives multiple input signals that are both required for functional activity in vivo. cAMP-stimulation induces a cGMP-dependent signaling cascade, leading to activation of kinase activity, and, independently, cAMP induces a GRAM-dependent translocation of GbpC toward the plasma membrane and cell cortex, where it may locally phosphorylate effector proteins, which are needed for proper biological activity.

Kruger, A., P. Batsios, et al. (2012). "Characterization of NE81, the first lamin-like nucleoskeleton protein in a unicellular organism." Mol Biol Cell 23(2): 360-370.
	Lamins build the nuclear lamina and are required for chromatin organization, gene expression, cell cycle progression, and mechanical stabilization. Despite these universal functions, lamins have so far been found only in metazoans. We have identified protein NE81 in Dictyostelium, which has properties that justify its denomination as a lamin-like protein in a lower eukaryote. This is based on its primary structure, subcellular localization, and regulation during mitosis, and its requirement of the C-terminal CaaX box as a posttranslational processing signal for proper localization. Our knockout and overexpression mutants revealed an important role for NE81 in nuclear integrity, chromatin organization, and mechanical stability of cells. All our results are in agreement with a role for NE81 in formation of a nuclear lamina. This function is corroborated by localization of Dictyostelium NE81 at the nuclear envelope in human cells. The discovery of a lamin-like protein in a unicellular organism is not only intriguing in light of evolution, it may also provide a simple experimental platform for studies of the molecular basis of laminopathies.

Kuhnert, O., O. Baumann, et al. (2012). "Functional characterization of CP148, a novel key component for centrosome integrity in Dictyostelium." Cell Mol Life Sci.
	The Dictyostelium centrosome consists of a layered core structure surrounded by a microtubule-nucleating corona. A tight linkage through the nuclear envelope connects the cytosolic centrosome with the clustered centromeres within the nuclear matrix. At G2/M the corona dissociates, and the core structure duplicates, yielding two spindle poles. CP148 is a novel coiled coil protein of the centrosomal corona. GFP-CP148 exhibited cell cycle-dependent presence and absence at the centrosome, which correlates with dissociation of the corona in prophase and its reformation in late telophase. During telophase, GFP-CP148 formed cytosolic foci, which coalesced and joined the centrosome. This explains the hypertrophic appearance of the corona upon strong overexpression of GFP-CP148. Depletion of CP148 by RNAi caused virtual loss of the corona and disorganization of interphase microtubules. Surprisingly, formation of the mitotic spindle and astral microtubules was unaffected. Thus, microtubule nucleation complexes associate with centrosomal core components through different means during interphase and mitosis. Furthermore, CP148 RNAi caused dispersal of centromeres and altered Sun1 distribution at the nuclear envelope, suggesting a role of CP148 in the linkage between centrosomes and centromeres. Taken together, CP148 is an essential factor for the formation of the centrosomal corona, which in turn is required for centrosome/centromere linkage.

Linkner, J., B. Nordholz, et al. (2012). "Highly effective removal of floxed Blasticidin S resistance cassettes from Dictyostelium discoideum mutants by extrachromosomal expression of Cre." Eur J Cell Biol 91(2): 156-160.
	The inactivation of proteins in cells is inevitable to study their physiological role in various cellular processes. In contrast to strategies to alter the amount of active proteins in cells, only a gene knockout guarantees complete removal of the protein of interest. For Dictyostelium discoideum cells, the gene replacement construct typically consists of a Blasticidin S resistance (Bsr) cassette flanked by fragments of the target gene to allow insertion by homologous recombination. More advanced knockout constructs additionally carry loxP sites on both sides of the Bsr cassettes for subsequent removal of the selection marker by transient expression of Cre recombinase, thus allowing generation of multiple knockouts using just a single selection marker. However, due to its design, the available neomycin selection-based Cre expression plasmid occasionally tends to integrate into the genome and also yield only a moderate number of transfectants in liquid media. In some cases, for instance in SCAR-null cells, it was not possible to remove the Bsr cassette without stable integration of the Cre expression vector into the genome. To circumvent these difficulties we designed the extrachromosomal Cre-recombinase expression vector pTX-NLS-Cre. We verified the greatly improved efficacy of this novel Cre-loxP approach by removal of the Bsr cassette in five different cell lines including the SCAR-null mutant. As a consequence, this vector will be a highly valuable means for the rapid generation of single or multiple mutants remaining sensitive to the most reliable selection markers Blasticidin S and neomycin.

Lobanov, M. Y. and O. V. Galzitskaya (2012). "Occurrence of disordered patterns and homorepeats in eukaryotic and bacterial proteomes." Mol Biosyst 8(1): 327-337.
	Combining the motif discovery and disorder protein segment identification in PDB allows us to create the first and largest library of disordered patterns. At present the library includes 109 disordered patterns. Here we offer a comprehensive analysis of the occurrence of selected disordered patterns and 20 homorepeats of 6 residues long in 123 proteomes. 27 disordered patterns occur sparsely in all considered proteomes, but the patterns of low-complexity-homorepeats-appear more often in eukaryotic than in bacterial proteomes. A comparative analysis of the number of proteins containing homorepeats of 6 residues long and the disordered selected patterns in these proteomes has been performed. The matrices of correlation coefficients between numbers of proteins where at least once a homorepeat of six residues long for each of 20 types of amino acid residues and 109 disordered patterns from the library appears in 9 kingdoms of eukaryota and 5 phyla of bacteria have been calculated. As a rule, the correlation coefficients are higher inside the considered kingdom than between them. The largest fraction of homorepeats of 6 residues belongs to Amoebozoa proteomes (D. discoideum), 46%. Moreover, the longest uninterrupted repeats belong to S306 from D. discoideum (Amoebozoa). Homorepeats of some amino acids occur more frequently than others and the type of homorepeats varies across different proteomes, . For example, E6 appears most frequent for all considered proteomes for Chordata, Q6 for Arthropoda, S6 for Nematoda. The averaged occurrence of multiple long runs of 6 amino acids in a decreasing order for 97 eukaryotic proteomes is as follows: Q6, S6, A6, G6, N6, E6, P6, T6, D6, K6, L6, H6, R6, F6, V6, I6, Y6, C6, M6, W6, and for 26 bacterial proteomes it is A6, G6, P6, and the others occur seldom. This suggests that such short similar motifs are responsible for common functions for nonhomologous, unrelated proteins from different organisms.

Meza, I., J. D. Diaz-Valencia, et al. (2012). "Molecular and functional characterization of an Entamoeba histolytica protein (EhMLCI) with features of a myosin essential light chain." Mol Biochem Parasitol 181(1): 17-28.
	Entamoeba histolytica, a protozoan parasite of humans, relays on its striking motility to survive and invade host tissues. Characterization of the molecular components involved in motile processes is crucial to understand its pathogenicity. Although protein components of myosin II hexamers have been predicted from E. histolytica genome data, only a heavy chain of myosin, EhmhcA, has been characterized so far. We have cloned an E. histolytica cDNA sequence that best matched Dictyostelium discoideum myosin essential light chain and found that the cloned sequence is transcribed as an mRNA of 0.445 kb which could encode a protein of 16.88 kDa, within the predicted range for a myosin light chain. In silico analyses revealed that the protein sequence, named EhMLCI, shows two consensus domains for binding MHC, but lacks the N-terminal sequence for actin binding, as in A2 type myosin essential light chains. A single EF-hand calcium-binding domain was identified in the C-terminus and several high score predictability sites for serine and tyrosine phosphorylation. Antibodies to recombinant EhMLCI identified two proteins of approximately 17 and 15 kDa in trophozoite extracts, the latter phophorylated in tyrosines. Serine phosphorylation was not detected. Immunomicroscopy revealed EhMLCI cortical and cytoplasmic distribution in trophozoites and true colocalization with EhmhcA determined by PCC. Co-immunoprecipitation corroborated EhMLCI interaction with EhmhcA. EhMLCI was also localized in actomyosin-containing complexes. Differential partition of phospho-tyrosinated EhMLCI into cell fractions containing the soluble form of EhmhcA and its lack of serine phosphorylation suggest its possible participation in a novel down regulatory mechanism of myosin II activity in E. histolytica.

Mir, H., J. Rajawat, et al. (2012). "Staurosporine induced poly (ADP-ribose) polymerase independent cell death in Dictyostelium discoideum." Indian J Exp Biol 50(1): 80-86.
	In the present study D. discoideum has been used as a model organism to understand the role of poly (ADP-ribose) polymerase (PARP) in caspase independent paraptotic cell death pathways. D. discoideum lacks caspases and Bcl-2 family proteins; nevertheless it has 9 potential genes for PARP. PARP has been known to get activated in various cell death associated diseases. In this study kinetics of cell death induced by staurosporine (STS), a bacterial alkaloid, was established to unravel the role of PARP. It was found that STS induced cell death in D. discoideum did not involve PARP activation, however it involved cathepsin D. Results indicated that an alternative mechanism may be existing in D. discoideum that lacks Bcl-2 family proteins for STS induced cell death that evades Bax involvement.

Nikolaeva, I., R. J. Huber, et al. (2012). "EGF-like peptide of Dictyostelium discoideum is not a chemoattractant but it does restore folate-mediated chemotaxis in the presence of signal transduction inhibitors." Peptides.
	A synthetic EGF-like (EGFL) peptide (DdEGFL1), equivalent to the first EGFL domain in the extracellular matrix protein CyrA, has previously been shown to enhance random cell motility and cAMP-mediated chemotaxis in Dictyostelium discoideum. However the role of DdEGFL1 as a potential chemoattractant had not been addressed. In this study, a micropipette assay and an under-agarose migration assay showed that DdEGFL1 is not a chemoattractant for Dictyostelium cells. A radial bioassay was used to show that DdEGFL1 does not significantly enhance folate-mediated chemotaxis in contrast to its chemokinetic effect during chemotaxis toward cAMP. However, DdEGFL1 was able to rescue chemotaxis toward folate when the pathway was inhibited by pharmacological agents that inhibit known components of the signaling cascade (e.g. phosphatidylinositol 3-kinase, phospholipase A2, tyrosine kinases, and calmodulin). These data suggest that DdEGFL1 may activate a novel motility pathway that when coupled with folic acid receptor activation, can maintain the normal migratory response to folic acid in vegetative cells. Together, this data provides new insight into the function of EGFL repeats during Dictyostelium chemotaxis and the existence of a novel motility pathway regulated by EGFL peptides and/or repeats in this model organism.

Nunez-Corcuera, B., J. L. Birch, et al. (2012). "Transcriptional Repression by a bZIP Protein Regulates Dictyostelium Prespore Differentiation." PLoS One 7(1): e29895.
	In response to the signaling polyketide DIF-1 DimB directly activates transcription of the ecmB gene in pstB cells; a subset of the prestalk cells that are the precursors of the basal disc. We show that the promoter of pspA, a prespore-specific gene, also contains a DimB binding site. Mutation of this site causes ectopic expression in the prestalk region and ChIP analysis shows that DIF-1 induces binding of DimB to the pspA promoter. DIF-1 represses pspA gene expression in a suspension cell assay but this repression is abrogated in a dimB null strain. These results suggest a coupled control mechanism, whereby the same DIF-DimB signaling pathway that directly activates ecmB gene expression directly represses pspA gene expression.

Pears, C. J., C. A. Couto, et al. (2012). "The role of ADP-ribosylation in regulating DNA double-strand break repair." Cell Cycle 11(1): 48-56.
	ADP-ribosylation is the post translational modification of proteins catalysed by ADP-ribosyltransferases (ARTs). ADP-ribosylation has been implicated in a wide variety of cellular processes including cell growth and differentiation, apoptosis and transcriptional regulation. Perhaps the best characterised role, however, is in DNA repair and genome stability where ADP-ribosylation promotes resolution of DNA single strand breaks. Although ADP-ribosylation also occurs at DNA double strand breaks (DSBs), which ARTs catalyse this reaction and the molecular basis of how this modification regulates their repair remains a matter of debate. Here we review recent advances in our understanding of how ADP-ribosylation regulates DSB repair. Specifically, we highlight studies using the genetic model organism Dictyostelium, in addition to vertebrate cells that identify a third ART that accelerates DSB repair by non-homologous end-joining through promoting the interaction of repair factors with DNA lesions. The implications of these data with regards to how ADP-ribosylation regulates DNA repair and genome stability are discussed.

Renfro, D. P., B. K. McIntosh, et al. (2012). "GONUTS: the Gene Ontology Normal Usage Tracking System." Nucleic Acids Res 40(Database issue): D1262-1269.
	The Gene Ontology Normal Usage Tracking System (GONUTS) is a community-based browser and usage guide for Gene Ontology (GO) terms and a community system for general GO annotation of proteins. GONUTS uses wiki technology to allow registered users to share and edit notes on the use of each term in GO, and to contribute annotations for specific genes of interest. By providing a site for generation of third-party documentation at the granularity of individual terms, GONUTS complements the official documentation of the Gene Ontology Consortium. To provide examples for community users, GONUTS displays the complete GO annotations from seven model organisms: Saccharomyces cerevisiae, Dictyostelium discoideum, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus and Arabidopsis thaliana. To support community annotation, GONUTS allows automated creation of gene pages for gene products in UniProt. GONUTS will improve the consistency of annotation efforts across genome projects, and should be useful in training new annotators and consumers in the production of GO annotations and the use of GO terms. GONUTS can be accessed at http://gowiki.tamu.edu. The source code for generating the content of GONUTS is available upon request.

Rosel, D., T. Khurana, et al. (2012). "TOR complex 2 (TORC2) in Dictyostelium suppresses phagocytic nutrient capture independently of TORC1-mediated nutrient sensing." J Cell Sci 125(Pt 1): 37-48.
	The TOR protein kinase functions in two distinct complexes, TOR complex 1 (TORC1) and 2 (TORC2). TORC1 is required for growth in response to growth factors, nutrients and the cellular energy state; TORC2 regulates AKT signaling, which can modulate cytoskeletal polarization. In its ecological niche, Dictyostelium engulf bacteria and yeast for nutrient capture. Despite the essential role of TORC1 in control of cellular growth, we show that nutrient particle capture (phagocytosis) in Dictyostelium is independent of TORC1-mediated nutrient sensing and growth regulation. However, loss of Dictyostelium TORC2 components Rictor/Pia, SIN1/RIP3 and Lst8 promotes nutrient particle uptake; inactivation of TORC2 leads to increased efficiency and speed of phagocytosis. In contrast to phagocytosis, we show that macropinocytosis, an AKT-dependent process for cellular uptake of fluid phase nutrients, is not regulated by either of the TOR complexes. The integrated and balanced regulation of TORC1 and TORC2 might be crucial in Dictyostelium to coordinate growth and energy needs with other essential TOR-regulated processes.

Shu, S., X. Liu, et al. (2012). "Actin cross-linking proteins cortexillin I and II are required for cAMP signaling during Dictyostelium chemotaxis and development." Mol Biol Cell 23(2): 390-400.
	Starvation induces Dictyostelium amoebae to secrete cAMP, toward which other amoebae stream, forming multicellular mounds that differentiate and develop into fruiting bodies containing spores. We find that the double deletion of cortexillin (ctx) I and II alters the actin cytoskeleton and substantially inhibits all molecular responses to extracellular cAMP. Synthesis of cAMP receptor and adenylyl cyclase A (ACA) is inhibited, and activation of ACA, RasC, and RasG, phosphorylation of extracellular signal regulated kinase 2, activation of TORC2, and stimulation of actin polymerization and myosin assembly are greatly reduced. As a consequence, cell streaming and development are completely blocked. Expression of ACA-yellow fluorescent protein in the ctxI/ctxII-null cells significantly rescues the wild-type phenotype, indicating that the primary chemotaxis and development defect is the inhibition of ACA synthesis and cAMP production. These results demonstrate the critical importance of a properly organized actin cytoskeleton for cAMP-signaling pathways, chemotaxis, and development in Dictyostelium.

Sultana, H., G. Neelakanta, et al. (2012). "Ectopic expression of Cyclase associated protein CAP restores the streaming and aggregation defects of Adenylyl Cyclase A deficient Dictyostelium discoideum cells." BMC Dev Biol 12(1): 3.
	ABSTRACT: BACKGROUND: Cell adhesion, an integral part of D. discoideum development, is important for morphogenesis and regulated gene expression in the multicellular context and is required to trigger cell-differentiation. G-protein linked adenylyl cyclase pathways are crucially involved and a mutant lacking the aggregation specific adenylyl cyclase ACA does not undergo multicellular development. RESULTS: Here, we have investigated the role of cyclase-associated protein (CAP), an important regulator of cell polarity and F-actin/G-actin ratio in the aca mutant. We show that ectopic expression of GFP-CAP improves cell polarization, streaming and aggregation in aca cells, but it fails to completely restore development. Our studies indicate a requirement of CAP in the ACA dependent signal transduction for progression of the development of unicellular amoebae into multicellular structures. The reduced expression of the cell adhesion molecule DdCAD1 together with csA is responsible for the defects in aca cells to initiate multicellular development. Early development was restored by the expression of GFP-CAP that enhanced the DdCAD1 transcript levels and to a lesser extent the csA mRNA levels. CONCLUSIONS: Collectively, our data shows a novel role of CAP in regulating cell adhesion mechanisms during development that might be envisioned to unravel the functions of mammalian CAP during animal embryogenesis.

Thomas Sosa, R., M. M. Weber, et al. (2012). "A Single beta Adaptin Contributes to AP1 and AP2 Complexes and Clathrin Function in Dictyostelium." Traffic 13(2): 305-316.
	The assembly of clathrin-coated vesicles is important for numerous cellular processes, including nutrient uptake and membrane organization. Important contributors to clathrin assembly are four tetrameric assembly proteins, also called adaptor proteins (APs), each of which contains a beta subunit. We identified a single beta subunit, named beta1/2, that contributes to both the AP1 and AP2 complexes of Dictyostelium. Disruption of the gene encoding beta1/2 resulted in severe defects in growth, cytokinesis and development. Additionally, cells lacking beta1/2 displayed profound osmoregulatory defects including the absence of contractile vacuoles and mislocalization of contractile vacuole markers. The phenotypes of beta1/2 null cells were most similar to previously described phenotypes of clathrin and AP1 mutants, supporting a particularly important contribution of AP1 to clathrin pathways in Dictyostelium cells. The absence of beta1/2 in cells led to significant reductions in the protein amounts of the medium-sized subunits of the AP1 and AP2 complexes, establishing a role for the beta subunit in the stability of the medium subunits. Dictyostelium beta1/2 could resemble a common ancestor of the more specialized beta1 and beta2 subunits of the vertebrate AP complexes. Our results support the essential contribution of a single beta subunit to the stability and function of AP1 and AP2 in a simple eukaryote.

Vilches, S., N. Jimenez, et al. (2012). "The Aeromonas dsbA mutation decreased their virulence by triggering type III secretion system but not flagella production." Microb Pathog 52(2): 130-139.
	Pathogenesis of Aeromonas species have been reported to be associated with virulence factors such as lipopolysaccharides (LPS), bacterial toxins, bacterial secretion systems, flagella, and other surface molecules. Dsb (Disulfide bond) proteins play an important role in catalyzing disulfide bond formation in proteins within the periplasmic space. An A. hydrophila dsbA mutant with attenuated virulence using Dictyostelium amoebae as an alternative host model was identified. The attenuated virulence was tested in other animal models (by intraperitoneal injection in fish and mice) and was correlated with the presence of a defective type III secretion system for the first time in non enteric bacteria. The dsbA mutation was shown in several enteric bacteria to involve the outer membrane secretin. The defect in Aeromonas also seems to involve the outer membrane secretin homologue named AscC. However, unlike what happen in Escherichia coli, no changes in motility or flagella expression were observed for A. hydrophila dsbA mutants. The loss of E. coli motility caused by deletion of dsbA is likely due to defective disulfide bond formation in FlgI, a component of the flagella. No disulfide bond formation in FlgI homologues in Aeromonas flagella biogenesis, either polar or lateral, could be expected according to their amino acid residues sequences.

von Buelow, J., A. Mueller-Lucks, et al. (2012). "Functional characterization of a novel aquaporin from Dictyostelium discoideum amoebae implies a unique gating mechanism." J Biol Chem.
	The social amoeba Dictyostelium discoideum is a widely used model organism for studying basic functions of protozoan and metazoan cells, such as osmoregulation and cell motility. There is evidence from other species that cellular water channels, aquaporins (AQP ), are central to both processes. Yet, data on D. discoideum AQPs is almost absent. Despite cloning of two putative D. discoideum AQPs, WacA and AqpA, water permeability has not been shown. Further, WacA and AqpA are expressed at the late multicellular stage and in spores but not in amoebae. We cloned a novel AQP, AqpB, from amoeboidal D. discoideum cells. Wildtype AqpB was impermeable to water, glycerol, and urea when expressed in Xenopus laevis oocytes. Neither stepwise truncation of the N-terminus nor selected point mutations activated the water channel. However, mutational truncation by 12 amino acids of an extraordinary long intracellular loop induced water permeability of AqpB hinting at a novel gating mechanism. This AqpB mutant was inhibited by mercuric chloride confirming the presence of a cysteine residue in the selectivity filter as predicted by our structure model. We detected AqpB by Western blot in a glycosylated and a non-glycosylated form throughout all developmental stages. When expressed in D. discoideum amoebae, AqpB-GFP fusion constructs localized to vacuolar structures, to the plasma membrane, and to lamellipodia-like membrane protrusions. We conclude, that the localization pattern in conjunction with channel gating may be indicative of AqpB functions in osmoregulation as well as cell motility of D. discoideum.

Xiong, H. and F. Rivero (2012). "Assaying Rho GTPase-dependent processes in Dictyostelium discoideum." Methods Mol Biol 827: 381-392.
	The model organism D. discoideum is well suited to investigate basic questions of molecular and cell biology, particularly those related to the structure, regulation, and dynamics of the cytoskeleton, signal transduction, cell-cell adhesion, and development. D. discoideum makes use of Rho-regulated signaling pathways to reorganize its cytoskeleton during chemotaxis, endocytosis, and cytokinesis. In this organism the Rho family encompasses 20 members, several belonging to the Rac subfamily, but there are no representatives of the Cdc42 and Rho subfamilies. Here we present protocols suitable for monitoring the actin polymerization response and the activation of Rac upon stimulation of aggregation competent cells with the chemoattractant cAMP.

Yan, J., V. Mihaylov, et al. (2012). "A Gbetagamma Effector, ElmoE, Transduces GPCR Signaling to the Actin Network during Chemotaxis." Dev Cell 22(1): 92-103.
	Activation of G protein-coupled receptors (GPCRs) leads to the dissociation of heterotrimeric G-proteins into Galpha and Gbetagamma subunits, which go on to regulate various effectors involved in a panoply of cellular responses. During chemotaxis, Gbetagamma subunits regulate actin assembly and migration, but the protein(s) linking Gbetagamma to the actin cytoskeleton remains unknown. Here, we identified a Gbetagamma effector, ElmoE in Dictyostelium, and demonstrated that it is required for GPCR-mediated chemotaxis. Remarkably, ElmoE associates with Gbetagamma and Dock-like proteins to activate the small GTPase Rac, in a GPCR-dependent manner, and also associates with Arp2/3 complex and F-actin. Thus, ElmoE serves as a link between chemoattractant GPCRs, G-proteins and the actin cytoskeleton. The pathway, consisting of GPCR, Gbetagamma, Elmo/Dock, Rac, and Arp2/3, spatially guides the growth of dendritic actin networks in pseudopods of eukaryotic cells during chemotaxis.

Zhang, D., H. van der Wel, et al. (2012). "Skp1 Prolyl 4-Hydroxylase of Dictyostelium Mediates Glycosylation-independent and -dependent Responses to O2 without Affecting Skp1 Stability." J Biol Chem 287(3): 2006-2016.
	Cytoplasmic prolyl 4-hydroxylases (PHDs) have a primary role in O(2) sensing in animals via modification of the transcriptional factor subunit HIFalpha, resulting in its polyubiquitination by the E3(VHL)ubiquitin (Ub) ligase and degradation in the 26 S proteasome. Previously thought to be restricted to animals, a homolog (P4H1) of HIFalpha-type PHDs is expressed in the social amoeba Dictyostelium where it also exhibits characteristics of an O(2) sensor for development. Dictyostelium lacks HIFalpha, and P4H1 modifies a different protein, Skp1, an adaptor of the SCF class of E3-Ub ligases related to the E3(VHL)Ub ligase that targets animal HIFalpha. Normally, the HO-Skp1 product of the P4H1 reaction is capped by a GlcNAc sugar that can be subsequently extended to a pentasaccharide by novel glycosyltransferases. To analyze the role of glycosylation, the Skp1 GlcNAc-transferase locus gnt1 was modified with a missense mutation to block catalysis or a stop codon to truncate the protein. Despite the accumulation of the hydroxylated form of Skp1, Skp1 was not destabilized based on metabolic labeling. However, hydroxylation alone allowed for partial correction of the high O(2) requirement of P4H1-null cells, therefore revealing both glycosylation-independent and glycosylation-dependent roles for hydroxylation. Genetic complementation of the latter function required an enzymatically active form of Gnt1. Because the effect of the gnt1 deficiency depended on P4H1, and Skp1 was the only protein labeled when the GlcNAc-transferase was restored to mutant extracts, Skp1 apparently mediates the cellular functions of both P4H1 and Gnt1. Although Skp1 stability itself is not affected by hydroxylation, its modification may affect the stability of targets of Skp1-dependent Ub ligases.

