CSM News Electronic Edition Volume 2, number 12 March 26, 1994 Please submit abstracts of your papers as soon as they have been accepted for publication by sending them to CSM-News@worms.cmsbio.nwu.edu. Back issues of CSM-News, the CSM Reference database and other useful information is available by anonymous ftp from worms.cmsbio.nwu.edu [129.105.233.50], via Gopher at the same address, or by World Wide Web through WWW.acns.nwu.edu. ============= Announcement ============= To: the Dicty community From: Bill Loomis and Doug Smith March 22, 1994 Amos Bairoch heads the organization that is in charge of the protein data base, SWISS-PROT. Discussion between us have lead to establishing Dictyostelium as one of five "privaledged organisms" in the database. This means that it will be easier to retrieve the amino acid sequences encoded by Dictyostelium genes submitted to any of the public domain files ( GenBank, EMBL etc.). Moreover, transfer to SWISSPROT will be more rapid and the genes will be partially anotated. The Dicty proteins can be conveniently accessed under DictyDB accession numbers: eg. myosin II heavy chain (mhcA) is DD01008. All of the "DDxxxxx" proteins are from Dicty. Together with Adam Kuspa we have proof read the list but would appreciate hearing of any remaining errors. The document (DICTY.TXT) at SWISS-PROT gives the full list. The file is growing rapidly and the annotation is proceeding. We hope this will be of value to all of us. Here is what Bairoch circulated a week or so ago: 2.2 What's happening with the model organisms As we announced in the last release we have selected a number of organisms that are the target of genome sequencing and/or mapping projects and for which we intend to: - Be as complete as possible. All sequences available at a given time should be immediately included in SWISS-PROT. This also includes sequence corrections and updates. - Provide a high level of annotations. - Cross-references to specialized database(s) that contain, among other data, some genetic information about the genes that code for these proteins. - Provide specific indices or documents. Thanks to a collaborative effort with Douglas Smith and Bill Loomis of UCSD we have added a fifth organism, Dictyostelium discoideum (slime mold), to our list of model organisms. Many new sequences were added at this release and a new document file (DICTY.TXT) lists all the D.discoideum sequence entries in SWISS-PROT and their corresponding gene names. At this release we also have started our collaboration with the group at the Sanger Genome Center in Hinxton (UK) and we have added 516 new C.elegans sequences; most of which are translation of sequencing data from the genome project. A new document file (CELEGANS.TXT) list all the C.elegans sequence entries in SWISS-PROT and their corresponding gene names and, when appropriate, their cosmid-derived names. Here is the current status of the five model organisms: Organism Database Index file Number of cross-referenced sequences -------------- ---------------------- -------------- --------- C.elegans WormPep CELEGANS.TXT 672 D.discoideum DictyDB DICTY.TXT 183 D.melanogaster FlyBase In preparation 600 E.coli EcoGene ECOLI.TXT 2555 S.cerevisiae LISTA (in preparation) YEAST.TXT 1731 2.4 Changes in the DR line We have added cross-references to the Dictyostelium discoideum genome database (DictyDB) (see section 2.2 of these notes). These cross- references are present in the DR lines: Data bank identifier: DICTYDB Primary identifier: Unique identifier attributed by DictyDB to the gene coding for the protein. Secondary identifier: The gene designation (name). A "-" is present when no gene name has yet been assigned. Example: DR DICTYDB; DD01047; MYOA. ========== Abstracts ========== The Level of Sequestered Calcium in Vegetative Amoebae of Dictyostelium discoideum Can Predict Post-aggregative Cell Fate Shweta Saran, M. Azhar, P.S. Manogaran, Gopal Pande and Vidyanand Nanjundiah Developmental Biology and Genetics Laboratory, Indian Institute of Science, Bangalore 560012, India DIFFERENTIATION, in press When vegetative amoebae of D. discoideum are labelled with chlortetracycline (CTC) and monitored for calcium-CTC fluorescence, they fall into two distinct classes that can be separated using a fluorescence-activated cell sorter. We name the classes F(+), meaning high fluorescence and F(-), meaning low fluorescence. Either F(+) or F(-) amoebae can be labelled with ruthenium red or rhodamine 123 and the original mixture re-constituted. The resulting slugs or fruiting bodies display ruthenium red or rhodamine 123 fluorescence in a pattern which indicates that F(+) amoebae are pre-stalk and F(-) amoebae are prespores. As expected, this committment is reversible: F(+) or F(-) amoebae can also develop by themselves. Pure F(+) slugs show a high level of calcium-CTC fluorescence in their anterior and little or none in their posterior. Pure F(-) slugs initially show no fluorescence, but after being labelled a second time with CTC display asimilar gradient of calcium-CTC fluorescence. We infer from this that genotypically identical cells raised in a common environment can differ in respect of the levels of sequestered calcium they contain and that this difference is correlated with future cell fate. We conjecture that the observed calcium differences are related to differences in cell cycle phases. ------------------------------------------------------------------ [End CSM-News, volume 2, number 12]