dictyNews Electronic Edition Volume 42, number 3 January 29, 2016 Please submit abstracts of your papers as soon as they have been accepted for publication by sending them to dicty@northwestern.edu or by using the form at http://dictybase.org/db/cgi-bin/dictyBase/abstract_submit. Back issues of dictyNews, the Dicty Reference database and other useful information is available at dictyBase - http://dictybase.org. Follow dictyBase on twitter: http://twitter.com/dictybase ========= Abstracts ========= Self-Generated Chemoattractant Gradients: Attractant Depletion Extends the Range and Robustness of Chemotaxis. Luke Tweedy, David A Knecht, Gillian M Mackay & Robert H Insall PLOS Biology, in press Chemotaxis is fundamentally important, but the sources of gradients in vivo are rarely well understood. Here we analyse self-generated chemotaxis, in which cells respond to gradients they have made themselves by breaking down globally available attractants, using both computational simulations and experiments. We show that chemoattractant degradation creates steep local gradients. This leads to surprising results, in particular the existence of a leading population of cells that moves highly directionally, while cells behind this group are undirected. This leading cell population is denser than those following, especially at high attractant concentrations. The local gradient moves with the leading cells as they interact with their surroundings, giving directed movement that is unusually robust and can operate over long distances. Even when gradients are applied from external sources, attractant breakdown greatly changes cells' responses and increases robustness. We also consider alternative mechanisms for directional decision-making and show that they do not predict the features of population migration we observe experimentally. Our findings provide useful diagnostics to allow identification of self-generated gradients, and suggest that self-generated chemotaxis is unexpectedly universal in biology and medicine. submitted by: Robert Insall [r.insall@beatson.gla.ac.uk] ——————————————————————————————————————— A computational method for the coupled solution of reaction– diffusion equations on evolving domains and manifolds: Application to a model of cell migration and chemotaxis G. MacDonald, J.A. Mackenzie, M. Nolan & R.H. Insall Journal of Computational Physics, in press In this paper, we devise a moving mesh finite element method for the approximate solution of coupled bulk–surface reaction–diffusion equations on an evolving two dimensional domain. Fundamental to the success of the method is the robust generation of bulk and surface meshes. For this purpose, we use a novel moving mesh partial differential equation (MMPDE) approach. The developed method is applied to model problems with known analytical solutions; these experiments indicate second-order spatial and temporal accuracy. Coupled bulk–surface problems occur frequently in many areas; in particular, in the modelling of eukaryotic cell migration and chemotaxis. We apply the method to a model of the two-way interaction of a migrating cell in a chemotactic field, where the bulk region corresponds to the extracellular region and the surface to the cell membrane. submitted by: Robert Insall [r.insall@beatson.gla.ac.uk] ——————————————————————————————————————— Use of a Probabilistic Motif Search to Identify Histidine Phosphotransfer Domain-Containing Proteins Defne Surujon and David I. Ratner PLoS ONE, 2016 The wealth of newly obtained proteomic information affords researchers the possibility of searching for proteins of a given structure or function. Here we describe a general method for the detection of a protein domain of interest in any species for which a complete proteome exists. In particular, we apply this approach to identify histidine phosphotransfer (HPt) domain-containing proteins across a range of eukaryotic species. From the sequences of known HPt domains, we created an amino acid occurrence matrix which we then used to define a conserved, probabilistic motif. Examination of various organisms either known to contain (plant and fungal species) or believed to lack (mammals) HPt domains established criteria by which new HPt candidates were identified and ranked. Search results using a probabilistic motif matrix compare favorably with data to be found in several commonly used protein structure/function databases: our method identified all known HPt proteins in the Arabidopsis thaliana proteome, confirmed the absence of such motifs in mice and humans, and suggests new candidate HPts in several organisms. Moreover, probabilistic motif searching can be applied more generally, in a manner both readily customized and computationally compact, to other protein domains; this utility is demonstrated by our identification of histones in a range of eukaryotic organisms. submitted by: David Ratner [diratner@amherst.edu] ——————————————————————————————————————— Rho signaling in Dictyostelium discoideum Francisco Rivero and Huajiang Xiong International Review of Cell and Molecular Biology Small GTPases of the Rho family are ubiquitous molecular switches involved in the regulation of most actin cytoskeleton dependent processes and many other processes not directly linked to actin. The soil ameba D. discoideum is a well established model organism for studies of the actin cytoskeleton and its regulation by signal transduction pathways. D. discoideum is equipped with a complex repertoire of Rho signaling components, with 20 Rho GTPases, more than 100 regulators (including exchange factors, GTPase activating proteins and gunanine nucleotide dissociation inhibitors) and nearly 80 effectors or components of effector complexes. In this review we examine the knowledge accumulated to date about proteins involved in Rho-regulated signaling pathways in D. discoideum, with an emphasis on functional studies. We integrate the information about individual components into defined signaling pathways, with a focus on three extensively investigated processes: chemotaxis, vesicle trafficking and cytokinesis. submitted by: Francisco Rivero [f.rivero-crespo@hull.ac.uk] ============================================================== [End dictyNews, volume 42, number 3]