Copy Link
Add to Bookmark
Report
dictyNews Volume 42 Number 03
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]
