196 research outputs found
Studies of Bacterial Branching Growth using Reaction-Diffusion Models for Colonial Development
Various bacterial strains exhibit colonial branching patterns during growth
on poor substrates. These patterns reflect bacterial cooperative
self-organization and cybernetic processes of communication, regulation and
control employed during colonial development. One method of modeling is the
continuous, or coupled reaction-diffusion approach, in which continuous time
evolution equations describe the bacterial density and the concentration of the
relevant chemical fields. In the context of branching growth, this idea has
been pursued by a number of groups. We present an additional model which
includes a lubrication fluid excreted by the bacteria. We also add fields of
chemotactic agents to the other models. We then present a critique of this
whole enterprise with focus on the models' potential for revealing new
biological features.Comment: 1 latex file, 40 gif/jpeg files (compressed into tar-gzip). Physica
A, in pres
Modeling branching and chiral colonial patterning of lubricating bacteria
In nature, microorganisms must often cope with hostile environmental
conditions. To do so they have developed sophisticated cooperative behavior and
intricate communication capabilities, such as: direct cell-cell physical
interactions via extra-membrane polymers, collective production of
extracellular "wetting" fluid for movement on hard surfaces, long range
chemical signaling such as quorum sensing and chemotactic (bias of movement
according to gradient of chemical agent) signaling, collective activation and
deactivation of genes and even exchange of genetic material. Utilizing these
capabilities, the colonies develop complex spatio-temporal patterns in response
to adverse growth conditions. We present a wealth of branching and chiral
patterns formed during colonial development of lubricating bacteria (bacteria
which produce a wetting layer of fluid for their movement). Invoking ideas from
pattern formation in non-living systems and using ``generic'' modeling we are
able to reveal novel survival strategies which account for the salient features
of the evolved patterns. Using the models, we demonstrate how communication
leads to self-organization via cooperative behavior of the cells. In this
regard, pattern formation in microorganisms can be viewed as the result of the
exchange of information between the micro-level (the individual cells) and the
macro-level (the colony). We mainly review known results, but include a new
model of chiral growth, which enables us to study the effect of chemotactic
signaling on the chiral growth. We also introduce a measure for weak chirality
and use this measure to compare the results of model simulations with
experimental observations.Comment: 50 pages, 24 images in 44 GIF/JPEG files, Proceedings of IMA
workshop: Pattern Formation and Morphogenesis (1998
Continuous and discrete models of cooperation in complex bacterial colonies
We study the effect of discreteness on various models for patterning in
bacterial colonies. In a bacterial colony with branching pattern, there are
discrete entities - bacteria - which are only two orders of magnitude smaller
than the elements of the macroscopic pattern. We present two types of models.
The first is the Communicating Walkers model, a hybrid model composed of both
continuous fields and discrete entities - walkers, which are coarse-graining of
the bacteria. Models of the second type are systems of reaction diffusion
equations, where the branching of the pattern is due to non-constant diffusion
coefficient of the bacterial field. The diffusion coefficient represents the
effect of self-generated lubrication fluid on the bacterial movement. We
implement the discreteness of the biological system by introducing a cutoff in
the growth term at low bacterial densities. We demonstrate that the cutoff does
not improve the models in any way. Its only effect is to decrease the effective
surface tension of the front, making it more sensitive to anisotropy. We
compare the models by introducing food chemotaxis and repulsive chemotactic
signaling into the models. We find that the growth dynamics of the
Communication Walkers model and the growth dynamics of the Non-Linear diffusion
model are affected in the same manner. From such similarities and from the
insensitivity of the Communication Walkers model to implicit anisotropy we
conclude that the increased discreteness, introduced be the coarse-graining of
the walkers, is small enough to be neglected.Comment: 16 pages, 10 figures in 13 gif files, to be published in proceeding
of CMDS
SkyMapper SEDs of nearby galaxies: quenching and bursting probed by a change index for star formation
The wish list of astronomers includes a tool that reveals quenching of star
formation in galaxies directly as it proceeds. Here, we present a
proof-of-concept for a new quenching-and-bursting diagnostic, a "change index"
for star formation, that requires only photometric data, provided they include
filters such as the violet bands used by SkyMapper. The index responds
mostly to changes in star-formation rate on a timescale of 20 to 500 Myr and is
nearly insensitive to dust extinction. It works effectively to distances of 100
to 150 Mpc. We explore its application to eight example galaxies in SkyMapper
DR2, including known E+A and Seyfert-1 galaxies. Owing to the degeneracies
inherent in broad-band photometry, the change index can only be a qualitative
indicator of changes in star-formation rate. But once the SkyMapper Southern
Survey is complete, the change index will be available for every spatial
resolution element of every galaxy in the Southern sky within its working
distance range.Comment: 20 pages, 14 figures, submitted to PAS
Information flow and optimization in transcriptional control
In the simplest view of transcriptional regulation, the expression of a gene
is turned on or off by changes in the concentration of a transcription factor
(TF). We use recent data on noise levels in gene expression to show that it
should be possible to transmit much more than just one regulatory bit.
Realizing this optimal information capacity would require that the dynamic
range of TF concentrations used by the cell, the input/output relation of the
regulatory module, and the noise levels of binding and transcription satisfy
certain matching relations. This parameter-free prediction is in good agreement
with recent experiments on the Bicoid/Hunchback system in the early Drosophila
embryo, and this system achieves ~90% of its theoretical maximum information
transmission.Comment: 5 pages, 4 figure
Spatio-selection in Expanding Bacterial Colonies
Segregation of populations is a key question in evolution theory. One
important aspect is the relation between spatial organization and the
population's composition. Here we study a specific example -- sectors in
expanding bacterial colonies. Such sectors are spatially segregated
sub-populations of mutants. The sectors can be seen both in disk-shaped
colonies and in branching colonies. We study the sectors using two models we
have used in the past to study bacterial colonies -- a continuous
reaction-diffusion model with non-linear diffusion and a discrete
``Communicating Walkers'' model. We find that in expanding colonies, and
especially in branching colonies, segregation processes are more likely than in
a spatially static population. One such process is the establishment of stable
sub- population having neutral mutation. Another example is the maintenance of
wild-type population along side with sub-population of advantageous mutants.
Understanding such processes in bacterial colonies is an important subject by
itself, as well as a model system for similar processes in other spreading
populations
Lubricating Bacteria Model for Branching growth of Bacterial Colonies
Various bacterial strains (e.g. strains belonging to the genera Bacillus,
Paenibacillus, Serratia and Salmonella) exhibit colonial branching patterns
during growth on poor semi-solid substrates. These patterns reflect the
bacterial cooperative self-organization. Central part of the cooperation is the
collective formation of lubricant on top of the agar which enables the bacteria
to swim. Hence it provides the colony means to advance towards the food. One
method of modeling the colonial development is via coupled reaction-diffusion
equations which describe the time evolution of the bacterial density and the
concentrations of the relevant chemical fields. This idea has been pursued by a
number of groups. Here we present an additional model which specifically
includes an evolution equation for the lubricant excreted by the bacteria. We
show that when the diffusion of the fluid is governed by nonlinear diffusion
coefficient branching patterns evolves. We study the effect of the rates of
emission and decomposition of the lubricant fluid on the observed patterns. The
results are compared with experimental observations. We also include fields of
chemotactic agents and food chemotaxis and conclude that these features are
needed in order to explain the observations.Comment: 1 latex file, 16 jpeg files, submitted to Phys. Rev.
- …