8,603 research outputs found
Unraveling Adaptation in Eukaryotic Pathways: Lessons from Protocells
Eukaryotic adaptation pathways operate within wide-ranging environmental
conditions without stimulus saturation. Despite numerous differences in the
adaptation mechanisms employed by bacteria and eukaryotes, all require energy
consumption. Here, we present two minimal models showing that expenditure of
energy by the cell is not essential for adaptation. Both models share important
features with large eukaryotic cells: they employ small diffusible molecules
and involve receptor subunits resembling highly conserved G-protein cascades.
Analyzing the drawbacks of these models helps us understand the benefits of
energy consumption, in terms of adjustability of response and adaptation times
as well as separation of cell-external sensing and cell-internal signaling. Our
work thus sheds new light on the evolution of adaptation mechanisms in complex
systems.Comment: accepted for publication in PLoS Computational Biology; 19 pages, 8
figure
Partial differential equations for self-organization in cellular and developmental biology
Understanding the mechanisms governing and regulating the emergence of structure and heterogeneity within cellular systems, such as the developing embryo, represents a multiscale challenge typifying current integrative biology research, namely, explaining the macroscale behaviour of a system from microscale dynamics. This review will focus upon modelling how cell-based dynamics orchestrate the emergence of higher level structure. After surveying representative biological examples and the models used to describe them, we will assess how developments at the scale of molecular biology have impacted on current theoretical frameworks, and the new modelling opportunities that are emerging as a result. We shall restrict our survey of mathematical approaches to partial differential equations and the tools required for their analysis. We will discuss the gap between the modelling abstraction and biological reality, the challenges this presents and highlight some open problems in the field
Self-similar dynamics of bacterial chemotaxis
Colonies of bacteria grown on thin agar plate exhibit fractal patterns as a
result of adaptation to their environments. The bacterial colony pattern
formation is regulated crucially by chemotaxis, the movement of cells along a
chemical concentration gradient. Here, the dynamics of pattern formation in
bacterial colony is investigated theoretically through a continuum model that
considers chemotaxis. In the case of the gradient sensed by the bacterium is
nearly uniform, the bacterial colony patterns are self-similar, which they look
the same at every scale. The scaling law of the bacterial colony growth has
been revealed explicitly. Chemotaxis biases the movement of bacterial
population in colony trend toward the chemical attractant. Moreover, the
bacterial colonies evolve long time as the traveling wave with sharp front.Comment: 4 pages, 3 figures, accepted by Phys. Rev. E (Brief Report
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.
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