6 research outputs found
Noise regulation by quorum sensing in low mRNA copy number systems
<p>Abstract</p> <p>Background</p> <p>Cells must face the ubiquitous presence of noise at the level of signaling molecules. The latter constitutes a major challenge for the regulation of cellular functions including communication processes. In the context of prokaryotic communication, the so-called quorum sensing (QS) mechanism relies on small diffusive molecules that are produced and detected by cells. This poses the intriguing question of how bacteria cope with the fluctuations for setting up a reliable information exchange.</p> <p>Results</p> <p>We present a stochastic model of gene expression that accounts for the main biochemical processes that describe the QS mechanism close to its activation threshold. Within that framework we study, both numerically and analytically, the role that diffusion plays in the regulation of the dynamics and the fluctuations of signaling molecules. In addition, we unveil the contribution of different sources of noise, intrinsic and transcriptional, in the QS mechanism.</p> <p>Conclusions</p> <p>The interplay between noisy sources and the communication process produces a repertoire of dynamics that depends on the diffusion rate. Importantly, the total noise shows a non-monotonic behavior as a function of the diffusion rate. QS systems seems to avoid values of the diffusion that maximize the total noise. These results point towards the direction that bacteria have adapted their communication mechanisms in order to improve the signal-to-noise ratio.</p
Theoretical Design of Paradoxical Signaling-Based Synthetic Population Control Circuit in E. coli
We have developed a mathematical framework to analyze the cooperative control of cell population homeostasis via paradoxical signaling in synthetic contexts. Paradoxical signaling functions through quorum sensing (where cells produce and release a chemical signal as a function of cell density). Precisely, the same quorum sensing signal provides both positive (proliferation) and negative (death) feedback in different signal concentration regimes. As a consequence, the relationship between intercellular quorum sensing signal concentration and net growth rate (cell proliferation minus death rates) can be non-monotonic. This relationship is a condition for robustness to certain cell mutational overgrowths and allows for increased stability in the presence of environmental perturbations. Here, we explore stability and robustness of a conceptualized synthetic circuit. Furthermore, we asses possible design principles that could exist among a subset of paradoxical circuit implementations. This analysis sparks the development a bio-molecular control theory to identify ideal underlying characteristics for paradoxical signaling control systems
Stochastic noise reduction upon complexification: positively correlated birth-death type systems
Cell systems consist of a huge number of various molecules that display
specific patterns of interactions, which have a determining influence on the
cell's functioning. In general, such complexity is seen to increase with the
complexity of the organism, with a concomitant increase of the accuracy and
specificity of the cellular processes. The question thus arises how the
complexification of systems - modeled here by simple interacting birth-death
type processes - can lead to a reduction of the noise - described by the
variance of the number of molecules. To gain understanding of this issue, we
investigated the difference between a single system containing molecules that
are produced and degraded, and the same system - with the same average number
of molecules - connected to a buffer. We modeled these systems using Ito
stochastic differential equations in discrete time, as they allow
straightforward analytical developments. In general, when the molecules in the
system and the buffer are positively correlated, the variance on the number of
molecules in the system is found to decrease compared to the equivalent system
without a buffer. Only buffers that are too noisy by themselves tend to
increase the noise in the main system. We tested this result on two model
cases, in which the system and the buffer contain proteins in their active and
inactive state, or protein monomers and homodimers. We found that in the second
test case, where the interconversion terms are non-linear in the number of
molecules, the noise reduction is much more pronounced; it reaches up to 20%
reduction of the Fano factor with the parameter values tested in numerical
simulations on an unperturbed birth-death model. We extended our analysis to
two arbitrary interconnected systems.Comment: 38 pages, 5 figures, to appear in J. Theor. Bio
Using Competing Bacterial Communication to Disassemble Biofilms
In recent years, bacterial infections have become a major
public health concern due to their ability to cooperate between
single and multiple species resisting to various forms
of treatments (e.g., antibiotics). One form of protection is
through biofilms, where the bacteria produce a protective
medium known as the Extracellular Polymeric Substances
(EPS). Researchers are pursuing new multi-disciplinary approaches
to treating and kerb the evolving process of these
infections through the biofilms, to lower the humans' antibiotic
dependence that can result in the so-called \super-
bugs". Although various solutions have been proposed to
break biofilms, they are based on applying drugs or using
nanoparticles. In this paper, we propose an alternative
approach, where bacteria will cooperate and surround the
biofilms to consume the nutrients. By hijacking the nutrients
in the environment and blocking the
ow from reaching
the biofilms, this will lead to starvation, forcing them to
break their structure. Preliminary simulations show that a
small action radius of quorum sensing molecules is needed
to maximise bacteria attraction to a particular location and
create the protective wall. Therefore, this formation is capable
of speeds up biofilm dispersal process by two hours
Slow protein fluctuations explain the emergence of growth phenotypes and persistence in clonal bacterial populations
One of the most challenging problems in microbiology is to understand how a
small fraction of microbes that resists killing by antibiotics can emerge in a
population of genetically identical cells, the phenomenon known as persistence
or drug tolerance. Its characteristic signature is the biphasic kill curve,
whereby microbes exposed to a bactericidal agent are initially killed very
rapidly but then much more slowly. Here we relate this problem to the more
general problem of understanding the emergence of distinct growth phenotypes in
clonal populations. We address the problem mathematically by adopting the
framework of the phenomenon of so-called weak ergodicity breaking, well known
in dynamical physical systems, which we extend to the biological context. We
show analytically and by direct stochastic simulations that distinct growth
phenotypes can emerge as a consequence of slow-down of stochastic fluctuations
in the expression of a gene controlling growth rate. In the regime of fast gene
transcription, the system is ergodic, the growth rate distribution is unimodal,
and accounts for one phenotype only. In contrast, at slow transcription and
fast translation, weakly non-ergodic components emerge, the population
distribution of growth rates becomes bimodal, and two distinct growth
phenotypes are identified. When coupled to the well-established growth rate
dependence of antibiotic killing, this model describes the observed fast and
slow killing phases, and reproduces much of the phenomenology of bacterial
persistence. The model has major implications for efforts to develop control
strategies for persistent infections.Comment: 26 pages, 7 figure