Related papers: Positive feedback and noise activate the stringent…
Pluripotent embryonic stem cells are of paramount importance for biomedical research thanks to their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent…
We propose a modelling framework to analyse the stochastic behaviour of heterogeneous, multi-scale cellular populations. We illustrate our methodology with a particular example in which we study a population with an oxygen-regulated…
Cells use signalling pathways as windows into the environment to gather information, transduce it into their interior, and use it to drive behaviours. MAPK (ERK) is a highly conserved signalling pathway in eukaryotes, directing multiple…
For millennia, cyanobacteria have evolved strategies for acclimatization to dynamic environments- this requires a molecular response system. Phosphate is essential for cellular integrity and metabolism, yet inorganic phosphate is often the…
Precise temporal coordination of gene expression is crucial for many developmental processes. One central question in developmental biology is how such coordinated expression patterns are robustly controlled. During embryonic development of…
This paper analyzes, in the context of a prokaryotic cell, the stochastic variability of the number of proteins when there is a control of gene expression by an autoregulation scheme. The goal of this work is to estimate the efficiency of…
We studied in silico effects of structural stress in Mycoplasma pneumoniae, a genome-reduced model bacterial organism, by tracking the damage propagating on its metabolic network after a deleterious perturbation. First, we analyzed failure…
We study the non-monotonic force-extension behaviour of helical ribbons using a new model for inextensible elastic strips. Unlike previous rod models our model predicts hysteresis behaviour for low-pitch ribbons of arbitrary material…
This paper studies the emergence of multi-stability and hysteresis in those systems that arise, under positive feedback, starting from monotone systems with well-defined steady-state responses. Such feedback configurations appear routinely…
The mitogen-activated protein kinase (MAPK) signaling cascade, an evolutionarily conserved motif present in all eukaryotic cells, is involved in coordinating critical cell-fate decisions, regulating protein synthesis, and mediating learning…
Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically; and the frequency spectrum of this chemical fluctuation carries valuable information about the mechanism and the dynamics of the intracellular…
How can a microorganism adapt to a variety of environmental conditions despite there exists a limited number of signal transduction machineries? We show that for any growing cells whose gene expression is under stochastic fluctuations,…
Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of…
We show that the effect of stress on the reproductive fitness of noisy cell populations can be modelled as first-passage time problem, and demonstrate that even relatively short-lived fluctuations in gene expression can ensure long-term…
Many types of bacteria can survive under stress by switching stochastically between two different phenotypes: the "normals" who multiply fast, but are vulnerable to stress, and the "persisters" who hardly multiply, but are resilient to…
Within the cell, biopolymers are often situated in constrained, fluid environments, e.g., cytoskeletal networks, stretched DNAs in chromatin. It is of paramount importance to understand quantitatively how they, utilizing their flexibility,…
Erythropoiesis is a mechanism for the production of red blood cells by cellular differentiation. It is based on amplification steps due to an interplay between renewal and differentiation in the successive cell compartments from stem cells…
Hysteresis and bet-hedging (random choice of phenotypes) are two different observations typically linked with multiplicity of phenotypes in biological systems. Hysteresis can be viewed as form of the system's persistent memory of past…
To maintain renewing epithelial tissues in a healthy, homeostatic state, (stem) cell divisions and differentiation need to be tightly regulated. Mechanisms of homeostatic control often rely on crowding control: cells are able to sense the…
Epigenetic mechanisms of silencing via heritable chromatin modifications play a major role in gene regulation and cell fate specification. We consider a model of epigenetic chromatin silencing in budding yeast and study the bifurcation…