Related papers: Oscillations and temporal signalling in cells
Gene expression is a biochemical process, where stochastic binding and un-binding events naturally generate fluctuations and cell-to-cell variability in gene dynamics. These fluctuations typically have destructive consequences for proper…
Collective oscillation of cells in a population has been reported under diverse biological contexts and with vastly different molecular constructs. Could there be common principles similar to those that govern spontaneous oscillation in…
The NF-kB signalling system is involved in a variety of cellular processes including immune response, inflammation, and apoptosis. Recent experiments have found oscillations in the nuclear-cytoplasmic translocation of the NF-kB…
We study a system of dynamical units, each of which shows excitable or oscillatory behavior, depending on the choice of parameters. When we couple these units with repressive bonds, we can control the duration of collective oscillations for…
Biological rhythms are generated by pacemaker organs, such as the heart pacemaker organ (the sinoatrial node) and the master clock of the circadian rhythms (the suprachiasmatic nucleus), which are composed of a network of autonomously…
We explore the joint effect of the intrinsic noise and time delay on the spatial pattern formation within a multi-scale mobile lattice model of the epithelium. The protein fluctuations are driven by transcription/translation processes in…
Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to…
Cell signaling, gene expression, and metabolism are affected by cell-cell heterogeneity and random changes in the environment. The effects of such fluctuations on cell signaling and gene expression have recently been studied intensively…
Oscillatory dynamics are common features of complex networks, often playing essential roles in regulating function. Across scales from gene regulatory networks to ecosystems, delayed feedback mechanisms are key drivers of system-scale…
In genomic applications, there is often interest in identifying genes whose time-course expression trajectories exhibit periodic oscillations with a period of approximately 24 hours. Such genes are usually referred to as circadian, and…
The time taken for gene expression varies not least because proteins vary in length considerably. This paper uses an abstract, tuneable Boolean regulatory network model to explore gene expression time variation. In particular, it is shown…
Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically-motivated mathematical models for cell differentiation that generically generate oscillations and hence…
The digital nature of genes combined with the associated low copy numbers of proteins regulating them is a significant source of stochasticity, which affects the phase of biochemical oscillations. We provide a theoretical framework for…
Stochasticity is both exploited and controlled by cells. Although the intrinsic stochasticity inherent in biochemistry is relatively well understood, cellular variation, or 'noise', is predominantly generated by interactions of the system…
We describe a mechanism for pronounced biochemical oscillations, relevant to microscopic systems, such as the intracellular environment. This mechanism operates for reaction schemes which, when modeled using deterministic rate equations,…
In biochemical signaling, information is often encoded in oscillatory signals. However, the advantages of such a coding strategy over an amplitude encoding scheme of constant signals remain unclear. Here we study the dynamics of a simple…
Understanding the interplay among processes that occur over different timescales is a challenging issue in the physics of systems regulation. In gene regulation, the timescales for changes in chromatin states can differ from those for…
We assess the impact of cell cycle noise on gene circuit dynamics. For bistable genetic switches and excitable circuits, we find that transitions between metastable states most likely occur just after cell division and that this…
Bioreactors are widely used in many industries to generate a range of products using various host cells e.g., yeast, insect, and mammalian cells. Depending on the process, product, and host cell, some bioreactors exhibit sustained periodic…
The structure of a genetic network is uncovered by studying its response to external stimuli (input signals). We present a theory of propagation of an input signal through a linear stochastic genetic network. It is found that there are…