Related papers: Discrete gene replication events drive coupling be…
Rhythms in electrical activity in the membrane of cells in the suprachiasmatic nucleus (SCN) are crucial for the function of the circadian timing system, which is characterized by the expression of the so-called clock genes. Intracellular…
Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. In 2000, Elowitz and Leibler showed that by rational design of the reaction network, and using existing…
Circadian rhythms are biological rhythms of approximately 24 h that persist even under constant conditions without environmental daily cues. The molecular circadian clock machinery generates the physiological rhythms, which can be…
A wide range of organisms features molecular machines, circadian clocks, which generate endogenous oscillations with ~24 h periodicity and thereby synchronize biological processes to diurnal environmental fluctuations. Recently, it has…
The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce…
The circadian clocks keeping time of day in many living organisms rely on self-sustained biochemical oscillations which can be entrained by external cues, such as light, to the 24-hour cycle induced by Earth rotation. However, environmental…
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…
It is possible that there are post-translational circadian oscillators that continue functioning in the absence of negative feedback transcriptional repression in many cell types from diverse organisms. Apart from the KaiABC system from…
The metazoan genome is replicated in precise cell lineage specific temporal order. However, the mechanism controlling this orchestrated process is poorly understood as no molecular mechanisms have been identified that actively regulate the…
Oscillatory gene circuits are ubiquitous to biology and are involved in fundamental processes of cell cycle, circadian rhythms and developmental systems. The synthesis of small, non-natural oscillatory genetic circuits have been…
Biological oscillators are very diverse but can be classified based on dynamical motifs such as the types of feedback loops present. The S. Elongatus circadian clock is a remarkable phosphorylation-based oscillator that can be reconstituted…
Eukaryotic cells are often exposed to fluctuations in growth conditions as well as endogenous and exogenous stress-related agents. In addition, during development global patterns of gene transcription change dramatically, and these changes…
Humans, like almost all animals, are phase-locked to the diurnal cycle. Most of us sleep at night and are active through the day. Because we have evolved to function with this cycle, the circadian rhythm is deeply ingrained and even…
We introduce and analyze an extension of the mixed feedback loop model of Fran\c{c}ois and Hakim. Our extension includes an additional promoter state and allows for reversible protein sequestration, which was absent from the original…
We propose a revisited version of the in vivo model of the cyanobacterial circadian clock. Our aim is to address the lack of robustness predicted for the mutant cyanobacteria without transcriptional regulation of the original model. For…
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…
Isogenic Escherichia coli growing exponentially in a constant environment display large variation in growth-rates, division-sizes and generation-times. It is unclear how these seemingly random cell cycles can be reconciled with the precise…
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
The circadian clock can adapt itself to external cues, but the molecular mechanisms and regulatory networks governing circadian oscillations' transient adjustments are still largely unknown. Here we consider the specific case of circadian…