Related papers: Protein sequestration versus Hill-type repression …
Periodic forcing of nonlinear oscillators leads to a large number of dynamic behaviors. The coupling of the cell-cycle to the circadian clock provides a biological realization of such forcing. Using high throughput single-cell microscopy,…
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…
Temperature compensation is a notable property of circadian oscillators that indicates the insensitivity of the oscillator system's period to temperature changes; the underlying mechanism, however, is still unclear. We investigated the…
Biochemical circadian rhythm oscillations play an important role in many signalling mechanisms. In this work, we explore some of the biophysical mechanisms responsible for sustaining robust oscillations by constructing a minimal but…
Objective: The circadian rhythm synchronizes physiological and behavioural patterns with the 24-hour light-dark cycle. Disruption to the circadian rhythm is linked to various health conditions, though optimal methods to describe these…
Circadian clocks exhibit the robustness of period and plasticity of phase against environmental changes such as temperature and nutrient conditions. Thus far, however, it is unclear how both are simultaneously achieved. By investigating…
Circadian clocks ubiquitous in life forms ranging bacteria to multi-cellular organisms, often exhibit intrinsic temperature compensation; the period of circadian oscillators is maintained constant over a range of physiological temperatures,…
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…
Common models of circadian rhythms are constructed as compartmental reactions of well mixed biochemicals involving a negative-feedback loop containing several intermediate reaction steps in order to enable oscillations. Spatial transport of…
Intrinsically disordered protein regions (IDRs) are found across all domains of life and are characterized by a lack of stable 3D structure. Nevertheless, IDRs play critical roles in the most tightly regulated cellular processes, including…
The development of systemic approaches in biology has put emphasis on identifying genetic modules whose behavior can be modeled accurately so as to gain insight into their structure and function. However most gene circuits in a cell are…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
Autonomous circadian clocks drive daily rhythms in physiology and behaviour. A network of coupled neurons, the suprachiasmatic nucleus (SCN), serves as a robust self-sustained circadian pacemaker. Synchronization of this timer to the…
Circadian rhythms are acquired through evolution to increase the chances for survival through synchronizing with the daylight cycle. Reliable synchronization is realized through two trade-off properties: regularity to keep time precisely,…
Molecular circadian clocks, that are found in all nucleated cells of mammals, are known to dictate rhythms of approximately 24 hours (circa diem) to many physiological processes. This includes metabolism (e.g., temperature, hormonal blood…
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…
To understand the sophisticated control mechanisms of the human's endocrine system is a challenging task that is a crucial step towards precise medical treatment of many disfunctions and diseases. Although mathematical models describing the…
The in vivo circadian clock in single cyanobacteria is studied here by time-lapse fluorescence microscopy when the temperature is lowered below 25{\deg}C . We first disentangle the circadian clock behavior from the bacterial cold shock…
Transcription factors are proteins that regulate gene activity by activating or repressing gene transcription. A special class of transcriptional repressors operates via a short-range mechanism, making local DNA regions inaccessible to…
Oscillatory chemical reactions often serve as a timing clock of cellular processes in living cells. The temporal dynamics of protein concentration levels is thus of great interest in biology. Here we propose a theoretical framework to…