Related papers: Oscillations and temporal signalling in cells
Delay is an inherent feature of genetic regulatory networks. It represents the time required for the assembly of functional regulator proteins. The protein production process is complex, as it includes transcription, translocation,…
For cellular biochemical reaction systems where the numbers of molecules is small, significant noise is associated with chemical reaction events. This molecular noise can give rise to behavior that is very different from the predictions of…
We examine fluctuation effects due to the low copy number of proteins involved in pattern-forming dynamics within a bacterium. We focus on a stochastic model of the oscillating MinCDE protein system regulating accurate cell division in E.…
Many transcription factors bind to DNA with a remarkable lack of specificity, so that regulatory binding sites compete with an enormous number of non-regulatory 'decoy' sites. For an auto-regulated gene, we show decoy sites decrease noise…
It has been recently shown that the exponential growth rate of a population of bacterial cells starting from a single cell shows transient oscillations due to early synchronized bursts of division. These oscillations are enhanced by cell…
Regulation of intrinsic noise in gene expression is essential for many cellular functions. Correspondingly, there is considerable interest in understanding how different molecular mechanisms of gene expression impact variations in protein…
In this work, the dynamics of fluctuations in gene expression time series is investigated. By using collected data of gene expression from yeast and human organisms, we found that the fluctuations of gene expression level and its average…
We study the dynamics of intracellular calcium oscillations in the presence of proteins that bind calcium on multiple sites and that are generally believed to act as passive calcium buffers in cells. We find that multisite calcium-binding…
Living systems regulate many aspects of their behavior through periodic oscillations of molecular concentrations, which function as `biochemical clocks.' These clocks are intrinsically subject to thermal fluctuations, so that the duration…
Gene products (RNAs, proteins) often occur at low molecular counts inside individual cells, and hence are subject to considerable random fluctuations (noise) in copy number over time. Not surprisingly, cells encode diverse regulatory…
Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biological processes, including development,…
Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multi-component mathematical framework for translation we uncover…
Auto-regulatory feedback loops are one of the most common network motifs. A wide variety of stochastic models have been constructed to understand how the fluctuations in protein numbers in these loops are influenced by the kinetic…
Gene expression is inherently a noisy process which manifests as cell-to-cell variability in time evolution of proteins. Consequently, events that trigger at critical threshold levels of regulatory proteins exhibit stochasticity in their…
Gene regulatory networks must relay information from extracellular signals to downstream genes in an efficient, timely and coherent manner. Many complex functional tasks such as the immune response require system-wide broadcasting of…
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…
The dynamic behaviors of microRNA and mRNA under external stress are studied with biological experiments and mathematics models. In this study, we developed a mathematic model to describe the biological phenomenon and for the first time…
Many cellular components are present in such low numbers that individual stochastic production and degradation events lead to significant fluctuations in molecular abundances. Although feedback control can, in principle, suppress such…
In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…
We show that the simplest stochastic epidemiological models with spatial correlations exhibit two types of oscillatory behaviour in the endemic phase. In a large parameter range, the oscillations are due to resonant amplification of…