Related papers: Quantifying mRNA synthesis and decay rates using s…
Regulatory genes called small RNAs (sRNAs) are known to play critical roles in cellular responses to changing environments. For several sRNAs, regulation is effected by coupled stoichiometric degradation with messenger RNAs (mRNAs). The…
The processes, resulting in the transcription of RNA, are intrinsically noisy. It was observed experimentally that the synthesis of mRNA molecules is driven by short, burst-like, events. An accurate prediction of the protein level often…
Tight regulation of messenger RNA (mRNA) stability is essential to ensure accurate gene expression in response to developmental and environmental cues. mRNA stability is controlled by mRNA decay pathways, which have traditionally been…
The rate of mRNA translation depends on the initiation, elongation, and termination rates of ribosomes along the mRNA. These rates depend on many "local" factors like the abundance of free ribosomes and tRNA molecules in the vicinity of the…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…
In this paper we study an important global regulation mechanism of transcription of biological cells using specific macro-molecules, 6S RNAs. The functional property of 6S RNAs is of blocking the transcription of RNAs when the environment…
A wealth of new research has highlighted the critical roles of small RNAs (sRNAs) in diverse processes such as quorum sensing and cellular responses to stress. The pathways controlling these processes often have a central motif comprising…
Gene expression is a fundamental process in a living system. The small RNAs (sRNAs) is widely observed as a global regulator in gene expression. The inherent nonlinearity in this regulatory process together with the bursty production of…
We build a simple model for feedback systems involving small RNA (sRNA) molecules based on the iron metabolism system in the bacterium E. coli, and compare it with the corresponding system in H. pylori which uses purely transcriptional…
Small, non-coding RNAs (sRNAs) play important roles as genetic regulators in prokaryotes. sRNAs act post-transcriptionally via complementary pairing with target mRNAs to regulate protein expression. We use a quantitative approach to compare…
Down regulation of mRNA translation is an important problem in various bio-medical domains ranging from developing effective medicines for tumors and for viral diseases to developing attenuated virus strains that can be used for…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles due to differences in transcription time, degradation rate and RNA processing kinetics. Recent studies have shown that a…
Transcription of genes is the focus of most forms of regulation of gene expression. Even though careful biochemical experimentation has revealed the molecular mechanisms of transcription initiation for a number of different promoters in…
Large-scale simultaneous mRNA translation and the resulting competition for the available ribosomes has important implications to the cell's functioning and evolution. Developing a better understanding of the intricate correlations between…
Small non-coding RNAs can exert significant regulatory activity on gene expression in bacteria. In recent years, substantial progress has been made in understanding bacterial gene expression by sRNAs. However, recent findings that…
The ribosomal density along the coding region of the mRNA molecule affect various fundamental intracellular phenomena including: protein production rates, organismal fitness, ribosomal drop off, and co-translational protein folding. Thus,…
Single cell experiments of simple regulatory networks can markedly differ from cell population experiments. Such differences arise from stochastic events in individual cells that are averaged out in cell populations. For instance, while…
MicroRNAs are small noncoding RNAs that regulate genes post-transciptionally by binding and degrading target eukaryotic mRNAs. We use a quantitative model to study gene regulation by inhibitory microRNAs and compare it to gene regulation by…
Protein synthesis rates are determined, at the translational level, by properties of the transcript's sequence. The efficiency of an mRNA can be tuned by varying the ribosome binding sites controlling the recruitment of the ribosomes, or…