相关论文: Bistability of an In Vitro Synthetic Autoregulator…
A self-regulatory genetic circuit, where a protein acts as a positive regulator of its own production, is known to be a simplest form of biological network with a positive feedback loop. Although at least three components, DNA, RNA, and the…
A simple stochastic model of a self regulating gene that displays bistable switching is analyzed. While on, a gene transcribes mRNA at a constant rate. Transcription factors can bind to the DNA and affect the gene's transcription rate.…
Bistable biochemical switches are ubiquitous in gene regulatory networks and signal transduction pathways. Their switching dynamics, however, are difficult to study directly in experiments or conventional computer simulations, because…
The bistable gene regulatory switch controlling the transition from lysogeny to lysis in bacteriophage lambda presents a unique challenge to quantitative modeling. Despite extensive characterization of this regulatory network, the origin of…
Synthetic biology is a growing interdisciplinary field, with far-reaching applications, which aims to design biochemical systems that behave in a desired manner. With the advancement of strand-displacement DNA computing, a large class of…
Mixed feedback loops combining transcriptional and post-transcriptional regulations are common in cellular regulatory networks. They consist of two genes, encoding a transcription factor and a small non-coding RNA (sRNA), which mutually…
Bistability plays a central role in the gene regulatory networks (GRNs) controlling many essential biological functions, including cellular differentiation and cell cycle control. However, establishing the network topologies that can…
The design and implementation of regulation motifs ensuring robust perfect adaptation are challenging problems in synthetic biology. Indeed, the design of high-yield robust metabolic pathways producing, for instance, drug precursors and…
Background: MicroRNAs, post-transcriptional repressors of gene expression, play a pivotal role in gene regulatory networks. They are involved in core cellular processes and their dysregulation is associated to a broad range of human…
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…
Riboswitches, structured elements in the untranslated regions of messenger RNAs, regulate gene expression by binding specific metabolites. We introduce a kinetic network model that describes the functions of riboswitches at the systems…
miRNAs serve as crucial post-transcriptional regulators in various essential cell fate decision. However, the contribution of the mRNA-miRNA mutual regulation to bistability is not fully understood. Here, we built a set of mathematical…
Genetic switch systems with mutual repression of two transcription factors are studied using deterministic methods (rate equations) and stochastic methods (the master equation and Monte Carlo simulations). These systems exhibit bistability,…
Small regulatory RNAs (sRNAs) are short non-coding RNAs in bacteria capable of post-transcriptional regulation. sRNAs have recently gained attention as tools in basic and applied sciences for example to fine-tune genetic circuits or…
We analyze three simple genetic circuits which involve transcriptional regulation and feedback: the autorepressor, the switch and the repressilator, that consist of one, two and three genes, respectively. Such systems are commonly simulated…
In this paper, we study through mathematical modelling the combined effect of transcriptional and translational regulation by proteins and small noncoding RNAs (sRNA) in a genetic feedback motif that has an important role in the survival of…
We investigate dynamics of a kinetic model of inhibitory autoregulation as exemplified when a protein inhibits its own production by interfering with its messenger RNA, known in molecular biology as translational autoregulation. We first…
DNA strand displacement (SD) reactions are central to the operation of many synthetic nucleic acid systems, including molecular circuits, sensors, and machines. Over the years, a broad set of design frameworks has emerged to accommodate…
Negative and positive transcriptional feedback loops are present in natural and synthetic genetic oscillators. A single gene with negative transcriptional feedback needs a time delay and sufficiently strong nonlinearity in the transmission…
Bifunctional enzymes, which catalyze both the forward and reverse steps of a substrate modification reaction, arise naturally in bacterial two-component signaling systems and metabolic regulation. Beyond their well-known role in conferring…