Delay and noise induced regime shift and enhanced stability in gene expression dynamics

Yang, Tao; Zhang, Chun; Zeng, Chunhua; Zhou, Guoqiong; Han, Qun; Tian, Dong; Zhang, Huili

doi:10.1088/1742-5468/2014/12/p12015

Cited by 33 publications

(13 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the framework of differential equations, such processes can be modeled as a time delay (Yang et al. , Zeng et al. ).…”

Section: Introductionmentioning

confidence: 99%

“…In other words, the density-dependent effects are not instantaneous; rather, they have a time lag (D'Odorico et al 2013, Guttal et al 2013. In the framework of differential equations, such processes can be modeled as a time delay (Yang et al 2014a. Delay and bistability have been extensively studied (Masoller 2001, Bratsun et al 2005, Gupta et al 2013), but the impacts of time delays on bistable lake eutrophication ecosystems are not clear.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Stochastic ecological kinetics of regime shifts in a time‐delayed lake eutrophication ecosystem

et al. 2017

Self Cite

View full text Add to dashboard Cite

Abstract. Lake eutrophication ecosystems tend to exhibit bistable kinetics with two preferential configurations of oligotrophic and eutrophic states, and perturbations in the environmental parameters can cause regime shifts between two alternative stable states, yielding catastrophic regime shifts. In this article, we study stochastic kinetics of regime shifts in a time-delayed lake eutrophication ecological system, where the environmental parameters are assumed to be disturbed by both input and loss external noises. The dynamical behavior of stochastic delay on the regime shifts between oligotrophic and eutrophic states is analyzed using numerical simulations. Time delays in loss and recycling processes are considered. It is shown from time series and probability distribution that noises and delays can induce regime shifts between two stable states. Theoretical analyses are used to support our numerical simulations. By using the mean first passage time (MFPT) technique, we also discuss the escape time problem between two stable states in time-delayed ecosystems. A detailed study of the MFPT depending on various noise characteristics is performed, and the main results are compared for different cases of time delays.

show abstract

“…In the framework of differential equations, such processes can be modeled as a time delay (Yang et al. , Zeng et al. ).…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Stochastic ecological kinetics of regime shifts in a time‐delayed lake eutrophication ecosystem

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…Here x is the concentration of the transcription factor (TF) monomer, α the basal synthesis reaction rate of the TF, β the maximal rate of phosphorylated dimer TF activator, γ the degradation rate, and c the concentration of x needed for half-maximal induction. By introducing the environmental fluctuation, this model has been widely investigated due to its role of representativeness [23][24][25][26][27][28][29][30][31]. Note that the effect of a carrying capacity of the environment on the production of the TF has been included in this model.…”

Section: A Simple Gene Transcription Regulatory Systemmentioning

confidence: 99%

Effects of restrained degradation on gene expression and regulation

et al. 2020

View full text Add to dashboard Cite

The effects of carrying capacity of environment K for degradation (the K effect for short) on the constitutive gene expression and a simple genetic regulation system, are investigated by employing a stochastic Langevin equation combined with the corresponding Fokker-Planck equation for the two stochastic systems subjected to internal and external noises. This K effect characterizes the limited degradation ability of the environment for RNA or proteins, such as insufficient catabolic enzymes. The K effect could significantly change the distribution of mRNA copy-number in constitutive gene expression, and interestingly, it leads to the Fano factor slightly larger than 1 if only the internal noise exists. Therefore, that the recent experimental measurements suggests the Fano factor deviates from 1 slightly (Science 346 (2014) 1533), probably originates from the K effect. The K effects on the steady and transient properties of genetic regulation system, have been investigated in detail.It could enhance the mean first passage time significantly especially when the noises are weak and reduce the signal-to-noise ratio in stochastic resonance substantially.

show abstract

“…9,10 The existence of two major ingredients, the positive feedback loop involved in dynamical system and the additional nonlinearity, contribute to the phenomenon of bistability. [25][26][27] According to previous works, 9,12,[28][29][30] noise is pervasive in the gene expression events. On occasion, these events show burst-like dynamical behaviors.…”

Section: Introductionmentioning

confidence: 99%

Lévy noise-induced transitions in gene regulatory networks

Wu¹,

Chen²,

Zheng³

et al. 2017

Preprint

View full text Add to dashboard Cite

Important effects of noise on a one-dimensional gene expression model involving a single gene have recently been discussed. However, few works have been devoted to the transition in two-dimensional models which include the interaction of genes. Therefore, we investigate here, a quantitative two-dimensional model (MeKS network) of gene expression dynamics describing the competence development in the B. subtilis under the influence of L évy as well as Brownian motions, where noises can do the B. subtilis a favor in nutrient depletion. To analyze the transitions between the vegetative and the competence regions therein, two deterministic quantities, the mean first exit time (MFET) and the first escape probability (FEP) from a microscopic perspective, as well as their averaged versions from a macroscopic perspective, are applied. The relative contribution factor (RCF), the ratio of non-Gaussian and Gaussian noise strengths, is adopted to implement optimal control in these transitions. Schematic representations indicate that there exists an optimum choice that makes the transition occurring at the highest probability. Additionally, we use a geometric concept, the stochastic basin of attraction, to exhibit a pictorial comprehension about the influence of the L évy motion on the basin stability of the competence state.

show abstract

Delay and noise induced regime shift and enhanced stability in gene expression dynamics

Cited by 33 publications

References 45 publications

Stochastic ecological kinetics of regime shifts in a time‐delayed lake eutrophication ecosystem

Stochastic ecological kinetics of regime shifts in a time‐delayed lake eutrophication ecosystem

Effects of restrained degradation on gene expression and regulation

Lévy noise-induced transitions in gene regulatory networks

Contact Info

Product

Resources

About