Stochastic suppression of gene expression oscillators under intercell coupling.

This paper examines the dynamics of an ensemble of hysteresis-based genetic relaxation oscillators, focusing on the influence of noise and cell-to-cell coupling on the appearance of new dynamical regimes. In particular, we show that control of the coupling strength and noise can effectively change the dynamics of the system leading to behaviors such as clustering, synchronous and asynchronous oscillations, and suppression. Moreover, under certain conditions an optimal amount of noise can lead to increased order in the system. The results obtained are correlated with relevant biological processes that occur in living organisms.

[1]  R. Steuer Effects of stochasticity in models of the cell cycle: from quantized cycle times to noise-induced oscillations. , 2004, Journal of theoretical biology.

[2]  Peter Jung,et al.  Noise in Spatially Extended Systems , 2001 .

[3]  D. Bray Protein molecules as computational elements in living cells , 1995, Nature.

[4]  M. Elowitz,et al.  Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[5]  D. Sherrington Stochastic Processes in Physics and Chemistry , 1983 .

[6]  Zhonghuai Hou,et al.  Internal noise stochastic resonance of synthetic gene network , 2005 .

[7]  Jürgen Kurths,et al.  Constructive effects of fluctuations in genetic and biochemical regulatory systems. , 2003, Bio Systems.

[8]  B. Bainbridge,et al.  Genetics , 1981, Experientia.

[9]  K. Aihara,et al.  A model of periodic oscillation for genetic regulatory systems , 2002 .

[10]  A. Penzkofer,et al.  CHEMICAL PHYSICS LETTERS , 1976 .

[11]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[12]  J. Kurths,et al.  Coherence Resonance in a Noise-Driven Excitable System , 1997 .

[13]  P. Swain,et al.  Stochastic Gene Expression in a Single Cell , 2002, Science.

[14]  宁北芳,et al.  疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .

[15]  D. Gillespie A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions , 1976 .

[16]  Ertugrul M. Ozbudak,et al.  Regulation of noise in the expression of a single gene , 2002, Nature Genetics.

[17]  P. Kloeden,et al.  Numerical Solution of Stochastic Differential Equations , 1992 .

[18]  A. Arkin,et al.  Stochastic mechanisms in gene expression. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[19]  J. Hasty,et al.  Translating the noise , 2002, Nature Genetics.

[20]  Gürol M. Süel,et al.  An excitable gene regulatory circuit induces transient cellular differentiation , 2006, Nature.

[21]  Luonan Chen,et al.  Synchronizing Genetic Oscillators by Signaling Molecules , 2005, Journal of biological rhythms.

[22]  N. Kampen,et al.  Stochastic processes in physics and chemistry , 1981 .

[23]  BMC Bioinformatics , 2005 .

[24]  J. Raser,et al.  Noise in Gene Expression: Origins, Consequences, and Control , 2005, Science.

[25]  Mads Kærn,et al.  Noise in eukaryotic gene expression , 2003, Nature.

[26]  Jeff Hasty,et al.  Designer gene networks: Towards fundamental cellular control. , 2001, Chaos.

[27]  C. Gardiner Handbook of Stochastic Methods , 1983 .

[28]  Kazuyuki Aihara,et al.  Modeling genetic switches with positive feedback loops. , 2003, Journal of theoretical biology.

[29]  S. Leibler,et al.  Biological rhythms: Circadian clocks limited by noise , 2000, Nature.

[30]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[31]  M. Elowitz,et al.  A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[32]  J. Hasty,et al.  Synchronizing genetic relaxation oscillators by intercell signaling , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[33]  P. Swain,et al.  Intrinsic and extrinsic contributions to stochasticity in gene expression , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[34]  M. Ehrenberg,et al.  Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[35]  H. McAdams,et al.  Circuit simulation of genetic networks. , 1995, Science.

[36]  T. Kepler,et al.  Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. , 2001, Biophysical journal.

[37]  J. Raser,et al.  Control of Stochasticity in Eukaryotic Gene Expression , 2004, Science.

[38]  J. Hasty,et al.  Noise-based switches and amplifiers for gene expression. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[39]  P. Swain,et al.  Gene Regulation at the Single-Cell Level , 2005, Science.

[40]  David McMillen,et al.  Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks , 2004, BMC Bioinformatics.

[41]  E. Hill Journal of Theoretical Biology , 1961, Nature.

[42]  Nature Genetics , 1991, Nature.

[43]  Nancy Kopell,et al.  Synchrony in a Population of Hysteresis-Based Genetic Oscillators , 2004, SIAM J. Appl. Math..

[44]  W. Ebeling Stochastic Processes in Physics and Chemistry , 1995 .

[45]  A. Ninfa,et al.  Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli , 2003, Cell.

[46]  Bard Ermentrout,et al.  Simulating, analyzing, and animating dynamical systems - a guide to XPPAUT for researchers and students , 2002, Software, environments, tools.