Control, exploitation and tolerance of intracellular noise

Noise has many roles in biological function, including generation of errors in DNA replication leading to mutation and evolution, noise-driven divergence of cell fates, noise-induced amplification of signals, and maintenance of the quantitative individuality of cells. Yet there is order to the behaviour and development of cells. They operate within strict parameters and in many cases this behaviour seems robust, implying that noise is largely filtered by the system. How can we explain the use, rejection and sensitivity to noise that is found in biological systems? An exploration of the sources and consequences of noise calls for the use of stochastic models.

[1]  D. Koshland,et al.  Non-genetic individuality: chance in the single cell , 1976, Nature.

[2]  D. Gillespie Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[3]  O. Berg A model for the statistical fluctuations of protein numbers in a microbial population. , 1978, Journal of theoretical biology.

[4]  S. Swain Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences , 1984 .

[5]  C. W. Gardiner,et al.  Handbook of stochastic methods - for physics, chemistry and the natural sciences, Second Edition , 1986, Springer series in synergetics.

[6]  J. Abraham,et al.  An invertible element of DNA controls phase variation of type 1 fimbriae of Escherichia coli. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[7]  I. Herskowitz,et al.  Regulation by the yeast mating-type locus of STE12, a gene required for cell-type-specific expression , 1987, Molecular and cellular biology.

[8]  T. Kurtz Approximation of Population Processes , 1987 .

[9]  L. Hartwell,et al.  Checkpoints: controls that ensure the order of cell cycle events. , 1989, Science.

[10]  M. Ko,et al.  The dose dependence of glucocorticoid‐inducible gene expression results from changes in the number of transcriptionally active templates. , 1990, The EMBO journal.

[11]  M. Ko,et al.  A stochastic model for gene induction. , 1991, Journal of theoretical biology.

[12]  T. Hunter,et al.  Phosphopeptide mapping and phosphoamino acid analysis by two-dimensional separation on thin-layer cellulose plates. , 1991, Methods in enzymology.

[13]  G. Oster,et al.  What drives the translocation of proteins? , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Gerald R. Fink,et al.  Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: Regulation by starvation and RAS , 1992, Cell.

[15]  P. Lansdorp,et al.  Lineage commitment in human hemopoiesis involves asymmetric cell division of multipotent progenitors and does not appear to be influenced by cytokines , 1993, Journal of cellular physiology.

[16]  Frank Moss,et al.  Noise enhancement of information transfer in crayfish mechanoreceptors by stochastic resonance , 1993, Nature.

[17]  C. Stevens,et al.  An evaluation of causes for unreliability of synaptic transmission. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[18]  D. Hood,et al.  Tetrameric repeat units associated with virulence factor phase variation in Haemophilus also occur in Neisseria spp. and Moraxella catarrhalis. , 1996, FEMS microbiology letters.

[19]  C. Svanborg,et al.  Type 1 fimbrial expression enhances Escherichia coli virulence for the urinary tract. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[20]  John P. Miller,et al.  Broadband neural encoding in the cricket cereal sensory system enhanced by stochastic resonance , 1996, Nature.

[21]  R. Heinrich,et al.  The Regulation of Cellular Systems , 1996, Springer US.

[22]  D. Fell Understanding the Control of Metabolism , 1996 .

[23]  S. Leibler,et al.  Robustness in simple biochemical networks , 1997, Nature.

[24]  P. Sternberg,et al.  Evolution of cell lineage. , 1997, Current opinion in genetics & development.

[25]  S. Fields,et al.  Transcriptional activation upon pheromone stimulation mediated by a small domain of Saccharomyces cerevisiae Ste12p , 1997, Molecular and cellular biology.

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

[27]  W. Khalil,et al.  Interaction of Doxorubicin with phospholipid monolayer and liposomes. , 1998, Biophysical chemistry.

[28]  K. Mukhopadhyay,et al.  Conformation induction in melanotropic peptides by trifluoroethanol: fluorescence and circular dichroism study. , 1998, Biophysical chemistry.

[29]  D. Bray,et al.  Origins of individual swimming behavior in bacteria. , 1998, Biophysical journal.

[30]  S. Tapscott,et al.  Modeling stochastic gene expression: implications for haploinsufficiency. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[31]  H. Seifert,et al.  Differential roles of homologous recombination pathways in Neisseria gonorrhoeae pilin antigenic variation, DNA transformation and DNA repair , 1998, Molecular microbiology.

[32]  A. Arkin,et al.  Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. , 1998, Genetics.

[33]  C. J.,et al.  Predicting Temporal Fluctuations in an Intracellular Signalling Pathway , 1998 .

[34]  J. Greenblatt,et al.  GAL4 is regulated by the RNA polymerase II holoenzyme-associated cyclin-dependent protein kinase SRB10/CDK8. , 1999, Molecular cell.

[35]  J. W. Little,et al.  Robustness of a gene regulatory circuit , 1999, The EMBO journal.

[36]  J. Hacker,et al.  A novel mechanism of phase variation of virulence in Staphylococcus epidermidis: evidence for control of the polysaccharide intercellular adhesin synthesis by alternating insertion and excision of the insertion sequence element IS256 , 1999, Molecular microbiology.

[37]  A. Arkin,et al.  It's a noisy business! Genetic regulation at the nanomolar scale. , 1999, Trends in genetics : TIG.

[38]  Frank Moss,et al.  Use of behavioural stochastic resonance by paddle fish for feeding , 1999, Nature.

[39]  U. Alon,et al.  Robustness in bacterial chemotaxis , 2022 .

[40]  K. Kohn Molecular interaction map of the mammalian cell cycle control and DNA repair systems. , 1999, Molecular biology of the cell.

[41]  T. Msadek When the going gets tough: survival strategies and environmental signaling networks in Bacillus subtilis. , 1999, Trends in microbiology.

[42]  D. Bray,et al.  A free-energy-based stochastic simulation of the Tar receptor complex. , 1999, Journal of molecular biology.

[43]  David I. K. Martin,et al.  Epigenetic inheritance at the agouti locus in the mouse , 1999, Nature Genetics.

[44]  Julie A. Theriot,et al.  Cooperative symmetry-breaking by actin polymerization in a model for cell motility , 1999, Nature Cell Biology.

[45]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

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

[47]  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.

[48]  D. Gillespie The chemical Langevin equation , 2000 .

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

[50]  S. Hultgren,et al.  Bacterial pili: molecular mechanisms of pathogenesis. , 2000, Current opinion in microbiology.

[51]  S. Hultgren,et al.  Bad bugs and beleaguered bladders: interplay between uropathogenic Escherichia coli and innate host defenses. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[52]  J. White,et al.  Channel noise in neurons , 2000, Trends in Neurosciences.

[53]  G. Odell,et al.  The segment polarity network is a robust developmental module , 2000, Nature.

[54]  Michael A. Gibson,et al.  Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels , 2000 .

[55]  Ivan Sadowski,et al.  Two Regulators of Ste12p Inhibit Pheromone-Responsive Transcription by Separate Mechanisms , 2000, Molecular and Cellular Biology.

[56]  Adam P. Arkin Self-Organized Biological Dynamics and Nonlinear Control: Signal processing by biochemical reaction networks , 2000 .

[57]  L. Serrano,et al.  Engineering stability in gene networks by autoregulation , 2000, Nature.

[58]  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.

[59]  D. A. Baxter,et al.  Modeling transcriptional control in gene networks—methods, recent results, and future directions , 2000, Bulletin of mathematical biology.

[60]  Anirvan M. Sengupta,et al.  Engineering aspects of enzymatic signal transduction: photoreceptors in the retina. , 2000, Biophysical journal.

[61]  J. Doyle,et al.  Robust perfect adaptation in bacterial chemotaxis through integral feedback control. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[62]  I. Sadowski,et al.  Multiple Signals Regulate GALTranscription in Yeast , 2000, Molecular and Cellular Biology.

[63]  M. Rodnina,et al.  Ribosome fidelity: tRNA discrimination, proofreading and induced fit. , 2001, Trends in biochemical sciences.

[64]  Identification of a Group 1-Like Capsular Polysaccharide Operon for Vibrio vulnificus , 2001, Infection and Immunity.

[65]  R. Young,et al.  Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. , 2001, Genes & development.

[66]  B. Hallet,et al.  Playing Dr Jekyll and Mr Hyde: combined mechanisms of phase variation in bacteria. , 2001, Current opinion in microbiology.

[67]  B. Séraphin,et al.  Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion , 2001, The EMBO journal.

[68]  M. Thattai,et al.  Intrinsic noise in gene regulatory networks , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[69]  A. Arkin Synthetic cell biology. , 2001, Current opinion in biotechnology.

[70]  A. Kierzek,et al.  The Effect of Transcription and Translation Initiation Frequencies on the Stochastic Fluctuations in Prokaryotic Gene Expression* , 2001, The Journal of Biological Chemistry.

[71]  Hiroaki Kitano,et al.  Foundations of systems biology , 2001 .

[72]  D. A. Baxter,et al.  Modeling Circadian Oscillations with Interlocking Positive and Negative Feedback Loops , 2001, The Journal of Neuroscience.

[73]  Nicolas Le Novère,et al.  STOCHSIM: modelling of stochastic biomolecular processes , 2001, Bioinform..

[74]  A. Bren,et al.  Changing the direction of flagellar rotation in bacteria by modulating the ratio between the rotational states of the switch protein FliM. , 2001, Journal of molecular biology.

[75]  J. Rine,et al.  The rye mutants identify a role for Ssn/Srb proteins of the RNA polymerase II holoenzyme during stationary phase entry in Saccharomyces cerevisiae. , 2001, Genetics.

[76]  D. Gillespie Approximate accelerated stochastic simulation of chemically reacting systems , 2001 .

[77]  T. Brill,et al.  Spectroscopy of Hydrothermal Reactions 15. The pH and Counterion Effects on the Decarboxylation Kinetics of the Malonate System , 2001 .

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

[79]  S. Fraser,et al.  Modeling a hox gene network in silico using a stochastic simulation algorithm. , 2002, Developmental biology.

[80]  A. Goldbeter,et al.  Robustness of circadian rhythms with respect to molecular noise , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[81]  D. Gillespie The Chemical Langevin and Fokker−Planck Equations for the Reversible Isomerization Reaction† , 2002 .

[82]  J. Ferrell Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. , 2002, Current opinion in cell biology.

[83]  G. Odell,et al.  Robustness, Flexibility, and the Role of Lateral Inhibition in the Neurogenic Network , 2002, Current Biology.

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

[85]  Leslie M Loew,et al.  Computational cell biology: spatiotemporal simulation of cellular events. , 2002, Annual review of biophysics and biomolecular structure.

[86]  Adam P Arkin,et al.  Fifteen minutes of fim: control of type 1 pili expression in E. coli. , 2002, Omics : a journal of integrative biology.

[87]  S. Leibler,et al.  Mechanisms of noise-resistance in genetic oscillators , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[88]  J. Doyle,et al.  Robustness as a measure of plausibility in models of biochemical networks. , 2002, Journal of theoretical biology.

[89]  M. Thattai,et al.  Attenuation of noise in ultrasensitive signaling cascades. , 2002, Biophysical journal.

[90]  J. Doyle,et al.  Reverse Engineering of Biological Complexity , 2002, Science.

[91]  J. Rawlings,et al.  Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics , 2002 .

[92]  S. Leibler,et al.  Establishment of developmental precision and proportions in the early Drosophila embryo , 2002, Nature.

[93]  J. Ross,et al.  Signal Processing by Simple Chemical Systems , 2002 .

[94]  C. Rao,et al.  Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm , 2003 .

[95]  Jeffrey W. Smith,et al.  Stochastic Gene Expression in a Single Cell , 2022 .