A delay model for noise-induced bi-directional switching

Nonlinearity

Volumn 22, Issue 12, 2009, Pages 2845-2859

  Lei, Jinzhi ^a   He, Guowei ^b   Liu, Haoping ^c,d   Nie, Qing ^d  

^a TSINGHUA UNIVERSITY   (China)

^b INSTITUTE OF MECHANICS   (China)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 70450241137     PISSN: 09517715     EISSN: 13616544     Source Type: Journal    
DOI: 10.1088/0951-7715/22/12/003     Document Type: Article

References (52)

1. Acar M, Mettetal J T and van Oudenaarden A 2008 Stochastic switching as a survival strategy in fluctuating environments Nature Genet. 40 471-5
2. Alon U 2007 An Introduction to Systems Biology (London: Chapman and Hall/CRC)
3. Atkinson M R, Savageau M A, Myers J T and Ninfa A J 2003 Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113 597-607
4. Austin D W, Allen M S, McCollum J M, Dar R D, Wilgus J R, Sayler G S, Samatova N F, Cox C D and Simpson M L 2006 Gene network shaping of inherent noise spectra Nature 439 608-11
5. Barik D, Paul M R, Baumann W T, Cao Y and Tyson J J 2008 Stochastic simulation of enzyme-catalyzed reactions with disparate time scales Biophy. J. 95 3563-74
6. Becskei A, Séraphin B and Serrano L 2001 Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion EMBO J. 20 2528-35
7. Bennett R and Johnson A 2005 Mating in Candida albicans and the search for a sexual cycle Annu. Rev. Microbiol. 59 233-55
8. Bratsun D, Volfson D, Tsimring L S and Hasty J 2005 Delay-induced stochastic oscillations in gene regulation Proc. Natl Acad. Sci. USA 102 14593-8
9. Cherry J L and Adler F R 2000 How to make a biological switch J. Theor. Biol. 203 117-33
10. Chen K C, Calzone L, Csikasz-Nagy A, Cross F R, Novak B and Tyson J J 2004 Integrative analysis of cell cycle control in budding yeast Mol. Biol. Cell. 15 3841-62
11. Chou C, Zhang Y, Zhao R and Nie Q 2007 Numerical methods for stiff reaction-diffusion systems Discrete Contin. Dyn. Syst. B 7 515-25
12. Conrad E, Mayo A E, Ninfa A J and Forger D B 2008 Rate constants rather than biochemical mechanism determine behavior of genetic clocks J. R. Soc. Interface 5 S9-15
13. Cooke K L and Grossman Z 1982 Discrete delay, distributed delay and stability switches J. Math. Anal. Appl. 86 592-627
14. Elowitz M B, Levine A J, Siggia E D and Swain P S 2002 Stochastic gene expression in a single cell Science 297 1183-6
15. Ferrell J E Jr 2002 Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability Curr. Opin. Chem. Biol. 6 140-8
16. Gardner T S, Cantor C R and Collins J J 2000 Construction of a genetic toggle switch in Escherichia coli. Nature 403 339-42
17. Golding I, Paulsson J, Zawilski S M and Cox E C 2005 Real-time kinetics of gene activity in individual bacteria Cell 123 1025-36
18. Hale J 1977 Theory of Functional Differential Equations (Berlin: Springer)
19. Hasty J, Pradiness J, Dolnik M and Collins J J 2000 Noise-based switches and amplifiers for gene expression Proc. Natl Acad. Sci. USA 97 2075-80
20. Huang G, Wang H, Chou S, Nie X, Chen J and Liu H 2006 Bistable expression of WOR1, a master regulator of white-opaque switching in Candida albicans Proc. Natl Acad. Sci. USA 103 12813-18
21. Kaufmann B B, Yang Q, Mettetal J T and van Oudenaarden A 2007 Heritable stochastic switching revealed by single-cell genealogy PLoS Biol. 5 e239
22. Kaufmann B B and van Oudenaarden A 2007 Stochastic gene expression: from single molecules to the proteome Curr. Opin. Genet. Dev. 17 107-12
23. Kærn M, Elston T C, Blake W J and Collins J J 2005 Stochasticity in gene expression: from theories to phenotypes Nature Rev. Genet. 6 451-64
24. Kerszberg M 2004 Noise, delays, robustness, canalization and all that Curr. Opin. Genet. Devices 14 440-5
25. Kvaal C, Lachke S A, Srikantha T, Daniels K, McCoy J and Soll D R 1999 Misexpression of the opaque-phase-specific gene PEP1 (SAP1) in the white phase of Candida albicans confers increased virulence in a mouse model of cutaneous infection Infect. Immun. 67 6652-62
26. Lei J 2009 Stochasticity in single gene expression with both intrinsic noise and fluctuation in kinetic parameters J. Theor. Biol. 256 485-92
27. Lewis J 2003 Autoinhibition with transcriptional delay: a simple mechanism for the zebrafish somitogenesis oscillator Curr. Biol. 13 1398-408
28. Maamar H and Dubnau D 2005 Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop Mol. Microbiol. 56 615-24
29. Maheshri N and O'Shea E K 2007 Living with noisy genes: how cells function reliably with inherent variability in gene expression Annu. Rev. Biophys. Biomol. Struct. 36 413-34
30. Monk N 2003 Oscillatory expression of Hes1, p53, and NF-κ B driven by transcriptional time delays Curr. Biol. 13 1409-13
31. olde Scheper T, Klinkenberg D, Pennartz C and van Pelt J 1999 A mathematical model for the intracellular circadian rhythm generator J. Neurosci. 19 40-7
32. Ozbudak E M, Thattai M, Lim H N, Shraiman B I and van Oudenaarden A 2004 Multistability in the lactose utilization networks of Escherichia coli. Nature 427 737-40
33. Paulsson J 2004 Summing up the noise in gene networks Nature 427 415-8
34. Raj A and van Oudenaarden A 2008 Nature, nurture, or chance: stochastic gene expression and its consequences Cell 135 216-26
35. Rikkerink E H, Magee B B and Magee P T 1988 Opaque-white phenotype transition: a programmed morphological transition in Candida albicans J. Bacteriol. 170 895-9
36. Schaffer W M 1974 Optimal reproductive effort in fluctuating environments Am. Naturalist. 108 783-90
37. Samoilov M S, Price G and Arkin A P 2006 From fluctuations to phenotypes: the physiology of noise Sci. STKE 2006 re17
38. Santilln M and Mackey M C 2008 Quantitative approaches to the study of bistability in the lac operon of Escherichia coli. J. R. Soc. Interface 5 S29-39
39. Shahrezaei V, Ollivier J F and Swain P S 2008 Colored extrinsic fluctuations and stochastic gene expression Mol. Syst. Biol. 4 1-9
40. Shahrezaei V and Swain P S 2008 The stochastic nature of biochemical networks Curr. Opin. Biotechnol. 19 369-74
41. Slutsky B, Staebell M, Anderson J, Risen L, Pfaller M and Soll D R 1987 'White-opaque transition': a second high-frequency switching system in Candida albicans J. Bacteriol. 169 189-97 (Pubitemid 17228707)
42. Soll D R, Morrow B and Srikantha T 1993 High-frequency phenotypic switching in Candida albicans Trends Genet. 9 61-5
43. Soll D R 1997 Gene regulation during high-frequency switching in Candida albicans Microbiology 143 279-88
44. Sriram K, Soliman S and Fages F 2009 Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans J. Theor. Biol. 258 71-88
45. Stearns S C 1976 Life-history tactics: a review of the ideas Quart. Rev. Biol. 51 3-7
46. Swain P S, Elowitz M B and Siggia E D 2002 Intrinsic and extrinsic contributions to stochasticity in gene expression Proc. Natl Acad. Sci. USA 99 12795-800
47. Tian T and Burrage K 2006 Stochastic models for regulatory networks of the genetic toggle switch Proc. Natl Acad. Sci. USA 103 8372-7
48. Tsuboi R et al 1994 Pathogenesis of superficial mycoses J. Med. Vet. Mycol. (Suppl.) 32 91-104
49. Veening J, Smits W K and Kuipers O P 2008 Bistability, epigenetics, and bet-hedging in bacteria Annu. Rev. Microbiol. 62 193-210
50. Wang L, Walker B L, Iannaccone S, Bhatt D, Kennedy P J and Tse W T 2009 Bistable switches control memory and plasticity in cellular differentiation Proc. Natl Acad. Sci. USA 106 6638-43
51. Yan G, Lee T J, Mori S, Nevins J R and You L 2008 A bistable Rb-E2F switch underlies the restriction point Nature Cell Biol. 10 476-82
52. Zordan R E, Galgoczy D J and Johnson A D 2006 Epigenetic properties of white-opaque switching in Candida albicans are based on a self-sustaining transcriptional feedback loop Proc. Natl Acad. Sci. USA 103 12807-12