Internal noise-driven circadian oscillator in Drosophila

Biophysical Chemistry

Volumn 145, Issue 2-3, 2009, Pages 57-63

  Li, Qianshu ^a   Li, Hengyu ^a  

^a BEIJING INSTITUTE OF TECHNOLOGY   (China)

Author keywords

Circadian rhythms; Intrinsic coherence resonance; Noise sustained oscillator

Indexed keywords

ARTICLE; CIRCADIAN RHYTHM; CONTROLLED STUDY; DROSOPHILA; MATHEMATICAL MODEL; NEGATIVE FEEDBACK; NOISE; OSCILLATION; POSITIVE FEEDBACK; PRIORITY JOURNAL; STEADY STATE;

ANIMALS; CIRCADIAN RHYTHM; DROSOPHILA; MODELS, BIOLOGICAL; STOCHASTIC PROCESSES;

EID: 70350205601     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2009.08.009     Document Type: Article

References (58)

1. Moore-Ede M.C., Sulzman F.M., and Fuller C.A. The Clocks that Time Us: Physiology of the Circadian Timing System (1982), Harvard University Press, Cambridge, MA
2. Edmunds L.N. Cellular and Molecular Bases of Biological Clocks (1988), Springer, New York
3. Dunlap J.C. Molecular Bases for Circadian Clocks. Cell 96 (1999) 271-290
4. Young M.W. Life's 24-hour clock: molecular control of circadian rhythms in animal cells. Trends Biochem. Sci. 25 (2000) 601-606
5. Williams J.A., and Sehgal A. Molecular components of the circadian system in Drosophila. Annu. Rev. Physiol. 63 (2001) 729-755
6. Young M.W., and Kay S.A. Time zones: a comparative genetics of circadian clocks. Nat. Rev. Genet. 2 (2001) 702-715
7. Reppert S.M., and Weaver D.R. Molecular analysis of mammalian circadian rhythms. Annu. Rev. Physiol. 63 (2001) 647-676
8. Hardin P.E., Hall J.C., and Rosbash M. Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels. Nature 343 (1990) 536-540
9. Goldbeter A. A model for circadian oscillations in the Drosophila period protein (PER). Proc. R. Soc. Lond. B 261 (1995) 319-324
10. Ruoff P., Rensing L., Kommedal R., and Mohsenzadeh S. Modeling temperature compensation in chemical and biological oscillators. Chronobiol. Int. 14 (1997) 499-510
11. Leloup J.C., and Goldbeter A. A model for circadian rhythms in Drosophila incorporating the formation of a complex between PER and TIM proteins. J. Biol. Rhythms 13 (1998) 70-87
12. Scheper T., Klinkenberg D., Pennartz C., and van Pelt J. A mathematical model for the intracellular circadian rhythm generator. J. Neurosci. 19 (1999) 40-47
13. Lee K., Loros J.J., and Dunlap J.C. Interconnected feedback loops in the Neurospora circadian system. Science 289 (2000) 107-110
14. Glossop N., Lyons L.C., and Hardin P.E. Interlocked feedback loops within the Drosophila circadian oscillator. Science 286 (1999) 766-768
15. Bae K., Lee C., Sidote D., Chuang K., and Edery I. Circadian regulation of a Drosophila homolog of the mammalian clock gene: PER and TIM function as positive regulators. Mol. Cell. Biol. 18 (1998) 6142-6151
16. Shearman L.P., et al. Interacting molecular loops in the mammalian circadian clock. Science 288 (2000) 1013-1019
17. Kuczenski R.S., Hong K.C., Garcia-Ojalvo J., and Lee K.H. PERIOD-TIMELESS interval timer may require an additional feedback loop. Plos Comput. Biol. 3 (2007) 1468-1476
18. Tyson J.J., Hong C.I., Thron C.D., and Novak B. A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM. Biophys. J. 77 (1999) 2411-2417
19. Smolen P., Baxter D.A., and Byrne J.H. Modeling circadian oscillations with interlocking positive and negative feedback loops. J. Neurosci. 21 (2001) 6644-6656
20. Smolen P., Baxter D.A., and Byrne J.H. A reduced model clarifies the role of feedback loops and time delays in the Drosophila circadian oscillator. Biophys. J. 83 (2002) 2349-2359
21. Hastings M.H. Circadian clockwork: two loops are better than one. Nat. Rev. Neurosci. 1 (2000) 143-146
22. Tsai T.Y., et al. Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science 321 (2008) 126-129
23. Barkai N., and Leibler S. Circadian clocks limited by noise. Nature 403 (2000) 267-268
24. Gonze D., Halloy J., and Goldbeter A. Robust of circadian rhythms with respect to molecular noise. Proc. Natl Acad. Sci. U. S. A. 99 (2002) 673-678
25. Kepler T.B., and Elston T.C. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. Biophys. J. 81 (2001) 3116-3136
26. Steuer R., Zhou C., and Kurths J. Constructive effects of fluctuations in genetic and biochemical regulatory systems. Biosystems 72 (2003) 241-251
27. Shuai J.W., and Jung P. Optimal intracellular calcium signaling. Phys. Rev. Lett. 88 (2002) 068102
28. Perc M., Gosak M., and Marhl M. Periodic calcium waves in coupled cells induced by internal noise. Chem. Phys. Lett. 437 (2007) 143-147
29. Perc M., Gosak M., and Marhl M. From stochasticity to determinism in the collective dynamics of diffusively coupled cells. Chem. Phys. Lett. 421 (2006) 106-110
30. Gosaka M., Marhl M., and Perc M. Chaos out of internal noise in the collective dynamics of diffusively coupled cells. Eur. Phys. J. B 62 (2008) 171-177
31. Gammaitoni L., Hänggi P., Jung P., and Marchesoni F. Stochastic resonance. Rev. Mod. Phys. 70 (1998) 223-287
32. Pikovsky A.S., and Kurths J. Coherence resonance in a noisedriven excitable system. Phys. Rev. Lett. 78 (1997) 775-778
33. Perc M. Spatial coherence resonance in excitable media. Phys. Rev. E 72 (2005) 016207
34. Gosaka M., Marhl M., and Perc M. Spatial coherence resonance in excitable biochemical media induced by internal noise. Biophys. Chemist. 128 (2007) 210-214
35. Vilar J.M.G., Kueh H.Y., Barkai N., and Leibler S. Mechanisms of noise-resistance in genetic oscillators. Proc. Natl Acad. Sci. U. S. A. 99 (2002) 5988-5992
36. Hou Z., and Xin H. Internal noise stochastic resonance in a circadian clock system. J. Chem. Phys. 119 (2003) 11508-11512
37. Li Q., and Lang X. Internal noise-sustained circadian rhythms in a Drosophila model. Biophys. J. 94 (2008) 1983-1994
38. Bratsun D., Volfson D., Tsimring L.S., and Hasty J. Delay-induced stochastic oscillations in gene regulation. Proc. Natl Acad. Sci. U. S. A. 102 (2005) 14593-14598
39. Endery I., Zwiebel L., Dembinska M., and Rosbash M. Temporal phosphorylation of the Drosophila period protein. Proc. Natl Acad. Sci. U. S. A. 91 (1994) 2260-2264
40. Van Kampen N.G. Stochastic Processes in Physics and Chemistry (1981), North-Holland, Amsterdam
41. Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81 (1977) 2340-2361
42. Gillespie D.T. The chemical Langevin equation. J. Chem. Phys. 113 (2000) 297-306
43. Hu G., Ditzinger T., Ning C.Z., and Haken H. Stochastic resonance without external periodic force. Phys. Rev. Lett. 71 (1993) 807-810
44. Schimid G., Goychuk I., and Hänggi P. Stochastic resonance as a collective property of ion channel assemblies. Europhys. Lett. 56 (2001) 22-28
45. Shuai J.W., and Jung P. Entropically enhanced excitability in small systems. Phys. Rev. Lett. 95 (2005) 114501
46. Higham D.J. An algorithmic introduction to numberical simulation of stochastic differential equations. SIAM Rev. 43 (2001) 525-546
47. Qian H., Saffarian S., and Elson E.L. Concentration fluctuations in a mesoscopic oscillating chemical reaction system. Proc. Natl Acad. Sci. U. S. A. 99 (2002) 10376-10381
48. Hilborn R.C., and Erwin J.D. Stochastic coherence in an oscillatory gene circuit model. J. Theor. Biol. 253 (2008) 349-354
49. Lindner B., García-Ojalvo J., Neiman A., and Schimansky-Geier L. Effects of noise in excitable systems. Phys. Rep. 392 (2004) 321-424
50. Pittendrigh C. On temperature independence in the clock system controlling emergence time in Drosophila. Proc. Natl Acad. Sci. U. S. A. 40 (1954) 1018-1029
51. Konopka R.J. C. Pittendrigh, D. Orr, Reciprocal behaviour associated with altered homeostasis and photosensitivity of Drosophila clock mutants. J. Neurogenet. 6 (1989) 1-10
52. Press W.H., Teukolsky S.A., Vetterling W.T., and Flannery B.P. Numerical Recipes in C (1992), Cambridge University Press, Cambridge
53. Gracheva M.E., and Gunton J.D. Intercellular communication via intracellular calcium oscillations. J. Theor. Biol. 221 (2003) 513-518
54. Gracheva M.E., Toral R., and Gunton J.D. Stochastic effects in intercellular calcium spiking in Hepatocytes. J. Theor. Biol. 212 (2001) 111-125
55. Gonze D., Halloy J., and Gaspard P. Biochemical clocks and molecular noise: theoretical study of robustness factors. J. Chem. Phys. 116 (2002) 10997-11010
56. Gaspard P. The correlation time of mesoscopic chemical clocks. J. Chem. Phys. 117 (2002) 8905-8916
57. Rao C.V., Wolf D.W., and Arkin A.P. Control, exploitation and tolerance of intracellular noise. Nature 420 (2002) 231-237
58. Zhang J., Hou Z., and Xin H. System-size biresonance for intracellular calcium signaling. Chem. Phys. Chem. 5 (2004) 1041-1045