Enhanced entrainability of genetic oscillators by period mismatch

Journal of the Royal Society Interface

Volumn 10, Issue 81, 2013, Pages

  Hasegawa, Yoshihiko ^a   Arita, Masanori ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

Dynamical systems; Entrainment; Genetic oscillator

Indexed keywords

AIR ENTRAINMENT; DYNAMICAL SYSTEMS;

BIOLOGICAL OSCILLATORS; CELLULAR COMPONENTS; COUPLING STRENGTHS; EXTERNAL STIMULUS; FLOQUET MULTIPLIER; FUNDAMENTAL MODELS; GENETIC OSCILLATORS; PASSIVE MECHANISM;

RELAXATION OSCILLATORS;

MESSENGER RNA;

ARTICLE; BIOLOGICAL OSCILLATOR; CELL COMPONENT; CELL CYCLE; CELL STIMULATION; MATHEMATICAL MODEL; NONHUMAN; RNA TRANSCRIPTION; BIOLOGICAL MODEL; BIOLOGICAL RHYTHM; FEEDBACK SYSTEM; GENETICS; PHYSIOLOGY; TIME;

BIOLOGICAL CLOCKS; FEEDBACK, PHYSIOLOGICAL; MODELS, BIOLOGICAL; TIME FACTORS;

MLCS; MLOWN;

EID: 84875743821     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2012.1020     Document Type: Article

References (54)

1. Novák B, Tyson JJ. 2008 Design principles of biochemical oscillators. Nat. Rev. 9, 981-991. (doi:10.1038/nrm2530)
2. Roenneberg T, Morse D. 1993 Two circadian oscillators in one cell. Nature 362, 362-364. (doi:10.1038/362362a0)
3. Morse D, Hastings JW, Roenneberg T. 1994 Different phase responses of the two circadian oscillators in Gonyaulax. J. Biol. Rhythms 9, 263-274. (doi:10.1177/074873049400900307)
4. Gonze D, Goldbeter A. 2000 Entrainment versus chaos in a model for a circadian oscillator driven by light-dark cycles. J. Stat. Phys. 101, 649-663. (doi:10.1023/A:1026410121183)
5. Bell-Pedersen D, Cassone VM, Earnest DJ, Golden SS, Hardin PE, Thomas TL, Zoran MJ. 2005 Circadian rhythms from multiple oscillators: lessons from diverse organisms. Nat. Rev. 6, 544-556. (doi:10. 1038/nrg1633)
6. Goodwin BC. 1965 Oscillatory behavior in enzymatic control processes. Adv. Enzyme Regulat. 3, 425-437. (doi:10.1016/0065-2571(65)90067-1)
7. Wagner A. 2005 Circuit topology and the evolution of robustness in two-gene circadian oscillators. Proc. Natl Acad. Sci. USA 102, 11 775-11 780. (doi:10. 1073/pnas.0501094102)
8. Trané C, Jacobsen EW. 2007 On robustness as the rationale behind multiple feedback loops in the circadian clock. In 2nd Conf. Foundations of Systems Biology in Engineering (FOSBE), pp. 439-444, 9-12 September, Stuttgart, Germany.
9. Hafner M, Sacré P, Symul L, Sepulchre R, Koeppl H. 2010 Multiple feedback loops in circadian cycles: robustness and entrainment as selection criteria. In 7th Int. Workshop on Computational Systems Biology (eds M Nykter, P Ruusuvuori, C Carlberg & O Yli-Harja), pp. 43-46, 16-18 June, Luxembourg. (http://www.cs.tut.fi/wcsb10/)
10. Hastings MH. 2000 Circadian clockwork: two loops are better than one. Nat. Rev. 1, 143-146. (doi:10.1038/35039080)
11. Benzi R, Sutera A, Vulpiani A. 1981 The mechanism of stochastic resonance. J. Phys. A 14, L453. (doi:10. 1088/0305-4470/14/11/006)
12. McNamara B, Wiesenfeld K. 1989 Theory of stochastic resonance. Phys. Rev. A 39, 4854-4869. (doi:10.1103/PhysRevA.39.4854)
13. Jung P, Hänggi P. 1991 Amplification of small signals via stochastic resonance. Phys. Rev. A 44, 8032-8042. (doi:10.1103/PhysRevA.44.8032)
14. Jung P, Behn U, Pantazelou E, Moss F. 1992 Collective response in globally coupled bistable systems. Phys. Rev. A 46, R1709-R1712. (doi:10. 1103/PhysRevA.46.R1709)
15. Gammaitoni L, Hänggi P, Jung P, Marchesoni F. 1998 Stochastic resonance. Rev. Mod. Phys. 70, 223-287. (doi:10.1103/RevModPhys.70.223)
16. McDonnell MD, Stocks NG, Pearce CEM, Abbott D. 2008 Stochastic resonance. Cambridge, UK: Cambridge University Press.
17. McDonnell MD, Abbott D. 2009 What is stochastic resonance? Definitions, misconceptions, debates, and its relevance to biology. PLoS Comput. Biol. 5, e1000348. (doi:10.1371/journal.pcbi.1000348)
18. Hasegawa Y, Arita M. 2011 Escape process and stochastic resonance under noise-intensity fluctuation. Phys. Lett. A 375, 3450-3458. (doi:10.1016/j. physleta.2011.07.054)
19. Astumian RD, Bier M. 1994 Fluctuation driven ratchets: molecular motors. Phys. Rev. Lett. 72, 1766-1769. (doi:10.1103/PhysRevLett.72.1766)
20. Astumian RD. 1997 Thermodynamics and kinetics of a Brownian motor. Science 276, 917-922. (doi:10. 1126/science.276.5314.917)
21. Frey E, Kroy K. 2005 Brownian motion: a paradigm of soft matter and biological physics. Ann. Phys. 14, 20-50. (doi:10.1002/andp.200410132)
22. Hänggi P, Marchesoni F. 2009 Artificial Brownian motors: controlling transport on the nanoscale. Rev. Mod. Phys. 81, 387-442. (doi:10.1103/ RevModPhys.81.387)
23. Hasegawa Y, Arita M. 2012 Fluctuating noise drives Brownian transport. J. R. Soc. Interface 9, 3554-3563. (doi:10.1098/rsif.2012.0603)
24. 4 model of kink-antikink nucleation. Phys. Rev. Lett. 76, 2609-2612. (doi:10.1103/PhysRevLett.76.2609)
25. Nakao H, Arai K, Kawamura Y. 2007 Noise-induced synchronization and clustering in ensembles of uncoupled limit-cycle oscillators. Phys. Rev. Lett. 98, 184101. (doi:10.1103/PhysRevLett.98.184101)
26. Teramae J, Tanaka D. 2004 Robustness of the noise-induced phase synchronization in a general class of limit cycle oscillators. Phys. Rev. Lett. 93, 204103. (doi:10.1103/PhysRevLett.98.204103)
27. Tessone CJ, Mirasso CR, Toral R, Gunton JD. 2006 Diversity-induced resonance. Phys. Rev. Lett. 97, 194101. (doi:10.1103/PhysRevLett.97.194101)
28. Sharma VK. 2003 Adaptive significance of circadian clocks. Chronobiol. Int. 20, 901-919. (doi:10.1081/CBI-120026099)
29. Beaver LM, Gvakharia BO, Vollintine TS, Hege DM, Stanewsky R, Giebultowicz JM. 2002 Loss of circadian clock function decreases reproductive fitness in males of Drosophila melanogaster. Proc. Natl Acad. Sci. USA 19, 2134-2139. (doi:10.1073/pnas.032426699)
30. Dodd AN, Salathia N, Hall A, Kévei E, Tóth R, Nagy F, Hibberd JM, Millar AJ, Webb AAR. 2005 Plant circadian clocks increase photosynthesis, growth, survival and competitive advantage. Science 309, 630-633. (doi:10.1126/science.1115581)
31. Woelfle MA, Ouyang Y, Phanvijhitsiri K, Johnson CH. 2004 The adaptive value of circadian clocks: an experimental assessment in cyanobacteria. Curr. Biol. 14, 1481-1486. (doi:10.1016/j.cub.2004.08.023)
32. Gonze D, Bernard S, Waltermann C, Kramer A, Herzel H. 2005 Spontaneous synchronization of coupled circadian oscillators. Biophys. J. 89, 120-129. (doi:10.1529/biophysj.104.058388)
33. Liu AC et al. 2007 Intercellular coupling confers robustness against mutations in the SCN circadian clock network. Cell 129, 605-616. (doi:10.1016/j. cell.2007.02.047)
34. Tsai TY-C, Choi YS, Ma W, Pomerening JR, Tang C, Ferrell Jr. JE. 2008 Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science 321, 126-129. (doi:10. 1126/science.1156951)
35. Zhou T, Zhang J, Yuan Z, Chen L. 2008 Synchoronization of genetic oscillators. Chaos 18, 037126.
36. Komin N, Murza AC, Hernández-García E, Toral R. 2010 Synchronization and entrainment of coupled circadian oscillators. Interface Focus 1, 167-176. (doi:10.1098/rsfs.2010.0327)
37. Elowitz MB, Leibler S. 2000 A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338. (doi:10.1038/35002125)
38. FitzHugh R. 1961 Impulses and physiological states in theoretical models of nerve membrane. Biophys. J. 1, 445-466. (doi:10.1016/S0006-3495(61)86902-6)
39. Nagumo J, Arimoto S, Yoshizawa S. 1962 An active pulse transmission line simulating nerve axon. Proc. IRE 50, 2061-2070.
40. Kuramoto Y. 2003 Chemical oscillations, waves, and turbulence. Mineola, NY: Dover publications.
41. Izhikevich EM. 2007 Dynamical systems in neuroscience: the geometry of excitability and bursting. Cambridge, MA: MIT Press.
42. Pikovsky A, Rosenblem M, Kurths J. 2001 Synchronization: a universal concept in nonlinear sciences. Cambridge, UK: Cambridge University Press.
43. Schwemmer MA, Lewis T. 2012 The theory of weakly coupled oscillators. In Phase response curves in neuroscience: theory, experiment and analysis (eds N Schultheiss, A Prinz, R. Butera), pp. 3-31. Berlin, Germany: Springer.
44. Klausmeier CA. 2008 Floquet theory: a useful tool for understanding nonequilibrium dynamics. Theor. Ecol. 1, 153-161. (doi:10.1007/s12080-008-0016- 2)
45. Guckenheimer J, Holmes P. 1983 Nonlinear oscillations, dynamical systems, and bifurcations of vector fields. Berlin, Germany: Springer.
46. Crawford JD. 1991 Introduction to bifurcation theory. Rev. Mod. Phys. 63, 991-1037. (doi:10. 1103/RevModPhys.63.991)
47. Wiesenfeld K, McNamara B. 1985 Period-doubling systems as small-signal amplifiers. Phys. Rev. Lett. 55, 13-16. (doi:10.1103/PhysRevLett.55.13)
48. Wiesenfeld K, McNamara B. 1986 Small-signal amplification in bifurcating dynamical systems. Phys. Rev. A 33, 629-642. (doi:10.1103/PhysRevA.33.629)
49. Honma K, Honma S. 1988 Circabidian rhythm: its appearance and disappearance in association with a bright light pulse. Experientia 44, 981-983. (doi:10.1007/BF01939893)
50. Koern M, Elston TC, Blake WJ, Collins JJ. 2005 Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. 6, 451-464. (doi:10.1038/nrg1615)
51. Patnaik PR. 2006 External, extrinsic and intrinsic noise in cellular systems: analogies and implications for protein synthesis. Biotechnol. Mol. Biol. Rev. 1, 121-127.
52. Maheshri N, O'Shea EK. 2007 Living with noisy genes: how cells function reliably with inherent variability in gene expression. Annu. Rev. Biophys. Biomol. Struct. 36, 413-434. (doi:10.1146/annurev. biophys.36.040306.132705)
53. Rausenberger J, Fleck C, Timmer J, Kollmann M. 2009 Signatures of gene expression noise in cellular systems. Progr. Biophys. Mol. Biol. 100, 57-66. (doi:10.1016/j.pbiomolbio.2009.06.003)
54. Diambra L, Malta CP. 2012 Modeling the emergence of circadian rhythms in a clock neuron network. PLoS ONE 7, e33912. (doi:10.1371/journal.pone. 0033912)