메뉴 건너뛰기




Volumn 335, Issue , 2013, Pages 222-234

Signatures of nonlinearity in single cell noise-induced oscillations

Author keywords

Intrinsic noise; Linear noise approximation; Master equations; Oscillations; Stochastic differential equations

Indexed keywords

BIFURCATION; BIOCHEMISTRY; EQUATION; NONLINEARITY; STOCHASTICITY; THEORETICAL STUDY;

EID: 84881013625     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2013.06.021     Document Type: Article
Times cited : (48)

References (59)
  • 2
    • 80051671001 scopus 로고    scopus 로고
    • Sustained oscillations for density dependent Markov processes
    • Baxendale P., Greenwood P. Sustained oscillations for density dependent Markov processes. J. Math. Biol. 2011, 63:433-457.
    • (2011) J. Math. Biol. , vol.63 , pp. 433-457
    • Baxendale, P.1    Greenwood, P.2
  • 3
    • 0019974626 scopus 로고
    • Role of feedback inhibition in stabilizing the classical operon
    • Bliss R., Painter P., Marr A. Role of feedback inhibition in stabilizing the classical operon. J. Theor. Biol. 1982, 97:177-193.
    • (1982) J. Theor. Biol. , vol.97 , pp. 177-193
    • Bliss, R.1    Painter, P.2    Marr, A.3
  • 4
    • 81255149550 scopus 로고    scopus 로고
    • The effect of loss of immunity on noise-induced sustained oscillations in epidemics
    • Chaffee J., Kuske R. The effect of loss of immunity on noise-induced sustained oscillations in epidemics. Bull. Mathe. Biol. 2011, 73:2552-2574.
    • (2011) Bull. Mathe. Biol. , vol.73 , pp. 2552-2574
    • Chaffee, J.1    Kuske, R.2
  • 6
    • 64949184133 scopus 로고    scopus 로고
    • Enhanced stochastic oscillations in autocatalytic reactions
    • Dauxois T., Di Patti F., Fanelli D., McKane A. Enhanced stochastic oscillations in autocatalytic reactions. Phys. Rev. E 2009, 79:036112.
    • (2009) Phys. Rev. E , vol.79 , pp. 036112
    • Dauxois, T.1    Di Patti, F.2    Fanelli, D.3    McKane, A.4
  • 7
    • 33644877313 scopus 로고    scopus 로고
    • Optimal observability of sustained stochastic competitive inhibition oscillations at organellar volumes
    • Davis K., Roussel M. Optimal observability of sustained stochastic competitive inhibition oscillations at organellar volumes. FEBS J. 2006, 273:84-95.
    • (2006) FEBS J. , vol.273 , pp. 84-95
    • Davis, K.1    Roussel, M.2
  • 8
    • 84900149029 scopus 로고    scopus 로고
    • Mid-range ultradian rhythms in Drosophila and the circadian clock problem
    • Springer Netherlands, D. Lloyd, E.L. Rossi (Eds.)
    • Dowse H.B. Mid-range ultradian rhythms in Drosophila and the circadian clock problem. Ultradian Rhythms from Molecules to Mind 2008, 175-199. Springer Netherlands. D. Lloyd, E.L. Rossi (Eds.).
    • (2008) Ultradian Rhythms from Molecules to Mind , pp. 175-199
    • Dowse, H.B.1
  • 9
    • 0242490781 scopus 로고    scopus 로고
    • Fast evaluation of fluctuations in biochemical networks with the linear noise approximation
    • Elf J., Ehrenberg M. Fast evaluation of fluctuations in biochemical networks with the linear noise approximation. Genome Res. 2003, 13:2475-2484.
    • (2003) Genome Res. , vol.13 , pp. 2475-2484
    • Elf, J.1    Ehrenberg, M.2
  • 10
    • 4244202604 scopus 로고
    • Stochastic resonance without external periodic force
    • Gang H., Ditzinger T., Ning C., Haken H. Stochastic resonance without external periodic force. Phys. Rev. Lett. 1993, 71:807-810.
    • (1993) Phys. Rev. Lett. , vol.71 , pp. 807-810
    • Gang, H.1    Ditzinger, T.2    Ning, C.3    Haken, H.4
  • 13
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie D. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 1977, 81:2340-2361.
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.1
  • 14
    • 0034225547 scopus 로고    scopus 로고
    • The chemical Langevin equation
    • Gillespie D. The chemical Langevin equation. J. Chem. Phys. 2000, 113:297.
    • (2000) J. Chem. Phys. , vol.113 , pp. 297
    • Gillespie, D.1
  • 15
    • 34249950625 scopus 로고    scopus 로고
    • Stochastic simulation of chemical kinetics
    • Gillespie D. Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem. 2007, 58:35-55.
    • (2007) Annu. Rev. Phys. Chem. , vol.58 , pp. 35-55
    • Gillespie, D.1
  • 16
    • 66649109136 scopus 로고    scopus 로고
    • Noise-induced breakdown of the Michaelis-Menten equation in steady-state conditions
    • Grima R. Noise-induced breakdown of the Michaelis-Menten equation in steady-state conditions. Phys. Rev. Lett. 2009, 102:218103.
    • (2009) Phys. Rev. Lett. , vol.102 , pp. 218103
    • Grima, R.1
  • 17
    • 77956247381 scopus 로고    scopus 로고
    • An effective rate equation approach to reaction kinetics in small volumes. theory and application to biochemical reactions in nonequilibrium steady-state conditions
    • Grima R. An effective rate equation approach to reaction kinetics in small volumes. theory and application to biochemical reactions in nonequilibrium steady-state conditions. J. Chem. Phys. 2010, 133:035101.
    • (2010) J. Chem. Phys. , vol.133 , pp. 035101
    • Grima, R.1
  • 18
    • 84860114415 scopus 로고    scopus 로고
    • A study of the accuracy of moment-closure approximations for stochastic chemical kinetics
    • Grima R. A study of the accuracy of moment-closure approximations for stochastic chemical kinetics. J. Chem. Phys. 2012, 136:154105.
    • (2012) J. Chem. Phys. , vol.136 , pp. 154105
    • Grima, R.1
  • 19
    • 58149269561 scopus 로고    scopus 로고
    • Modelling reaction kinetics inside cells
    • Grima R., Schnell S. Modelling reaction kinetics inside cells. Essays Biochem. 2008, 45:41.
    • (2008) Essays Biochem. , vol.45 , pp. 41
    • Grima, R.1    Schnell, S.2
  • 20
    • 80052396994 scopus 로고    scopus 로고
    • How accurate are the nonlinear chemical Fokker-Planck and chemical Langevin equations?
    • Grima R., Thomas P., Straube A. How accurate are the nonlinear chemical Fokker-Planck and chemical Langevin equations?. J. Chem. Phys. 2011, 135:084103.
    • (2011) J. Chem. Phys. , vol.135 , pp. 084103
    • Grima, R.1    Thomas, P.2    Straube, A.3
  • 21
    • 0345790286 scopus 로고    scopus 로고
    • Internal noise stochastic resonance in a circadian clock system
    • Hou Z., Xin H. Internal noise stochastic resonance in a circadian clock system. J. Chem. Phys. 2003, 119:11508.
    • (2003) J. Chem. Phys. , vol.119 , pp. 11508
    • Hou, Z.1    Xin, H.2
  • 22
    • 24644511779 scopus 로고    scopus 로고
    • Multiscale analysis of stochastic delay differential equations
    • Klosek M., Kuske R. Multiscale analysis of stochastic delay differential equations. Multiscale Model. Simulation 2005, 3:706-729.
    • (2005) Multiscale Model. Simulation , vol.3 , pp. 706-729
    • Klosek, M.1    Kuske, R.2
  • 24
    • 84880997562 scopus 로고
    • Limit theorems and diffusion approximations for density dependent Markov chains. In: Stochastic Systems: Modeling, Identification and Optimization, I, Springer
    • Kurtz, T., 1976. Limit theorems and diffusion approximations for density dependent Markov chains. In: Stochastic Systems: Modeling, Identification and Optimization, I, Springer, pp. 67-78.
    • (1976) , pp. 67-78
    • Kurtz, T.1
  • 25
    • 33847630066 scopus 로고    scopus 로고
    • Sustained oscillations via coherence resonance in SIR
    • Kuske R., Gordillo L.F., Greenwood P. Sustained oscillations via coherence resonance in SIR. J. Theor. Biol. 2007, 245:459-469.
    • (2007) J. Theor. Biol. , vol.245 , pp. 459-469
    • Kuske, R.1    Gordillo, L.F.2    Greenwood, P.3
  • 26
    • 84859091952 scopus 로고    scopus 로고
    • Persistent cell-autonomous circadian oscillations in fibroblasts revealed by six-week single-cell imaging of PER2::LUC bioluminescence
    • Leise T., Wang C., Gitis P., Welsh D. Persistent cell-autonomous circadian oscillations in fibroblasts revealed by six-week single-cell imaging of PER2::LUC bioluminescence. PLoS ONE 2012, 7:e33334.
    • (2012) PLoS ONE , vol.7
    • Leise, T.1    Wang, C.2    Gitis, P.3    Welsh, D.4
  • 27
    • 44049103351 scopus 로고    scopus 로고
    • Internal noise-sustained circadian rhythms in a Drosophila model
    • Li Q., Lang X. Internal noise-sustained circadian rhythms in a Drosophila model. Biophys. J. 2008, 94:1983-1994.
    • (2008) Biophys. J. , vol.94 , pp. 1983-1994
    • Li, Q.1    Lang, X.2
  • 28
    • 0035828638 scopus 로고    scopus 로고
    • Stochastic resonance with explicit internal signal
    • Li Q., Zhu R. Stochastic resonance with explicit internal signal. J. Chem. Phys. 2001, 115:6590.
    • (2001) J. Chem. Phys. , vol.115 , pp. 6590
    • Li, Q.1    Zhu, R.2
  • 29
    • 34249937560 scopus 로고    scopus 로고
    • Amplified biochemical oscillations in cellular systems
    • McKane A., Nagy J., Newman T., Stefanini M. Amplified biochemical oscillations in cellular systems. J. Stat. Phys. 2007, 128:165-191.
    • (2007) J. Stat. Phys. , vol.128 , pp. 165-191
    • McKane, A.1    Nagy, J.2    Newman, T.3    Stefanini, M.4
  • 30
    • 84862675384 scopus 로고    scopus 로고
    • Central and peripheral circadian clocks in mammals
    • Mohawk J., Green C., Takahashi J. Central and peripheral circadian clocks in mammals. Annu. Rev. Neurosci. 2012, 35:445-462.
    • (2012) Annu. Rev. Neurosci. , vol.35 , pp. 445-462
    • Mohawk, J.1    Green, C.2    Takahashi, J.3
  • 31
    • 8844256589 scopus 로고    scopus 로고
    • Circadian gene expression in individual fibroblasts. cell-autonomous and self-sustained oscillators pass time to daughter cells
    • Nagoshi E., Saini C., Bauer C., Laroche T., Naef F., Schibler U. Circadian gene expression in individual fibroblasts. cell-autonomous and self-sustained oscillators pass time to daughter cells. Cell 2004, 119:693-705.
    • (2004) Cell , vol.119 , pp. 693-705
    • Nagoshi, E.1    Saini, C.2    Bauer, C.3    Laroche, T.4    Naef, F.5    Schibler, U.6
  • 32
    • 56749160113 scopus 로고    scopus 로고
    • Design principles of biochemical oscillators
    • Novák B., Tyson J. Design principles of biochemical oscillators. Nat. Rev. Mol. Cell Biol. 2008, 9:981-991.
    • (2008) Nat. Rev. Mol. Cell Biol. , vol.9 , pp. 981-991
    • Novák, B.1    Tyson, J.2
  • 34
    • 79957877141 scopus 로고    scopus 로고
    • Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reaction systems-an analytical theory
    • Qian H. Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reaction systems-an analytical theory. Nonlinearity 2011, 24:R19.
    • (2011) Nonlinearity , vol.24
    • Qian, H.1
  • 35
    • 84860127314 scopus 로고    scopus 로고
    • Discreteness-induced concentration inversion in mesoscopic chemical systems
    • Ramaswamy R., González-Segredo N., Sbalzarini I., Grima R. Discreteness-induced concentration inversion in mesoscopic chemical systems. Nat. Commun. 2012, 3:779.
    • (2012) Nat. Commun. , vol.3 , pp. 779
    • Ramaswamy, R.1    González-Segredo, N.2    Sbalzarini, I.3    Grima, R.4
  • 38
    • 0035847473 scopus 로고    scopus 로고
    • On the influence of noise on the critical and oscillatory behavior of a predator-prey model. coherent stochastic resonance at the proper frequency of the system
    • Rozenfeld A., Tessone C., Albano E., Wio H. On the influence of noise on the critical and oscillatory behavior of a predator-prey model. coherent stochastic resonance at the proper frequency of the system. Phys. Lett. A 2001, 280:45-52.
    • (2001) Phys. Lett. A , vol.280 , pp. 45-52
    • Rozenfeld, A.1    Tessone, C.2    Albano, E.3    Wio, H.4
  • 39
    • 66049138052 scopus 로고    scopus 로고
    • Fluctuations and oscillations in a simple epidemic model
    • Rozhnova G., Nunes A. Fluctuations and oscillations in a simple epidemic model. Phys. Rev. E 2009, 79:041922.
    • (2009) Phys. Rev. E , vol.79 , pp. 041922
    • Rozhnova, G.1    Nunes, A.2
  • 41
    • 0033669189 scopus 로고    scopus 로고
    • A network of protein-protein interactions in yeast
    • Schwikowski B., Uetz P., Fields S. A network of protein-protein interactions in yeast. Nat. Biotechnol. 2000, 18(12):1257-1261.
    • (2000) Nat. Biotechnol. , vol.18 , Issue.12 , pp. 1257-1261
    • Schwikowski, B.1    Uetz, P.2    Fields, S.3
  • 42
    • 84867127337 scopus 로고    scopus 로고
    • Non-linear corrections to the time-covariance function derived from a multi-state chemical master equation
    • Scott M. Non-linear corrections to the time-covariance function derived from a multi-state chemical master equation. IET Syst. Biol. 2012, 6:116.
    • (2012) IET Syst. Biol. , vol.6 , pp. 116
    • Scott, M.1
  • 43
    • 3042601065 scopus 로고    scopus 로고
    • Frequency domain chemical Langevin analysis of stochasticity in gene transcriptional regulation
    • Simpson M., Cox C., Sayler G., et al. Frequency domain chemical Langevin analysis of stochasticity in gene transcriptional regulation. J. Theor. Biol. 2004, 229:383-394.
    • (2004) J. Theor. Biol. , vol.229 , pp. 383-394
    • Simpson, M.1    Cox, C.2    Sayler, G.3
  • 45
    • 78650646338 scopus 로고    scopus 로고
    • Stochastic theory of large-scale enzyme-reaction networks. finite copy number corrections to rate equation models
    • Thomas P., Straube A., Grima R. Stochastic theory of large-scale enzyme-reaction networks. finite copy number corrections to rate equation models. J. Chem. Phys. 2010, 133:195101.
    • (2010) J. Chem. Phys. , vol.133 , pp. 195101
    • Thomas, P.1    Straube, A.2    Grima, R.3
  • 46
    • 84872565357 scopus 로고    scopus 로고
    • Computation of biochemical pathway fluctuations beyond the linear noise approximation using iNA
    • 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE doi:10.1109/BIBM.2012.6392668
    • Thomas, P., Matuschek, H., Grima, R., 2012. Computation of biochemical pathway fluctuations beyond the linear noise approximation using iNA. In: 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE. pp. 1-5. doi:10.1109/BIBM.2012.6392668.
    • (2012) , pp. 1-5
    • Thomas, P.1    Matuschek, H.2    Grima, R.3
  • 47
    • 84873681523 scopus 로고    scopus 로고
    • Molecular noise induces concentration oscillations in chemical systems with stable node steady states
    • Toner D., Grima R. Molecular noise induces concentration oscillations in chemical systems with stable node steady states. J. Chem. Phys. 2013, 138:055101.
    • (2013) J. Chem. Phys. , vol.138 , pp. 055101
    • Toner, D.1    Grima, R.2
  • 48
    • 2242458129 scopus 로고    scopus 로고
    • Biochemical oscillations
    • Springer, C.P. Fall, E.S. Marland, J.M. Wagner, J.J. Tyson (Eds.)
    • Tyson J. Biochemical oscillations. Computational Cell Biology 2002, 230-260. Springer. C.P. Fall, E.S. Marland, J.M. Wagner, J.J. Tyson (Eds.).
    • (2002) Computational Cell Biology , pp. 230-260
    • Tyson, J.1
  • 49
    • 0016659905 scopus 로고
    • Control of mitosis by a continuous biochemical oscillation. synchronization; spatially inhomogeneous oscillations
    • Tyson J., Kauffman S. Control of mitosis by a continuous biochemical oscillation. synchronization; spatially inhomogeneous oscillations. J. Math. Biol. 1975, 1:289-310.
    • (1975) J. Math. Biol. , vol.1 , pp. 289-310
    • Tyson, J.1    Kauffman, S.2
  • 51
    • 0001340421 scopus 로고
    • The expansion of the master equation
    • Van Kampen N. The expansion of the master equation. Adv. Chem. Phys. 1976, 245-309.
    • (1976) Adv. Chem. Phys. , pp. 245-309
    • Van Kampen, N.1
  • 53
    • 0037197850 scopus 로고    scopus 로고
    • Mechanisms of noise-resistance in genetic oscillators
    • Vilar J., Kueh H., Barkai N., Leibler S. Mechanisms of noise-resistance in genetic oscillators. Proc. Nat. Acad. Sci. 2002, 99:5988-5992.
    • (2002) Proc. Nat. Acad. Sci. , vol.99 , pp. 5988-5992
    • Vilar, J.1    Kueh, H.2    Barkai, N.3    Leibler, S.4
  • 54
    • 84867122511 scopus 로고    scopus 로고
    • Linear noise approximation is valid over limited times for any chemical system that is sufficiently large
    • Wallace E., Gillespie D., Sanft K., Petzold L. Linear noise approximation is valid over limited times for any chemical system that is sufficiently large. IET Syst. Biol. 2012, 6:102-115.
    • (2012) IET Syst. Biol. , vol.6 , pp. 102-115
    • Wallace, E.1    Gillespie, D.2    Sanft, K.3    Petzold, L.4
  • 55
    • 33749995740 scopus 로고    scopus 로고
    • Exact results for noise power spectra in linear biochemical reaction networks
    • Warren P., Tǎnase-Nicola S., ten Wolde P., et al. Exact results for noise power spectra in linear biochemical reaction networks. J. Chem. Phys. 2006, 125:144904.
    • (2006) J. Chem. Phys. , vol.125 , pp. 144904
    • Warren, P.1    Tǎnase-Nicola, S.2    ten Wolde, P.3
  • 56
    • 11144311974 scopus 로고    scopus 로고
    • Bioluminescence imaging of individual fibroblasts reveals persistent, independently phased circadian rhythms of clock gene expression
    • Welsh D., Yoo S., Liu A., Takahashi J., Kay S. Bioluminescence imaging of individual fibroblasts reveals persistent, independently phased circadian rhythms of clock gene expression. Curr. Biol. 2004, 14:2289-2295.
    • (2004) Curr. Biol. , vol.14 , pp. 2289-2295
    • Welsh, D.1    Yoo, S.2    Liu, A.3    Takahashi, J.4    Kay, S.5
  • 58
    • 0000342056 scopus 로고    scopus 로고
    • Internal stochastic resonance in a model system for intracellular calcium oscillations
    • Zhong S., Qi F., Xin H. Internal stochastic resonance in a model system for intracellular calcium oscillations. Chem. Phys. Lett. 2001, 342:583-586.
    • (2001) Chem. Phys. Lett. , vol.342 , pp. 583-586
    • Zhong, S.1    Qi, F.2    Xin, H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.