Abstract
The transition of gene switch induced by external noises (multiplicative external noise and additive external noise) and external signals is investigated in the genetic regulatory system. Results show that the state-to-state transition of gene switch as well as resonant behaviors, such as the explicit coherence resonance (ECR), implicit coherence resonance (ICR) and control parameter coherence biresonance (CPCBR), can appear when noises are injected into the genetic regulatory system. The ECR is increased with the increase of the control parameter value when starting from the supercritical Hopf bifurcation parameter point, and there exists a critical control parameter value for the occurrence of ECR. However, the ICR is decreased as the control parameter value is increased when starting from the subcritical Hopf bifurcation point. In particular, the coherence of ECR is higher and more sensitive to noise than that of ICR. When an external signal is introduced into the system, the enhancement or suppression of the CPCBR and the number of peaks strongly depend on the frequency and amplitude of the external signal. Furthermore, the gene regulation system can selectively enhance or decrease the noise-induced oscillation signals at preferred frequency and amplitude of an external signal.
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References
Ahsan RC, Madhu C, Rob E (2015) Stochastic S-system modeling of gene regulatory network. Cogn Neurodyn 9:535–547
Bressloff PC (2014) Chapter 6 Stochastic gene expression and regulatory networks. In: Stochastic processes in cell biology. Interdisciplinary applied mathematics, vol 41. Springer, Dordrecht, pp 269–340
Caravagna G, Mauri G, d’Onofrio A (2013) The interplay of intrinsic and extrinsic bounded noises in biomolecular networks. PLoS ONE 8(2):e51174
Chaudhury S (2015) Modeling the effect of transcriptional noise on switching in gene networks in a genetic bistable switch. J Biol Phys 41:235–246
Chen BS, Hsu CY (2012) Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing. BMC Syst Biol 6(1):1–15
de Franciscis S, Caravagna G, d’Onofrio A arXiv preprint arXiv:1410.6993
de Franciscis S, Caravagna G, d’Onofrio A (2014) Bounded noises as a natural tool to model extrinsic fluctuations in biomolecular networks. Nat Comput 13:297–307
Gillespie DT (2000) The chemical Langevin equation. J Chem Phys 113:297–306
Góra PF (2005) Population explosion suppressed by noise: stationary distributions and how to simulate them. New J Phys 7:36(1-10)
Hasty J, Dolnik M, Rottschäfer V, Collins JJ (2002) Synthetic gene network for entraining and amplifying cellular oscillations. Phys Rev Lett 88:148101(1-4)
Hou ZH, Yang LF, Xin HW (1999) Stochastic bi-resonance without external signal in the CO + O2 catalytic oxidation reaction system. J Chem Phys 111:1592–1594
Kuang J, Tang M, Yu JS (2013) The mean and noise of protein numbers in stochastic gene expression. J Math Biol 67:261–291
Li QS, Lang XF (2006) Internal signal transmission in one-way coupled excitable system: Noise and coupling effects. Phys Rev E 74:031905(1-6)
Li YP, Li QS (2006) Implicit and explicit internal signal stochastic resonance in calcium ion oscillations. Chem Phys Lett 417:498–502
Mackey MC, Tyran-Kamińska M (2015) The limiting dynamics of a bistable molecular switch with and without noise. J Math Biol 73:1–29
Meister A, Du C, Li YH, Wong WH (2014) Modeling stochastic noise in gene regulatory. Syst Quant Biol 2(1):1–29
Munsky B, Neuert G, van Oudenaarden A (2012) Using gene expression noise to understand gene regulation. Science 336:183–187
Pikovsky AS, Kurths J (1997) Coherence resonance in a noise-driven excitable system. Phys Rev Lett 78:775–778
Rao CV, Wolf DM, Arkin AP (2002) Control, exploitation and tolerance of intracellular noise. Nature (London) 420:231–237
Shi JC (2010) Signal transduction and amplification in a circadian oscillator: interaction between two colored noises. J Theor Biol 265:565–571
Shi JC, Luo M, Dong T (2009) The selectivity of noise and coupling for coherence biresonance and array-enhanced coherence biresonance in coupled neural systems. BioSystems 98:85–90
Strelkowa N (2014) Stochastic complexity analysis in synthetic biology. Emerg Complex Comput 5:161–194
Thomas P, Matuschek H, Grima R (2013) How reliable is the linear noise approximation of gene regulator networks? BMC Genom 14(4):1–5
Toral R, Mirasso CR, Gunton JD (2003) System size coherence resonance in coupled FitzHugh–Nagumo models. Europhys Lett 61:162–167
Wang S, Xu J, Liu F, Wang W (2004) Improvement of signal transmission through spike-timing-dependent plasticity in neural networks. Eur Phys J (B) 39:351–356
Wang ZW, Hou ZH, Xin HW, Zhang ZZ (2007) Engineered internal noise stochastic resonator in gene network: a model study. Biophys Chem 125:281–285
Wang CJ, Yi M, Yang KL, Yang LJ (2012) Time delay induced transition of gene switch and stochastic resonance in a genetic transcriptional regulatory model. BMC Syst Biol 6(Suppl. 1):S9(1-16)
Yi M, Jia Y (2005) Light-noise-induced suprathreshold circadian oscillations and coherent resonance in Drosophila. Phys Rev E 72:012902(1-4)
Yi M, Jia Y, Liu Q, Li JR, Zhu CL (2006) Enhancement of internal-noise coherence resonance by modulation of external noise in a circadian oscillator. Phys Rev E 73:041923(1-8)
Yu G, Yi M, Jia Y, Tang J (2009) A constructive role of internal noise on coherence resonance induced by external noise in a calcium oscillation system. Chaos Solitons Fractals 41(1):273–283
Zhou CS, Kurths J, Hu B (2001) Array-enhanced coherence resonance: nontrivial effects of heterogeneity and spatial independence of noise. Phys Rev Lett 87:098101–098104
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The authors acknowledge the financial support of the Natural Science Foundation of Guangxi Province No: 2013GXNSFAA019019 and the Natural Science Foundation of Guangxi Province No: 2013GXNSFAA019041.
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Shi, JC., Luo, M., Dong, T. et al. External Noise and External Signal Induced Transition of Gene Switch and Coherence Resonance in the Genetic Regulatory System. Acta Biotheor 65, 135–150 (2017). https://doi.org/10.1007/s10441-017-9307-6
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DOI: https://doi.org/10.1007/s10441-017-9307-6