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Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems

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  • Zhou, Peipei
  • Cai, Shuiming
  • Liu, Zengrong
  • Chen, Luonan
  • Wang, Ruiqi

Abstract

To understand how a complex biomolecular network functions, a decomposition or a reconstruction process of the network is often needed so as to provide new insights into the regulatory mechanisms underlying various dynamical behaviors and also to gain qualitative knowledge of the network. Unfortunately, it seems that there are still no general rules on how to decompose a complex network into simple modules. An alternative resolution is to decompose a complex network into small modules or subsystems with specified functions such as switches and oscillators and then integrate them by analyzing the interactions between them. The main idea of this approach can be illustrated by considering a bidirectionally coupled network in this paper, i.e., coupled Toggle switch and Repressilator, and analyzing the occurrence of various dynamics, although the theoretical principle may hold for a general class of networks. We show that various biomolecular signals can be shaped by regulating the coupling between the subsystems. The approach presented here can be expected to simplify and analyze even more complex biological networks.

Suggested Citation

  • Zhou, Peipei & Cai, Shuiming & Liu, Zengrong & Chen, Luonan & Wang, Ruiqi, 2013. "Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems," Chaos, Solitons & Fractals, Elsevier, vol. 50(C), pages 115-126.
    • Handle: RePEc:eee:chsofr:v:50:y:2013:i:c:p:115-126
    DOI: 10.1016/j.chaos.2012.11.011
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    1. Naama Barkai & Stanislas Leibler, 2000. "Circadian clocks limited by noise," Nature, Nature, vol. 403(6767), pages 267-268, January.
    2. Marcel Tigges & Tatiana T. Marquez-Lago & Jörg Stelling & Martin Fussenegger, 2009. "A tunable synthetic mammalian oscillator," Nature, Nature, vol. 457(7227), pages 309-312, January.
    3. Jesse Stricker & Scott Cookson & Matthew R. Bennett & William H. Mather & Lev S. Tsimring & Jeff Hasty, 2008. "A fast, robust and tunable synthetic gene oscillator," Nature, Nature, vol. 456(7221), pages 516-519, November.
    4. Michael B. Elowitz & Stanislas Leibler, 2000. "A synthetic oscillatory network of transcriptional regulators," Nature, Nature, vol. 403(6767), pages 335-338, January.
    5. Eric H. Davidson, 2010. "Emerging properties of animal gene regulatory networks," Nature, Nature, vol. 468(7326), pages 911-920, December.
    6. Matthew Freeman, 2000. "Feedback control of intercellular signalling in development," Nature, Nature, vol. 408(6810), pages 313-319, November.
    7. Olaf Sporns & Rolf Kötter, 2004. "Motifs in Brain Networks," PLOS Biology, Public Library of Science, vol. 2(11), pages 1-1, October.
    8. Ertugrul M. Ozbudak & Mukund Thattai & Han N. Lim & Boris I. Shraiman & Alexander van Oudenaarden, 2004. "Multistability in the lactose utilization network of Escherichia coli," Nature, Nature, vol. 427(6976), pages 737-740, February.
    9. Albert Goldbeter, 2002. "Computational approaches to cellular rhythms," Nature, Nature, vol. 420(6912), pages 238-245, November.
    10. Timothy S. Gardner & Charles R. Cantor & James J. Collins, 2000. "Construction of a genetic toggle switch in Escherichia coli," Nature, Nature, vol. 403(6767), pages 339-342, January.
    11. Attila Becskei & Luis Serrano, 2000. "Engineering stability in gene networks by autoregulation," Nature, Nature, vol. 405(6786), pages 590-593, June.
    12. Murat Acar & Attila Becskei & Alexander van Oudenaarden, 2005. "Enhancement of cellular memory by reducing stochastic transitions," Nature, Nature, vol. 435(7039), pages 228-232, May.
    13. Savaş Tay & Jacob J. Hughey & Timothy K. Lee & Tomasz Lipniacki & Stephen R. Quake & Markus W. Covert, 2010. "Single-cell NF-κB dynamics reveal digital activation and analogue information processing," Nature, Nature, vol. 466(7303), pages 267-271, July.
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    1. Xu, Yong & Wu, Juan & Du, Lin & Yang, Hui, 2016. "Stochastic resonance in a genetic toggle model with harmonic excitation and Lévy noise," Chaos, Solitons & Fractals, Elsevier, vol. 92(C), pages 91-100.

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