IDEAS home Printed from https://ideas.repec.org/a/eee/chsofr/v45y2012i5p577-587.html
   My bibliography  Save this article

Periodic perturbation of genetic oscillations

Author

Listed:
  • Zhdanov, Vladimir P.

Abstract

Kinetics of gene expression may be oscillatory due to the feedbacks between the mRNA, non-coding RNA and protein synthesis. In complex genetic networks, the kinetic oscillations generated in one subnetwork may influence oscillations in another subnetwork. To clarify what may happen in such situations, we have performed a mean-field analysis and Monte Carlo simulations of periodic perturbation of the oscillatory kinetics of the simplest genetic network including a gene with negative regulation of the mRNA production by protein, obtained via mRNA translation and two steps of conversion. Our analysis shows universal and specific features of the kinetics under consideration. Our simulations indicate that due to fluctuations only some of these features can really be observed. Specifically, the main frequencies obtained by the Fourier expansion of the mean-field and Monte Carlo kinetics are found to be often similar except that the Monte Carlo distribution of frequencies near the main frequencies is somewhat wider.

Suggested Citation

  • Zhdanov, Vladimir P., 2012. "Periodic perturbation of genetic oscillations," Chaos, Solitons & Fractals, Elsevier, vol. 45(5), pages 577-587.
    • Handle: RePEc:eee:chsofr:v:45:y:2012:i:5:p:577-587
    DOI: 10.1016/j.chaos.2011.12.008
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0960077911002402
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.chaos.2011.12.008?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Y. Kobayashi & T. Shibata & Y. Kuramoto & A. S. Mikhailov, 2010. "Evolutionary design of oscillatory genetic networks," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 76(1), pages 167-178, July.
    2. Bottani, Samuel & Grammaticos, Basile, 2008. "A simple model of genetic oscillations through regulated degradation," Chaos, Solitons & Fractals, Elsevier, vol. 38(5), pages 1468-1482.
    3. Matthew R. Bennett & Wyming Lee Pang & Natalie A. Ostroff & Bridget L. Baumgartner & Sujata Nayak & Lev S. Tsimring & Jeff Hasty, 2008. "Metabolic gene regulation in a dynamically changing environment," Nature, Nature, vol. 454(7208), pages 1119-1122, August.
    4. Mengel, Benedicte & Krishna, Sandeep & Jensen, Mogens H. & Trusina, Ala, 2012. "Nested feedback loops in gene regulation," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(1), pages 100-106.
    5. M. Perc, 2009. "Stochastic resonance on paced genetic regulatory small-world networks: effects of asymmetric potentials," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 69(1), pages 147-153, May.
    6. Zhdanov, Vladimir P., 2011. "Periodic perturbation of the bistable kinetics of gene expression," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 390(1), pages 57-64.
    7. Shen, Jianwei & Liu, Zengrong & Zheng, Weixing & Xu, Fengdan & Chen, Luonan, 2009. "Oscillatory dynamics in a simple gene regulatory network mediated by small RNAs," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 388(14), pages 2995-3000.
    8. Zhang, Fengpan & Lu, Jinrui & Liu, Zhiguang & Chen, Aimin & Shen, Jianwei, 2010. "Effects of nonlinear degradation of protein on the oscillatory dynamics in a simple gene regulatory network," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(6), pages 1286-1295.
    9. 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.
    10. G. Bordyugov & A. Granada & H. Herzel, 2011. "How coupling determines the entrainment of circadian clocks," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 82(3), pages 227-234, August.
    11. Michael B. Elowitz & Stanislas Leibler, 2000. "A synthetic oscillatory network of transcriptional regulators," Nature, Nature, vol. 403(6767), pages 335-338, January.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Evgeni V Nikolaev & Eduardo D Sontag, 2016. "Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory," PLOS Computational Biology, Public Library of Science, vol. 12(4), pages 1-33, April.
    2. Singh, Vijai & Chaudhary, Dharmendra Kumar & Mani, Indra & Dhar, Pawan Kumar, 2016. "Recent advances and challenges of the use of cyanobacteria towards the production of biofuels," Renewable and Sustainable Energy Reviews, Elsevier, vol. 60(C), pages 1-10.
    3. Huang, Chengdai & Cao, Jinde & Xiao, Min, 2016. "Hybrid control on bifurcation for a delayed fractional gene regulatory network," Chaos, Solitons & Fractals, Elsevier, vol. 87(C), pages 19-29.
    4. Samanthe M Lyons & Wenlong Xu & June Medford & Ashok Prasad, 2014. "Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems," PLOS Computational Biology, Public Library of Science, vol. 10(3), pages 1-16, March.
    5. 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.
    6. Lucia Marucci & David A W Barton & Irene Cantone & Maria Aurelia Ricci & Maria Pia Cosma & Stefania Santini & Diego di Bernardo & Mario di Bernardo, 2009. "How to Turn a Genetic Circuit into a Synthetic Tunable Oscillator, or a Bistable Switch," PLOS ONE, Public Library of Science, vol. 4(12), pages 1-10, December.
    7. Miles Miller & Marc Hafner & Eduardo Sontag & Noah Davidsohn & Sairam Subramanian & Priscilla E M Purnick & Douglas Lauffenburger & Ron Weiss, 2012. "Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity," PLOS Computational Biology, Public Library of Science, vol. 8(7), pages 1-18, July.
    8. Luna Rizik & Loai Danial & Mouna Habib & Ron Weiss & Ramez Daniel, 2022. "Synthetic neuromorphic computing in living cells," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    9. Jin Wang & Bo Huang & Xuefeng Xia & Zhirong Sun, 2006. "Funneled Landscape Leads to Robustness of Cell Networks: Yeast Cell Cycle," PLOS Computational Biology, Public Library of Science, vol. 2(11), pages 1-10, November.
    10. Avraham E Mayo & Yaakov Setty & Seagull Shavit & Alon Zaslaver & Uri Alon, 2006. "Plasticity of the cis-Regulatory Input Function of a Gene," PLOS Biology, Public Library of Science, vol. 4(4), pages 1-1, March.
    11. Ankit Gupta & Mustafa Khammash, 2022. "Frequency spectra and the color of cellular noise," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    12. Bottani, Samuel & Grammaticos, Basile, 2008. "A simple model of genetic oscillations through regulated degradation," Chaos, Solitons & Fractals, Elsevier, vol. 38(5), pages 1468-1482.
    13. Margherita Carletti & Malay Banerjee, 2019. "A Backward Technique for Demographic Noise in Biological Ordinary Differential Equation Models," Mathematics, MDPI, vol. 7(12), pages 1-16, December.
    14. Jun Feng & Zhenting Li & Shizhen Zhang & Chun Bao & Jingxian Fang & Yun Yin & Bolei Chen & Lei Pan & Bing Wang & Yu Zheng, 2023. "A Microimage-Processing-Based Technique for Detecting Qualitative and Quantitative Characteristics of Plant Cells," Agriculture, MDPI, vol. 13(9), pages 1-16, September.
    15. Weiyue Ji & Handuo Shi & Haoqian Zhang & Rui Sun & Jingyi Xi & Dingqiao Wen & Jingchen Feng & Yiwei Chen & Xiao Qin & Yanrong Ma & Wenhan Luo & Linna Deng & Hanchi Lin & Ruofan Yu & Qi Ouyang, 2013. "A Formalized Design Process for Bacterial Consortia That Perform Logic Computing," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-9, February.
    16. Konstantinos I Papadimitriou & Guy-Bart V Stan & Emmanuel M Drakakis, 2013. "Systematic Computation of Nonlinear Cellular and Molecular Dynamics with Low-Power CytoMimetic Circuits: A Simulation Study," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-24, February.
    17. Inés P Mariño & Alexey Zaikin & Joaquín Míguez, 2017. "A comparison of Monte Carlo-based Bayesian parameter estimation methods for stochastic models of genetic networks," PLOS ONE, Public Library of Science, vol. 12(8), pages 1-25, August.
    18. Dhiman, Aman & Poria, Swarup, 2018. "Allee effect induced diversity in evolutionary dynamics," Chaos, Solitons & Fractals, Elsevier, vol. 108(C), pages 32-38.
    19. Javier Santos-Moreno & Eve Tasiudi & Hadiastri Kusumawardhani & Joerg Stelling & Yolanda Schaerli, 2023. "Robustness and innovation in synthetic genotype networks," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    20. T. Ochiai & J. C. Nacher, 2007. "Stochastic analysis of autoregulatory gene expression dynamics," Mathematical and Computer Modelling of Dynamical Systems, Taylor & Francis Journals, vol. 14(4), pages 377-388, November.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:chsofr:v:45:y:2012:i:5:p:577-587. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Thayer, Thomas R. (email available below). General contact details of provider: https://www.journals.elsevier.com/chaos-solitons-and-fractals .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.