IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-30478-2.html
   My bibliography  Save this article

Complex dynamics in a synchronized cell-free genetic clock

Author

Listed:
  • Lukas Aufinger

    (Physics Department - E14, Technical University Munich)

  • Johann Brenner

    (Physics Department - E14, Technical University Munich)

  • Friedrich C. Simmel

    (Physics Department - E14, Technical University Munich)

Abstract

Complex dynamics such as period doubling and chaos occur in a wide variety of non-linear dynamical systems. In the context of biological circadian clocks, such phenomena have been previously found in computational models, but their experimental study in biological systems has been challenging. Here, we present experimental evidence of period doubling in a forced cell-free genetic oscillator operated in a microfluidic reactor, where the system is periodically perturbed by modulating the concentration of one of the oscillator components. When the external driving matches the intrinsic period, we experimentally find period doubling and quadrupling in the oscillator dynamics. Our results closely match the predictions of a theoretical model, which also suggests conditions under which our system would display chaotic dynamics. We show that detuning of the external and intrinsic period leads to more stable entrainment, suggesting a simple design principle for synchronized synthetic and natural genetic clocks.

Suggested Citation

  • Lukas Aufinger & Johann Brenner & Friedrich C. Simmel, 2022. "Complex dynamics in a synchronized cell-free genetic clock," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30478-2
    DOI: 10.1038/s41467-022-30478-2
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-30478-2
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-022-30478-2?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
    ---><---

    References listed on IDEAS

    as
    1. 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.
    2. Michael B. Elowitz & Stanislas Leibler, 2000. "A synthetic oscillatory network of transcriptional regulators," Nature, Nature, vol. 403(6767), pages 335-338, January.
    3. Claus O. Wilke & Jia Lan Wang & Charles Ofria & Richard E. Lenski & Christoph Adami, 2001. "Evolution of digital organisms at high mutation rates leads to survival of the flattest," Nature, Nature, vol. 412(6844), pages 331-333, July.
    4. Barbora Lavickova & Nadanai Laohakunakorn & Sebastian J. Maerkl, 2020. "A partially self-regenerating synthetic cell," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    5. David T. Riglar & David L. Richmond & Laurent Potvin-Trottier & Andrew A. Verdegaal & Alexander D. Naydich & Somenath Bakshi & Emanuele Leoncini & Lorena G. Lyon & Johan Paulsson & Pamela A. Silver, 2019. "Bacterial variability in the mammalian gut captured by a single-cell synthetic oscillator," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    6. Tal Danino & Octavio Mondragón-Palomino & Lev Tsimring & Jeff Hasty, 2010. "A synchronized quorum of genetic clocks," Nature, Nature, vol. 463(7279), pages 326-330, January.
    7. Laurent Potvin-Trottier & Nathan D. Lord & Glenn Vinnicombe & Johan Paulsson, 2016. "Synchronous long-term oscillations in a synthetic gene circuit," Nature, Nature, vol. 538(7626), pages 514-517, October.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Se Ho Park & Seokmin Ha & Jae Kyoung Kim, 2023. "A general model-based causal inference method overcomes the curse of synchrony and indirect effect," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    2. Jung Hun Park & Gábor Holló & Yolanda Schaerli, 2024. "From resonance to chaos by modulating spatiotemporal patterns through a synthetic optogenetic oscillator," Nature Communications, Nature, vol. 15(1), pages 1-13, December.

    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. Jung Hun Park & Gábor Holló & Yolanda Schaerli, 2024. "From resonance to chaos by modulating spatiotemporal patterns through a synthetic optogenetic oscillator," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Ankit Gupta & Mustafa Khammash, 2022. "Frequency spectra and the color of cellular noise," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    3. 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.
    4. Lucas Henrion & Juan Andres Martinez & Vincent Vandenbroucke & Mathéo Delvenne & Samuel Telek & Andrew Zicler & Alexander Grünberger & Frank Delvigne, 2023. "Fitness cost associated with cell phenotypic switching drives population diversification dynamics and controllability," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    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. Duncan Ingram & Guy-Bart Stan, 2023. "Modelling genetic stability in engineered cell populations," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    7. Volkov, Evgeny & Hellen, Edward H., 2021. "The effect of characteristic times on collective modes of two quorum sensing coupled identical ring oscillators," Chaos, Solitons & Fractals, Elsevier, vol. 151(C).
    8. Betz, Ulrich A.K. & Arora, Loukik & Assal, Reem A. & Azevedo, Hatylas & Baldwin, Jeremy & Becker, Michael S. & Bostock, Stefan & Cheng, Vinton & Egle, Tobias & Ferrari, Nicola & Schneider-Futschik, El, 2023. "Game changers in science and technology - now and beyond," Technological Forecasting and Social Change, Elsevier, vol. 193(C).
    9. Das, Saureesh, 2022. "Recurrence quantification and bifurcation analysis of electrical activity in resistive/memristive synapse coupled Fitzhugh–Nagumo type neurons," Chaos, Solitons & Fractals, Elsevier, vol. 165(P1).
    10. 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.
    11. 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.
    12. Shunsuke Kawasaki & Hiroki Ono & Moe Hirosawa & Takeru Kuwabara & Shunsuke Sumi & Suji Lee & Knut Woltjen & Hirohide Saito, 2023. "Programmable mammalian translational modulators by CRISPR-associated proteins," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    13. 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.
    14. 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.
    15. Bottani, Samuel & Grammaticos, Basile, 2008. "A simple model of genetic oscillations through regulated degradation," Chaos, Solitons & Fractals, Elsevier, vol. 38(5), pages 1468-1482.
    16. Masa Tsuchiya & Vincent Piras & Alessandro Giuliani & Masaru Tomita & Kumar Selvarajoo, 2010. "Collective Dynamics of Specific Gene Ensembles Crucial for Neutrophil Differentiation: The Existence of Genome Vehicles Revealed," PLOS ONE, Public Library of Science, vol. 5(8), pages 1-10, August.
    17. 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.
    18. Arturo Marín & Héctor Tejero & Juan Carlos Nuño & Francisco Montero, 2013. "The Advantage of Arriving First: Characteristic Times in Finite Size Populations of Error-Prone Replicators," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-12, December.
    19. 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.
    20. Onelia Gagliano & Camilla Luni & Yan Li & Silvia Angiolillo & Wei Qin & Francesco Panariello & Davide Cacchiarelli & Joseph S. Takahashi & Nicola Elvassore, 2021. "Synchronization between peripheral circadian clock and feeding-fasting cycles in microfluidic device sustains oscillatory pattern of transcriptome," Nature Communications, Nature, vol. 12(1), pages 1-12, December.

    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:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30478-2. 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: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    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.