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Complex dynamics in a synchronized cell-free genetic clock

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  • 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
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    References listed on IDEAS

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    1. 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.
    2. 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.
    3. 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.
    4. Michael B. Elowitz & Stanislas Leibler, 2000. "A synthetic oscillatory network of transcriptional regulators," Nature, Nature, vol. 403(6767), pages 335-338, January.
    5. 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.
    6. Barbora Lavickova & Nadanai Laohakunakorn & Sebastian J. Maerkl, 2020. "A partially self-regenerating synthetic cell," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    7. 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.
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    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.

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