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Emergent digital bio-computation through spatial diffusion and engineered bacteria

Author

Listed:
  • Alex J. H. Fedorec

    (University College London)

  • Neythen J. Treloar

    (University College London)

  • Ke Yan Wen

    (University College London)

  • Linda Dekker

    (University College London)

  • Qing Hsuan Ong

    (University College London)

  • Gabija Jurkeviciute

    (University College London)

  • Enbo Lyu

    (University College London)

  • Jack W. Rutter

    (University College London)

  • Kathleen J. Y. Zhang

    (University College London)

  • Luca Rosa

    (University College London)

  • Alexey Zaikin

    (University College London
    University College London)

  • Chris P. Barnes

    (University College London)

Abstract

Biological computing is a promising field with potential applications in biosafety, environmental monitoring, and personalized medicine. Here we present work on the design of bacterial computers using spatial patterning to process information in the form of diffusible morphogen-like signals. We demonstrate, mathematically and experimentally, that single, modular, colonies can perform simple digital logic, and that complex functions can be built by combining multiple colonies, removing the need for further genetic engineering. We extend our experimental system to incorporate sender colonies as morphogen sources, demonstrating how one might integrate different biochemical inputs. Our approach will open up ways to perform biological computation, with applications in bioengineering, biomaterials and biosensing. Ultimately, these computational bacterial communities will help us explore information processing in natural biological systems.

Suggested Citation

  • Alex J. H. Fedorec & Neythen J. Treloar & Ke Yan Wen & Linda Dekker & Qing Hsuan Ong & Gabija Jurkeviciute & Enbo Lyu & Jack W. Rutter & Kathleen J. Y. Zhang & Luca Rosa & Alexey Zaikin & Chris P. Bar, 2024. "Emergent digital bio-computation through spatial diffusion and engineered bacteria," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49264-3
    DOI: 10.1038/s41467-024-49264-3
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    References listed on IDEAS

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    1. Joaquin Caro-Astorga & Kenneth T. Walker & Natalia Herrera & Koon-Yang Lee & Tom Ellis, 2021. "Bacterial cellulose spheroids as building blocks for 3D and patterned living materials and for regeneration," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
    2. Ximing Li & Luna Rizik & Valeriia Kravchik & Maria Khoury & Netanel Korin & Ramez Daniel, 2021. "Synthetic neural-like computing in microbial consortia for pattern recognition," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    3. Yeqing Zong & Haoqian M. Zhang & Cheng Lyu & Xiangyu Ji & Junran Hou & Xian Guo & Qi Ouyang & Chunbo Lou, 2017. "Insulated transcriptional elements enable precise design of genetic circuits," Nature Communications, Nature, vol. 8(1), pages 1-13, December.
    4. Javier Macia & Ricard Sole, 2014. "How to Make a Synthetic Multicellular Computer," PLOS ONE, Public Library of Science, vol. 9(2), pages 1-13, February.
    5. Lewis Grozinger & Martyn Amos & Thomas E. Gorochowski & Pablo Carbonell & Diego A. Oyarzún & Ruud Stoof & Harold Fellermann & Paolo Zuliani & Huseyin Tas & Angel Goñi-Moreno, 2019. "Pathways to cellular supremacy in biocomputing," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    6. Michael B. Elowitz & Stanislas Leibler, 2000. "A synthetic oscillatory network of transcriptional regulators," Nature, Nature, vol. 403(6767), pages 335-338, January.
    7. Alvin Tamsir & Jeffrey J. Tabor & Christopher A. Voigt, 2011. "Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’," Nature, Nature, vol. 469(7329), pages 212-215, January.
    8. Javier Macia & Romilde Manzoni & Núria Conde & Arturo Urrios & Eulàlia de Nadal & Ricard Solé & Francesc Posas, 2016. "Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia," PLOS Computational Biology, Public Library of Science, vol. 12(2), pages 1-24, February.
    9. 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.
    10. 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.
    11. Attila Becskei & Luis Serrano, 2000. "Engineering stability in gene networks by autoregulation," Nature, Nature, vol. 405(6786), pages 590-593, June.
    12. Peter Rugbjerg & Nils Myling-Petersen & Andreas Porse & Kira Sarup-Lytzen & Morten O. A. Sommer, 2018. "Diverse genetic error modes constrain large-scale bio-based production," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
    13. Sergi Regot & Javier Macia & Núria Conde & Kentaro Furukawa & Jimmy Kjellén & Tom Peeters & Stefan Hohmann & Eulàlia de Nadal & Francesc Posas & Ricard Solé, 2011. "Distributed biological computation with multicellular engineered networks," Nature, Nature, vol. 469(7329), pages 207-211, January.
    14. Sarah Guiziou & Pauline Mayonove & Jerome Bonnet, 2019. "Hierarchical composition of reliable recombinase logic devices," Nature Communications, Nature, vol. 10(1), pages 1-7, December.
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