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Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia

Author

Listed:
  • Javier Macia
  • Romilde Manzoni
  • Núria Conde
  • Arturo Urrios
  • Eulàlia de Nadal
  • Ricard Solé
  • Francesc Posas

Abstract

Engineered synthetic biological devices have been designed to perform a variety of functions from sensing molecules and bioremediation to energy production and biomedicine. Notwithstanding, a major limitation of in vivo circuit implementation is the constraint associated to the use of standard methodologies for circuit design. Thus, future success of these devices depends on obtaining circuits with scalable complexity and reusable parts. Here we show how to build complex computational devices using multicellular consortia and space as key computational elements. This spatial modular design grants scalability since its general architecture is independent of the circuit’s complexity, minimizes wiring requirements and allows component reusability with minimal genetic engineering. The potential use of this approach is demonstrated by implementation of complex logical functions with up to six inputs, thus demonstrating the scalability and flexibility of this method. The potential implications of our results are outlined.Author Summary: Synthetic biological circuits have been built for different purposes. Nevertheless, the way these devices have been designed so far present several limitations: complex genetic engineering is required to implement complex circuits, and once the parts are built, they are not reusable. We proposed to distribute the computation in several cellular consortia that are physically separated, thus ensuring implementation of circuits independently of their complexity and using reusable components with minimal genetic engineering. This approach allows an easy implementation of multicellular computing devices for secretable inputs or biosensing purposes.

Suggested Citation

  • 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.
  • Handle: RePEc:plo:pcbi00:1004685
    DOI: 10.1371/journal.pcbi.1004685
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    References listed on IDEAS

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    1. Subhayu Basu & Yoram Gerchman & Cynthia H. Collins & Frances H. Arnold & Ron Weiss, 2005. "A synthetic multicellular system for programmed pattern formation," Nature, Nature, vol. 434(7037), pages 1130-1134, April.
    2. Tae Seok Moon & Chunbo Lou & Alvin Tamsir & Brynne C. Stanton & Christopher A. Voigt, 2012. "Genetic programs constructed from layered logic gates in single cells," Nature, Nature, vol. 491(7423), pages 249-253, November.
    3. 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.
    4. Roberta Kwok, 2010. "Five hard truths for synthetic biology," Nature, Nature, vol. 463(7279), pages 288-290, January.
    5. 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.
    6. Jeff Hasty & David McMillen & J. J. Collins, 2002. "Engineered gene circuits," Nature, Nature, vol. 420(6912), pages 224-230, November.
    7. Michael B. Elowitz & Stanislas Leibler, 2000. "A synthetic oscillatory network of transcriptional regulators," Nature, Nature, vol. 403(6767), pages 335-338, January.
    8. 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.
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    Cited by:

    1. Joaquín Gutiérrez Mena & Sant Kumar & Mustafa Khammash, 2022. "Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

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