Skip to main content
SpringerLink
Log in

Quantitative Analysis of the Spatiotemporal Dynamics of a Synthetic Predator–Prey Ecosystem

  • Protocol
  • First Online:
Synthetic Gene Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 813))

Abstract

A major focus in synthetic biology is the rational design and implementation of gene circuits to control dynamics of individual cells and, increasingly, cellular populations. Population-level control is highlighted in recent studies which attempt to design and implement synthetic ecosystems (or engineered microbial consortia). On the one hand, these engineered systems may serve as a critical technological foundation for practical applications. On the other hand, they may serve as well-defined model systems to examine biological questions of broad relevance. Here, using a synthetic predator–prey ecosystem as an example, we illustrate the basic experimental techniques involved in system implementation and characterization. By extension, these techniques are applicable to the analysis of other microbial-based synthetic or natural ecosystems.

These authors contributed equally to this work.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Gardner, T. S., Cantor, C. R., and Collins, J. J. (2000) Construction of a genetic toggle switch in Escherichia coli, Nature 403, 339–342.

    Article  PubMed  CAS  Google Scholar 

  2. Atkinson, M. R., Savageau, M. A., Myers, J. T., and Ninfa, A. J. (2003) Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli, Cell 113, 597–607.

    Article  PubMed  CAS  Google Scholar 

  3. Ham, T. S., Lee, S. K., Keasling, J. D., and Arkin, A. P. (2008) Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory, PLoS ONE 3, e2815.

    Article  PubMed  Google Scholar 

  4. Lou, C., Liu, X., Ni, M., Huang, Y., Huang, Q., Huang, L., Jiang, L., Lu, D., Wang, M., Liu, C., Chen, D., Chen, C., Chen, X., Yang, L., Ma, H., Chen, J., and Ouyang, Q. (2010) Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch, Mol Syst Biol 6.

    Google Scholar 

  5. Kobayashi, H., Kærn, M., Araki, M., Chung, K., Gardner, T. S., Cantor, C. R., and Collins, J. J. (2004) Programmable cells: Interfacing natural and engineered gene networks, Proceedings of the National Academy of Sciences of the United States of America 101, 8414–8419.

    Article  PubMed  CAS  Google Scholar 

  6. Kramer, B. P., Viretta, A. U., Baba, M. D.-E., Aubel, D., Weber, W., and Fussenegger, M. (2004) An engineered epigenetic transgene switch in mammalian cells, Nat Biotech 22, 867–870.

    Article  CAS  Google Scholar 

  7. Tan, C., Marguet, P., and You, L. (2009) Emergent bistability by a growth-modulating positive feedback circuit, Nat Chem Biol 5, 842–848.

    Article  PubMed  CAS  Google Scholar 

  8. Stricker, J., Cookson, S., Bennett, M. R., Mather, W. H., Tsimring, L. S., and Hasty, J. (2008) A fast, robust and tunable synthetic gene oscillator, Nature 456, 516–519.

    Article  PubMed  CAS  Google Scholar 

  9. Elowitz, M. B., and Leibler, S. (2000) A synthetic oscillatory network of transcriptional regulators, Nature 403, 335–338.

    Article  PubMed  CAS  Google Scholar 

  10. Fung, E., Wong, W. W., Suen, J. K., Bulter, T., Lee, S.-G., and Liao, J. C. (2005) A synthetic gene-metabolic oscillator, Nature 435, 118–122.

    Article  PubMed  CAS  Google Scholar 

  11. Tigges, M., Denervaud, N., Greber, D., Stelling, J., and Fussenegger, M. (2010) A synthetic low-frequency mammalian oscillator, Nucl. Acids Res. 38, 2702–2711.

    Article  PubMed  CAS  Google Scholar 

  12. Swinburne, I. A., Miguez, D. G., Landgraf, D., and Silver, P. A. (2008) Intron length increases oscillatory periods of gene expression in animal cells, Genes & Development 22, 2342–2346.

    Article  CAS  Google Scholar 

  13. Tigges, M., Marquez-Lago, T. T., Stelling, J., and Fussenegger, M. (2009) A tunable synthetic mammalian oscillator, Nature 457, 309–312.

    Article  PubMed  CAS  Google Scholar 

  14. Hooshangi, S., Thiberge, S., and Weiss, R. (2005) Ultrasensitivity and noise propagation in a synthetic transcriptional cascade, Proceedings of the National Academy of Sciences of the United States of America 102, 3581–3586.

    Article  PubMed  CAS  Google Scholar 

  15. Anderson, J. C., Voigt, C. A., and Arkin, A. P. (2007) Environmental signal integration by a modular AND gate, Mol Syst Biol 3.

    Google Scholar 

  16. Win, M. N., and Smolke, C. D. (2008) Higher-Order Cellular Information Processing with Synthetic RNA Devices, Science 322, 456–460.

    Article  PubMed  CAS  Google Scholar 

  17. Zhan, J., Ding, B., Ma, R., Ma, X., Su, X., Zhao, Y., Liu, Z., Wu, J., and Liu, H. (2010) Develop reusable and combinable designs for transcriptional logic gates, Mol Syst Biol 6.

    Google Scholar 

  18. Friedland, A. E., Lu, T. K., Wang, X., Shi, D., Church, G., and Collins, J. J. (2009) Synthetic Gene Networks That Count, Science 324, 1199–1202.

    Article  PubMed  CAS  Google Scholar 

  19. Levskaya, A., Chevalier, A. A., Tabor, J. J., Simpson, Z. B., Lavery, L. A., Levy, M., Davidson, E. A., Scouras, A., Ellington, A. D., Marcotte, E. M., and Voigt, C. A. (2005) Synthetic biology: Engineering Escherichia coli to see light, Nature 438, 441–442.

    Article  PubMed  CAS  Google Scholar 

  20. Weber, W., Kramer, B. P., and Fussenegger, M. (2007) A genetic time-delay circuitry in mammalian cells, Biotechnology and Bioengineering 98, 894–902.

    Article  PubMed  CAS  Google Scholar 

  21. Weber, W., Stelling, J., Rimann, M., Keller, B., Daoud-El Baba, M., Weber, C. C., Aubel, D., and Fussenegger, M. (2007) A synthetic time-delay circuit in mammalian cells and mice, Proceedings of the National Academy of Sciences of the United States of America 104, 2643–2648.

    Article  CAS  Google Scholar 

  22. Danino, T., Mondragon-Palomino, O., Tsimring, L., and Hasty, J. (2010) A synchronized quorum of genetic clocks, Nature 463, 326–330.

    Article  PubMed  CAS  Google Scholar 

  23. Marguet, P., Tanouchi, Y., Spitz, E., Smith, C., and You, L. (2010) Oscillations by Minimal Bacterial Suicide Circuits Reveal Hidden Facets of Host-Circuit Physiology, PLoS ONE 5, e11909.

    Article  PubMed  Google Scholar 

  24. Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H., and Weiss, R. (2005) A synthetic multicellular system for programmed pattern formation, Nature 434, 1130–1134.

    Article  PubMed  CAS  Google Scholar 

  25. Sohka, T., Heins, R., and Ostermeier, M. (2009) Morphogen-defined patterning of Escherichia coli enabled by an externally tunable band-pass filter, Journal of Biological Engineering 3, 10.

    Article  PubMed  Google Scholar 

  26. Tabor, J. J., Salis, H. M., Simpson, Z. B., Chevalier, A. A., Levskaya, A., Marcotte, E. M., Voigt, C. A., and Ellington, A. D. (2009) A Synthetic Genetic Edge Detection Program, 137, 1272–1281.

    Google Scholar 

  27. Brenner, K., Karig, D. K., Weiss, R., and Arnold, F. H. (2007) Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium, Proceedings of the National Academy of Sciences of the United States of America 104, 17300–17304.

    Article  CAS  Google Scholar 

  28. You, L., Cox, R. S., Weiss, R., and Arnold, F. H. (2004) Programmed population control by cell-cell communication and regulated killing, Nature 428, 868–871.

    Article  PubMed  CAS  Google Scholar 

  29. Tamsir, A., Tabor, J. J., and Voigt, C. A. (2011) Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’, Nature 469, 212–215.

    Article  PubMed  CAS  Google Scholar 

  30. Balagadde, F. K., Song, H., Ozaki, J., Collins, C. H., Barnet, M., Arnold, F. H., Quake, S. R., and You, L. (2008) A synthetic Escherichia coli predator-prey ecosystem, Mol Syst Biol 4.

    Google Scholar 

  31. Weber, W., Daoud-El Baba, M., and Fussenegger, M. (2007) Synthetic ecosystems based on airborne inter- and intrakingdom communication, Proceedings of the National Academy of Sciences of the United States of America 104, 10435–10440.

    Article  CAS  Google Scholar 

  32. Miller, M. B., and Bassler, B. L. (2001) Quorum Sensing in Bacteria, Annual Review of Microbiology 55, 165–199.

    Article  PubMed  CAS  Google Scholar 

  33. Pai, A., Tanouchi, Y., Collins, C. H., and You, L. (2009) Engineering multicellular systems by cell-cell communication, Current Opinion in Biotechnology 20, 461–470.

    Article  PubMed  CAS  Google Scholar 

  34. Waters, C. M., and Bassler, B. L. (2005) Quorum Sensing: Cell-to-Cell Com-munication in Bacteria, Annual Review of Cell and Developmental Biology 21, 319–346.

    Article  PubMed  CAS  Google Scholar 

  35. Song, H., Payne, S., Gray, M., and You, L. (2009) Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem, Nat Chem Biol 5, 929–935.

    Article  PubMed  CAS  Google Scholar 

  36. Kerr, B., Riley, M. A., Feldman, M. W., and Bohannan, B. J. M. (2002) Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors, Nature 418, 171–174.

    Article  PubMed  CAS  Google Scholar 

  37. Chuang, J. S., Rivoire, O., and Leibler, S. (2009) Simpson’s Paradox in a Synthetic Microbial System, Science 323, 272–275.

    Article  PubMed  CAS  Google Scholar 

  38. Shou, W., Ram, S., and Vilar, J. M. G. (2007) Synthetic cooperation in engineered yeast populations, Proceedings of the National Academy of Sciences of the United States of America 104, 1877–1882.

    Article  CAS  Google Scholar 

  39. Acar, M., Mettetal, J. T., and van Oudenaarden, A. (2008) Stochastic switching as a survival strategy in fluctuating environments, Nat Genet 40, 471–475.

    Article  PubMed  CAS  Google Scholar 

  40. Kim, H. J., Boedicker, J. Q., Choi, J. W., and Ismagilov, R. F. (2008) Defined spatial structure stabilizes a synthetic multispecies bacterial community, Proceedings of the National Academy of Sciences of the United States of America 105, 18188–18193.

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was partially supported by the National Institutes of Health (5R01CA118486), a National Science Foundation CAREER award (LY), a DuPont Young Professorship (LY), a David and Lucile Packard Fellowship (LY), and a Department of Homeland Security Graduate Fellowship (SP).

Author information

Authors and Affiliations

  1. Department of Biomedical Engineering, Duke University, Durham, NC, USA

    Stephen Payne & Robert Phillip Smith

  2. Department of Biomedical Engineering, Institute for Genome Sciences and Policy, Center for Systems Biology, Duke University, Durham, NC, USA

    Lingchong You

Authors
  1. Stephen Payne
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Robert Phillip Smith
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lingchong You
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Lingchong You .

Editor information

Editors and Affiliations

  1. Inst. Biologie II, Zentrum für Biologische Signalstudien, Universität Freiburg, Stübeweg 51, Freiburg, 79108, Germany

    Wilfried Weber

  2. Dept. Ingenieurwissenschaften, Biosysteme (BSSE), ETH Zürich, Mattenstr. 26, Basel, 4058, Switzerland

    Martin Fussenegger

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Payne, S., Smith, R.P., You, L. (2012). Quantitative Analysis of the Spatiotemporal Dynamics of a Synthetic Predator–Prey Ecosystem. In: Weber, W., Fussenegger, M. (eds) Synthetic Gene Networks. Methods in Molecular Biology, vol 813. Humana Press. https://doi.org/10.1007/978-1-61779-412-4_19

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-412-4_19

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-411-7

  • Online ISBN: 978-1-61779-412-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation