Hill Kinetics Meets P Systems: A Case Study on Gene Regulatory Networks as Computing Agents in silico and in vivo

  • Thomas Hinze
  • Sikander Hayat
  • Thorsten Lenser
  • Naoki Matsumaru
  • Peter Dittrich
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4860)

Abstract

Modeling and simulation of biological reaction networks is an essential task in systems biology aiming at formalization, understanding, and prediction of processes in living organisms. Currently, a variety of modeling approaches for specific purposes coexists. P systems form such an approach which owing to its algebraic nature opens growing fields of application. Here, emulating the dynamical system behavior based on reaction kinetics is of particular interest to explore network functions. We demonstrate a transformation of Hill kinetics for gene regulatory networks (GRNs) into the P systems framework. Examples address the switching dynamics of GRNs acting as NAND gate and RS flip-flop. An adapted study in vivo experimentally verifies both practicability for computational units and validity of the system model.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Alon, U.: An Introduction to Systems Biology. Chapman & Hall, Sydney, Australia (2006)MATHGoogle Scholar
  2. 2.
    Barbacari, N., et al.: Gene Regulatory Network Modelling by Membrane Systems. In: Freund, R., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2005. LNCS, vol. 3850, pp. 162–178. Springer, Heidelberg (2006)Google Scholar
  3. 3.
    Bernardini, F., et al.: Quorum Sensing P Systems. Theor. Comp. Sci. 371, 20–33 (2007)MATHCrossRefMathSciNetGoogle Scholar
  4. 4.
    Busi, N., et al.: Computing with Genetic Gates, Proteins, and Membranes. In: Hoogeboom, H.J., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2006. LNCS, vol. 4361, pp. 233–249. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  5. 5.
    Fontana, F., et al.: Discrete Solutions to Differential Equations by Metabolic P Systems. Theor. Comput. Sci. 372(1), 165–182 (2007)MATHCrossRefMathSciNetGoogle Scholar
  6. 6.
    Gardner, T.S., et al.: Construction of a Genetic Toggle Switch in Escherichia coli. Nature 403, 339–342 (2000)CrossRefGoogle Scholar
  7. 7.
    Hastings, J., et al.: Bacterial Bioluminescence. Annu. Rev. Microbiol. 31, 549–595 (1977)CrossRefGoogle Scholar
  8. 8.
    Hayat, S., et al.: Towards in vivo Computing: Quantitative Analysis of an Artificial Gene Regulatory Network Behaving as a RS Flip-Flop. In: Proc. Bionetics (2006)Google Scholar
  9. 9.
    Hinze, T., et al.: A Protein Substructure Based P System for Description and Analysis of Cell Signalling Networks. In: Hoogeboom, H.J., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2006. LNCS, vol. 4361, pp. 409–423. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  10. 10.
    Hoops, S., et al.: Copasi: a COmplex PAthway SImulator. Bioinf. 22, 3067–3074 (2006)CrossRefGoogle Scholar
  11. 11.
    Manca, V.: Metabolic P Systems for Biomolecular Dynamics. Progress in Natural Sciences 17(4), 384–391 (2006)MathSciNetGoogle Scholar
  12. 12.
    Mestl, T., et al.: A Mathematical Framework for Describing and Analysing Gene Regulatory Networks. J. Theor. Biol. 176, 291–300 (1995)CrossRefGoogle Scholar
  13. 13.
    Miller, M., et al.: Quorum Sensing in Bacteria. Annu. Rev. Microbiol. 55, 165–199 (2001)CrossRefGoogle Scholar
  14. 14.
    Păun, A., et al.: Modeling Signal Transduction Using P Systems. In: Hoogeboom, H.J., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2006. LNCS, vol. 4361, pp. 100–122. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  15. 15.
    Păun, G.: Computing with Membranes. J. Comp. Syst. Sci. 61(1), 108–143 (2000)CrossRefGoogle Scholar
  16. 16.
    Păun, G.: Membrane Computing: An Introduction. Springer, Berlin (2002)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Thomas Hinze
    • 1
  • Sikander Hayat
    • 2
  • Thorsten Lenser
    • 1
  • Naoki Matsumaru
    • 1
  • Peter Dittrich
    • 1
  1. 1.Friedrich-Schiller-Universität Jena, Bio Systems Analysis Group, Ernst-Abbe-Platz 1–4, D-07743 JenaGermany
  2. 2.Universität des Saarlandes, Computational Biology Group, Center for Bioinformatics, P.O. Box 15 11 50, D-66041 SaarbrückenGermany

Personalised recommendations