Abstract
We analyse an enhanced specification of VICE, a hypothetical prokaryote with a genome as basic as possible. Besides the most common metabolic pathways of prokaryotes in interphase, VICE also posseses a regulatory feedback circuit based on the enzyme phosphofructokinase. We use as formal description language a fragment of the stochastic π-calculus. Simulations are run on BEAST, an abstract machine specially tailored to run in silico experimentations. Two kinds of virtual experiments have been carried out, depending on the way nutrients are supplied to VICE. The result of our experimentations in silico confirm that our virtual cell “survives” in an optimal environment, as it exhibits the homeostatic property similary to real living cells. Additionally, oscillatory patterns in the concentration of fructose-6-phosphate and fructose-1,6-bisphosphate show up, similar to the real ones.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Almaas, E., Kowács, B., et al.: Global organization of metabolic fluxes in the bacterium. Escherichia Coli. Nature 427, 839–843 (2004)
Buchholz, A., Takors, R., Wandrey, C.: Quantification of intracellular metabolites in escherichia coli k12 using liquid chromatographic-electrospray ionization tandem mass spectrometric techniques. Analytical Biochemistry 295, 129–137 (2001)
Cao, Y., Li, H., Petzold, L.: Efficient formulation of the stochastic simulation algorithm for chemically reacting system. Journal of Chemical Physics 121, 4059–4067 (2004)
Cardelli, L., Phillips, A.: A correct abstract machine for stochastic pi-calculus. In: Procs. BioConcur (2004)
Chiarugi, D., Curti, M., Degano, P., Marangoni, R.: ViCe: a VIrtual CEll. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 207–220. Springer, Heidelberg (2005)
Curti, M., Degano, P., Priami, C., Baldari, C.T.: Modelling biochemical pathways through enhanced π-calculus. Theoretical Computer Science (to appear, 2004)
Degano, P., Priami, C.: Enhanced operational semantics. ACM Computing Surveys 28(2), 352–354 (1996)
Demin, O.V., Kholodenko, B.N., Westerhoff, H.V.: Control analysis of stationary forced oscillations. Journal of Physical Chemistry 103, 10696–10710 (1999)
Diaz Ricci, J.C.: Adp modulates the dynamic behavior of the glycolytic pathway of escherichia coli. Biochemical and Biophysical Research Communications 271, 244–249 (2000)
Edwards, J., Ibarra, R., Palsson, B.: In silico prediction of escherichia coli metabolic capabilities are consistent with experimental data. Nature Biotechnology 19, 125–130 (2001)
Masaru, T., et al.: E–CELL: software environment for whole–cell simulation. Bioinformatics 15, 72–84 (1998)
Fong, S., Marciniak, J., Palsson, B.: Description and interpretation on adaptive evolution of escherichia coli k-12 mg1655 by using a genome-scale in silico metabolic model. Journal of Bacteriology 185, 6400–6408 (2003)
Gibson, M., Bruck, J.: Efficient exact stochastic simulation of hcemical systems with many species and many channels. Journal of Physical Chemistry 104, 1876–1889 (2005)
Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81(25), 2340–2361 (1977)
Hammes, G.G., Shimmel, P.R.: The Enzymes. In: Boyer, P.D. (ed.), vol. 2. Academic Press, New York (1970)
Heinrich, R., Schuster, S.: The regulation of cellular systems. Chapman and Hall, Boca Raton (1996)
Higgins, J.: A chemical mechanism for oscillation of glycolytic intermediates in yeast cell. Proceeding of National Academy Science USA 51, 989–994 (1964)
Kholodenko, B.N., Hoek, J.B., Westerhoff, H.V., Brown, G.C.: Quantification of information tranfer via cellular transduction pathways. FEBS letters 414, 430–434 (1997)
Kitano, H.: Foundations of System Biology. MIT Press, Cambridge (2002)
Koonin, E.V.: How many genes can make a cell:the minimal-gene-set concept. Annual Review Genomics and Human Genetics 01, 99–116 (2000)
Loew, L.M., Schaff, J.C.: The virtual cell: a software environment for computational cell biology. Trends Biotechnology 19(10), 401–406 (2001)
Milner, R.: Communicating and Mobile Systems: the π-calculus. Cambridge Univ. Press, Cambridge (1999)
Mushegian, A.R., Koonin, E.V.: A minimal gene set fir cellular life derived by comparison of complete bacterial genome. Proceedings of National Academy of Science USA 93, 10268–10273 (1996)
Petzold, L., Li, H.: Logarithmic direct method for discrete stochastic simulation of chemically reacting systems (2006), http://www.engineering.ucsb.edu/cse/Files/ldm0513.pdf
Priami, C.: Stochastic π-calculus. The Computer Journal 38(6), 578–589 (1995)
Priami, C., Regev, A., Silverman, W., Shapiro, E.: Application of a stochastic passing-name calculus to representation and simulation of molecular processes. Information Processing Letters 80, 25–31 (2001)
Reed, J., Palsson, B.: Thirteen years of building contraint-based in silico models of escherichia coli. Journal of Bacteriology 185, 2692–2699 (2003)
Regev, A., Shapiro, E.: Cells as computations. Nature 419, 343 (2002)
Regev, A., Silverman, W., Shapiro, E.: Representation and simulation of biochemical processes using the π-calculus process algebra. In: Pacific Symposium of Biocomputing (PSB 2001), pp. 459–470 (2001)
Schuster, S., Kahn, D., Westerhoff, H.V.: Modular analysis of the control of complex metabolic pathways. Biophysical Chemistry 48, 1–17 (1993)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Chiarugi, D., Chinellato, M., Degano, P., Brutto, G.L., Marangoni, R. (2006). Feedbacks and Oscillations in the Virtual Cell VICE. In: Priami, C. (eds) Computational Methods in Systems Biology. CMSB 2006. Lecture Notes in Computer Science(), vol 4210. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11885191_7
Download citation
DOI: https://doi.org/10.1007/11885191_7
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-46166-1
Online ISBN: 978-3-540-46167-8
eBook Packages: Computer ScienceComputer Science (R0)