Hybrid modeling of cell signaling and transcriptional reprogramming and its application in C. elegans development

Frontiers in Genetics

Volumn 2, Issue NOV, 2011, Pages

  Fertig, Elana J ^a   Danilova, Ludmila V ^a   Favorov, Alexander V ^a,b,c   Ochs, Michael F ^a,d  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b STATE RESEARCH INSTITUTE OF GENETICS AND SELECTION OF INDUSTRIAL MICROORGANISMS   (Russian Federation)

^c VAVILOV INSTITUTE OF GENERAL GENETICS   (Russian Federation)

^d JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Cell signaling; Computational molecular biology; Development; Probabilistic models; Stochastic processes; Transcriptional reprogramming

Indexed keywords

CAENORHABDITIS ELEGANS;

EID: 84855367309     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2011.00077     Document Type: Article

References (36)

1. Arkin, A., Ross, J., and McAdams, H. H. (1998). Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected escherichia coli cells. Genetics 149, 1633-1648.
2. Berset, T. A., Hoier, E. F., and Hajnal, A. (2005). The C. elegans homolog of the mammalian tumor suppressor dep-1/scc1 inhibits egfr signaling to regulate binary cell fate decisions. Genes Dev. 19, 1328-1340.
3. Burdine, R. D., Branda, C. S., and Stern, M. J. (1998). EGL-17(FGF) expression coordinates the attraction of the migrating sex myoblasts with vulval induction in C. elegans. Development 125, 1083-1093.
4. Euling, S., and Ambros, V. (1996). Heterochronic genes control cell cycle progress and developmental competence of C. elegans vulva precursor cells. Cell 84, 667-676.
5. Fisher, J., Piterman, N., Hajnal, A., and Henzinger, T. A. (2007). Predictive modeling of signaling crosstalk during C. elegans vulval development. PLoS Comput. Biol. 3, e92. doi:10.1371/journal.pcbi.0030092
6. Fujioka, A., Terai, K., Itoh, R. E., Aoki, K., Nakamura, T., Kuroda, S., Nishida, E., and Matsuda, M. (2006). Dynamics of the ras/erk mapk cascade as monitored by fluorescent probes. J. Biol. Chem. 281, 8917-8926.
7. Geva-Zatorsky, N., Rosenfeld, N., Itzkovitz, S., Milo, R., Sigal, A., Dekel, E., Yarnitzky, T., Liron, Y., Polak, P., Lahav, G., and Alon, U. (2006). Oscillations and variability in the p53 system. Mol. Syst. Biol. 2:2006:0033.
8. Gillespie, D. T. (1976). A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 22, 403-434.
9. Giurumescu, C. A., Sternberg, P. W., and Asthagiri, A. R. (2006). Intercellular coupling amplifies fate segregation during Caenorhabditis elegans vulval development. Proc. Natl. Acad. Sci. U.S.A. 103, 1331-1336.
10. Giurumescu, C. A., Sternberg, P. W., and Asthagiri, A. R. (2009). Predicting phenotypic diversity and the underlying quantitative molecular transitions. PLoS Comput. Biol. 5, e1000354. doi:10.1371/journal.pcbi.1000354
11. Greenwald, I. (2005). LIN-12/Notch signaling in C. elegans. WormBook 1-16.
12. Greenwald, I., Sternberg, P., and Horvitz, H. (1983). The lin-12 locus specifies cell fates in Caenorhabditis elegans. Cell 34, 435-444.
13. Gygi, S. P., Rochon, Y., Franza, B. R., and Aebersold, R. (1999). Correlation between protein and mrna abundance in yeast. Mol. Cell. Biol. 19, 1720-1730.
14. Kierzek, A., Zhou, L., and Wanner, B. (2010). Stochastic kinetic model of two component system signalling reveals all-or-none, graded and mixed mode stochastic switching responses. Mol. Biosyst. 6, 531-542.
15. Kim, S., Li, H., Dougherty, E., Cao, N., Chen, Y., Bittner, M., and Suh, E. (2002). Can markov chain models minic biological regulation? J. Biol. Syst. 10, 431-445.
16. Kinnunen, T., Huang, Z., Townsend, J., Gatdula, M. M., Brown, J. R., Esko, J. D., and Turnbull, J. E. (2005). Heparan 2-o-sulfotransferase, hst-2, is essential for normal cell migration in Caenorhabditis elegans. Proc. Natl. Acad. Sci. U.S.A. 102, 1507-1512.
17. Li, C., Nagasaki, M., Ueno, K., and Miyano, S. (2009). Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional petri net with extension. BMC Syst. Biol. 3, 42. doi:10.1186/1752-0509-3-42
18. Li, H., Cao, Y., Petzold, L. R., and Gillespie, D. T. (2008). Algorithms and software for stochastic simulation of biochemical reacting systems. Biotechnol. Prog. 24, 56-61.
19. Locasale, J. W., Shaw, A. S., and Chakraborty, A. K. (2007). Scaffold proteins confer diverse regulatory properties to protein kinase cascades. Proc. Natl. Acad. Sci. U.S.A. 104, 13307-13312.
20. Mayer, B. J., Blinov, M. L., and Loew, L. M. (2009). Molecular machines or pleiomorphic ensembles: signaling complexes revisited. J. Biol. 8, 81.
21. McAdams, H. H., and Arkin, A. (1997). Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. U.S.A. 94, 814-819.
22. Meier-Schellersheim, M., Xu, X., Angermann, B., Kunkel, E. J., Jin, T., and Germain, R. N. (2006). Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method. PLoS Comput. Biol. 2, e82. doi:10.1371/journal.pcbi.0020082
23. Moraru, I., Schaff, J. C., Slepchenko, B. M., Blinov, M. L., Morgan, F., Lakshminarayana, A., Gao, F., Li, Y., and Loew, L. M. (2008). Virtual cell modelling and simulation software environment. IET Syst. Biol. 2, 352-362.
24. Novak, B., and Tyson, J. J. (2004). A model for restriction point control of the mammalian cell cycle. J. Theor. Biol. 230, 563-579.
25. Ohmachi, M., Rocheleau, C. E., Church, D., Lambie, E., Schedl, T., and Sundaram, M. V. (2002). C. elegans ksr-1 and ksr-2 have both unique and redundant functions and are required for mpk-1 erk phosphorylation. Curr. Biol. 12, 427-433.
26. Sadot, A., Fisher, J., Barak, D., Admanit, Y., Stern, M. J., Hubbard, E. J. A., and Harel, D. (2008). Toward verified biological models. IEEE/ACM Trans. Comput. Biol. Bioinform. 5, 223-234.
27. Sako, Y., Minoguchi, S., and Yanagida, T. (2000). Single-molecule imaging of egfr signalling on the surface of living cells. Nat. Cell Biol. 2, 168-172.
28. Shea, M. A., and Ackers, G. K. (1985). The or control system of bacteriophage lambda. A physical-chemical model for gene regulation. J. Mol. Biol. 181, 211-230.
29. Shmulevich, I., Dougherty, E. R., Kim, S., and Zhang, W. (2002). Probabilistic boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18, 261-274.
30. Sprinzak, D., Lakhanpal, A., Lebon, L., Santat, L. A., Fontes, M. E., Anderson, G. A., Garcia-Ojalvo, J., and Elowitz, M. B. (2010). Cis-interactions between notch and delta generate mutually exclusive signalling states. Nature 465, 86-90.
31. Sternberg, P. W. (2005). Vulval development. WormBook 1-28.
32. Sulston, J., and Horvitz, H. (1977). Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. Dev. Biol. 56, 110-156.
33. Sun, X., and Hong, P. (2007). Computational modeling of Caenorhabditis elegans vulval induction. Bioinformatics 23, i499-i507.
34. Sundaram, M. V. (2006). RTK/Ras/MAPK signaling. WormBook 1-19.
35. Ullah, M., Schmidt, H., Cho, K. H., and Wolkenhauer, O. (2006). Deterministic modelling and stochastic simulation of biochemical pathways using matlab. Syst. Biol. (Stevenage) 153, 53-60.
36. Velculescu, V. E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M. A., Bassett, D. E. J., Hieter, P., Vogelstein, B., and Kinzler, K. W. (1997). Characterization of the yeast transcriptome. Cell 88, 243-251.