Positive feedbacks contribute to the robustness of the cell cycle with respect to molecular noise

Lecture Notes in Control and Information Sciences

Volumn 407, Issue , 2010, Pages 283-295

  Gonze, Didier ^a   Hafner, Marc ^b,c,d  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^b EPFL   (Switzerland)

^c UNIVERSITY OF ZURICH   (Switzerland)

^d SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCUIT OSCILLATIONS; STOCHASTIC CONTROL SYSTEMS; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

ATTRACTIVITY; CATALYTIC ACTIVATION; LIMIT CYCLE OSCILLATION (LCO); MODIFIED MODEL; MOLECULAR NOISE; POSITIVE FEEDBACK LOOP; REGULATORY FEEDBACK LOOPS; STOCHASTIC SIMULATIONS;

FEEDBACK;

EID: 77958190724     PISSN: 01708643     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-642-16135-3_23     Document Type: Article

References (43)

1. Barkai, N., Leibler, S.: Circadian clocks limited by noise. Nature 403, 267-268 (2000)
2. Becker-Weimann, S., Wolf, J., Herzel, H., Kramer, A.: Modeling feedback loops of the Mammalian circadian oscillator. Biophys J. 87, 3023-3034 (2004)
3. Brunner, M., Kaldi, K.: Interlocked feedback loops of the circadian clock of Neurospora crassa. Mol. Microbiol. 68, 255-262 (2008)
4. Calatay, T., Turcotte, M., Elowitz, M. B., Garcia-Ojalvo, J., Suel, G. M.: Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 139, 512-522 (2009)
5. Cheng, P., Yang, Y., Liu, Y.: Interlocked feedback loops contribute to the robustness of the Neurospora circadian clock. Proc. Natl. Acad. Sci. USA 98, 7408-7413 (2001)
6. Ciliberto, A., Novak, B., Tyson, J. J.: Steady states and oscillations in the p53/Mdm2 network. Cell Cycle 4, 488-493 (2005)
7. Cross, F. R.: Two redundant oscillatory mechanisms in the yeast cell cycle. Dev. Cell 4, 741-752 (2003)
8. Elowitz, M. B., Leibler, S.: A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338 (2000)
9. Forger, D. B., Peskin, C. S.: Stochastic simulation of the mammalian circadian clock. Proc. Natl. Acad. Sci. USA 102, 321-324 (2005)
10. Gérard, C., Goldbeter, A.: Temporal self-organization of the cyclin/Cdk network driving the mammalian cell cycle. Proc. Natl. Acad. Sci. USA 106, 21643-21648 (2010)
11. Gillespie, D. T.: Exact Stochastic Simulation of Coupled Chemical Reactions. J. Phys. Chem. 81, 2340-2361 (1977)
12. Glossop, N. R., Lyons, L. C., Hardin, P. E.: Interlocked feedback loops within the Drosophila circadian oscillator. Science 286, 766-768 (1999)
13. Goldbeter, A.: A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase. Proc. Natl. Acad. Sci. USA 88, 9107-9111 (1991)
14. Goldbeter, A.: Modeling the mitotic oscillator driving the cell division cycle. Comments on Theor. Biol. 3, 75-107 (1993)
15. Goldbeter, A.: A model for circadian oscillations in the Drosophila period protein (PER). Proc. Biol. Sci. 261, 319-324 (1995)
16. Goldbeter, A.: Biochemical Oscillations and Cellular Rhythms: The molecular bases of periodic and chaotic behaviour. Cambridge University Press, Cambridge (1996)
17. Goldbeter, A., Gonze, D., Houart, G., Leloup, J. C., Halloy, J., Dupont, G.: From simple to complex oscillatory behavior in metabolic and genetic control networks. Chaos 11, 247-260 (2001)
18. Goldbeter, A.: Computational approaches to cellular rhythms. Nature 420, 238-245 (2002)
19. Gonze, D., Halloy, J., Goldbeter, A.: Robustness of circadian rhythms with respect to molecular noise. Proc. Natl. Acad. Sci. USA 99, 673-678 (2002)
20. Gonze, D., Halloy, J., Gaspard, P.: Biochemical clocks and molecular noise: Theoretical study of robustness factors. J. Chem. Phys. 116, 10997-11101 (2002)
21. Gonze, D., Goldbeter, A.: Circadian rhythms and molecular noise. Chaos 16, 026110 (2006)
22. Goodwin, B. C.: Oscillatory behavior in enzymatic control processes. Adv. Enzyme Regul. 3, 425-438 (1965)
23. Hafner, M., Koeppl, H., Hasler, M., Wagner, A.: 'Glocal' robustness analysis and model discrimination for circadian oscillators. PLoS Comput. Biol. 5, e1000534 (2009)
24. Hafner, M., Koeppl, H., Wagner, A.: Evolution of Feedback Loops in Oscillatory Systems. In: Third International Conference on Foundations of Systems Biology in Engineering, pp. 157-160 (2009), http://arxiv.org/abs/1003. 1231
25. Hasty, J., Dolnik, M., Rottschaefer, V., Collins, J. J.: Synthetic gene network for entraining and amplifying cellular oscillations. Phys. Rev. Lett. 88, 148101 (2002)
26. Kapuy, O., He, E., Lopez-Aviles, S., Uhlmann, F., Tyson, J. J., Novak, B.: System-level feedbacks control cell cycle progression. FEBS Lett. 583, 3992-3998 (2009)
27. Kar, S., Baumann, W. T., Paul, M. R., Tyson, J. J.: Exploring the roles of noise in the eukaryotic cell cycle. Proc. Natl. Acad. Sci. USA 106, 6471-6476 (2009)
28. Kollmann, M., Lovdok, L., Bartholomé, K., Timmer, J., Sourjik, V.: Design principles of a bacterial signalling network. Nature 438, 504-507 (2005)
29. Kummer, U., Krajnc, B., Pahle, J., Green, A. K., Dixon, C. J., Marhl, M.: Transition from stochastic to deterministic behavior in calcium oscillations. Biophys J. 89, 1603-1611 (2005)
30. Leloup, J. C., Goldbeter, A.: Toward a detailed computational model for the mammalian circadian clock. Proc. Natl. Acad. Sci. USA 100, 7051-7056 (2003)
31. Meyer, T., Stryer, L.: Molecular model for receptor-stimulated calcium spiking. Proc. Natl. Acad. Sci. USA 85, 5051-5055 (1988)
32. Novak, B., Tyson, J. J.: Design principles of biochemical oscillators. Nat. Rev. Mol. Cell. Biol. 9, 981-991 (2008)
33. Pomerening, J. R.: Positive-feedback loops in cell cycle progression. FEBS Lett. (in press)
34. Pourquié, O.: The vertebrate segmentation clock. J. Anat. 199, 169-175 (2001)
35. Rao, C., Arkin, A.: Stochastic chemical kinetics and the quasi steady-state assumption: application to the Gillespie algorithm. J. Chem. Phys. 118, 4999-5010 (2003)
36. Sabouri-Ghomi, M., Ciliberto, A., Kar, S., Novak, B., Tyson, J. J.: Antagonism and bistability in protein interaction networks. J. Theor. Biol. 250, 209-218 (2002)
37. Shearman, L. P., Sriram, S., Weaver, D. R., Maywood, E. S., Chaves, I., Zheng, B., Kume, K., Lee, C. C., van der Horst, G. T., Hastings, M. H., Reppert, S.: Interacting molecular loops in the mammalian circadian clock. Science 288, 1013-1019 (2002)
38. Smolen, P., Baxter, D. A., Byrne, J. H.: Interlinked dual-time feedback loops can enhance robustness to stochasticity and persistence of memory. Phys. Rev. E 79, 31902 (2009)
39. Stelling, J., Gilles, E. D., Doyle, F. J.: Robustness properties of circadian clock architectures. Proc. Natl. Acad. Sci. USA 101, 13210-13215 (2004)
40. Stricker, J., Cookson, S., Bennett, M. R., Mather, W. H., Tsimring, L. S., Hasty, J.: A fast, robust and tunable synthetic gene oscillator. Nature 456, 516-519 (2008)
41. Tsai, T. Y., Choi, Y. S., Ma, W., Pomerening, J. R., Tang, C., Ferrell, J. E.: Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science 321, 126-129 (2008)
42. Vilar, J. M., Kueh, H. Y., Barkai, N., Leibler, S.: Mechanisms of noiseresistance in genetic oscillators. Proc. Natl. Acad. Sci. USA 99, 5988-5992 (2002)
43. Wagner, A.: Circuit topology and the evolution of robustness in two-gene circadian oscillators. Proc. Natl. Acad. Sci. USA 102, 11775-11780 (2005)