A stochastic model correctly predicts changes in budding yeast cell cycle dynamics upon periodic expression of CLN2

PLoS ONE

Volumn 9, Issue 5, 2014, Pages

  Oguz, Cihan ^a   Palmisano, Alida ^a,b   Laomettachit, Teeraphan ^c   Watson, Layne T ^a,b   Baumann, William T ^b   Tyson, John J ^a  

^a VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

^b Virginia Polytechnic Institute and State University   (United States)

^c KING MONGKUT'S UNIVERSITY OF TECHNOLOGY THONBURI   (Thailand)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLINE; CLN2 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; CELL CULTURE; CELL CYCLE; CELL CYCLE G1 PHASE; CELL SIZE; CLN2 GENE; CONTROLLED STUDY; GENETIC ALGORITHM; GENETIC STRAIN; NONHUMAN; PHENOTYPE; PREDICTION; STOCHASTIC MODEL; WILD TYPE; YEAST CELL; BIOLOGICAL MODEL; CYTOLOGY; GENE EXPRESSION REGULATION; GENETICS; MUTATION; SACCHAROMYCES CEREVISIAE; STATISTICS;

CELL CYCLE; CELL SIZE; CYCLINS; GENE EXPRESSION REGULATION, FUNGAL; MODELS, BIOLOGICAL; MUTATION; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; STOCHASTIC PROCESSES;

EID: 84901207678     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0096726     Document Type: Article

References (25)

1. Jackman J, O'Connor PM (2001) Methods for synchronizing cells at specific stages of the cell cycle. Current protocols in cell biology: 8-3.
2. Futcher B (1999) Cell cycle synchronization. Methods in cell science 21: 79-86.
3. Davis PK, Ho A, Dowdy SF (2001) Biological methods for cell-cycle synchronization of mammalian cells. Biotechniques 30: 1322-1331. (Pubitemid 32523842)
4. Manukyan A, Abraham L, Dungrawala H, Schneider BL (2011) Synchronization of yeast. In: Cell Cycle Synchronization, Springer. pp. 173-200.
5. Morgan DO (2007) The cell cycle: principles of control. New Science Press.
6. Bloom J, Cross FR (2007) Multiple levels of cyclin specificity in cell-cycle control. Nature Reviews Molecular Cell Biology 8: 149-160. (Pubitemid 46432532)
7. Charvin G, Cross F, Siggia E (2009) Forced periodic expression of G1 cyclins phase-locks the budding yeast cell cycle. Proceedings of the National Academy of Sciences 106: 6632-6637.
8. Laomettachit T (2011) Mathematical modeling approaches for dynamical analysis of protein regulatory networks with applications to the budding yeast cell cycle and the circadian rhythm in cyanobacteria. Ph.D. thesis, Virginia Institute of Technology. ETDs website. Available: http://scholar.lib.vt.edu/ theses/available/etd-11072011-021528/. Accessed 2014 Apr 14.
9. Oguz C, Laomettachit T, Chen KC, Watson LT, Baumann WT, et al. (2013) Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model. BMC systems biology 7: 53.
10. Di Talia S, Skotheim JM, Bean JM, Siggia ED, Cross FR (2007) The effects of molecular noise and size control on variability in the budding yeast cell cycle. Nature 448: 947-951. (Pubitemid 47312778)
11. Wang P, Randhawa R, Shaffer CA, Cao Y, Baumann WT (2008) Converting macromolecular regulatory models from deterministic to stochastic formulation. In: Proceedings of the 2008 Spring simulation multiconference. Society for Computer Simulation International, pp. 385-392.
12. Kügler P (2012) Moment fitting for parameter inference in repeatedly and partially observed stochastic biological models. PloS One 7: e43001.
13. Li B, You L (2013) Predictive power of cell-to-cell variability. Quantitative Biology 1: 131-139.
14. Poovathingal SK, Gunawan R (2010) Global parameter estimation methods for stochastic biochemical systems. BMC Bioinformatics 11: 414.
15. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, et al. (2003) Global analysis of protein expression in yeast. Nature 425: 737-741. (Pubitemid 37314318)
16. Cross FR, Archambault V, Miller M, Klovstad M (2002) Testing a mathematical model of the yeast cell cycle. Molecular biology of the cell 13: 52-70. (Pubitemid 34106058)
17. Charvin G, Cross FR, Siggia ED (2008) A microuidic device for temporally controlled gene expression and long-term fluorescent imaging in unperturbed dividing yeast cells. PloS One 3: e1468.
18. Turner JJ, Ewald JC, Skotheim JM (2012) Cell size control in yeast. Current Biology 22: R350-R359.
19. Johnston G, Pringle J, Hartwell L (1977) Coordination of growth with cell division in the yeast Saccharomyces cerevisiae. Experimental cell research 105: 79-98. (Pubitemid 8066451)
20. Nurse P, Fantes P (1981) Cell cycle controls in fission yeast: a genetic analysis. The cell cycle: 85-98.
21. Novak B, Tyson JJ (1997) Modeling the control of DNA replication in fission yeast. Proceedings of the National Academy of Sciences 94: 9147-9152. (Pubitemid 27357797)
22. Alberghina L, Smeraldi C, Ranzi BM, Porro D (1998) Control by nutrients of growth and cell cycle progression in budding yeast, analyzed by double-tag flow cytometry. Journal of bacteriology 180: 3864-3872. (Pubitemid 28361582)
23. Avraham N, Soifer I, Carmi M, Barkai N (2013) Increasing population growth by asymmetric segregation of a limiting resource during cell division. Molecular systems biology 9.
24. Lord P, Wheals A (1981) Variability in individual cell cycles of Saccharomyces cerevisiae. Journal of cell science 50: 361-376. (Pubitemid 12225997)
25. Bi E, Park HO (2012) Cell polarization and cytokinesis in budding yeast. Genetics 191: 347-387.