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Song R, Peng W, Liu P, Acar M. A cell size- and cell cycle-aware stochastic model for predicting time-dynamic gene network activity in individual cells. BMC SYSTEMS BIOLOGY 2015; 9:91. [PMID: 26646617 PMCID: PMC4673848 DOI: 10.1186/s12918-015-0240-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/02/2015] [Indexed: 11/29/2022]
Abstract
Background Despite the development of various modeling approaches to predict gene network activity, a time dynamic stochastic model taking into account real-time changes in cell volume and cell cycle stages is still missing. Results Here we present a stochastic single-cell model that can be applied to any eukaryotic gene network with any number of components. The model tracks changes in cell volume, DNA replication, and cell division, and dynamically adjusts rates of stochastic reactions based on this information. By tracking cell division, the model can maintain cell lineage information, allowing the researcher to trace the descendants of any single cell and therefore study cell lineage effects. To test the predictive power of our model, we applied it to the canonical galactose network of the yeast Saccharomyces cerevisiae. Using a minimal set of free parameters and across several galactose induction conditions, the model effectively captured several details of the experimentally-obtained single-cell network activity levels as well as phenotypic switching rates. Conclusion Our model can readily be customized to model any gene network in any of the commonly used cells types, offering a novel and user-friendly stochastic modeling capability to the systems biology field. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0240-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ruijie Song
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 501, New Haven, CT, 06511, USA. .,Systems Biology Institute, Yale University, 840 West Campus Drive, West Haven, CT, 06516, USA.
| | - Weilin Peng
- Systems Biology Institute, Yale University, 840 West Campus Drive, West Haven, CT, 06516, USA. .,Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA.
| | - Ping Liu
- Systems Biology Institute, Yale University, 840 West Campus Drive, West Haven, CT, 06516, USA. .,Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA.
| | - Murat Acar
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 501, New Haven, CT, 06511, USA. .,Systems Biology Institute, Yale University, 840 West Campus Drive, West Haven, CT, 06516, USA. .,Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA. .,Department of Physics, Yale University, 217 Prospect Street, New Haven, CT, 06511, USA.
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Salerno L, Cosentino C, Merola A, Bates DG, Amato F. Validation of a model of the GAL regulatory system via robustness analysis of its bistability characteristics. BMC SYSTEMS BIOLOGY 2013; 7:39. [PMID: 23680044 PMCID: PMC3698211 DOI: 10.1186/1752-0509-7-39] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 04/26/2013] [Indexed: 11/29/2022]
Abstract
Background In Saccharomyces cerevisiæ, structural bistability generates a bimodal expression of the galactose uptake genes (GAL) when exposed to low and high glucose concentrations. This indicates that yeast cells can decide between using either the limited amount of glucose or growing on galactose under changing environmental conditions. A crucial requirement for any plausible mechanistic model of this system is that it reproduces the robustness of the bistable response observed in vivo against inter-individual parametric variability and fluctuating environmental conditions. Results We show how a control-theoretic analysis of the robustness of a model of the GAL regulatory network may be used to establish the model’s plausibility in characterizing the persistent memory of different carbon sources, without the need for extensive simulations. Chemical Reaction Network Theory is used to establish that the proposed network model is compatible with structural bistability. The robustness of each of the two operative conditions against fluctuations of the species concentrations is demonstrated by studying the Domains of Attraction of the corresponding equilibrium points. Finally, we use a global robustness analysis method based on Semi-Definite Programming to evaluate the modification of the bistable steady states induced by multiple parametric variations throughout bounded regions of the parameter space. Conclusions Our analysis provides convincing evidence for the robustness, and hence plausibility, of the GAL regulatory network model. The proposed workflow also demonstrates the power of analytical methods from control theory to provide a direct quantitative characterization of the dynamics of multistable biomolecular regulatory systems without recourse to extensive computer simulations.
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Affiliation(s)
- Luca Salerno
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi Magna Græcia di Catanzaro, Catanzaro, Italy
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