title: Analysis of stochastic strategies in bacterial competence: a master equation approach.
abstract: Competence is a transiently differentiated state that certain bacterial cells reach when faced with a stressful environment. Entrance into competence can be attributed to the excitability of the dynamics governing the genetic circuit that regulates this cellular behavior. Like many biological behaviors, entrance into competence is a stochastic event. In this case cellular noise is responsible for driving the cell from a vegetative state into competence and back. In this work we present a novel numerical method for the analysis of stochastic biochemical events and use it to study the excitable dynamics responsible for competence in Bacillus subtilis. Starting with a Finite State Projection (FSP) solution of the chemical master equation (CME), we develop efficient numerical tools for accurately computing competence probability. Additionally, we propose a new approach for the sensitivity analysis of stochastic events and utilize it to elucidate the robustness properties of the competence regulatory genetic circuit. We also propose and implement a numerical method to calculate the expected time it takes a cell to return from competence. Although this study is focused on an example of cell-differentiation in Bacillus subtilis, our approach can be applied to a wide range of stochastic phenomena in biological systems.
authors.affiliation: Department of Mechanical and Industrial Engineering, University of California, Santa Barbara, Santa Barbara, California, USA.
authors.forename: Sandra H
authors.initials: SH
authors.lastname: Dandach
authors.forename: Mustafa
authors.initials: M
authors.lastname: Khammash
mesh_terms: D000465:Algorithms; D001412:Bacillus subtilis / Q000235:genetics / Q000502:physiology; D001426:Bacterial Proteins / Q000235:genetics / Q000502:physiology; D053263:Gene Regulatory Networks / Q000235:genetics / Q000502:physiology*; D008954:Models, Biological; D009010:Monte Carlo Method; D013269:Stochastic Processes; D049490:Systems Biology / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics / Q000502:physiology
chemical_list: D001426:Bacterial Proteins; D014157:Transcription Factors; C087449:comK protein, Bacillus subtilis