Biomaterial Database

Modeling synthetic gene oscillators. 2012

Erin L O'Brien, and Elizabeth Van Itallie, and Matthew R Bennett

Department of Biochemistry & Cell Biology, Rice Univeristy, 6100 Main St., Houston, TX, USA.

Genetic oscillators have long held the fascination of experimental and theoretical synthetic biologists alike. From an experimental standpoint, the creation of synthetic gene oscillators represents a yardstick by which our ability to engineer synthetic gene circuits can be measured. For theorists, synthetic gene oscillators are a playground in which to test mathematical models for the dynamics of gene regulation. Historically, mathematical models of synthetic gene circuits have varied greatly. Often, the differences are determined by the level of biological detail included within each model, or which approximation scheme is used. In this review, we examine, in detail, how mathematical models of synthetic gene oscillators are derived and the biological processes that affect the dynamics of gene regulation.

UI	MeSH Term	Description	Entries
D008957	Models, Genetic	Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.	Genetic Models,Genetic Model,Model, Genetic
D005246	Feedback	A mechanism of communication within a system in that the input signal generates an output response which returns to influence the continued activity or productivity of that system.	Feedbacks
D005786	Gene Expression Regulation	Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.	Gene Action Regulation,Regulation of Gene Expression,Expression Regulation, Gene,Regulation, Gene Action,Regulation, Gene Expression
D005813	Genes, Synthetic	Biologically functional sequences of DNA chemically synthesized in vitro.	Artificial Genes,Synthetic Genes,Artificial Gene,Gene, Artificial,Gene, Synthetic,Genes, Artificial,Synthetic Gene
D001683	Biological Clocks	The physiological mechanisms that govern the rhythmic occurrence of certain biochemical, physiological, and behavioral phenomena.	Biological Oscillators,Oscillators, Endogenous,Pacemakers, Biological,Biologic Clock,Biologic Oscillator,Biological Pacemakers,Clock, Biologic,Clocks, Biological,Oscillator, Biologic,Oscillators, Biological,Pacemaker, Biologic,Pacemakers, Biologic,Biologic Clocks,Biologic Oscillators,Biologic Pacemaker,Biologic Pacemakers,Biological Clock,Biological Oscillator,Biological Pacemaker,Clock, Biological,Clocks, Biologic,Endogenous Oscillator,Endogenous Oscillators,Oscillator, Biological,Oscillator, Endogenous,Oscillators, Biologic,Pacemaker, Biological
D053263	Gene Regulatory Networks	Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.	Gene Circuits,Gene Modules,Gene Networks,Transcriptional Networks,Gene Module,Circuit, Gene,Circuits, Gene,Gene Circuit,Gene Network,Gene Regulatory Network,Module, Gene,Modules, Gene,Network, Gene,Network, Gene Regulatory,Network, Transcriptional,Networks, Gene,Networks, Gene Regulatory,Networks, Transcriptional,Regulatory Network, Gene,Regulatory Networks, Gene,Transcriptional Network

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