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Environment-sensing Mechanisms of Gene Expression and their Effects on the Dynamics of Genetic Circuits across Cell Generations

Research output: Book/ReportDoctoral thesisCollection of Articles

Details

Original languageEnglish
PublisherTampere University of Technology
Number of pages65
ISBN (Electronic)978-952-15-3686-1
ISBN (Print)978-952-15-3678-6
Publication statusPublished - 25 Jan 2016
Publication typeG5 Doctoral dissertation (article)

Publication series

NameTampere University of Technology. Publication
PublisherTampere University of Technology
Volume1367
ISSN (Print)1459-2045

Abstract

In genetic circuits, the constituent genes do not interact only between themselves, they are also affected by regulatory molecules of the host cells that support the circuits’ operation and by the environmental conditions. These factors, along with the intrinsic noise in gene expression, affect the functioning of the circuits. As such, to understand the structure of natural circuits and to engineer functional synthetic circuits, one needs to characterize thoroughly how external factors and perturbations from the environment may affect their behavior.

This thesis focused on two cellular mechanisms through which the dynamics of gene expression becomes environment dependent: the intake of gene expression regulatory molecules from the media and the σ factor competition. The first mechanism determines the dynamics by which inducer molecules in the media enter the cell cytoplasm and trigger or repress the expression of the target gene. The second mechanism allows cells to change its gene expression profile to adapt to specific stress conditions.

Following the characterization of the effects of these mechanisms on the expression dynamics of individual genes from live, single cell measurements, we then performed in silico assessments on how these effects at the single gene level propagate to the circuit level. Here, the dynamics of genetic circuits was observed in both non-dividing and dividing cell populations, where errors in the partitioning of molecules in cell division occur and introduce significant variance between sister cells.

From these studies, with the knowledge on the factors of the host cells and their environment sensing mechanisms, more predictive models of the circuits’ dynamics are expected to emerge. The models would further help in identifying what circuit composition, properties of the host strains and environmental conditions are needed for the circuits to exhibit the desired behavior.

Field of science, Statistics Finland

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