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Title:Modeling heterogeneity in the microbial world
Author(s):Cole, Jr., John Andrew
Director of Research:Luthey-Schulten, Zaida
Doctoral Committee Chair(s):Goldenfeld, Nigel
Doctoral Committee Member(s):Chemla, Yann; Kuehn, Seppe
Department / Program:Physics
Discipline:Physics
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):Stochastic gene expression, metabolism
Abstract:No two living cells are identical. Like tiny, squishy snowflakes, even seemingly identical cells (belonging to isogenic populations, and living under macroscopically similar conditions), will experience variations in their local microenvironments and in the numbers of gene copies, messenger RNAs, proteins, and other macromolecules that constitute their make up, and importantly, dictate their behavior. In this thesis I will employ the methods of systems biology, stochastic simulation, and mathematical analysis to investigate some of the causes and outcomes of this type of biological variability in the microbial world. This document is divided into four main chapters. The first focuses on how the stochastic expression of metabolic enzymes affects the growth and metabolic pathway usage of individual Escherichia coli cells. The second chapter deals with how E. coli cells in colonies diverge behaviorally as a function of their location, and how they naturally tend to cooperate in a previously unknown form of crossfeeding. Finally, the third and fourth chapters deal with details of how gene expression stochasticity itself arises, with an eye toward the effects that DNA replication have on mRNA and protein statistics (and what that means for interpreting single molecule experiments).
Issue Date:2017-10-10
Type:Text
URI:http://hdl.handle.net/2142/99301
Rights Information:Copyright 2017 John A. Cole Jr.
Date Available in IDEALS:2018-03-13
Date Deposited:2017-12


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