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The Development of RNA-based Control Systems to Regulate Signaling and Dictate Cell Fate in a Model MAPK Pathway

Citation

Galloway, Kate Elizabeth (2012) The Development of RNA-based Control Systems to Regulate Signaling and Dictate Cell Fate in a Model MAPK Pathway. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/CBBN-GX03. https://resolver.caltech.edu/CaltechTHESIS:06072012-150636005

Abstract

Cells integrate extracellular information via native signaling pathways to spatially and temporally coordinate complex tasks such as development and the immune response. Cellular programming holds the potential of harnessing the sophisticated and complex biological processes of living cells for diverse applications. In the last decade, cellular reprogramming has emerged as a viable therapeutic strategy. In large, reprogramming strategies have relied on statically programmed levels of gene expression to alter cellular behaviors. To construct more sophisticated programs requires dynamic control of expression and strategies for the facile construction of complex control architectures. Additionally, the application of synthetic programs to the control of native regulatory pathways requires the development of tools for interfacing with these pathways, as well as the construction of stringent controllers. Further, control systems composed of modular and tunable elements will facilitate the expansion of synthetic circuitry to a wide array of natural networks with varying system properties.

Here we describe the development of RNA-based control systems to regulate signaling and dictate cell fate in a model mitogen-activated protein kinase (MAPK) pathway. We construct networks of RNA-based control systems that interface with the Saccharomyces cerevisiae mating pathway to dictate entry into one of three programmed alternative fates dependent on environmental stimuli. We present a readily translatable method for identifying control points within natural networks that enable the construction of a modular interface between synthetic circuitry and native networks. In building these networks, we demonstrate the rational tuning of circuit performance via the exchange of well-defined parts to compose networks capable of actuating changes in cellular behavior in response to environmental cues. Further, we construct network architectures which facilitate reduced interference from simultaneously integrated opposing programs and identified sensitive parameters for engineering robust circuit performance. Finally, we present the development of a novel RNA-based control element for the regulation of both synthetic and endogenous transcripts. This work provides a model for engineering systems that regulate signaling and direct cell fate which may be applied to additional decision-making pathways to advance tissue engineering strategies, treat diseases, and study the behavior of natural regulatory networks.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Network, topology, synthetic biology, systems biology, control systems, fate, MAPK, RNA-based controllers, RNA
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemical Engineering
Minor Option:Biology
Awards:Everhart Distinguished Graduate Student Lecture Series, 2011
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Smolke, Christina D.
Thesis Committee:
  • Tirrell, David A. (chair)
  • Murray, Richard M.
  • Elowitz, Michael B.
  • Smolke, Christina D.
Defense Date:18 May 2012
Non-Caltech Author Email:katie.galloway (AT) gmail.com
Funders:
Funding AgencyGrant Number
National Institutes of HealthR01GM086663
Record Number:CaltechTHESIS:06072012-150636005
Persistent URL:https://resolver.caltech.edu/CaltechTHESIS:06072012-150636005
DOI:10.7907/CBBN-GX03
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:7146
Collection:CaltechTHESIS
Deposited By: Kate Galloway
Deposited On:01 Oct 2014 18:09
Last Modified:03 Oct 2019 23:56

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