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Experimental and Theoretical Frameworks for Enabling Environmental Synthetic Biology


Marken, John Paul (2023) Experimental and Theoretical Frameworks for Enabling Environmental Synthetic Biology. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/h50w-p058.


Although the field of synthetic biology has made great advances toward becoming a mature engineering discipline over its first quarter-century, the vast majority of these efforts have focused on improving the design and performance of genetic circuits intended to operate in well-controlled, laboratory settings. The goal of safely deploying engineered microbes to reliably perform their programmed functions in natural, uncontrolled environments begets its own set of foundational challenges that will require new frameworks that shift our existing mindsets about the way we engineer biological systems.

These frameworks, because they focus on enabling system properties that were not priorities for conventional synthetic biology research, can constitute a new field of research which I refer to as environmental synthetic biology. The central priorities of environmental synthetic biology include (1) developing and characterizing effective ways to introduce engineered biological systems into natural environments, (2) ensuring that the performance of these systems can remain robust and predictable in the face of environmental variability, (3) developing and characterizing ways to control and monitor the behavior of an engineered system after deployment in an inaccessible environment, and (4) developing fundamental architectures to enable autonomous system operation and adaptation within environmental contexts.

In this thesis, I present the initial steps towards the development of three frame- works that address these priorities of environmental synthetic biology. The first framework, described in Chapter 2, demonstrates the potential of using DNA as the substrate for addressable and adaptable intercellular communication in engineered populations. This enables the ability to one day create multicellular systems that can autonomously reconfigure their own architecture in the face of changing environmental conditions. The second framework, described in Chapters 3 and 4, presents a new mathematical representation of biomolecular reaction systems that enables geometric bounds on the space of possible behaviors under all possible configurations for a particular system architecture. The third, ongoing framework emphasizes the importance of explicitly incorporating the physiological state of the host cell into the assessment of a genetic circuit’s behavior by exploring the impact of cellular growth arrest on transcriptional response curves. The preliminary results of this work are presented in Chapter 5.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Synthetic Biology, Systems Biology
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Bioengineering
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Murray, Richard M.
Thesis Committee:
  • Elowitz, Michael B. (chair)
  • Hay, Bruce A.
  • Newman, Dianne K.
  • Murray, Richard M.
Defense Date:9 May 2023
Funding AgencyGrant Number
NSF Graduate Research FellowshipDGE-1745301
Army Research Office (ARO)W911NF-09-D-0001
Army Research Office (ARO)W911NF-19-2-0026
Record Number:CaltechTHESIS:05292023-181810775
Persistent URL:
Related URLs:
URLURL TypeDescription adapted for Ch. 2 adapted for Ch. 4
Marken, John Paul0000-0001-9696-088X
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:15225
Deposited By: John Marken
Deposited On:09 Jun 2023 15:04
Last Modified:20 Jun 2023 18:48

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