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Applying engineering principles to the design and construction of transcriptional devices

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dc.contributor.author Shetty, Reshma P
dc.date.accessioned 2008-05-27T20:53:42Z
dc.date.available 2008-05-27T20:53:42Z
dc.date.issued 2008-05-27T20:53:42Z
dc.identifier.uri http://hdl.handle.net/1721.1/41843
dc.description Ph.D. thesis (user submitted) en
dc.description.abstract The aim of this thesis is to consider how fundamental engineering principles might best be applied to the design and construction of engineered biological systems. I begin by applying these principles to a key application area of synthetic biology: metabolic engineering. Abstraction is used to compile a desired system function, reprogramming bacterial odor, to devices with human-defined function, then to biological parts, and finally to genetic sequences. Standardization is used to make the process of engineering a multi-component system easier. I then focus on devices that implement digital information processing through transcriptional regulation in Escherichia coli. For simplicity, I limit the discussion to a particular type of device, a trancriptional inverter, although much of the work applies to other devices as well. First, I discuss basic issues in transcriptional inverter design. Identification of key metrics for evaluating the quality of a static device behavior allows informed device design that optimizes digital performance. Second, I address the issue of ensuring that transcriptional devices work in combination by presenting a framework for developing standards for functional composition. The framework relies on additional measures of device performance, such as error rate and the operational demand the device places on the cellular chassis, in order to proscribe standard device signal thresholds. Third, I develop an experimental, proof-of-principle implementation of a transcriptional inverter based on a synthetic transcription factor derived from a zinc finger DNA binding domain and a leucine zipper dimerization domain. Zinc fingers and leucine zippers offer a potential scalable solution to the challenge of building libraries of transcription-based logic devices for arbitrary information processing in cells. Finally, I extend the principle of physical composition standards from parts and devices to the vectors that propagate those parts and devices. The new vectors support the assembly of biological systems. Taken together, the work helps to advance the transformation of biological system design from an ad hoc, artisanal craft to a more predictable, engineering discipline. en
dc.language.iso en_US en
dc.subject synthetic biology en
dc.subject biological engineering en
dc.subject transcriptional logic en
dc.subject transcription-based logic en
dc.subject engineered biological systems en
dc.subject PoPS en
dc.subject BioBrick standard biological part en
dc.subject abstraction en
dc.subject standardization en
dc.title Applying engineering principles to the design and construction of transcriptional devices en
dc.type Thesis en


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