Synthesis and verification of designs for chemical production in microbes.
Speaker: Dr. Saurabh Srivastava
Date: 31 January 2013 Time: 15:00-16:00
Location: "Alkiviades C. Payatakes" Seminar Room, FORTH, Heraklion, Crete
Host: Polyvios Pratikakis


In this talk we present a synthesis and verification system for the rational design of enzymatic pathways for microbial chemical production.

Synthetic biologists create novel unnatural organisms by inserting, modifying, or deleting DNA sequences within a host organism. Typically bacteria (Echerichia coli) or yeast (Saccharomyces cerevisiae) are the organisms of choice for transformation because they are well-studied model organisms and their biochemistry is fairly well known. While the experimental procedures exist, the inference and validation of designs is lacking. It is non-trivial or even impossible to do manual exploration of the space of engineering possibilities, or to ensure non-interference of the engineered pathway with the existing metabolic map.

Exploring the space of engineering possibilities is a synthesis problem, and ensuring non-interference is a verification problem. We have designed a synthesis and verification system for predicting novel enzymatic pathways. Given a desired target chemical that we want the organism to secrete, we predict a pathway to engineer, by predicting the genes to insert. We then verify that the inserted genes will not interfere, or will have minimal interference with the organism's native metabolic map.

We have employed the tool to predict wet-lab experiments and the design verification can save weeks to months of wet-lab work.


Saurabh Srivastava is an Assistant Research Engineer with a joint appointment between the Computer Science and Bioengineering departments at UC Berkeley. From 2010-12 he was a Computing Innovations Fellow at UC Berkeley. His current research agenda involves applying program synthesis techniques to aid experimental work in synthetic and systems biology. He finished his PhD in 2010 from University of Maryland, College Park on SMT solver based techniques for program synthesis.

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