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Quantifying Bacterial Evolvability

News: The Barrick lab webpages may be unavailable from December 28 to January 15 as the lab moves to UT Austin.

News: I have accepted an assistant professor position in the Department of Chemistry and Biochemistry at The University of Texas at Austin and will be starting my lab there in January 2011. «Official Announcement»

News: Two undergraduates I mentor win first-place prizes at the 2010 UURAF for their posters! Congratulations to James Dittmar for Mutator Alleles May Still Fix Late in Evolution and Mark Kauth for Evolution of E. coli in Changing Environments.

Presentation: "Re-sequencing hundreds of E. coli genomes: finding non-SNP mutations, analyzing mixed populations, and knowing what you don't know" given at MSU for the GEDD next-gen sequencing seminar series on 2010-03-19. pdf

I am broadly interested in understanding evolution as a creative force.

How does new information about the environment become fixed in genomes over evolutionary time? How do different kinds of mutations affect the ability to further adapt? What limits the speed of adaptation in a given population? What does the organization of information in a genome tell us about its past? Can we map fitness landscapes and chart what evolutionary trajectories are likely to be realized? How are microbial genomes evolving in the wild? Can we harness evolutionary processes to generate organisms or molecules that do useful tasks? Can we anticipate and frustrate the unfortunate evolution of microbial pathogens and cancers? Can we predict what mutations will sabotage the ingenious man-made contraptions of synthetic biology?

Answering these questions requires a systems level knowledge that spans the disciplines of evolutionary biology, microbiology, molecular biology, biochemistry, and computer science. My approach is to use several model systems that allow one to manipulate the evolutionary process and follow the dynamics of evolution in real time: (1) experiments with digital organisms (Avida), (2) in vitro selection and evolution experiments with functional nucleic acids (DNA and RNA), and (3) experiments with bacteria (E. coli). There is an element of chance in evolution, and these systems allow one to compare many replicate experiments to quantitatively understand the diversity of possible outcomes. They also allow perfect control of the environment, so that the influences of various factors on evolutionary paths and the biochemical roles of individual mutations can be unambiguously teased apart.

Currently, I am reconstructing the fine-scale dynamics of mutations within E. coli populations from a 20-year evolution experiment using next-generation DNA sequencing and high-throughput genotyping methods, modeling these dynamics to understand the evolutionary forces at work, and searching for examples where bacteria with lower fitness than other contending lineages in the same population eventually prevail because they have greater evolutionary potential.

I am a postdoctoral fellow in the laboratories of Richard Lenski and Charles Ofria at Michigan State University.

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Topic revision: r41 - 03 Dec 2010 - 13:19:50 - Main.JeffreyBarrick
 
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