Faculty

Barrick, Jeffrey
Assistant Professor, Dept. of Chemistry and Biochemistry

E-mail

Website

Main Office: MBB 1.436BA
Phone: 471-3247

Alternate Office: MBB 1.436
Phone: 471-5568

Mailing Address:
Institute for Cellular and Molecular Biology
The University of Texas at Austin
1 University Station
Austin, TX 78712

Graduate Student

• Hammerling, Michael - Graduate Student
• Meyer, Austin - Graduate Student
• Renda, Brian - Graduate Student
• Wolf, Lindsey - Graduate Student

Staff

• Barnhart, Craig - Staff



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Research Summary:

My laboratory uses experiments with populations of microorganisms, nucleic acids, and digital organisms to study evolution in action with the ultimate goal of harnessing evolution as a creative force for synthetic biology. To ask how different types of mutations impact evolutionary potential, we are using deep sequencing to monitor the competitive dynamics of spontaneous beneficial mutations in these populations and also engineering specific genomic changes. Molecular biology and biochemistry approaches are used to link the cell physiological effects of mutations to how they affect competitive fitness at the organism level, and bioinformatics and comparative genomics are used to investigate whether similar mutational pathways are important in nature. Other research interests include investigating the functions of cryptic genomic elements and using mark-recapture techniques on microbial genomes to watch them as they evolve in complex wild and pathogenic populations.


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Publications:

2011	Jerome, J.P., Bell, J.A., Plovanich-Jones, A.E., Barrick, J.E., Brown, C.T., Mansfield, L.S., Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a noval host, PLoS ONE 6:316-399.
2011	Woods, R.J., Barrick, J.E., Cooper, T.F, Shrestha, U., Kauth, M.R., Lenski, R.E., Second-order selection for evovability in a large Escherichia coli population., Science 331:1433-1436.
2010	Barrick, J.E., Kauth, M.R., Strelioff, C.C., and Lenski, R.E., Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects., Mol. Biol. Evol. 27:1338-1347.
2009	Barrick, J.E. and Lenski, R.E., Genome-wide mutational diversity in an evolving population of Escherichia coli., Cold Spring Harbor Symp. Quant. Biol. 74:119-129.
2009	Barrick, J.E., Yu, D.S., Yoon, S.H., Jeong, H, Oh, T.K., Schneider, D., Lenski, R.E., and Kim, J.F., Genome evoluation and adaptation in a long-term experiment with Escherichia coli., Nature 461:1243-1247.
2008	Weinberg, Z., Regulski, E.E., Hammond, M.C., Barrick, J.E., Yao, Z., Ruzzo, W.L., and Breaker, R.R., The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches., RNA 14:822-828.
2008	Regulski, E.E., Moy, R.H., Weinberg, Z., Barrick, J.E., Yao, Z., Ruzzo, W.L., and Breaker, R.R., A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism., Mol. Microbiol. 68:918-932.
2007	Barrick, J.E., and Breaker, R.R., The Power of Riboswitches, Scientific American 296 (1):50-57.
2007	Roth, A., Winkler, W.C., Regulski, E.E., Lee, B.W., Lim, J., Jona, I., Barrick, J.E., Ritwik, A., Kim, J.N., Welz, R., Iwata-Reuyl, D., Breaker, R.R., A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain., Nat. Struct. Mol. Biol. 14 (4):308-317.
2007	Yao, Z., Barrick, J.E., Weinberg, Z., Neph, S., Breaker, R.R., Tompa M., Ruzzo, W.L., A computational pipeline for high-throughput discovery of cis-regulatory noncoding RNA in prokaryotes., PLOS Comput. Biol. 3:e126.
2007	Weinberg, Z., Barrick, J.E., Yao, Z., Roth, A., Kim, J.N., Gore, J., Wang, J.X., Lee, E.R., Block, K.F., Sudarsan, N, Neph, S., Tompa, M., Ruzzo, W.L., Breaker, R.R., Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline., Nucleic Acids Res. 35:4809-4819.
2007	Barrick, J.E. and Breaker R.R., The structures, distributions, and mechanisms of metabolite-binding riboswitches., Genome Biology 8:R239.
2006	Sudarsan,N., Hammond, M.C., Block, K.F., Welz, R., Barrick, J.E., Roth, A., Breaker, R.R., Tandem riboswitch architectures exhibit complex gene control functions., Science 314:300-304.
2006	Puerta-Fernandez, E., Barrick, J.E., Roth, A., and Breaker, R.R., Identification of a new, non-coding RNA in extremophilic eubacteria, Proc. Natl. Acad. Sci U.S.A. 103:19490-19495.
2006	Lenski, R.E., Barrick, J.E., and Ofria, C., Balancing Robustness and Evolvability, PLoS Biology 4:e428.
2005	Barrick, J.E., Sudarsan, N., Weinberg, Z., Ruzzo, W.L., and Breaker, R.R., 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promotor., RNA 11:774-784.
2005	Corbino, K.A., Barrick, J.E., Lim, J., Welz, R., Tucker, B.J., Puskarz, I., Mandel, M., Rudnick, N.D., and Breaker, R.R., Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria., Genome Biol. 6:R70.
2004	Nahvi, A., Barrick, J.E., and Breaker, R.R., Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes., Nucleic Acids Res. 32:143-150.
2004	Barrick, J.E., Corbino, K.A., Winkler, W.C., Nahvi, A., Mandal, M., Collins, J., Lee, M., Roth, A., Sudarsan, N., Jona, I., Wickiser, J.K., and Breaker, R.R., New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control., Proc. Natl. Acad. Sci. U.S.A. 101:6421-6426.
2004	Mandel, M., Lee, M., Barrick, J.E., Weinberg, Z., Emilsson, G.M. Ruzzo, W.L., and Breaker, R.R., A glycine-dependent riboswitch that uses cooperative binding to control gene expression., Science 306:275-279.
2003	Barrick, J.E., and Roberts, R.W., Achieving specificity in selected and wild-type N peptide-RNA complexes: The importance of discrimination against noncognate RNA targets., Biochemistry 42:12998-13007.
2003	Winkler, W.C., Nahvi, A., Sudarsan, N., Barrick, J.E., and Breaker, R.R., An mRNA structure that controls gene expression by binding S-adenosylmethionine., Nat. Struct. Biol. 10:701-707.
2003	Sudarsan, N., Barrick, J.E., and Breaker, R.R., Metabolite-binding RNA domains are present in the genes of eukaryotes., RNA 9:644-647.
2003	Mandal, M., Boese, B., Barrick, J.E., Winkler, W.C., and Breaker, R.R., Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria., Cell 113:577-586.
2002	Barrick, J.E., and Roberts, R.W., Sequence analysis of an artificial family of RNA-binding peptides., Protein Sci. 11:2688-2696.
2001	Barrick, J.E., Takahashi, T.T., Balakin, A., and Roberts, R.W., Selection of RNA-binding peptides using mRNA-peptide fusions., Methods 23:287-293.
2001	Barrick, J.E., Takahashi, T.T., Ren, J.S., Xia, T.B., and Roberts, R.W., Large libraries reveal diverse solutions to an RNA recognition problem., Proc. Natl. Acad. Sci. U.S.A. 98:12374-12378.
2000	Liu, R.H., Barrick, J.E., Szostak, J.W. and Roberts, R.W., Optimized synthesis of RNA-protein fusions for in vitro protein selection., Methods Enzymol. 318:268-293.