Microbial Evolution (PMB 290)

Plant and Microbial Biology 290
Seminar in Microbial Genomics
Spring 2004
Course Control Number: 71445

Meeting Time: Wednesday, 4-5 pm, 107 Mulford

Contact Information

John Taylor
        jtaylor@nature.berkeley.edu
        321 Koshland Hall
        510-642-5366

Week	Date	Person	Topic/Papers
1	21-Jan	Organizational Meeting
2	28-Jan	John Taylor	Gibson.PLoS.2003. DeRisi.Science.1997. Ideker.Science.2001.
3	4-Feb	Shannon Peters	Tunlid.CurOpMicro.2002. Liu.PlantCell.2003.
4	11-Feb	Tom Sharpton	Zimmer.PNAS.2000. Chang.MolMicrobiol.2002.
5	18-Feb	Gyaneshwar Prasad	Transcriptome changes of Escherichia coli during nitrogen and sulfur limited slow growth
6	25-Feb	Sarah Archer-Evans	Bozdech.PLoS.2003. Le Roche. Science.2003.
7	3-Mar	Lee Chae	Eisen. PNAS.1998. Townsend.GenomeBiology.2002.
8	10-Mar	Jeff Townsend
9	17-Mar	Scott Blich
break	24-Mar	Spring Break and Neurospora Conference
10	31-Mar	Sarah Brown
11	7-Apr	Eugenia Ramos	Read.Nature.2003. Wolfgang.PNAS.2003. Salama.PNAS.2000.
12	14-Apr	Bill Feil
13	21-Apr	European Fungal Genetics Conference
14	28-Apr	Betty Gilbert	Papers for Takao Kasuga's presentation
15	5-May	Takao Kasuga

Selected References - Genomics Seminar Endnote Library 2004

Introduction

Derisi, J. L., V. R. Iyer, and P. O. Brown. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680-686.
Gibson, G. 2003. Microarray analysis: Genome-scale hypothesis scanning. PLoS 1:28-29
Ideker, T., V. Thorsson, J. A. Ranish, R. Christmas, J. Buhler, J. K. Eng, R. Bumgarner, D. R. Goodlett, R. Aebersold, and L. Hood. 2001. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292:929-934.
Khodursky, A. B., B. J. Peter, N. R. Cozzarelli, D. Botstein, P. O. Brown, and C. Yanofsky. 2000. DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 97:12170-12175.

Analysis

Alter, O., P. O. Brown, and D. Botstein. 2003. Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proceedings of the National Academy of Sciences of the United States of America 100:3351-3356.
Eisen, M. B., P. T. Spellman, P. O. Brown, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of the United States of America 95:14863-14868.
Grosu, P., J. P. Townsend, D. L. Hartl, and D. Cavalieri. 2002. Pathway processor: A tool for integrating whole-genome expression results into metabolic networks. Genome Research 12:1121-1126.
Townsend, J. P., and D. L. Hartl. 2002. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genomebiology 3:research0071.1-0071.16.
Troyanskaya, O. G., M. E. Garber, P. O. Brown, D. Botstein, and R. B. Altman. 2002. Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics 18:1454-1461.

Bacteria

Chang, D. E., D. J. Smalley, and T. Conway. 2002. Gene expression profiling of Escherichia coli growth transitions: an expanded stringent response model. Molecular Microbiology 45:289-306.
Conway, T., and G. K. Schoolnik. 2003. Microarray expression profiling: capturing a genome-wide portrait of the transcriptome. Molecular Microbiology 47:879-889.
Cooper, T., D. Rozen, and R. Lenski. 2003. Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. PNAS (USA) 100:1072-1077.
Corbin, R. W., O. Paliy, F. Yang, J. Shabanowitz, M. Platt, C. E. Lyons, K. Root, J. McAuliffe, M. I. Jordan, S. Kustu, E. Soupene, and D. F. Hunt. 2003. Toward a protein profile of Escherichia coli: Comparison to its transcription profile. Proceedings of the National Academy of Sciences of the United States of America 100:9232-9237.
Karlyshev, A. V., P. C. F. Oyston, K. Williams, G. C. Clark, R. W. Titball, E. A. Winzeler, and B. W. Wren. 2001. Application of high-density array-based signature-tagged mutagenesis to discover novel Yersinia virulence-associated genes. Infection & Immunity 69:7810-7819.
Khodursky, A. B., B. J. Peter, N. R. Cozzarelli, D. Botstein, P. O. Brown, and C. Yanofsky. 2000. DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 97:12170-12175.
Read, T. D., S. N. Peterson, N. Tourasse, L. W. Baillie, I. T. Paulsen, K. E. Nelson, H. Tettelin, D. E. Fouts, J. A. Eisen, S. R. Gill, E. K. Holtzapple, O. A. Okstad, E. Helgason, J. Rilstone, M. Wu, J. F. Kolonay, M. J. Beanan, R. J. Dodson, L. M. Brinkac, M. Gwinn, R. T. DeBoy, R. Madpu, S. C. Daugherty, A. S. Durkin, D. H. Haft, and et al. 2003. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423:81-86.
Salama, N., K. Guillemin, T. K. McDaniel, G. Sherlock, L. Tompkins, and S. Falkow. 2000. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proceedings of the National Academy of Sciences of the United States of America 97:14668-14673.
Soupene, E., W. C. van Heeswijk, J. Plumbridge, V. Stewart, D. Bertenthal, H. Lee, G. Prasad, O. Paliy, P. Charernnoppakul, and S. Kustu. 2003. Physiological studies of Escherichia coli strain MG1655: Growth defects and apparent cross-regulation of gene expression. Journal of Bacteriology 185:5611-5626.
Wendisch, V. F., D. P. Zimmer, A. Khodursky, B. Peter, N. Cozzarelli, and S. Kustu. 2001. Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays. Analytical Biochemistry 290:205-213.
Zimmer, D. P., E. Soupene, H. L. Lee, V. F. Wendisch, A. B. Khodursky, B. J. Peter, R. A. Bender, and S. Kustu. 2000. Nitrogen regulatory protein C-controlled genes of Escherichia coli: Scavenging as a defense against nitrogen limitation. Proceedings of the National Academy of Sciences of the United States of America 97:14674-14679.

Comparative genomics

Cliften, P., P. Sudarsanam, A. Desikan, L. Fulton, B. Fulton, J. Majors, R. Waterston, B. A. Cohen, and M. Johnston. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301:71-76.
Kellis, M., N. Patterson, M. Endrizzi, B. Birren, and E. S. Lander. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254.
Oshiro, G., L. M. Wodicka, M. P. Washburn, J. R. Yates, D. J. Lockhart, and E. A. Winzeler. 2002. Parallel identification of new genes in Saccharomyces cerevisiae. Genome Research 12:1210-1220.
Read, T. D., S. N. Peterson, N. Tourasse, L. W. Baillie, I. T. Paulsen, K. E. Nelson, H. Tettelin, D. E. Fouts, J. A. Eisen, S. R. Gill, E. K. Holtzapple, O. A. Okstad, E. Helgason, J. Rilstone, M. Wu, J. F. Kolonay, M. J. Beanan, R. J. Dodson, L. M. Brinkac, M. Gwinn, R. T. DeBoy, R. Madpu, S. C. Daugherty, A. S. Durkin, D. H. Haft, and et al. 2003. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423:81-86.
Wolfgang, M. C., B. R. Kulasekara, X. Y. Liang, D. Boyd, K. Wu, Q. Yang, C. G. Miyada, and S. Lory. 2003. Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America 100:8484-8489.

Natural variation

Backhus, L. E., J. DeRisi, P. O. Brown, and L. F. Bisson. 2003. Functional genomic analysis of a commercial wine strain of Saccharomyces cerevisiae under different nitrogen conditions (vol 1, pg 111, 2001). FEMS Yeast Research 4:123.
Cavalieri, D., J. P. Townsend, and D. L. Hartl. 2000. Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proceedings of the National Academy of Sciences of the United States of America 97:12369-12374.
Salama, N., K. Guillemin, T. K. McDaniel, G. Sherlock, L. Tompkins, and S. Falkow. 2000. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proceedings of the National Academy of Sciences of the United States of America 97:14668-14673.
Townsend, J. P., D. Cavalieri, and D. L. Hartl. 2003. Population genetic variation in genome-wide gene expression. Molecular Biology & Evolution 20:955-963.
Winzeler, E. A., C. I. Castillo-Davis, G. Oshiro, D. Liang, D. R. Richards, Y. Y. Zhou, and D. L. Hartl. 2003. Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays. Genetics 163:79-89.
Winzeler, E. A., D. R. Richards, A. R. Conway, A. L. Goldstein, S. Kalman, M. J. McCullough, J. H. McCusker, D. A. Stevens, L. Wodicka, D. J. Lockhart, and R. W. Davis. 1998. Direct allelic variation scanning of the yeast genome. Science 281:1194-1197.

Fungi other than yeast

Cowen, L. E., L. M. Kohn, and J. B. Anderson. 2001. Divergence in fitness and evolution of drug resistance in experimental populations of Candida albicans. Journal of Bacteriology 183:2971-2978.
Liu, J., Blaylock, L.A., Endre, G., Cho, J., Town, C.D., VandenBosch, K.A., Harrision, M.J. 2003. Transcript Profiling Coupled with Spatial Expression Analyses Reveals Genes Involved in Distinct Developmental Stages of an Arbuscular Mycorrhizal Symbiosis. Plant Cell 15:2106-2123.
Tunlid, A., and N. J. Talbot. 2002. Genomics of parasitic and symbiotic fungi. Current Opinion in Microbiology 5:513-519.
Tzung, K. W., R. M. Williams, S. Scherer, N. Federspiel, T. Jones, N. Hansen, V. Bivolarevic, L. Huizar, C. Komp, R. Surzycki, R. Tamse, R. W. Davis, and N. Agabian. 2001. Genomic evidence for a complete sexual cycle in Candida albicans. Proceedings of the National Academy of Sciences of the United States of America 98:3249-3253.

Pioneering methods

Lashkari, D. A., J. L. Derisi, J. H. McCusker, A. F. Namath, C. Gentile, S. Y. Hwang, P. O. Brown, and R. W. Davis. 1997. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proceedings of the National Academy of Sciences of the United States of America 94:13057-13062.
Lockhart, D. J., and E. A. Winzeler. 2000. Genomics, gene expression and DNA arrays. Nature 405:827-836.
Velculescu, V. E., L. Zhang, W. Zhou, J. Vogelstein, M. A. Basrai, D. E. Bassett, P. Hieter, B. Vogelstein, and K. W. Kinzler. 1997. Characterization of the yeast transcriptome. Cell 88:243-251.
Winzeler, E. A., and R. W. Davis. 1997. Functional analysis of the yeast genome. Current Opinion in Genetics & Development 7:771-776.
Winzeler, E. A., B. Lee, J. H. McCusker, and R. W. Davis. 1999a. Whole genome genetic-typing in yeast using high-density oligonucleotide arrays. Parasitology 118:S73-S80.

Proteomics

Corbin, R. W., O. Paliy, F. Yang, J. Shabanowitz, M. Platt, C. E. Lyons, K. Root, J. McAuliffe, M. I. Jordan, S. Kustu, E. Soupene, and D. F. Hunt. 2003. Toward a protein profile of Escherichia coli: Comparison to its transcription profile. Proceedings of the National Academy of Sciences of the United States of America 100:9232-9237.
Gygi, S. P., Y. Rochon, B. R. Franza, and R. Aebersold. 1999. Correlation between protein and mRNA abundance in yeast. Molecular & Cellular Biology 19:1720-1730.
Ideker, T., V. Thorsson, J. A. Ranish, R. Christmas, J. Buhler, J. K. Eng, R. Bumgarner, D. R. Goodlett, R. Aebersold, and L. Hood. 2001. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292:929-934.
Khodursky, A. B., B. J. Peter, N. R. Cozzarelli, D. Botstein, P. O. Brown, and C. Yanofsky. 2000. DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 97:12170-12175.

Protists

Bozdech, Z., M. Llinas, B. L. Pulliam, E. D. Wong, J. Zhu, and J. L. DeRisi. 2003. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS 1:85-100.
Le Roch, K. G., Y. Y. Zhou, P. L. Blair, M. Grainger, J. K. Moch, J. D. Haynes, P. De la Vega, A. A. Holder, S. Batalov, D. J. Carucci, and E. A. Winzeler. 2003. Discovery of gene function by expression profiling of the malaria parasite life cycle. Science 301:1503-1508.

Yeast

Arava, Y., Y. L. Wang, J. D. Storey, C. L. Liu, P. O. Brown, and D. Herschlag. 2003. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America 100:3889-3894.
Birrell, G. W., J. A. Brown, H. I. Wu, G. Giaever, A. M. Chu, R. W. Davis, and J. M. Brown. 2002. Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents. Proceedings of the National Academy of Sciences of the United States of America 99:8778-8783.
Birrell, G. W., G. Giaever, A. M. Chu, R. W. Davis, and J. M. Brown. 2001. A genome-wide screen in Saccharomyces cerevisiae for genes affecting UV radiation sensitivity. Proceedings of the National Academy of Sciences of the United States of America 98:12608-12613.
Brem, R. B., G. Yvert, R. Clinton, and L. Kruglyak. 2002. Genetic dissection of transcriptional regulation in budding yeast. Science 296:752-755.
Cho, R. J., M. J. Campbell, E. A. Winzeler, L. Steinmetz, A. Conway, L. Wodicka, T. G. Wolfsberg, A. E. Gabrielian, D. Landsman, D. J. Lockhart, and R. W. Davis. 1998. A genome-wide transcriptional analysis of the mitotic cell cycle. Molecular Cell 2:65-73.
Chu, S., J. Derisi, M. Eisen, J. Mulholland, D. Botstein, P. O. Brown, and I. Herskowitz. 1998. The transcriptional program of sporulation in budding yeast. Science 282:699-705.
Deutschbauer, A. M., R. M. Williams, A. M. Chu, and R. W. Davis. 2002. Parallel phenotypic analysis of sporulation and postgermination growth in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America 99:15530-15535.
Dunham, M. J., H. Badrane, T. Ferea, J. Adams, P. O. Brown, F. Rosenzweig, and D. Botstein. 2002. Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America 99:16144-16149.
Ferea, T. L., D. Botstein, P. O. Brown, and R. F. Rosenzweig. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proceedings of the National Academy of Sciences of the United States of America 96:9721-9726.
Gasch, A. P., P. T. Spellman, C. M. Kao, O. Carmel-Harel, M. B. Eisen, G. Storz, D. Botstein, and P. O. Brown. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Molecular Biology of the Cell 11:4241-4257.
Gerton, J. L., J. DeRisi, R. Shroff, M. Lichten, P. O. Brown, and T. D. Petes. 2000. Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America 97:11383-11390.
Giaever, G., A. M. Chu, L. Ni, C. Connelly, L. Riles, S. Veronneau, S. Dow, A. Lucau-Danila, K. Anderson, B. Andre, A. P. Arkin, A. Astromoff, M. El Bakkoury, R. Bangham, R. Benito, S. Brachat, S. Campanaro, M. Curtiss, K. Davis, A. Deutschbauer, K. D. Entian, P. Flaherty, F. Foury, D. J. Garfinkel, M. Gerstein, R. W. Davis, and et al. 2002. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387-391.
Gu, Z. L., L. M. Steinmetz, X. Gu, C. Scharfe, R. W. Davis, and W. H. Li. 2003. Role of duplicate genes in genetic robustness against null mutations. Nature 421:63-66.
Kuhn, K. M., J. L. DeRisi, P. O. Brown, and P. Sarnow. 2001. Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Molecular & Cellular Biology 21:916-927.
Nautiyal, S., J. L. DeRisi, and E. H. Blackburn. 2002. The genome-wide expression response to telomerase deletion in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America 99:9316-9321.
Primig, M., R. M. Williams, E. A. Winzeler, G. G. Tevzadze, A. R. Conway, S. Y. Hwang, R. W. Davis, and R. E. Esposito. 2000. The core meiotic transcriptome in budding yeasts. Nature Genetics 26:415-423.
Raghuraman, M. K., E. A. Winzeler, D. Collingwood, S. Hunt, L. Wodicka, A. Conway, D. J. Lockhart, R. W. Davis, B. J. Brewer, and W. L. Fangman. 2001. Replication dynamics of the yeast genome. Science 294:115-121.
Spellman, P. T., G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein, and B. Futcher. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9:3273-3297.
Steinmetz, L. M., H. Sinha, D. R. Richards, J. I. Spiegelman, P. J. Oefner, J. H. McCusker, and R. W. Davis. 2002. Dissecting the architecture of a quantitative trait locus in yeast. Nature 416:326-330.
Tani, T. H., A. Khodursky, R. M. Blumenthal, P. O. Brown, and R. G. Matthews. 2002. Adaptation to famine: A family of stationary-phase genes revealed by microarray analysis. Proceedings of the National Academy of Sciences of the United States of America 99:13471-13476.
ter Linde, J. J. M., H. Liang, R. W. Davis, H. Y. Steensma, J. P. van Dijken, and J. T. Pronk. 1999. Genome-wide transcriptional analysis of aerobic and anaerobic chemostat cultures of Saccharomyces cerevisiae. Journal of Bacteriology 181:7409-7413.
Winzeler, E. A., D. D. Shoemaker, A. Astromoff, H. Liang, K. Anderson, B. Andre, R. Bangham, R. Benito, J. D. Boeke, H. Bussey, A. M. Chu, C. Connelly, K. Davis, F. Dietrich, S. W. Dow, E. L. B. M, F. Foury, S. H. Friend, E. Gentalen, G. Giaever, J. H. Hegemann, T. Jones, M. Laub, H. Liao, N. Liebundguth, R. W. Davis, and et al. 1999b. Functional characterization of the S-cerevisiae genome by gene deletion and parallel analysis. Science 285:901-906.

Virus

Wang, D., L. Coscoy, M. Zylberberg, P. C. Avila, H. A. Boushey, D. Ganem, and J. L. DeRisi. 2002. Microarray-based detection and genotyping of viral pathogens. Proceedings of the National Academy of Sciences of the United States of America 99:15687-15692.

Plant and Microbial Biology 290 Seminar in Microbial Genomics Spring 2004 Course Control Number: 71445

Meeting Time: Wednesday, 4-5 pm, 107 Mulford

Plant and Microbial Biology 290
Seminar in Microbial Genomics
Spring 2004
Course Control Number: 71445