CURSO PRECONGRESO GENÓMICA EVOLUTIVA Y COMPARADA

XXIV Congreso Nacional de la Sociedad Mexicana de Bioquímica, A.C.

CURSO PRECONGRESO GENÓMICA EVOLUTIVA Y COMPARADA

PUERTO VALLARTA, JALISCO, 29 octubre – 4 noviembre

BIBLIOGRAFÍA SELECCIONADA

BIBLIOGRAFÍA GENERAL

· Baxevanis AD, Ouellette BFF. 2001. Bioinformatics. A Practical Guide to the Analysis of Genes and Proteins. Wiley-Interscience, 2^nd ed. 432p.

· Brown TA. 2000. Genomes. Wiley-Liss, 1^st ed. 608p.

· Li W-H. 1997. Molecular Evolution. Sinauer Assoc. 432 p.

· Page RDM, Holmes EC. 1998. Molecular Evolution. A Phylogenetic Approach. Blackwell Science Inc. 352.

TEORÍA 1

INTRODUCCIÓN

· Brown TA. 2000. Genomes. 14. Patterns of genome evolution. Wiley-Liss, 1^st ed. 367 – 390 pp.

TEORÍA 2

BIOINFORMÁTICA

· Mark Patterson and Michaela Handel (Editors); Steven Brenner & Fran Lewiter (Guest Editors). 1998. Trends Guide to Bioinformatics. Elsevier Science. 33 pp.

TEORÍA 3

GENÓMICA EVOLUTIVA

· MY Galperin, EV Koonin. 2001. Comparative genome analysis (C15). En: Bioinformatics. A practical guide to the analysis of genes and proteins. AD Baxevanis, BFF Ouellette (eds.) Wiley-Interscience, 2^nd ed. 359 – 390 pp.

TEORÍA 4

GENÓMICA FUNCIONAL (ver referencias en Discusión 4)

CÓMPUTO 1

BASES DE DATOS Y ALINEAMIENTO DE SECUENCIAS

· Minoru Kanehisa. 1998, Databases of biological information. pag 24 a 26 en: Trends Guide to Bioinformatics (Ver referencia completa en Teoría 2 arriba)

· William R. Pearson. 2000. Protein sequence comparison and Protein evolution. Tutorial - ISMB2000. 53 pp

CÓMPUTO 2

ANÁLISIS FILOGENÉTICO

· Barton GJ. 2001. Creation and analysis of protein multiple sequence alignments (C9). En: Bioinformatics. A practical guide to the analysis of genes and proteins. AD Baxevanis, BFF Ouellette (eds.) Wiley-Interscience, 2^nd ed. 215 – 232 pp.

· FSL Brinkman, DD Leipe. 2001. Pylogenetic analysis (C14). En: Bioinformatics. A practical guide to the analysis of genes and proteins. AD Baxevanis, BFF Ouellette (eds.) Wiley-Interscience, 2^nd ed. 332 – 358 pp.

DISCUSIÓN 1

BIOLOGÍA GENÓMICA

Texto básico:

· Brown TA. 2000. Genomes. 14. Patterns of genome evolution. Wiley-Liss, 1^st ed. 367 – 390 pp.

Artículos:

1. Brent R. 2000. Genomic biology. Cell 100:169-183.

2. Gogarten JP, Olendzenski L. 1999. Orthologs, paralogs and genome comparisons. Curr Opin Genet Dev 9:630-636.

3. Koonin EV, Aravind L, Kondrashov AS. 2000. The impact of comparative genomics on our understanding of evolution. Cell 101:573-576.

DISCUSIÓN 2

GENÓMICA ESTRUCTURAL

Texto básico:

· Hogue CWV. 2001. Structure Databases (C5). En: Bioinformatics. A practical guide to the analysis of genes and proteins. AD Baxevanis, BFF Ouellette (eds.) Wiley-Interscience, 2^nd ed. 83 – 110 pp.

Artículos:

1. Chothia C. 1992. Proteins. One thousand families for the molecular biologist. Nature 357:543-544.

2. Denton M, Marshall C. 2001. Protein folds: laws of form revisited. Nature 410:417.

3. Thornton JM, Orengo CA, Todd AE, Pearl FM. 1999. Protein folds, functions and evolution. J Mol Biol 293:333-342.

DISCUSIÓN 3

GENÓMICA EVOLUTIVA

Texto básico:

Artículos:

1. Kyrpides N, Overbeek R, Ouzounis C. 1999. Universal protein families and the functional content of the last universal common ancestor. J Mol Evol 49:413-423.

2. Tekaia F, Lazcano A, Dujon B. 1999. The genomic tree as revealed from whole proteome comparisons. Genome Res 9:550-557.

3. Wolf YI, Rogozin IB, Grishin NV, Koonin EV. 2002. Genome trees and the tree of life. Trends Genet 2002 Sep;18(9):472-479.

DISCUSIÓN 4

GENÓMICA FUNCIONAL

Texto básico:

· David Eisenberg, Edward M. Marcotte, Ioannis Xenarios & Todd O. Yeates. 2000. Protein function in the post-genomic era Nature 405, 823'826

Artículos:

1. Roy A Jensen 2001. Orthologs and paralogs - we need to get it right Genome Biology 2(8):interactions1002.1-1002.3.

2. Martijn Huynen, Berend Snel, Warren Lathe III, and Peer Bork 2000. Predicting Protein Function by Genomic Context: Quantitative Evaluation and Qualitative Inferences. Genome Res 10:1204-1210.

3. Christian von Mering, Roland Krause, Berend Snel, Michael Cornell, Stephen G. Oliver, Stanley Fields & Peer Bork. 2002. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417:399-403.

CONFERENCIA 1

Julio Collado-Vides

· Benitez-Bellon E, Moreno-Hagelsieb G, Collado-Vides J. 2002. Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA. Genome Biol 3:R0013.

· Perez-Rueda E, Collado-Vides J. 2001. Common history at the origin of the position-function correlation in transcriptional regulators in archaea and bacteria. J Mol Evol 53:172-179.

· Moreno-Hagelsieb G, Trevino V, Perez-Rueda E, et al. 2001. Transcription unit conservation in the three domains of life: a perspective from Escherichia coli. Trends Genet 17:175-177.

CONFERENCIA 2

Mario Soberón

· Miranda-Rios J, Navarro M, Soberon M. 2001. A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria. Proc Natl Acad Sci U S A 2001 Aug 14;98(17):9736-41.

Comentario en: Stormo GD, Ji Y. 2001. Proc Natl Acad Sci U S A 2001 Aug 14;98(17):9465-9467.

· Lopez O, Morera C, Miranda-Rios J, et al. 2001. Regulation of gene expression in response to oxygen in Rhizobium etli: role of FnrN in fixNOQP expression and in symbiotic nitrogen fixation. Bacteriol 2001 Dec;183(24):6999-7006.

· Gomez I, Oltean DI, Gill SS, et al. 2000. Mapping the epitope in cadherin-like receptors involved in Bacillus thuringiensis Cry1A toxin interaction using phage display. J Biol Chem 2001 Aug 3;276(31):28906-28912.

CONFERENCIA 3

Enrique Morett

· Chaney M, Grande R, Wigneshweraraj SR, et al. 2001. Binding of transcriptional activators to sigma 54 in the presence of the transition state analog ADP-aluminum fluoride: insights into activator mechanochemical action. Genes Dev 15:2282-2294.

· Juarez K, Flores H, Davila S, et al. 2000. Reciprocal domain evolution within a transactivator in a restricted sequence space. Proc Natl Acad Sci U S A 97:3314-3318.

· Grande RA, Valderrama B, Morett E. 1999. Suppression analysis of positive control mutants of NifA reveals two overlapping promoters for Klebsiella pneumoniae rpoN. J Mol Biol 294:291-298.

CONFERENCIA 4

Jean-Philippe Vielle-Calzada

· Hecht V, Vielle-Calzada JP, Hartog MV, et al. 2001. The Arabidopsis somatic embryogenesis receptor kinase 1 gene is expressed in developing ovules and embryos and enhances embryogenic competence in culture. Plant Physiol 2001 Nov;127(3):803-816.

· Vielle-Calzada JP, Baskar R, Grossniklaus U. 2000. Delayed activation of the paternal genome during seed development. Nature 2000 Mar 2;404(6773):91-94.

· Vielle-Calzada JP, Thomas J, Spillane C, et al. 1999. Maintenance of genomic imprinting at the Arabidopsis medea locus requires zygotic DDM1 activity. Genes Dev 1999 Nov 15;13(22):2971-2982.

CONFERENCIA 5

Linda Kohn

· Cowen LE, Anderson JB, Kohn LM. 2002. Evolution of drug resistance in Candida albicans. Annu Rev Microbiol 2002;56:139-165.

· Cowen LE, Nantel A, Whiteway MS, et al. 2002. Population genomics of drug resistance in Candida albicans. Proc Natl Acad Sci U S A 2002 Jul 9;99(14):9284-9289.

· Carbone I, Kohn LM. 2001. A microbial population-species interface: nested cladistic and coalescent inference with multilocus data. Mol Ecol 2001 Apr;10(4):947-964.

· Cowen LE, Kohn LM, Anderson JB. 2001. Divergence in fitness and evolution of drug resistance in experimental populations of Candida albicans. J Bacteriol 183:2971-2978.

CONFERENCIA 6

Jeremy Glasner

· Perna NT, Plunkett G 3rd, Burland V, et al. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529-533.

Comentario en: Eisen JA. 2001. Nature 409:463,465-456.

· Richmond CS, Glasner JD, Mau R, et al. 1999. Genome-wide expression profiling in Escherichia coli K-12. Nucleic Acids Res 27:3821-3835.

· Blattner FR, Plunkett G 3rd, Bloch CA, et al. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453-74.

CONFERENCIA 7

Valeria Souza

· Sandner L, Eguiarte LE, Navarro A, et al. 2001. The elements of the locus of enterocyte effacement in human and wild mammal isolates of Escherichia coli: evolution by assemblage or disruption? Microbiology 147:3149-3158.

· Peek AS, Souza V, Eguiarte LE, Gaut BS. 2001. The interaction of protein structure, selection, and recombination on the evolution of the type-1 fimbrial major subunit (fimA) from Escherichia coli. J Mol Evol 52:193-204.

· V Souza, LE Eguiarte. 1997. Bacteria gone native vs. bacteria gone awry?: Plasmidic transfer and bacterial evolution. Proc Natl Acad Sci U S A 94:5501-5503.

CONFERENCIA 8

Nikos Kyrpides

· Bhattacharyya A, Stilwagen S, Ivanova N, et al. 2002. Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains. Proc Natl Acad Sci U S A 99:12403-12408.

· Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA. 1999. Protein interaction maps for complete genomes based on gene fusion events. Nature 402:86-90.

· Kyrpides NC, Olsen GJ. 1999. Archaeal and bacterial hyperthermophiles: horizontal gene exchange or common ancestry? Trends Genet 15:298-299.

· Comentario sobre: Aravind L, et al. 1998. Trends Genet 14:442-444.

· Kyrpides N, Overbeek R, Ouzounis C. 1999. Universal protein families and the functional content of the last universal common ancestor. J Mol Evol 49:413-423.

CONFERENCIA 9

Bernard Dujon

· Teixeira M, Dujon B, Fabre E. 2002. Genome-wide nuclear morphology screen identifies novel genes involved in nuclear architecture and gene-silencing in Saccharomyces cerevisiae. J Mol Biol 321:551.

· Fischer G, Neuveglise C, Durrens P, et al. 2001. Evolution of gene order in the genomes of two related yeast species. Genome Res 11:2009-2019.

· Llorente B, Malpertuy A, Neuveglise C, et al. 2000. Genomic exploration of the hemiascomycetous yeasts: 18. Comparative analysis of chromosome maps and synteny with Saccharomyces cerevisiae. FEBS Lett 487:101-112.

· Ricchetti M, Fairhead C, Dujon B. 1999. Mitochondrial DNA repairs double-strand breaks in yeast chromosomes. Nature 402:96-100.

· Tekaia F, Lazcano A, Dujon B. 1999. The genomic tree as revealed from whole proteome comparisons. Genome Res 9:550-557.

CONFERENCIA 10

Michael Gray

· Lin S, Zhang H, Spencer DF, et al. 2002. Widespread and extensive editing of mitochondrial mRNAS in dinoflagellates. J Mol Biol 320:727-739.

· Gray MW, Burger G, Lang BF. The origin and early evolution of mitochondria. Genome Biol 2:R1018.

· Nedelcu AM, Lee RW, Lemieux C, et al. 2000. The complete mitochondrial DNA sequence of Scenedesmus obliquus reflects an intermediate stage in the evolution of the green algal mitochondrial genome. Genome Res 10:819-831.

· Burger G, Zhu Y, Littlejohn TG, et al. 2000. Complete sequence of the mitochondrial genome of Tetrahymena pyriformis and comparison with Paramecium aurelia mitochondrial DNA. J Mol Biol 297:365-380.

· Gray MW, Burger G, Lang BF. 1999. Mitochondrial evolution. Science 283:1476-1481.

CONFERENCIA 11

Diego González-Halphen

· Funes S, Davidson E, Claros MG, et al. 2002. The typically mitochondrial DNA-encoded ATP6 subunit of the F1F0-ATPase is encoded by a nuclear gene in Chlamydomonas reinhardtii. J Biol Chem. 277:6051-6058.

· Perez-Martinez X, Antaramian A, Vazquez-Acevedo M, et al. 2001. Subunit II of cytochrome c oxidase in Chlamydomonad algae is a heterodimer encoded by two independent nuclear genes. J Biol Chem 276:11302-11309.

· Perez-Martinez X, Vazquez-Acevedo M, Tolkunova E, et al. 2000. Unusual location of a mitochondrial gene. Subunit III of cytochrome C oxidase is encoded in the nucleus of Chlamydomonad algae. J Biol Chem 275:30144-30152.