Comparative Microbial Genomics: A Bioinformatics Approach

Autumn 2002

Course Syllabus

The classes will be held on Wednesday mornings, from 8:00 - 12:00 in building 208, room 007. The first lecture will be on Wednesday, 4 September, 2002. The course will end on Wednesday, 4 December, 2002. Please note that the project reports are due on Wednesday, 4 December, 2002. For those who would like a brief overview of basic molecular biology/genetics, have a look at my lecture notes for an Introductory Genetics course. For a background in Bioinformatics, see the lecture notes for the CBS Introduction to Bioinformatics" course. Date Topic # of Bacterial Genomes September 4 Introduction and Taxonomy of Microbial Genomes 97 September 11 DNA Atlases for Visualisation of Genomic Positional Information 100 September 18 Localisation of DNA Structures within chromosomes 101 September 25 Global Prediction of Chromatin Binding Sites 103 October 2 Comparison of 15 sequenced yeast genomes 105 October 9 Genomic Transcriptional Analysis 109 AUTUMN BREAK October 23 Annotation of Microbial Genomes 112 October 30 Microbial Proteome Comparisons 114 November 6 Prediction of Chromosomal Replication Origins 115 November 13 Projects Begin 119 December 4 Final Reports Due 126 Link to feedback page Wednesday, 4 September, 2002 Bacterial Taxonomy and Introduction to Sequenced Microbial Genomes. Lecture 1 - Comparative Microbial Genomics - Introductory Lecture - 10 minutes break for coffee Lecture 2 - Introduction to Bacterial Taxonomy (given by Professor Stephen On, from the Danish Veterinary Institute) - 10 minutes break Computer Excercises - What Has Been Sequenced? Archaeal Genomes Bacterial Genomes - 10 minutes break for MORE coffee, tea, or whatever. Journal Club - What Is Still Out there? "Estimating prokaryotic diversity and its limits", Thomas P. Curtis, William T. Sloan, and Jack W. Scannell, Proc. Natl. Acad. Sci. USA, Vol. 99, Issue 16, 10494-10499, August 6, 2002 Also see the commentary on this article: "How many species of prokaryotes are there?", Bess B. Ward, Proc. Natl. Acad. Sci. USA, Vol. 99, Issue 16, 10234-10236, August 6, 2002 Wednesday, 11 September, 2002 DNA Atlases to Visualise Whole Genome Information. Lecture 1 - Introduction to DNA Atlases Link to PowerPoint file    Link to PDF file of E.coli Structure Atlas paper Lecture 2 - DNA Genome Atlases Link to PDF file of "Three Views" paper describing the BaseAtlas, StructureAtlas, RepeatAtlas and GenomeAtlas      Link to web page with background information on DNA Structure Atlas parameters Journal Club - Comparative Genomics of Streptococcus agalactiae. "Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae", Hervé Tettelin, Vega Masignani, Michael J.Cieslewicz, Jonathan A. Eisen, Scott Peterson, Michael R. Wessels, Ian T. Paulsen, Karen E. Nelson, Immaculada Margarit, Timothy D. Read, Lawrence C. Madoff, Alex M. Wolf, Maureen J. Beanan, Lauren M. Brinkac, Sean C. Daugherty, Robert T. DeBoy, A. Scott Durkin, James F. Kolonay , Ramana Madupu , Matthew R. Lewis, Diana Radune, Nadezhda B. Fedorova, David Scanlan, Hoda Khouri, Stephanie Mulligan, Heather A. Carty, Robin T. Cline, Susan E. Van Aken, John Gill, Maria Scarselli, Marirosa Mora, Emilia T. Iacobini, Cecilia Brettoni, Giuliano Galli, Massimo Mariani, Filippo Vegni, Domenico Maione, Daniela Rinaudo, Rino Rappuoli, John L. Telford, Dennis L. Kasper, Guido Grandi, and Claire M. Fraser, Proc. Natl. Acad. Sci. USA, Early Edition available online (accessed on September 6, 2002). Link to PDF file Wednesday, 18 September, 2002 Localisation of DNA Structures within chromosomes. Lecture 1a - DNA is like Coca-cola Lecture 1b - A-DNA and Z-DNA in sequenced chromosomes Link to PowerPoint file    Link to web page version of the lecture notes Link to PDF file of paper , "Bias of purine stretches in sequenced chromosomes", Computers and Chemistry, 26:531-541, (2002). Link to PDF file of Encyclopedia review article , "DNA Structure: A-, B-, and Z-DNA Families", The Encyclopedia of Life Sciences, (Macmillan Publishers, London, 2002). Link to web page with fractions of cruciforms in sequenced genomes. Lecture 2 - Cruciform Atlases Link to PDF file of "Genome Gymnastics" preprint describing Cruciform Atlases Link to PDF file of reprint of "Visualisation and Significance of DNA Structural Motifs in the Campylobacter jejuni Genome" (Genome Letters, 1:16-25, 2002.) Link to web page with fractions of cruciforms in sequenced genomes. Computer Excercises - Make your own genome atlas. Wednesday, 25 September, 2002 Chromatin Binding Sites and Gene Expression Lecture 1 - Chromatin Binding Sites and Gene Expression. References: PDF of "Genome organisation and chromatin structure in Escherichia coli" (Biochimie, 83:201-212, 2001.)      Link to web page about this article. PDF of "DNA microarray analysis of fim mutations in Escherichia coli" (Molecular Genetics and Genomics, 267:721-729, 2002.) Journal Club - Comparative Genomics of Yersinia pestis. "Genome sequence of Yersinia pesti KIM", Deng W, Burland V, Plunkett G 3rd, Boutin A, Mayhew GF, Liss P, Perna NT, Rose DJ, Mau B, Zhou S, Schwartz DC, Fetherston JD, Lindler LE, Brubaker RR, Plano GV, Straley SC, McDonough KA, Nilles ML, Matson JS, Blattner FR, Perry RD., J. Bact., 184:4601-4611, August, 2002. Supplemental reading: Carsten Friis,    Lars Juhl Jensen,    and David W. Ussery, "Visualisation of Pathogenicity Regions in Bacteria", Genetica, 108:47-51, (2000).        [PubMed]        PDF file         [cover] Link to Yersinia pestis pPCP1 atlases. Link to S. typhimurium DT104 atlases. Link to E. coli pO157 atlases. Computer Excercises - Make your own genome atlas. Wednesday, 2 October, 2002 Yeast Genomics. (Jure Piskur, guest lecturer) Husk!! Journal club starts at kl. 8.00 this morning. "The genome sequence of Schizosaccharomyces pombe", Val Wood, et al., Nature, 415:871-880, February, 2002. Link to PDF file Lecture 1 - Comparison of 15 different yeast genomes. Link to web page with atlases for Saccharomyces cerevisiae chromosomes. Link to web page with atlases for Schizosaccharomyces pombe chromosomes. Lecture 2 - Comparison of yeast mitochondrial genomes. "Inheritance and organisation of the mitochondrial genome differ between two Saccharomyces yeasts" (Petersen RF, Langkjaer RB, Hvidtfeldt J, Gartner J, Palmen W, Ussery DW, Piskur J., J. Mol. Biol., 318:627-636 (May, 2002). Link to PDF file Computer Excercises - Make your own genome atlas. Wednesday, 9 October, 2002 Genomic Transcriptional Analysis. (Henrik Bjørn Nielsen) AUTUMN BREAK (week 42) Wednesday, 23 October, 2002 Lecture 1 - Introduction to Gene Annotation in Microbial Genomes. (Marie Skovgaard) Lecture 2 - On the Quality of Annotation in Prokaryotic Genomes.(Marie Skovgaard) "On the total number of genes and their length distribution in complete microbial genomes" (Marie Skovgaard, Lars Juhl Jensen, Søren Brunak, David W. Ussery, and Anders Krogh , Trends in Genetics, 17:425-428, (2001). Link to PDF file Journal Club - Oceanobacillus iheyensis genome "Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments.", Takami H, Takaki Y, Uchiyama I., Nucleic Acids Research, 30:3927-3925, September, 2002. PNAS online version, with supplemental information Link to PDF file Link to web page with atlases for the Oceanobacillus iheyensis genome. Computer Excercises - Make your own genome atlas. Wednesday, 30 October, 2002 Microbial Proteome Comparisons. Lecture 1 - Comparison of Proteomes COGs link (Clusters of Orthologous Groups of proteins) . NCBI's list of Microbial Genomes (note COGs link for each genome [proteome]) . Lecture 2 - Comparison of Pseudomonas aeruginosa and Pseudomonas putida. Background reading: "Structural analysis of DNA sequence: Evidence for lateral gene transfer in Thermotoga maritima" (Peder Worning, Lars Juhl Jensen, Karen E. Nelson, Søren Brunak, and David W. Ussery, Nucleic Acids Research, 28:706-709, (2000). Link to PDF file "A phylogenomic approach to microbial evolution" (Thomas Sicheritz-Ponten and Siv G. Andersson, Nucleic Acids Research, 29:545-5529, (2001). Link to PDF file Journal Club - Thermosynechococcus elongatus genome "Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1.", Nakamura et al., DNA Research, 9:123-130, August, 2002. Link to PDF file Supplemental information PDF file Link to web page with atlases for the Thermosynechococcus elongatus genome. Computer Excercises - Make your own genome atlas. Wednesday, 6 November, 2002 Prediction of Chromosomal Replication Origin. (Peder Worning) Journal Club - Brucella suis genome "The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts.", Takami H, Takaki Y, Uchiyama I., Proc. Natl. Acad. Sci. USA, 99:13148-13153, September, 2002. PNAS online version, with supplemental information Link to PDF file Link to web page with atlases for the Brucella suis genome. Related articles: Brucella melitensis genome papers. Brucella melitensis genome paper:Proc. Natl. Acad. Sci. USA, 99:443-448, January, 2002     PNAS online version with supplemental information Link to PDF file Commentary for Brucella melitensis genome paper (good background reading):Proc. Natl. Acad. Sci. USA, 99:1-3, January, 2002     PNAS commentary about Brucella melitensisgenome paper. Link to PDF file Link to web page with atlases for the Brucella melintensis genome. Wednesday, 13 November, 2002 Group Projects begin Journal Club - Oceanobacillus iheyensis genome "Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments.", Takami H, Takaki Y, Uchiyama I., Nucleic Acids Research, 30:3927-3925, September, 2002. PNAS online version, with supplemental information Link to PDF file Link to web page with atlases for the Oceanobacillus iheyensis genome. Wednesday, 20 November, 2002 Journal Club - Shigella flexneri genome "Genome sequence of Shigella flexner 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157.", Q. Jin, et al., Nucleic Acids Res, 30:4432-4441, October, 2002. Link to PDF file Link to web page with atlases for the Shigella flexneri genome. Wednesday, 27 November, 2002 Journal Club - Bifidobacterium longum genome "The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract.", Mark A. Schell, et al., Proc. Natl. Acad. Sci. USA, 99:14422-14427, 29 October, 2002. Link to PDF file Link to web page with atlases for the Bifidobacterium longum genome. Wednesday, 4 December, 2002 Final Reports Due Back to Dave's CBS Courses page        CBS Bioinformatics Course page