7.437 Topics in Molecular Biological Oceanography:

Genomic Approaches in Marine Science

Spring 2003

Required Reading

Class 1 (Overview and scope - Hahn and Shank)

Roger Brent (2000) Genomic Biology. Cell 100:169-183

Greg Gibson (2002) Microarrays in ecology and evolution. Molecular ecology 11: 17-24

O.G. Vukmirovic and S.M. Tilghman (2000) Exploring genome space. Nature 405: 820-822

S. Broder and J.C. Venter (2000) Whole genomes: the foundation of new biology and medicine. Curr Opin Biotechnol 11: 581-585.

- Hahn notes

- Shank notes
 
 

 Class 2 (Genome projects - McArthur) Olson, M.V. (2001) Clone by clone by clone. Nature 409: 816-818

Baltimore, D. (2001) Our genome unveiled. Nature 409: 814-816

Adams, M.D., et al. (2000) The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.

Myers, E.W., et al. (2000) A whole-genome assembly of Drosophila. Science 287: 2196-2204.
 

- McArthur powerpoint presentation

- Giardia genome project
 

 Class 3 (Cancelled due to snow)  (Feb 18)
 
 

Class 4 (Genomics in microbial evolution and diversity - Webb)(Feb 25)

Carl R. Woese  (2000)  Interpreting the universal phylogenetic tree.  PNAS 97: 8392?8396

Jason Raymond, Olga Zhaxybayeva, J. Peter Gogarten, Sveta Y. Gerdes, Robert E. Blankenship (2002) Whole-Genome Analysis of Photosynthetic Prokaryotes. Science 298: 1616-1620

J. Peter Gogarten, W. Ford Doolittle, and Jeffrey G. Lawrence  (2002) Prokaryotic Evolution in Light of Gene Transfer.   Mol. Biol. Evol. 19(12):2226?2238.
 

Supplementary readings:

A. E. Murray, D. Lies, G. Li, K. Nealson, J. Zhou, and J. M. Tiedje (2001) DNA-DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes.  PNAS 98: 9853-9858

W. Ford Doolittle (1999) Phylogenetic Classification and the Universal Tree.  Science 284: 2124-2128

Carl R. Woese  (1998) The universal ancestor. Proc. Natl. Acad. Sci. USA  95:  6854?6859

   Class 5 (Genome-genome interactions - Gast)   (Tues, Mar 4) Nancy A.Moran.  Microbial Minimalism: Genome Reduction in Bacterial Pathogens  (2002) Cell  108:583-586

N A Moran & A Mira (2001)  The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. genomebiology

J.T. Dessens, G. Margos, M.C. Rodriguez and R.E. Sinden Identification of Differentially Regulated Genes of Plasmodium by Suppression Subtractive Hybridization. (2000) Parasitology Today, vol. 16, no. 8: 354-356.

Supplementary reading:

Peter T Hraber* and Jennifer W Weller (2001)  On the species of origin: diagnosing the source of symbiotic transcripts. Genomebiology
 
 

 Class 6 (Genomics and microbial ecology I - Sievert)  (Tues, Mar 11) Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich S, Gates CM, Feldman RA, Spudich JL, Spudich EN, DeLong EF (2000). Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. Science 289 (5486): 1902-1906

O. Béjà, Marcelino T. Suzuki, Eugene V. Koonin, L. Aravind, Andrew Hadd, Linh P. Nguyen, Rachel Villacorta, Mojgan Amjadi, Corey Garrigues, Stevan B.
Jovanovich, Robert A. Feldman, Edward F. DeLong. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environmental Microbiology, Volume 2, Number 5 (October 2000), pp. 516-529

Rappé M. S., S. A. Connon, K. L. Vergin, S. J. Giovannoni (2002). Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418 630-633.
 

Supplementary readings:

Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. APPLIED AND ENVIRONMENTAL MICROBIOLOGY 66 (6): 2541-2547.

Karl D. M. (2002) Microbiological oceanography: Hidden in a sea of microbes. Nature 415: 590-591

Ball K. D. and J. T. Trevors (2002) Bacterial genomics: the sue of DNA microarrays and bacterial artificial chromosomes. Journal of Microbiological Methods 49: 275-284

Beja O, Spudich EN, Spudich JL, Leclerc M, DeLong EF (2001) Proteorhodopsin phototrophy in the ocean. Nature 411 (6839): 786-789
 

- Sievert presentation
 

 Class 7 (Comparative genomics - Hahn)    (Tues, Mar 18) Cristian Cañestro, Susan Bassham and John H Postlethwait (2003) Seeing chordate evolution through the Ciona genome sequence.  Genome Biology 4: 208.1-208.5

James W. Thomas and Jeffrey W. Touchman (2002) Vertebrate genome sequencing: building a backbone for comparative genomics. Trends in Genetics 18:104-108.

Jürg Spring (2002) Genome duplication strikes back.  Nature Genetics 31: 128-129.

Sarah F. Smith, Philip Snell, Frank Gruetzner, Anthony J. Bench, Thomas Haaf, Judith A. Metcalfe, Anthony R. Green, and Greg Elgar (2002) Analyses of the Extent of Shared Synteny and Conserved Gene Orders between the Genome of Fugu rubripes and Human 20q. Genome Research 12: 776-784.
 

Supplementary paper:

Frazer et al (2003) Cross-species sequence comparisons: a review of methods and available resources.  Genome Res. 13:1-12.
 

- Hahn presentation

 March 25:  Spring Break
 

Class 8 (Population genomics - Shank)    (Wed, April 2)
 

Max Igman, Kaessmann, H., Paabo, S., and U. Gyllensten (2000) Mitochondrial genome variation and the origin of modern humans. Nature 408:708-713.

Gabor Marth et al. (2003) Sequence variations in the public human genome data reflect a bottlenecked population history. PNAS100:376-381.

Christian Schlotterer (2003) Hitchhiking mapping ? functional genomics from the population genetics perspective. Trends in Genetics10:32-38.

William Evans and Mary Relling (1999) Pharmacogenomics: translating functional genomics into rational therapeutics. Science 286:487-491.
 

Supplementary readings:

Marjorie Oleksiak, Churchill, G.A, and D.L. Crawford (2002) Variation in gene expression within and among natural populations. Nature Genetics 32:261-266.

William Black, Baer, C.F., Antolin, M.F., and DuTeau, N.M. (2001) Population genomics: Genome-wide sampling of insect populations. Annu. Rev. Entomol. 2001. 46:441?69

Howard McLeod and William Evans (2001) Pharmacogenomics: unlocking the human genome for better drug therapy. Annu. Rev. Pharmacol. Toxicol. 41:101-121.
 

- Shank presentation (powerpoint file)

- Shank reference list (pdf file)
 

 Class 9 (Functional genomics in non-model organisms - Erdner)(Wed, April 9)  

Kamath, R.S., et al. (2003). Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421:231-237.

Kuhn, E. (2001). From library screening to microarray technology:  Strategies to determine gene expression profiles and to identify  differentially regulated genes in plants. Ann. Bot. 87:139-155

Lippmeier, J.C., A.M. Brown and K.E Apt (2002). Isolation of algal genes  by functional complementation of yeast. J. Phycol. 38:529-533.

- Erdner presentation


Class 10 (Genomics and microbial ecology II - Sogin) (cancelled)

Readings to be determined
 

Class 11 (Toxicogenomics - Handley)   (Wed, April 16)
 

Gracey AY, Cossins AR.    Application of microarray technology in environmental and comparative physiology.   Annu Rev Physiol. 2003;65:231-59.

Thomas RS, Rank DR, Penn SG, Zastrow GM, Hayes KR, Pande K, Glover E, Silander T, Craven MW, Reddy JK, Jovanovich SB, Bradfield CA.   Identification of toxicologically predictive gene sets using cDNA microarrays. Mol Pharmacol. 2001 Dec;60(6):1189-94.

Patrick Larkin, Leroy C. Folmar, Michael J. Hemmer, Arianna J. Poston, and Nancy D. Denslow.  Expression Profiling of Estrogenic Compounds Using a Sheepshead Minnow
cDNA Macroarray.  2003.  Environmental Health Perspectives ï VOLUME 111 | MAY 2003

- Handley presentation


 

Class 12 (Proteomics - Dyhrman)   (Wed, April 23)
 
 

J.L. Lo´ pez, A. Marina, J. Va´ zquez, G. Alvarez.  (2002)   A proteomic approach to the study of the marine mussels Mytilus edulis and M. galloprovincialis.  Marine Biology 141:217-223

Pandey A, Mann M. (2000) Proteomics to study genes and genomes. Nature. 2000 Jun 15;405(6788):837-46.

Phizicky E, Bastiaens PI, Zhu H, Snyder M, Fields S. (2003)  Protein analysis on a proteomic scale. Nature. 2003 Mar 13;422(6928):208-15.
 

- Dyhrman presentation

Class 13 (Bioinformatics - McArthur)   (Wed, April 30)
 
 

Kanehisa & Bork (2003) Bioinformatics in the post-sequence era.  Nature Genetics Suppl. 33:305-310.

Jamison (2003) Open Bioinformatics.  Bioinformatics 19: 679-680.

Ouzounis (2002)  Bioinformatics and the theoretical foundations of molecular biology.  Bioinformatics 18:377-378.

Roos et al (2002)  Mining the Plasmodium genome database to define organellar function:  what does the apicoplast do?  Phil. Tr. Roy. Soc. Lond. B. 357:35-46.

Bahl et al (2003) PlasmoDB:  The Plasmodium genome resource.  Nucl. Acids Res. 31: 212-215.

Classes 14-15 (WSF Genomics panel (proposal review) ? students and faculty)   (Wed, May 7, 14)