Rocap Lab Website

OCEAN 539 B

Environmental Genomics

Winter 2007

Readings

This page contains links to the journal articles we will be discussing in class, and some background papers for lecture and labs. Papers might not be accessible from a non-UW computer. Let me know if you have any problems with this page from on campus.

Week 1 Background: DeLong, 2005. Microbial Community Genomics in the Ocean

Week 2 Background: DeLong, 2005. Microbial Community Genomics in the Ocean Discussion: Venter et al. 2004 Environmental genome shotgun sequencing of the Sargasso Sea (led by Vaughn)

Week 3 Background: Delsuc et al.2005 Phylogenomics and the reconstruction of the tree of life Discussion: Giovannoni et al. 2005 Genomic streamlining in a cosmopolitan oceanic bacterium (led by Colleen E)

Week 4 Background: Holder& Lewis, 2003 Phylogeny estimation: Traditional and Bayesian Approaches Discussion: Snel et al. 2002 Genomes in Flux: the evolution of archaeal and proteobacterial gene content (led by Min)

Week 5 Background: Francke et al. 2005 Reconstructing the metabolic network of a bacterium from its genome Discussion: Howard et al. 2006, Bacterial taxa that limit sulfur flux from the ocean (led by Michele)

Week 6 No Class: ASLO

Week 7 Background Gogarten et al, Horizontal gene transfer, genome innovation and evolution Discussion Zhaxybayeva et al. 2006. Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events (led by Emily)

Week 8 Background: Armbrust et al. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Discussion: Strous et al, 2006. Deciphering the evolution and metabolism of an anammox bacterium from a community genome (led by Sara) and Discussion: Li et al. 2006, Phylogenomic analysis identifies red algal genes of endosymbiotic origin in the chromalveolates (led by Colleen D.)

Week 9 Background: Shendure et al. 2004 Advanced Sequencing Technologies: Methods and Goals Ram et al. 2005. Community Proteomics of a natural microbial biofim (led by Julie) and Angly et al. 2006, The marine viromes of four oceanic regions (Led by Jess)

Week 10 Class presentation of projects

Ocean 220 is an experiental course in which you will practice the scientific method from A-Z. During spring break, we will convene in the San Juans to plan our research. Then we will cruise aboard one of the UW's research ships for 1-3 days collecting data. After this, you will finish up post-cruise lab work, interpret your findings, and write a research paper focussing on your efforts. This class has been called 'the most work I ever loved to do' by a previous year's students. This course is a requirement for oceanography majors and is strongly advised for all students studying geology, fisheries, oceanography, environmental biology and civil engineering. Ocean 220 will be offered in Spring 2009.

Go to the class web page.

 

Oceanography 443 and 444 form a two part independent research project series for majors in oceanography.

In Ocean 443 the quarter will be spent doing background research, selecting a research problem and formulating an hypothesis, and then writing a proposal to conduct the research necessary to address the problem/hypothesis. Three credits.

Oceanography 444 gives each student the opportunity to carry out the observational and sample collection phases of their research proposed in OCN 443. Depending on their chosen study site, students utilize one or more of the university's research vessels, the R/V Thomas G. Thompson the R/V Clifford A. Barnes and the R/V WeeLander to collect their samples. During the research cruise the students are responsible for the operation of all the major science systems on the ship including but not limited to the integrated positioning system, the seafloor acoustic imaging system, the acoustic Doppler Current profiler (ADCP), and the CTD-water sampling system. Back on land, the remainder of the quarter is spent processing samples, analyzing data and writing up the results. Students write a final paper, post their results on a web page they create and present their results orally in a public symposium. Five credits

In the 2005-2006 academic year students conducted their research projects in the Galapagos Islands!
You can still view our cruise page.

Ocean 443 homepage

Ocean 444 homepage

Oceanography 539D: Graduate course in environmental genomics. Includes literature discussion, computer lab, and independent bioinformatics research project. Will probably be offered next in 2010. 

See the class web page

 

HERE ARE THE READINGS FOR THIS QUARTER

 

Techniques of molecular analysis with emphasis on DNA methods, including PCR, DNA sequencing, RFLP, RAPD and VNTR analysis and cloning. Applications of these techniques to fisheries, aquaculture, oceanography, population and evolutionary studies, and other areas of science. Three credits Class Website

Note: This course is now taught by Prof. Lorenz Hauser.  Contact him about when it will next be offered.