Rocap Lab Website

Text and pic here

Instructions and tips for setting up the G5

Education

I am a sophomore pursuing a double major in Biochemistry and Microbiology and a minor in Marine Biology.

Research Interests

I became familiar with Dr. Rocap's work when she was a guest lecturer in my first marine biology class at UW. After class I contacted her and enquired about the possibility of doing undergraduate research.

Right now I'm working with Cedar doing bioinformatics on the Stramenopile Chloroplast Genomics Project, which falls under the NSF-funded umbrella program called the Assembling the Tree of Life Project. My responsibilities include analyzing, annotating and proof-reading the sequenced chloroplast genomes.

I'm looking forward to giving my first talk--entitled "The Annotation of Chloroplast Genomes: Discovering the Evolutionary History of Algal Stramenopiles"--in May at the Undergraduate Research Symposium.

Visiting Graduate Student Fall 2008 

Education
BS Biological Sciences. León University. Spain (2003)
MS Oceanography. Las Palmas de Gran Canaria University. Spain (2007)
Doctoral Student, Biological Oceanography. ICM Barcelona – CSIC (Spanish National Research Council) (2005-Present)

Research Interests: Ecology and population structure of uncultured marine protist.

I am doing my PhD in the Marine Science Institute of Barcelona in the Ramon Massana’s group. I am working with protists, in particular with one of the groups of the marine stramenopiles, the MAST-4. This is a heterotrophic flagellate of 2-3 µm of size that is still uncultured. Moreover, MAST-4 is globally distributed and has a significant cell abundance (Massana et al. 2006. EM 8:1515). Lately, I have developed a Q-PCR system to quantify it in marine samples.

Currently I came to the Gabrielle Rocap lab to try to amplify the ITS1 and ITS2 region (Internal Transcribed Spacer) of MAST-4 from environmental DNA to make clone libraries. Then I want to study the microdiversity of the group, if some ecotypes appear, and their relationship with environmental conditions, such as water temperature for example. Furthermore, if is interesting for my samples, I want to develop an automated ribosomal intergenic spacer analysis (ARISA).

Publications

Raquel Rodríguez-Martínez, Matthias Labrenz, Javier del Campo, Irene Forn, Klaus Jürgens and Ramon Massana. Distribution of the uncultured protist MAST-4 in the Indian Ocean, Drake Passage and Mediterranean Sea assessed by real-time quantitative PCR. Environmental Microbiology (in press).

José M. González, Beatriz Fernández-Gómez, Antoni Fernández-Guerra, Larua Gómez-Consarnau, Olga Sánchez, Montserrat Coll-Lladò, Javier del Campo, Lorena Escudero, Raquel Rodríguez-Martínez, Laura Alonso-Sáez. Mikel Latasa, Ian Paulsen, Olga Nedashkovskaya, Itziar Lekunberri, Jarone Pinhassi and Carlos Pedrós- Alió. Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria). PNAS June 2008

Francisco Fierro, Carlos García-Estrada, Nancy I. Castillo, Raquel Rodríguez, Tania Velasco-Conde, Juan-Francisco Martín. Transcriptional and bioinformatic análisis of the 56.8kb DNA region amplified in tandem repeats containing the penicillin gene cluster in Penicillium chrysogenum. Fungal Genetics and Biology. March 2006

  
 

Education: I am studying biological oceanography at the University of Washington.

Research Interests: I am working under Gabrielle Rocap and Michele Wrabel
studying phytoplankton community structure. I have been identifying phytoplankton
using microscopy. I have studied samples from the Benguela Current and will
be using a method of genetic fingerprinting (ARISA) for additional identifications.

Research interests: I am working under Gabrielle Rocap and Emily Nahas doing qPCR work on marine cyanobacteria, specifically Synechococcus. Just got done with a month long research cruise in the Northern Pacific collecting samples to quantify ecotypes of Synechoccocus in the upper 200 meters.

Education:

B.A. Biology and History. Pomona College. Claremont, CA (2008).

M.S. and Ph.D. Oceanography. University of Washington. Seattle, WA (2008-present)

Research Interests: Ecology of marine viruses

My interests in marine virology began with studying viruses in coral reef ecosystems during my undergraduate career at Pomona College. I focused on the distribution of human associated adenoviruses found in corals and water in Kane'ohe Bay, Hawaii and their potential for being used as a proxy for anthropogenic impact in the bay.

At the University of Washington, I am researching viruses that infect the diatom Pseudo-nitzschia. This marine phytoplankton can produce domoic acid, which results in amnesic shellfish poisoning if consumed. Diatoms are also incredibly important primary producers and therefore their propulations have a direct impact on the global carbon cycle. Viruses are important regulators of marine communities and have been shown to cause the demise of phytoplankton blooms, be important in lateral gene transfer, and influence nutrient cycling. The implications of better understanding the dynamics between viruses and Psuedo-nitzschia range from developing warning systems for communities affected by harmful algal blooms, clarifying the controls on carbon cycling, and more.

Currently, I am working on isolating and characterizing a virus that infects Pseudo-nitzschia. This is mostly culture dependent work, but also involves epifluoresent microscopy to count viruses, and some genomic techniques to sequence the genome of the isolated virus. Eventually, my research will focus more on viral interactions in the field using metagenomic approaches to understand the viral and phytoplankton communities.

Downloaded from the website. Compiled using:

env CFLAGS="-O3" ./configure --enable-threads --enable-lfs
-fast wasn't any better (seems to be for G5 only)

Had to drag and drop binaries to /usr/local/bin