Virginia Rich

I was a graduate student in the DeLong Lab, and am now a postdoctoral researcher at the University of Arizona, Tucson, in the Ecology and Evolutionary Biology Department. You can reach me at vrich {at] email.arizona.edu, and you can download my full C.V. here.

Thesis Project

Developing "Community Genome" Microarrays for Marine Microbial Ecology

Over the last 7+ years, Ed and his lab have constructed large-insert environmental clone libraries, made from the microbial fraction of seawater, taken from a variety of depths at several locations. As part of an NSF Microbial Observatory Grant to E.D., I have worked to leverage the sequence information in the Monterey Bay library to construct a "census" microarray for a portion of the native microbial community. This array is now allowing a higher-throughput mapping of microbes than has previously been possible.

Monterey Bay is a long-term ecological research site, with the efforts of several major research institutions focused on understanding the Bay's oceanography. DNA samples have been collected by the DeLong Lab at monthly intervals since 1998, in tandem with the Monterey Bay Aquarium Research Institute's (MBARI) Biological Oceanography Group (BOG) research cruises. We hope that by examining these archived DNA samples with the microarray, and by exploring the results of this multi-year census in the context of the BOG group's chemcial, physical and biological analyses, we can form a more complete picture of the dynamics of Monterey Bay microbial communities.

Publications

Rich, VI, Konstantinidis K, DeLong EF. 2008. A “genome proxy” oligonucleotide microarray for marine microbial ecology. Environmental Microbiology. 10: 506-521. link to article

DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM. Community genomics among stratified microbial assemblages in the ocean's interior. Science. 2006 Jan 27; 311(5760): 496-503. link to article

Horz HP, Rich V, Avrahami S, Bohannan BJ. Methane-oxidizing bacteria in a California upland grassland soil: diversity and response to simulated global chane. Appl Environ Microbiol. 2005 May; 71(5): 2642-52. link to article

Preston, CM, Suzuki M, Rich VI, Heidelberg J, Chavez F, DeLong EF. Detection and distribution of two novel form II RuBisCos in the Monterey Bay. Manuscript in preparation.

Education & Training

This is the abridged version; you can download my full C.V. here.

B.A. from U.C. Berkeley 1998 Molecular & Cellular Biology: Genetics Division Integrative Biology 1999-2002: Teaching and research positions at the University of Washington, Seattle, and U.W.'s Friday Harbor Labs 2003 - present: PhD student in the DeLong Lab, co-advised by Ed DeLong and by George Somero at Stanford's Hopkins Marine Station

Protocols

• All my microarray protocols

Preparing Poly-L-lysine Slides

Designing our 70-mer Oligo Probes using ArrayOligoSelector, a program developed by DeRisi lab

Post-processing Arrays

Using the Genetix QArray2 Arrayer

Links

• The Microbial Life Education Resources' pages on our Monterey Bay Microbial Observatory

• The Monterey Bay Sanctuary Integrated Monitoring Network (SIMoN) webpage for the Monterey Bay Microbial Observatory

• Microarrays.org A useful site created and maintained by the DeRisi Lab, UCSF.

• Our research apprenticeship The course website for a research apprenticeship that I helped developed and run at the University of Washington's Friday Harbor Labs in 2001 and 2002, entitled "The Morphogenesis and Development of Acetabularia, the Mermaid's Wineglass". The leaders of the teaching team were Dr. Garett Odell and Dr. Dina Mandoli.

• The Center for Cell Dynamics I worked with Dr.s Garry Odell, Victoria Foe, and George von Dassow at the CCD as a lab tech before returning to grad school. Their confocal microscopy images and modelling are simply amazing - sit down with a cup of coffee and enjoy looking through their incredibly informative, revealing art.

• The MBARI BOG The Monterey Bay Aquarium Research Institute's Biological Oceanography Group page.

• Julian Day calendar

• Coastal California in Motion A visually stunning movie of chlorophyll and wind off the central California coast in August 2006, made by the MBARI BOG folks.

• Sullivan Lab doing marine phage research.

• Orphan Lab working on anaerobic C- and S-cycling microbial communities.

• The Center for Cell Dynamics at the University of Washington's Friday Harbor Labs. These folks are amazing.