Virginia Rich: Difference between revisions

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I am a graduate student in the [[DeLong Lab]], you can reach me at vrich {at] mit DoT [edu]
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I am an Assistant Professor at the Ohio State University in Columbus, Ohio, in the Department of Microbiology.
 
=== This page is out-of-date! Please visit my lab group's wiki page at [[SWES-MEL]]! ===
 
You can download my full C.V. here [[Image:Rich_CV_2016_March_short.pdf]]
 
You can reach me at vrich {at] email.arizona.edu.
 
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===Current Projects===
[[Genes, isotopes, and ecosystem biogeochemistry: dissecting methane flux at the leading edge of global change.]]  A DOE-funded project led by Scott Saleska and myself, with Gene Tyson (University of Queensland), Patrick Crill (Stockholm University), Jeff Chanton (Florida State University), Changsheng Li and Steven Frolking (University of New Hampshire)
 
[[“Microbial Buffering”: Protecting the Great Barrier Reef against human impact.]] A project led by Gene Tyson at the University of Queensland, with David Bourne and Britta Schaffelke (Australian Institute for Marine Science), Matt Sullivan and myself (University of Arizona), and Jason Bragg (CSIRO)
 
===Publications===
'''Rich, VI''', Eppley J, Shi Y, Pham V, DeLong EF. 2010. '''Time-series investigation of a coastal microbial community in Monterey Bay, CA, using the “genome proxy” microarray.''' ''Environmental Microbiology.'' [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2010.02314.x/abstract link to article]
 
'''Rich, VI''', Konstantinidis K, DeLong EF. 2008. '''A “genome proxy” oligonucleotide microarray for marine microbial ecology'''. ''Environmental Microbiology.'' 10: 506-521. [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01471.x 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. 2006. '''Community genomics among stratified microbial assemblages in the ocean's interior'''. ''Science.'' 311: 496-503. [http://www.sciencemag.org/cgi/content/full/311/5760/496 link to article]
 
Horz HP, '''Rich V''', Avrahami S, Bohannan BJ. 2005. '''Methane-oxidizing bacteria in a California upland grassland soil: diversity and response to simulated global change'''. ''Applied and Environmental Microbiology''. 71: 2642-52. [http://aem.asm.org/cgi/content/full/71/5/2642?view=long&pmid=15870356 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''']].
 
December 2008 - August 2011: Postdoctoral researcher in the University of Arizona's Ecology and Evolutionary Biology department
 
January 2003 - September 2008: PhD student in the DeLong Lab, co-advised by Ed DeLong and by [http://www.stanford.edu/group/somero/ George Somero] at Stanford's [http://www-marine.stanford.edu/ Hopkins Marine Station]
 
1999-2002: Teaching and research positions at the [http://www.washington.edu University of Washington, Seattle], and U.W.'s [http://depts.washington.edu/fhl/ Friday Harbor Labs]
 
B.A. from [http://www.berkeley.edu U.C. Berkeley] 1998
* [http://mcb.berkeley.edu Molecular & Cellular Biology: Genetics Division]
* [http://ib.berkeley.edu Integrative Biology]
 


===Thesis Project===  
===Thesis Project===  
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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 [http://www.lternet.edu/microbial_ecology/ Microbial Observatory] Grant to E.D., I am trying 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 will then allow a higher-throughput mapping of species 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. I leveraged the sequence information in DeLong Lab's Monterey Bay large-insert environmental clone libraries to construct a "census" microarray for a portion of the native microbial community, for high-throughput tracking of microbes (including their population dynamics) at a finer level of resolution than is possible with marker genes (eg 16S rRNA gene) and for much lower cost than metagenomes (eg $45 per sample for triplicate hybridizations).   


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 [http://www.mbari.org Monterey Bay Aquarium Research Institute's] (MBARI) [http://www.mbari.org/bog/ 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.
===Protocols===
[[DeLong:Lab_Protocols:Microarray_Protocols|'''All my microarray protocols''']]


===Abridged C.V.===
[[Media:DeLongLab-Protocols-Microarray-VR_PLLslideprep.doc|Preparing Poly-L-lysine Slides]]
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[[Media:DeLong-Protocols-Microarray-VR_Protocol_OligoProbeDesign.doc‎|Designing our 70-mer Oligo Probes]] using ArrayOligoSelector, a program developed by DeRisi lab
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[[Image:G_headshot_website_small_motherinlawrespectfullyremoved.jpg]]
[[Media:DeLongLab-Protocols-Microarray-VR_ArrayPostProcessing.doc|Post-processing Arrays]]


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[[Media:DeLongLab-Protocols-Microarray-VR_Microarryer_Use.doc‎|Using the Genetix QArray2 Arrayer]]
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B.A. from [http://www.berkeley.edu U.C. Berkeley] 1998
* [http://mcb.berkeley.edu Molecular & Cellular Biology: Genetics Division]
* [http://ib.berkeley.edu Integrative Biology]


1999-2002: various teaching and research positions at the [http://www.washington.edu University of Washington, Seattle], and U.W.'s [http://depts.washington.edu/fhl/ Friday Harbor Labs]


2003 - present: PhD student in the DeLong Lab, co-advised by Ed DeLong and by [http://www.stanford.edu/group/somero/ George Somero] at Stanford's [http://www-marine.stanford.edu/ Hopkins Marine Station]
===Links===
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[[Media:DeLongLab_LabMembers_VR_CV.pdf|'''download full C.V. here''']]


===Publications===
'''Rich, VI''', DeLong EF. A “genome proxy” oligonucleotide microarray for marine microbial ecology. Manuscript in preparation.


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.  
* [http://www.eebweb.arizona.edu/Faculty/mbsulli/ Tucson Marine Phage Lab] led by Matt Sullivan, exploring marine phages and their hosts.


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. [http://www.sciencemag.org/cgi/content/full/311/5760/496 link to article]
* [http://web.gps.caltech.edu/faculty/orphan/index.html Orphan Lab] working on anaerobic C- and S-cycling microbial communities.


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. [http://aem.asm.org/cgi/content/full/71/5/2642?view=long&pmid=15870356 link to article]
* [http://serc.carleton.edu/microbelife/microbservatories/monterey/index.html The Microbial Life Education Resources' pages on our Monterey Bay Microbial Observatory]


===Links===
* [http://www.mbnms-simon.org/other/gen/project_info.php?pid=100236&proid=&form=pi The Monterey Bay Sanctuary Integrated Monitoring Network (SIMoN) webpage for the Monterey Bay Microbial Observatory]
* [[DeLong:Lab_Protocols:Microarray_Protocols|My microarray protocols]]


* [http://derisilab.ucsf.edu/microarray/index.html Microarrays.org site created and maintained by the DeRisi Lab, UCSF]


* [http://derisilab.ucsf.edu/microarray/index.html Microarrays.org] A useful site created and maintained by the DeRisi Lab, UCSF.


* [http://serc.carleton.edu/microbelife/microbservatories/monterey/index.html Microbial Life Education Resources' pages on the Monterey Bay Microbial Observatory]
* [http://courses.washington.edu/dmandoli/FHL.html 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.


* [http://www.mbnms-simon.org/other/gen/project_info.php?pid=100236&proid=&form=pi Monterey Bay Sanctuary Integrated Monitoring Network (SIMoN) webpage for the Monterey Bay Microbial Observatory]
*[http://raven.zoology.washington.edu/celldynamics/ 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.


* [http://www.mbari.org/bog/ the MBARI BOG (Biological Oceanography Group) page]
* [http://www.mbari.org/bog/ The MBARI BOG] The Monterey Bay Aquarium Research Institute's Biological Oceanography Group page.


* [http://www.geo.mtu.edu/~gbluth/Teaching/julian.noleap.html Julian Day calendar]
* [http://www.geo.mtu.edu/~gbluth/Teaching/julian.noleap.html Julian Day calendar]


* [http://www.mbari.org/bog/images/mb06_chl.mpeg 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.


* [http://www.mbari.org/bog/images/mb06_chl.mpeg awesome movie of chlorophyll and wind off the central California coast in August 2006, made by the MBARI BOG folks]
* [http://raven.zoology.washington.edu/celldynamics/about/index.html The Center for Cell Dynamics] at the University of Washington's Friday Harbor Labs. These folks are amazing.
 
* [http://courses.washington.edu/dmandoli/FHL.html Course website for research apprenticeship I helped run at Friday Harbor Labs in 2001 and 2002]
 
* [http://web.mit.edu/mbsulli/www/ Matt Sullivan's website on his Cyanophage research]
 
* [http://covecottage.bugaco.com/ Cove Cottage, a beautiful getaway in Downeast Maine]

Revision as of 12:14, 24 March 2016

I am an Assistant Professor at the Ohio State University in Columbus, Ohio, in the Department of Microbiology.

This page is out-of-date! Please visit my lab group's wiki page at SWES-MEL!

You can download my full C.V. here File:Rich CV 2016 March short.pdf

You can reach me at vrich {at] email.arizona.edu.

Current Projects

Genes, isotopes, and ecosystem biogeochemistry: dissecting methane flux at the leading edge of global change. A DOE-funded project led by Scott Saleska and myself, with Gene Tyson (University of Queensland), Patrick Crill (Stockholm University), Jeff Chanton (Florida State University), Changsheng Li and Steven Frolking (University of New Hampshire)

“Microbial Buffering”: Protecting the Great Barrier Reef against human impact. A project led by Gene Tyson at the University of Queensland, with David Bourne and Britta Schaffelke (Australian Institute for Marine Science), Matt Sullivan and myself (University of Arizona), and Jason Bragg (CSIRO)

Publications

Rich, VI, Eppley J, Shi Y, Pham V, DeLong EF. 2010. Time-series investigation of a coastal microbial community in Monterey Bay, CA, using the “genome proxy” microarray. Environmental Microbiology. link to article

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. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science. 311: 496-503. link to article

Horz HP, Rich V, Avrahami S, Bohannan BJ. 2005. Methane-oxidizing bacteria in a California upland grassland soil: diversity and response to simulated global change. Applied and Environmental Microbiology. 71: 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'''.

December 2008 - August 2011: Postdoctoral researcher in the University of Arizona's Ecology and Evolutionary Biology department

January 2003 - September 2008: PhD student in the DeLong Lab, co-advised by Ed DeLong and by George Somero at Stanford's Hopkins Marine Station

1999-2002: Teaching and research positions at the University of Washington, Seattle, and U.W.'s Friday Harbor Labs

B.A. from U.C. Berkeley 1998


Thesis Project

Developing "Community Genome" Microarrays for Marine Microbial Ecology

Monterey Bay is a long-term ecological research site, with the efforts of several major research institutions focused on understanding the Bay's oceanography. I leveraged the sequence information in DeLong Lab's Monterey Bay large-insert environmental clone libraries to construct a "census" microarray for a portion of the native microbial community, for high-throughput tracking of microbes (including their population dynamics) at a finer level of resolution than is possible with marker genes (eg 16S rRNA gene) and for much lower cost than metagenomes (eg $45 per sample for triplicate hybridizations).

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

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


  • 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.
  • 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.
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