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January 2008

Research News

SBI Research Feature: High-Throughput DNA Sequencing Technology at OSU

In 2007, a small group of researchers and OSU’s Center for Genome Research and Biocomputing, with help from the College of Veterinary Medicine and the Botany and Plant Pathology Department, purchased a high-throughput DNA sequencing machine called the Illumina 1G Genome Analyzer.  Its main advantages over traditional sequencing methods are lower costs, greater depth of sequencing and speed – it can sequence the entire genome of a bacterium in three days. Jeff Chang, assistant professor of Botany and Plant Pathology, is one of the users on the OSU campus. Click here to read a short Web interview where Jeff describes how the Illumina sequencer works, some of its applications, and the logistics to get started.

2008 SBI Undergraduate Internships

Do you know any undergraduates who would enjoy working on a summer project related to the subsurface biosphere? Please encourage them to apply for an SBI internship. SBI will support up to 15 interns this summer with the goal of stimulating interest in the subsurface biosphere and encouraging undergraduates to pursue graduate school. The program focuses on, but is not limited to, under-represented minority and women students. The SBI will support monthly hourly costs for each intern of up to $1000/month and $3000 total. This support can be augmented with research funds from the intern's faculty mentor. Applications will be reviewed on receipt. Approval is contingent on the availability of a faculty mentor and a suitable research project. Applicants are encouraged to seek out their own faculty mentor (see the SBI faculty directory) and to apply early because of the limited number of internships available. For more information please see

Upcoming Events

Thursday, January 17, 4:00 p.m., Portland State University. Nitrogen fixation and the marine nitrogen cycle (IGERT Earth's Subsurface Biosphere Seminar). Speaker: Dr. Douglas Capone, Professor of Biological Sciences, USC College of Letters, Arts and Sciences. FMI: Julie Cope, 7-9316.

Tuesday, January 22, 3:00 p.m., OSU STAG 208. Trees in pastures – managing soils through vegetation change (Botany and Plant Pathology Seminar). Speaker: Steve Sharrow, Professor, Rangeland Ecology and Management.

Wednesday, January 23, 3:30-4:30 p.m., ALS 4001. Evolutionary genomics of the fungal kingdom: a view from the chytrids (CGRB Seminar Series). Speaker: Jason Stajich, Department of Plant and Microbial Biology, University of California, Berkeley.

Monday, January 28, 4:00 p.m., ALS 4000. Soil microbial ecology: the world beneath our feet (Crop and Soil Science Seminar). Dave Myrold, Professor and Associate Head, Crop and Soil Science.

January 31. Deadline to submit abstracts for presentations at the Internation Union of Microbiological Societies. The meeting will be held August 5-9, 2008, in Istanbul, Turkey and will include gatherings of the International Congress of Bacteriology and Applied Microbiology, the International Congress of Mycology, and the Congress of Virology.

February 1. Deadline to submit abstracts for Genomes 2008 - Functional Genomics of Microorganisms - The meeting will be held April 8-11, 2008, at the Institut Pasteur, Paris, France. The emphasis of the meeting will be comparative analyses of pathogenic and environmental microbes, functional genomics, computational genomics and systems biology in the light of the new technological developments. Genomics has also dramatically changed studies concerning the interaction of microorganism with their environment or, for pathogens, symbionts or commensals, their host. The newest results in this field will also be discussed.

February 7th, 4:00 p.m., 193 Burt Hall, OSU. IGERT Earth's Subsurface Biosphere Seminar. Dr. Allan Konopka, Lab Fellow - Pacific Northwest National Laboratory.

Link to a calendar of other related events...


Funding Opportunities for Students

OSU Institute for Water and Watersheds Graduate Research Funding - The IWW supports graduate student projects that assist OSU faculty, state or local agencies that are responsible for examining issues related to long-term water and watershed management with a focus on creating sustainable solutions that balance resource stewardship with economic viability for local communities. The project should involve water resources related research in topics including but not limited to water resources science, water resources engineering, or water resources policy and management. The awards are not necessarily limited to students enrolled in the Water Resources Graduate Program but also in related fields such as agriculture, engineering, soil science, forestry, fisheries and wildlife, geosciences, sociology, political science, among others. Proposals due Monday, January 28

The National Academies Research Associateship Program - The Research Associateship awards are open to doctoral-level scientists and engineers (U.S and Foreign Nationals) who can apply their special knowledge and talents to research areas that are of interest to them and to the participating host laboratories and centers. Awards are available for Postdoctoral Associates (within 5 years of the doctorate) and Senior Associates (normally 5 years or more beyond the doctorate). Associates conduct research in residence at the participating host laboratory they have chosen. Applications due: February 1.

National Energy Technology Laboratory Methane Hydrates Fellowship Program (NETL/ MHFP) - This program supports postgraduate master's and Ph.D. students in the advancement of methane hydrate science. Interest is in projects that provide an improved understanding of the processes that control hydrate stability and their potential role in global climate including formation of methane hydrates in permafrost and seafloor settings and the fate of dissociated hydrates through sediments, the water column, and into the atmosphere. A fellow receives a stipend from the National Research Council while carrying out his or her proposed project. Applications due: February 1.

EcoInformatics Summer Institute (EISI) for undergraduate and early graduate students - The program will be held at the HJ Andrews Experimental Forest in the Oregon Cascades from June 16-August 22, 2008. Students receive a stipend, course credit, and hand-on experience in ecoinformatics - the integration of mathematics, computer science, statistics, and engineering with the study and management of ecosystems. The program is led by OSU faculty and sponsored by NSF and NIH. Applications due: February 15, 2007.

NASA Planetary Biology Internship - The NASA Planetary Biology Internship Program (PBI) provides opportunities to explore scientific questions of global scale about planet Earth. Each year the PBI program sponsors nine or ten interns who undertake summer research at NASA Research Centers or NASA-sponsored laboratories and academic institutions.Typical programs in which interns may become involved include global ecology and remote sensing; microbial ecology and bio-mineralization; advanced life support; origin and early evolution of life. Interns receive a stipend of $3200 for the 8 weeks plus travel support. Applications due: March 3.


Funding Opportunities for Faculty

National Ground Water Association - Ground Water Research Fund - NGWREF seeks to fund leading-edge programming that stimulates new knowledge, information, programs, and products to advance ground water science and technology. It particularly encourages and values those proposals that bridge the gap between research and practical applications of the research findings. In 2008 it will prioritize funding for projects that contribute to achieving the Foundation's mission related to sustainability and public concerns about ground water quality. Proposals up to $50,000 will be considered; typically, research grants may be provided in the $3,000 - $8,000 range. Grants are for one year. Proposals due: February 1, 2008.

NSF Biological Oceanography - The Biological Oceanography Program supports research in marine ecology broadly defined - relationships among marine organisms and their interactions with the environment of the sea. Projects that fall within the purview of the program may focus on marine environments ranging from estuarine and coastal systems to the deep sea, and also include studies in the Great Lakes. Areas of research include ecosystem and biogeochemical processes; community and population ecology; behavioral, reproductive and life-history ecology; physiological and chemical ecology; and evolutionary ecology. Proposals due: February 15, 2008. Marine Geology and Geophysics, Chemical Oceanography, and Ocean Drilling Program share this deadline.

National Research Initiative: Microbial Genome Sequencing Program FY 2008 - This call invites research proposals (i) to support high-throughput sequencing of the genomes of microorganisms (including viruses, bacteria, archaea, fungi, oomycetes, protists and agriculturally important nematodes) and (ii) to develop and implement strategies, tools and technologies to make currently available genome sequences more valuable to the user community. Example topics: novel aspects of microbial biochemistry, physiology, metabolism, development and cellular biology; the diversity and the roles microorganisms play in complex ecosystems and in global geochemical cycles; the impact that microorganisms have on the productivity and sustainability of agriculture and natural resources (e.g., forestry, soil and water), and on the safety and quality of the nation's food supply; and the organization and evolution of microbial genomes, and the mechanisms of transmission, exchange and reshuffling of genetic information. Proposals due: February 19, 2008.

NSF Chemical, Bioengineering, Environmental, and Transport Systems (CBET) - Environmental Engineering - The Environmental Engineering and Sustainability cluster supports engineering research with the goal of reducing adverse effects of solid, liquid, and gaseous discharges into land, fresh and ocean waters, and air that result from human activity and impair the value of those resources in the context of ecological tenets. This cluster focuses on research on innovative biological, chemical, and physical processes used alone or as components of engineered systems to restore the usefulness of polluted land, water, and air resources. Major areas of interest and activity in the program include developing innovative biological, chemical, and physical treatment processes to remove and degrade pollutants from water and air; measuring, modeling and predicting the movement and fate of pollutants in the environment; and developing and evaluating techniques to clean up polluted sites, such as landfills and contaminated aquifers, restore the quality of polluted water, air, and land resources and rehabilitate degraded ecosystems. Proposals due: March 1, 2008.

Don't forget that the SBI has funding available for proposal development and maintains a list of external grant opportunities related to the subsurface biosphere.

This newsletter is distributed by OSU's Subsurface Biosphere Initiative - an interdisciplinary consortium of faculty and students who share interests in underground ecosystems. The newsletter is distributed through the SBI email lists. To subscribe or unsubscribe, go to Questions, comments and newsletter topics may be sent to the Newsletters are also available on the Web at