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Tiny animal will be used to diagnose environmental problems

September 8, 2010
Bloomington, Indiana --

Environmental scientists seeking new ways to sense and diagnose impending environmental and human health disasters returned from Maine last week with new ideas about how to use a common water flea species, Daphnia pulex, as a modern era equivalent to the coal mine canary.

The nine-day event at Mount Desert Island Biological Laboratory (MDIBL) was a course for veteran scientists and scientists-in-training -- taught by a diverse array of scholars -- who are collectively creating a new field of science called "environmental genomics," largely centered around water flea genomes. Course planners at Indiana University and MDIBL intend for this gathering to occur every August.

"The point is to put into people's hands the knowledge and tools to use technological advancements in genomics research, and apply these to ecology and environmental health research," said John Colbourne, genomics director of the IU Bloomington Center of Genomics and Bioinformatics and one of the course's organizers. "We are helping people think about studying environmental stress by looking at what happens to whole populations from a genetic perspective. This knowledge may one day facilitate decisions on how to mitigate environmental threats, such as knowing the biochemical effects of dispersants used in response to the oil spill disaster in the Gulf of Mexico."

By employing high-throughput genomics techniques, scientists are able to study not merely the genome of a single water flea but the genomes of whole populations. Genomes are composed of all the genetic information of a living organism. By examining changes in the DNA and in the expression of genomes, scientists can see how animals' genes respond to environmental stress like organic pollutants, heavy metals, pharmaceuticals, parasites, changes in water chemistry, acidity, temperature and their mixtures. Even subtle changes in environmental conditions may represent serious health risks for animal populations in nature, including humans.

"We've documented how Daphnia populations have adapted to survive in metal-contaminated lakes," said Joe Shaw, co-organizer of the course and assistant professor at IU Bloomington's School of Public and Environmental Affairs. "We are definitely getting a sense for what organisms can tolerate and how they react physiologically and genomically when stressed."

The idea behind the new technology is that the water flea genome can serve as a complex litmus strip. By examining which genes are turned on or off in a given population of water fleas, the scientists believe they can determine the presence of biological hazards -- and their effects -- even at very low concentrations.

IU Bloomington Center for Genomics and Bioinformatics (CGB) staff lead the Daphnia Genomics Consortium and collaborate with other IU scientists who also manage the comprehensive database of Daphnia genetic information and publications known as wfleabase (http://wfleabase.org/), a sly nod to IU Bloomington's FlyBase, a similar resource for fruit fly scientists. Colbourne says that the CGB is poised to become a center of excellence for environmental genomics research.

"We are excited to partner with the CGB in this important effort launched by John Colbourne and Joe Shaw," said MDIBL Director Kevin Strange. "MDIBL has a long history in environmental research, and our scientists are committed to improving human health and the health of our environment. The research projects and the customized technologies used in the course are really modernizing the field."

Guest lecturers at the course were IU Bloomington Center for Genomics and Bioinformatics Director Peter Cherbas and Rudy Professor of Statistics Karen Kafadar, as well as Kansas State University's Michael Herman, the National Institute of Environmental Health Sciences' Douglas Bell, the Jackson Laboratory's Gary Churchill, the University of California Los Angeles' John Novembre, and Princeton University's Leonid Kruglyak.

"This course was an important step for environmental genomics -- I was happy to help kick it off," said Michael Herman, co-director of the Ecological Genomics Institute at Kansas State University. "Given the caliber of participants at this early phase of research, everyone gained from the hands-on experience of testing how the environment changes gene functions and from discussing how environment-gene interactions might influence ecological processes."

Course takers were given instruction in using a high-throughput Daphnia pulex microarray, which was developed by the IU Center for Genomics and Bioinformatics in partnership with Roche NimbleGen Inc. The microarray contains DNA from all the genes of the genome, to simultaneously conduct twelve assays on a single microscope glass slide and interrogate when genes are activated. Also provided was instruction in bioinformatics data analysis from MDIBL course organizer Ben King, with sections on experimental design, statistics and how to deal with millions of data points collected from a single experiment. Scientists with Indianapolis-based Beckman Coulter Inc. were also on hand to demonstrate the use of robots and automated protocols designed to help environmental genomicists do molecular biology research on large numbers of samples representing whole populations.

"We've learned through the Daphnia research consortium that a sure way to incite rapid growth of a critically important field of research is to be very open and make as much data and tools available to researchers as possible," Colbourne said. "This course was very much devised with the next generation of researchers in mind."

The course was organized by the IU Center for Genomics and Bioinformatics and the Mount Desert Island Biological Laboratory, partly as a function of the Indiana University Consortium for Environmental Genomics and Toxicology. Roche NimbleGen Inc. provided high-density NimbleGen Daphnia pulex gene-expression microarrays, reagents for sample labeling and downstream processing, and a NimbleGen MS 200 Microarray Scanner. Beckman Coulter Inc. provided access to the Biomek FXP automation workstation. California-based Life Technologies provided other necessary reagents.

To speak with Colbourne or Shaw, please contact David Bricker, University Communications, at 812-856-9035 or brickerd@indiana.edu.


Web version:
http://newsinfo.iu.edu/news/page/normal/15434.html