DOE JGI Science Highlights: Comparative genomics of social amoebae

Found in soils worldwide, slime molds such as Dictyostelium discoideum are perhaps best known by their behaviors in the presence or absence of food. When food is plentiful, the social amoeba behave as individuals, but when food is scarce, they come together to form multicellular “fruiting bodies” that look like a flower bud atop a single stalk or foot composed of a fifth of the amoebae that have sacrificed themselves for the group.

D. purpureum. (Photo by Chandra Jack, Rice University)

Studying social amoebae allow researchers to learn more multicellularity because they can exist in both single-cell and multicellular states. From a bioremediation perspective however, slime molds are important candidates in cleaning up sites contaminated with chemicals and radioactive materials.

JGI Science @ the Lesher on Walnut Creek Patch

Most of us don’t even think about the insides of cows, the genes of waterfleas or the behavioral genetics of pollinating bees, but the 250 expert researchers who sequence microbial species—and actually understand the results—also know how to translate heavy duty science into layman's language.

Read more on the Walnut Creek Patch

DOE JGI Science Highlights: First analysis of Trichoderma species as biocontrol agents

Trichoderma atroviride and T. virens are filamentous fungi commonly found in the soil and are good at protecting crops such as beans, tomatoes, strawberries and cotton against a range of fungal pathogens. Their ability to do so could offer bioenergy crop growers an alternative to chemical pesticide treatment. Both were selected for sequencing by the DOE JGI, and their improved assemblies were released in 2010.

Trichoderma atroviride (red) growing along the hyphae of a host fungus (green). 

(Photo by Verena Seidl, TU Vienna and Nick Read, Univ. of Edinburgh)

Roberts Wesleyan College in DOE JGI Undergraduate Research Program in Microbial Genome Annotation

Dr. Roll attended an informational workshop at the end of January at the DOE Joint Genome Institute in Walnut Creek, Calif. Since that time, he has been preparing plans and programs that will allow Roberts students to participate in this initiative in a hands-on manner. The College already has been assigned a specific genome for its research: Hydrogenbacter thermophilus DSM 6534.

Read more at GatesChiliPost.com

Methylmercury-producing bacterium in Shorelines

A newly decoded bacterial genome brings scientists one step closer to unlocking the secret behind the production of methylmercury, the chemical notorious for contaminating tuna and other seafood.

Most mercury pollution comes from the burning of fossil fuels. Once in the atmosphere, it seeps into the rain and gradually trickles down to the sea. Certain bacteria that thrive in sediments and soils then transform it into methylmercury, a much more dangerous neurotoxin which latches onto proteins and works its way up the food chain. 

Read more at Shorelines.

DOE JGI Science Highlights: Arabidopsis lyrata reference genome now available

Arabidopsis thaliana is a small flowering plant often used as a model system by researchers. As part of the 2006 Community Sequencing Program portfolio, the DOE JGI selected A. thaliana’s close relative A. lyrata for sequencing. By comparing their genomes and the genomes of other, related species, researchers could gain insight into plant genetics, specifically how they respond to disease and environmental stress.

Arabidopsis lyrata (Image by Outi Savolainen, University of Oulu, Finland)

In a report published online April 10, 2011 in Nature Genetics, a team of researchers led by collaborators Magnus Nordborg and Detlef Weigel and including DOE JGI’s Igor Grigoriev and Jeremy Schmutz at the HudsonAlpha Institute for Biotechnology compared the sequences of A. thaliana and A. lyrata.

Methylmercury-producing bacterium in Smithsonian Science

The new genome, sequenced at the California-based DOE Joint Genome Institute, and completed at Oak Ridge National Laboratory, was published in the Journal of Bacteriology. It lays the foundation for future research to examine the little understood mechanisms behind the production of methylmercury.

“We know a little about the bacteria that produce methylmercury but we don’t know the mechanism by which they produce it,” adds Cynthia Gilmour, co-author of the study and senior scientist at the Smithsonian Environmental Research Center in Edgewater, Md. “We are going to compare this genome with the genome of non-methylmercury producing bacteria, see what genes are different and try and figure out the mechanism.”

Read more at Smithsonian Science

Arabidopsis lyrata genome project in GenomeWeb

The international research team, led by investigators at the Max Planck Institute for Developmental Biology, compared the newly sequenced genome to the much smaller genome of the model organism A. thaliana. Their findings suggest that the pared down version of the genome found in A. thaliana reflects a spate of small deletions — many affecting transposons and non-protein coding sequences. The study appeared in the early, online version of Nature Genetics yesterday.

 

Read more on GenomeWeb

Brown mercury-producing bacterium in Medical News Today

"What is not known are the genes or the proteins that allow these bacteria to mediate the transformation," said ORNL's Steven Brown, who led a research team to sequence the genome of a bacterium in the Desulfovibrio genus that is capable of methylating mercury.

The new genome, sequenced at the California-based DOE Joint Genome Institute (JGI) and published in the Journal of Bacteriology, lays the foundation for future research to examine the little understood mechanisms behind the production of methylmercury. 

Read more in Medical News Today

Brown mercury-producing bacterium in ScienceDaily

Desulfovibrio desulfuricans strain ND132 is an organism that thrives in sediments and soils without oxygen -- the places in lakes, streams and wetlands where mercury contamination is converted to methylmercury. It is representative of a group of organisms that "breathe" sulfate instead of oxygen and are largely responsible for mercury methylation in nature. "This is the first Desulfovibrio genome that will methylate mercury that's been published," Brown said. "Now that we have this resource, we can take a comparative approach and look at what is different between the bacteria that can methylate mercury and those that are unable to."

Read more in ScienceDaily.

DOE JGI Science Highlights: ORNL collaboration to understand methylmercury production

Mercury pollution in aquatic environments has been a concern, though the contaminants are mainly sourced from industrial processes and fossil fuel combustion. Isolated from Chesapeake Bay sediment, the sulfate-reducing bacterium, Desulfovibrio desulfuricans strain ND132, can also produce the human neurotoxin methylmercury.

Color-enhanced photo from SEM image of sulfate-reducing Desulfovibrio desulfuricans in a biofilm matrix. (Image courtesy of PNNL via Flickr/Creative Commons)

“What is not known are the genes or the proteins that allow these bacteria to mediate the transformation,” said Oak Ridge National Laboratory’s Steven Brown.

Cheryl Kerfeld presents ASBMB award lecture

Cheryl A. Kerfeld, a structural biologist and the head of the U.S. Department of Energy Joint Genome Institute's Education and Structural Genomics Programs, has won the American Society for Biochemistry and Molecular Biology's Award for Exemplary Contributions to Education. Kerfeld will present her award lecture, titled "Sequence and Consequence," at 12:30 p.m. on April 10 at the Experimental Biology 2011 conference at the Walter E. Washington Convention Center in Washington, D.C.

Read more on FirstScience.com

DOE JGI's Cheryl Kerfeld among 2011 ASBMB awardees in Washington DC

Cheryl A. Kerfeld, a structural biologist and the head of the Department of Energy Joint Genome Institute's Education and Structural Genomics Program, won the ASBMB Award for Exemplary Contributions to Education. Kerfeld, who also serves as an adjunct professor at the University of California, Berkeley, was named the winner for encouraging effective teaching and learning of biochemistry and molecular biology through her own teaching, leadership in education, writing, educational research, mentoring and public enlightenment. 

Read more on News-Medical.net