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Institute for Genomics and Systems Biology, 454, Illumina, Center for Research in Agricultural Genomics, National Institute of Environmental Health Services, Virginia Bioinformatics, Vancouver Island University, NIH, Li-Cor, Tiger Woods Learning Center, U

Argonne's IGSB to Use 454, Illumina Sequencers for Microbial Research
The Institute for Genomics and Systems Biology, a joint venture of the Department of Energy's Argonne National Laboratory and the University of Chicago, said this week that it has acquired two second-generation sequencers: a Roche/454 GS FLX and an Illumina Genome Analyzer.
IGSB said it acquired the instruments primarily to support three research projects at Argonne: a study of how microbes in the soil facilitate carbon dioxide sequestration; a metagenomic study of the microbial population in time series plots at DOE's Fermi National Accelerator Laboratory; and another metagenomic study of the role of microbial communities in subsurface remediation of inorganic contaminates.
The systems will also be available to other Argonne and University of Chicago researchers who require DNA sequencing. IGSB said it also intends to make the instruments available to “select peer-reviewed proposals" from researchers from other organizations in the near future.

Spanish Center Buys 454 Sequencer for Melon Project
A new scientific institute in Spain plans to use a 454 sequencer for de novo sequencing of the muskmelon, a smooth-skinned type of melon group that includes the honeydew, Roche said last week.
The Center for Research in Agricultural Genomics in Barcelona recently bought a 454 Genome Sequencer FLX, and will use it for melon research and other projects. CRAG is a consortium between the Spanish National Research Council, the Institute for Food and Agricultural Research and Technology, and the Autonomous University of Barcelona, and is funded by several agricultural and seed companies.
The institute, which will focus on plant and animal genomics, will begin work with 200 employees, 50 of them scientists. It is expected to be fully operational in 2009 in a new building on the campus of the Autonomous University of Barcelona in nearby Bellaterra.
The project to sequence the 450-megabase melon genome will begin by the end of 2008, according to Roche. A pilot phase is already underway.
The GS FLX will initially be used for whole genome and BAC sequencing, small RNA analysis, and transcriptome sequencing.

NIEHS Plans to Contract Illumina for Sequencing Service
The National Institute of Environmental Health Services in Research Triangle Park, NC, plans to use Illumina’s sequencing service for small RNA expression profiling and resequencing, according to a presolicitation posted on the Federal Business Opportunities website this week.
The service involves two projects: generating a small RNA expression profiling dataset of 33-base signature tags, at least two million tags for each of six samples; and generating a resequencing dataset of 33-base signature tags, at least 250 megabases for each of six samples.
According to the website, the notice “is not a request for competitive proposals; however, all responses received within eight days from the date of publication of this synopsis will be considered by the government.”
If no responses are received within that time “to determine whether a qualified source is more advantageous to the government, the order will be issued to Illumina,” the website stated.

Virginia Tech Researchers, Collaborators Sequence Cattle Bacteria Brucella
Scientists at the Virginia Bioinformatics Institute at Virginia Tech and collaborators have sequenced the genome of the bacterium Brucella abortus strain S19.
B. abortus causes the disease brucellosis in cattle and can cause spontaneous abortions. Cows found to have the disease are usually killed. However, the S19 strain does not cause disease and is used as a vaccine to protect cattle against brucellosis.
Researchers are hoping that its genome may “hold the secret as to why other Brucella strains cause disease and trigger the abortion of developing embryos in livestock,” according to a VBI statement.
VBI collaborated with researchers at the National Animal Disease Center in Ames, Iowa, and Roche subsidiary 454 Life Sciences on the project, using 454’s GS FLX and GS 20 sequencers. The results of their study are published in the current issue of PLoS One.
By using both pyrosequencing and Sanger sequencing, the researchers assembled 99.5 percent of the 3.2 Mb genome after one day of sequencing. The S19 genome is comprised of two circular chromosomes: one that is 2,122,487 base pairs long and the other that is 1,161,449 base pairs long. The average length of the sequence reads in this study was 110 base pairs, according to the paper.
"Further studies are underway to characterize the short list of protein differences that appear to be involved in cellular processes ranging from lipid transport and metabolism to transcription and protein transport,” said VBI’s Cyberinfrastructure Group Project Director Oswald Crasta, who is the corresponding author on the paper. “We believe that this characterization will explain why strain S19 has been such a successful vaccine over the years and why infection with other strains leads to disease," Crasta added.
Funding for the S19 sequencing research came from VBI and the Commonwealth Research Initiative, and the data analysis was funded in part through a grant from the National Science Foundation. The preparation and submission of genomic sequences to GenBank were funded by the National Institute of Allergy and Infectious Diseases.

Vancouver Nets $400K for Shellfish Genomics Lab
The Canadian government has granted Vancouver Island University CDN$400,000 ($393,000) to start a genomics lab focused on studying shellfish.
The University said last week it plans to use the funding from Western Economic Diversification Canada, a department of the government of Canada, to expand the Centre for Shellfish Research by starting the Shellfish Genomics Laboratory.
Specifically, the money will go to buy genomics research equipment that will be used to help study biological and environmental stress factors inherent in shellfish.
VIU also plans to develop research tools to diagnose stress factors that are related to the transportation, pollution, and the environment in larvae and adult shellfish that are raised in hatcheries.

NIH Unveils Enhancements and Improvements for Peer Review
The National Institutes of Health unveiled last week during a meeting of advisors its plans to enhance and improve its peer review system.
The changes follow a year-long effort to solicit new ideas from a variety of interested stakeholders and administrators that generated thousands of comments, opinions, and criticisms, the NIH said.
The mandate on which the peer review working groups focused was to “fund the best science, by the best scientists, with the least administrative burden," said Lawrence Tabak, director of the National Institute of Dental and Craniofacial Research and a co-chair of the two groups.
The new peer review system would encourage and expand the Transformative Research Pathway, reduce the burden of multiple rounds of submission for the same application, ensure balanced reviews, and improve the transparency of the reviews, said NIH. The new policies also intend to improve the quality of reviews and shorten the length of applications dramatically to 12 pages and an eight-page appendix, said Taback.
“First-rate peer review is a cornerstone of what NIH does, but our reality of course is that the increasing breadth and complexity of science has created new challenges for peer review,” Tabak said at the meeting of the Advisory Committee to the Director.
The NIH expects that the changes will increase the flexibility of service for reviewers, and will formally acknowledge their efforts and give them further compensation for their time and effort. Another core idea of the new policies is that the NIH will develop a permanent process for continuous review of the system.
Some of the policy changes include the expanded use of flexible deadlines, and spreading a 12-session reviewer commitment period over a four- to six-year period, Tabak told the audience.
He also said that reviewers who have provided outstanding and sustained service for a minimum of 18 full study section meetings as chartered members may apply for an administrative supplement of up to $250,000. Reviewers also may request to be considered for Merit/Javits awards on a competitive basis.
As part of an effort to streamline the review process and to increase reliability, the scale by which peer reviewers must identify the merit of an application will be shortened from a 41-step scale to a 7-step scale.
The review process also will focus on central criteria such as the impact of the research, an investigator’s innovation or originality, and the feasibility of the project’s plan.
More information about the peer review plan can be found here.

Li-Cor Biosciences Provides DNA Sequencer for After-School Programs
Li-Cor Biosciences of Lincoln, Neb., is providing the Tiger Woods Learning Center in Anaheim, Calif., with a DNA sequencer, to be used in after-school science programs for children in grades five to 12.
"We are providing the TWLC with one of our DNA sequencing systems to further enhance the hands-on experience in two of their current programs," said Jeff Harford, LI-COR product manager, in a statement.
TWLC, which offers free enrichment classes in reading, math, science, and technology, will use the company’s Li-Cor 4300 Genetic Analyzer in two of its science programs.

Viral Metagenomics Research Hints at Potential Ecological Influence of Treated Waste
BOSTON - A team of researchers, led by University of South Florida marine microbiologist Mya Breitbart, has uncovered unexpected viruses — among them plant and insect viruses — in human fecal samples and in treated and untreated sewage. The work provides clues about viruses that could ultimately become bioindicators, flagging areas contaminated by human sewage. It may also have ecological implications, since recycled wastewater is increasingly being used as a source of water for irrigation.
Karyna Rosario, a graduate student in Breitbart’s lab, presented the work at the American Society for Microbiology meeting last week.
Although it’s possible to estimate the overall viral abundance in the environment, Rosario explained, identifying specific viruses is trickier. Metagenomics offers a potential solution, making it possible to look at viral diversity and discover viruses that would otherwise remain imperceptible.
Because viruses in the human gastrointestinal tract can influence human body functions and the microbial flora dwelling within, Breitbart and her team decided to explore this viral diversity. They first applied viral metagenomics to human fecal samples, extracting viral nucleic acids — either DNA or RNA — from filtered and purified human fecal samples. By sequencing these nucleic acids and comparing the sequences to those in available databases, they were able to start characterizing the viral flora in the feces of healthy humans.
The researchers found that some 60 percent of the DNA viral sequence was from unknown viruses. “There’s a lot of novelty in these genes and we have no clue what these sequences are,” Rosario said. Amongst the known genes, most sequences identified were from phages — viruses that infect bacteria.
While that made sense, Rosario said, given the abundance of bacteria in the human gut, the team still expected to find human viruses when they looked at the RNA virus metagenome. Instead, the viral sequences most often came from a plant pathogen called the pepper mild mottle virus or PMMoV, which causes malformation and mottling in pepper plants.
They found PMMoV in three different libraries, all of which were sequenced by high-throughput pyrosequencing by collaborators at the Genome Institute of Singapore: two libraries of RNA viral genes from one individual’s feces at different times and a third library from another individual.
And the pepper virus wasn’t just detected in those two individuals. When the researchers expanded their search to include 18 people from San Diego or Singapore, they found PMMoV sequence in the feces of 78 percent of those living in San Diego and 67 percent of those living in Singapore. It was also detected in every raw sewage sample tested in 11 states.
“The first guess is that it’s probably coming from our food,” Rosario said. But, as it turned out, those carrying PMMoV weren’t necessarily eating peppers. When Breitbart and her team tested a variety of foods for PMMoV, they didn’t find the virus in any of the fresh peppers tested. They did find it in several processed foods, though, including chili sauces, chili powder, and Indian curry.
Subsequent experiments indicated that the PMMoV that had passed through the human digestive system could successfully infect plants, suggesting humans unwittingly help the viruses get to their preferred hosts. “We are probably vectors of the virus,” Rosario said.
That made the researchers wonder what happens to the viruses in human waste when we treat sewage and convert it back into water — a process called wastewater reclamation. Because of water shortages in some areas, reclaimed water has increasingly become an alternative to other water sources for agricultural and other irrigation.
Breitbart’s team decided to use their metagenomic approach, combined with transmission electron microscopy and PCR analysis, to see whether DNA or RNA viruses from human waste survived sewage treatment. So far, they have discovered an abundance of viruses in the treated wastewater, including PMMoV and many unknown viral sequences.
Once again, there were surprises amongst the known genes. The RNA virus metagenome boasted a bounty of sequences from viruses that normally infect insects.
The team is continuing their characterization of these and other viruses in the reclaimed wastewater — work that may inform the way such water is used in the future. And, Rosario said, by combining metagenomics with complementary techniques, they hope to get a more complete understanding of what’s happening in that water source.
“Metagenomic sequencing can reveal the unexpected,” Rosario concluded. “It shows you what’s there, not just what you’re looking for.”
— By Andrea Anderson; originally published on GenomeWeb Daily News

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.