August 2010

The RNAi Core Facility -- a joint venture of the Duke Center for RNA Biology, the Institute for Genome Sciences & Policy and the Comprehensive Cancer Center -- has new (and improved) digs in the basement of the CARL Building.

Facility Manager James Pearson also reports that the facility has now completed five whole-genome screens, including one aimed to uncover the host factors for yellow fever in human cells. You can expect to see a published report on those results in the coming months.

James Pearson, Nicholas Barrows and colleagues have aready published a related report in The Journal of Biomolecular Screening on factors affecting the reproducibility between siRNA-based screens at the genome-scale. Through comparisons between identical RNAi screens for yellow fever host factors, they showed that the reproducibility of the "hit lists" generated depends greatly on the methods used for analysis. The findings led them to propose "that the entire data set derived from functional genome-scale screens, especially if publicly funded, should be made available as is done with data derived from gene expression and genome-wide association studies."

For more information about the services provided at the facility, contact James Pearson at james.pearson@duke.edu or 613-5132.

On another note, a reminder that the final Summer Fellows poster session will be held on August 6th from 10:00 to 11:30 in the IGSP lobby (CIEMAS 2nd floor). Stop by to hear from the undergradaute fellows about their research and findings.

Radio In Vivo: Genomic and Personalized Medicine
On WCOM's Radio In Vivo, Geoff Ginsburg spoke with Ernie Hood on new developments in genomic and personalized medicine.

Mail-In Genetic Testing Unreliable, Misleading
"Part of the problem for consumers is that when you hear genetic risk, it sounds formal and official, but the complexity is mind boggling even to the experts," Susanne Haga told ABC News.

Genetic Testing Raises Question of Patients' Reactions
The News & Observer features Alex Cho's efforts, along with colleagues in the IGSP Center for Genomic Medicine, to examine how changes to perceived risk for getting diabetes based on genetic tests influences behavior.

India Capable of Producing Lower-Cost HPV Vaccine
Vaccine manufacturers in India and other developing nations can produce a lower-cost HPV vaccine despite the complicated array of patent protections on the technology, Yahoo! News reports. The article is based on a study in Nature Biotechnology by Subha Chandrasekharan, Bob Cook-Deegan and recent graduate Swathi Padmanabhan.

Alzheimer's Gene Acts on Middle Aged People, Researchers Say
Bloomberg News featured new findings by Allen Roses and colleagues suggesting that middle-aged people carrying a high-risk variant of a gene linked to Alzheimer's already have less brain volume and do worse on tests of memory and learning.

Op-ed: Genes and a Sporting Chance
In an op-ed inspired by news that NFL wide receiver Chris Henry was suffering from degenerative brain damage at the time of his death, Hunt Willard writes "if some athletes - perhaps graced by their genome with better odds of success - might also have inherently better odds of a career- or life-threatening injury by virtue of the genes they've inherited, it adds a new dimension to the very thin line between what announcer [Jim] McKay called "the thrill of victory" and "the agony of defeat."

Op-ed: The Human Genome at Ten
In a Herald-Sun opinion piece, Susanne Haga says that "some have concluded that the genome revolution hasn't lived up to its billing. But, the truth is, it's really too soon to say."

NSF Award to Help Develop Mighty Mini Protein Factories
ECN Magazine featured research by Lingchong You aimed to create "miniscule cellular factories that create and pump out whatever he likes, such as a protein that the body cannot produce itself."

Controversies in Medicine: Direct-to-Consumer Genetic Testing
At this point in the evolution of the field of personalized medicine, it is clear that patients who wish to "take control" of their health should do so in collaboration with their health care provider, writes Geoff Ginsburg in Duke Med Magazine.

The State of Things: DNA Collection
On WUNC's The State of Things, Sara Katsanis discusses a new N.C. law that will allow law enforcement officers to collect DNA samples from suspects arrested for violent felonies. Learn more about the status of such "Katie's laws" here. An op-ed written by Katsanis and Chris Heaney on this topic ran in papers around the country.

Spatiotemporal Regulation of Cell-Cycle Genes by SHORTROOT Links Patterning and Growth
In Nature, Philip Benfey and colleagues provide evidence for a direct link between developmental regulators, specific components of the cell-cycle machinery and organ patterning. Read the news release.

Sex and Age Differences in Lipid Response to Chronic Infection with the Hepatitis C Virus
Jeanette McCarthy and colleagues report results in the Journal of Viral Hepatitis that show hepatitis C infection is associated with lower cholesterol levels in two US cohorts, and that this relationship varies by age and sex, suggesting a possible influence of sex hormones on host lipid response to the virus.

An Alignment-Free Method to Identify Candidate Orthologous Enhancers in Multiple Drosophila Genomes
In Bioinformatics, Uwe Ohler and colleagues describe an alignment-free method that identifies conserved enhancers in multiple diverged species. The software, data and results are available online.

Diagnosis of Partial Body Radiation Exposure in Mice Using Peripheral Blood Gene Expression Profiles
In PLoS One, John Chute, Joe Nevins, Joe Lucas and colleagues show that partial body irradiation, even to a single limb, generates a characteristic blood signature of radiation injury.

Evolutionary Genetics in Wild Primates: Combining Genetic Approaches with Field Studies of Natural Populations
In Trends in Genetics, Jenny Tung, Susan Alberts and Greg Wray say that, in combination with the rich history of behavioral, ecological and physiological work on natural primate populations, genetic approaches promise to provide a compelling picture of primate evolution in the past and in the present day.

Variation and Fitness Costs for Tolerance to Different Types of Herbivore Damage in Boechera stricta Genotypes with Contrasting Glucosinolate Structures
Tom Mitchell-Olds reports in New Phytologist evidence showing significant genetic variation for tolerance to different types of herbivores in Boechera stricta, a wild relative of Arabidopsis.

Immune Signatures Predict Prognosis in Localized Cancer
In Cancer Investigation, David Hsu and colleagues say that, "in aggregate, the gene expression signatures implicating specific components of the immune response hold prognostic import across solid tumors."

Serotonin Transporter Gene Moderates the Development of Emotional Problems Among Children Following Bullying Victimization
Avshalom Caspi, Terrie Moffit and colleagues report in the Journal of the American Academy of Child and Adolescent Psychology further evidence that the serotonin transporter gene moderates the risk of emotional disturbance after exposure to stressful events.

On July 8th, Allen Buchanan gave testimony on ethical issues in synthetic biology to The Presidential Commission for the Study of Bioethical Issues in Washington, D.C. The presentation was video recorded and is available online. Look for a feature on this topic in the September/October issue of GenomeLIFE.

Susanne Haga participated in a panel on direct-to-consumer testing at the FDA's Public Meeting on Oversight of Laboratory Developed Tests on July 20th.

IGSP researchers, including Susanne Haga, Genevieve Tindall and Julianne O'Daniel, have developed a discussion game designed to improve understanding of genetic concepts and associated ethical and policy issues via fun, informal interactions. The elements of the Genome Diner game are available for download online.

The National Institutes of Health invites applications proposing highly innovative research that will investigate the epigenetic basis of human diseases.

The National Institutes of Health is soliciting research grant applications that characterize epigenetic events involved in neurodevelopmental processes or propose to identify epigenome-wide marks associated with early environmental influences and vulnerability to mental disorders.

The National Institute of Allergy and Infectious Diseases invites applications for research focused on early stage product development projects to establish proof-of-concept for novel or emerging, rapid and innovative clinical diagnostic technologies, that do not involve nucleic acid amplification methods to detect NIAID Category A, B, or C Priority Pathogens and toxins.

The National Center for Research Resources will support development of a wide a range of new biomedical research tools, including core technologies used in genomics and proteomics

The National Institute of Allergy and Infectious Diseases will fund genomics research aimed to help understand why humans who receive transplants often suffer from immune system rejection.

The National Human Genome Research Institute will move into the next phase of its electronic medical records research program with grants that will give around $25.5 million over the next four years to fund investigators and to start a coordinating center to support the research.