February 2011

The next issue of GenomeLIFE will hit the stands soon. The special February/March issue will highlight researchers representing many different departments and disciplines at Duke who are all seeking fundamental biological insights with the help of new genomic technologies and a systems biology approach.

You'll get a glimpse of recent discoveries made in studies of the model plant Arabidopsis that have shown us that microRNA can move from cell to cell, how growth and development are linked and a way to make plants grow faster. You'll also meet researchers working on everything from microbes that live in some of the saltiest places on earth to sea urchin larva, nematode worms to mice and even red-eared slider turtles, to address questions about how cells and organisms deal with stress, change their fates and decide which sex they will be. Others featured are applying systems approaches in a more clinical arena, to dissect the networks underlying cancer's incredible diversity. In each and every case, the ultimate goal is the same: to get a little closer to understanding life in all its wonder and complexity.

Be sure to pick up a copy and, as always, if you have a story idea for a future GenomeLIFE issue, please drop us a line at igsp-news@duke.edu.

We'd also like to take this opportunity to recognize François Lutzoni in the Department of Biology as the newest member of the IGSP. The Lutzoni lab studies symbiosis in lichens and has recently sequenced the fungal and algal genomes of a representative lichen known as Cladonia grayi. Some of his work was featured in the cover story of the last GenomeLIFE issue. Welcome François!

IGSP Reviews Organization, Future Plans
The Chronicle reports that the IGSP will undergo an extensive, two-phase assessment. Learn more about the planning process now underway to design "IGSP 2.0" at genome.duke.edu.

Going Where No One Had Gone - Via Spreadsheet
A Forbes blog posts a series of videos in which Misha Angrist talks about his book "Here is a Human Being," which journalist Matthew Herper calls "a ripping good yarn and one of the best handbooks on the big changes coming from DNA sequencing."

Patents, Not Just Politics, Create Obstacles to University Stem-Cell Research
Information-sharing and patent issues are common throughout science, but the problem is especially severe within stem-cell research because of the field's birth amid political controversy, Bob Cook-Deegan says in The Chronicle of Higher Education.

Mind Reading: Geneticist Misha Angrist on Publishing His Genome. TMI?
Time Magazine's Healthland reports a Q & A with Misha Angrist about what it's like to make your genome public and write a book about it.

Report Urges Defense to Collect Genome Data on All Troops
In a nextgov.com article about a report that urges the Defense Department to collect human genome sequence data from military personnel, Bob Cook-Deegan says they do not make a deep or persuasive case on how genomic information could help Defense better manage conditions such as PTSD.

Friends With (Genetic) Benefits?
In reference to a study that suggests that when it comes to certain genes friends of a feather flock together, Misha Angrist tells Time Healthland that he believes a person's actual behavior and personality will always be more important than genetics when it comes to social behavior.

Sequencing Alone Doesn't Offer True Picture of Human Disease
To really understand disease, "you must have a robust way to test the functional relevance of mutations you find in patients," says Nicholas Katsanis in a release about his study in Nature Genetics on variants that can cause ciliopathies and interact with other disease-causing genes to yield other kinds of problems.

New Software Quantifies Leaf Venation Networks
ScienceBlog reports on a user-assisted software tool that extracts macroscopic vein structures directly from leaf images and another, developed in collaboration with Philip Benfey and John Harer, that allows analysis of the complex root network structure of crop plants.

Study Says Depression Gene Exists
A new meta-study supports the idea that the serotonin transporter gene really is a depression gene, an advance that Terrie Moffitt says will "close the chapter" on the controversy. The development was also reported by the Los Angeles Times and ABC News.

Transcription Initiation Patterns Indicate Divergent Strategies for Gene Regulation at the Chromatin Level
In PLoS Genetics, Uwe Ohler and Jun Zhu report evidence that promoter classes defined from 5' capped transcripts not only reflect differences in the initiation process at the core promoter but are also indicative of divergent transcriptional programs established within gene-proximal nucleosome organization.

Gene By Sex Interaction for Measures of Obesity in the Framingham Heart Study
In the International Journal of Obesity, Jeanette McCarthy reports data in support of a sex-influenced association between genetic variation in a gene known as LYPLAL1 and obesity-related traits.

Histone H3K4 Methylation Keeps Centromeres Open for Business
In the EMBO Journal, Beth Sullivan writes about a new study showing that open chromatin and satellite DNA transcription are linked to centromere maintenance.

A Stele-Enriched Gene Regulatory Network in the Arabidopsis Root
In Molecular Systems Biology, Philip Benfey and colleagues report data from high spatial resolution gene expression experiments and yeast one-hybrid and two-hybrid assays showing that upstream transcription factors are expressed in more diverse cell types than their targets and that promoters bound by a relatively large number of transcription factors correspond to key developmental regulators.

Outcrossing, Mitotic Recombination and Life-History Trade-Offs Shape Genome Evolution in Saccharomyces cerevisiae
In Proceedings of the National Academy of Sciences, Paul Magwene and colleagues provide new insights into the roles that both outcrossing and mitotic recombination play in shaping the genome architecture of the yeast S. cerevisiae.

Allele-Specific Gene Expression in a Wild Nonhuman Primate Population
In Molecular Ecology, Jenny Tung, Susan Alberts and Greg Wray report results illustrating how environmental and ecological data can be integrated into evolutionary genetic studies of functional variation in natural populations.

Comparative Expression Analysis of the Phosphocreatine Circuit in Extant Primates: Implications for Human Brain Evolution
In the Journal of Human Evolution, Greg Wray and colleagues provide evidence that proteins involved in supplying energy to the brain are expressed at higher levels in humans than in non-human primates, a shift that may have been been important in supporting the increased metabolic demands of the human brain.

For details and updates on IGSP seminars and events, see the Events Calendar.

A selection of upcoming events:

Tuesday, February 1st
Tuesday Seminar Series
Mike Resnick from NIEHS will present.

Tuesday, February 1st
Special Seminar
Tim Reddy of the HudsonAlpha Institute for Biotechnology will give a seminar entitled "Personal Functional Genomics: How Variation in Genome Sequence Impacts Gene Regulation" as part of recruitment for a joint faculty position in the IGSP and Department of Biostatistics and Bioinformatics.

Wednesday, February 2nd
Systems Biology Seminar
Gabriel Weinreb from UNC Chapel Hill will present "Causal Mapping as a Standardized Method to Model Biological Systems."

Thursday, February 3rd
Genomic and Personalized Medicine Forum
Vance Vanier, CEO and President of Navigenics, will present "The Advent of Personal Genomic Testing."

Monday, February 7th
Cancer Genomics Seminar
Christi Augustine will speak about targeted therapeutics for the treatment of melanoma.

Monday, February 7th
Computational Biology Seminar
Thomas Kepler will present "Quantitative Systems Vaccinology."

Friday, February 18th
Science & Society Journal Club
Kathryn Maxon will lead a discussion on a current topic at the intersection of science and society.

The National Institutes of Health will provide $1 million in funding for research projects that study how gene and protein expression affect prenatal development of organs in the lower urinary tract.

The National Institutes of Health seeks to stimulate research linking basic genomic discoveries to the prevention and alleviation of symptoms in patients suffering from chronic disorders.

The National Human Genome Research Institute has announced supplemental funding to promote the inclusion of standard phenotypic and environmental exposure measures selected from the PhenX Toolkit into existing population-based genomic studies supported by the NIH.

The National Institute on Drug Abuse is soliciting proposals on the pharmacogenetics of drug addiction.