Ah, Grant Review

Have strong feelings on the NIH grant review process? Well, here's your chance to sound off and vent your frustrations with a reader poll over at DrugMonkey's place. The purpose of the poll is to determine whether the number of summary statements and the review service changes the way researchers view the alleged flaws in the review process. If you've got a bone to pick because, for example, a really high percentage of your applications have received seriously flawed reviews, let your voice be heard so that maybe, just maybe, things might be better for the next generation of investigators.

Outsourcing Sequencing

At Science Progress, Scripps' Jeanne Loring explores the possibility that American researchers will soon be outsourcing their sequencing projects to China. China's sequencing capability is growing rapidly, she writes, pointing out that BGI has ordered 128 Illumina sequencers, bringing the total number of sequencers there to 157 — nearly double what the Broad Institute has. Instrument and reagent costs are only part of the price of sequencing, Loring says. "The Chinese will be able to achieve with DNA sequencing just what they attained in the manufacturing industry: the ability to do it cheaper and faster than anyone else," she says.

A Drug Company and the Poor

The New York Times profiles GlaxoSmithKline's Andrew Witty, particularly focusing on his efforts to help the poor. Witty has promised to limit the price of GSK drugs in poor countries to no more than 25 percent of what they charge in wealthy nations and to donate one-fifth of the profits from poor countries to build up their healthcare systems. Witty, of course, has his detractors. Daniel Berman, who began the Doctors Without Borders' Access Campaign says that moving vaccine technology to middle-income countries was "still a lot of smoke and mirrors" and that GSK's malaria-focused lab in Spain "still doesn't have a big enough budget to make a difference." Witty has won over others, including Oxfam's Sophia Tickell. "I'm in charge of an organization that can actually make a difference for people in the third world, and I am not going to be the person who, after X years, sits back and says, 'Oh, I wish I'd done more,'" Witty says.

CAREERS: Keeping the Balance

Tunisia Riley at Under the Microscope compiled a list of family-friendly companies in science, technology and health. She says that each of the companies on her list "have one or more of the following: a high percentage of women employees, good paid maternity/paternity leave, on-site childcare and a proven commitment to a work-life balance for their employees." And that list includes Cornell University, Eli Lily, and Genentech, among others.

This Week in PNAS

This week in the PNAS Early Edition, researchers show a relationship between RNA polymerases II and III by using ChIP-Seq studies to map their in vivo binding sites throughout the human genome. In the investigation of two cell lines, GM12878 and K562, Pol II was found to bind near many known Pol III genes, as well as a number of previously unidentified Pol III targets. The team also found that transcription factors normally associated with Pol II transcription were also closely connected with Pol-III-transcribed genes. Their results refute the previous expectation that RNA polymerases operate independently from one another, showing that Pol II and Pol III can work together to globally coordinate gene expression.

Research of out of Iowa State University demonstrates that AtIWS1, a protein implicated with the post-recruitment and transcription elongation processes of RNA polymerase II in Arabadopsis thaliana, is required for brassinosteroid-induced gene expression. The researchers found that loss-of-function mutations in AtIWS1 resulted in overall dwarfism, hypersensitivity to a transcription elongation inhibitor, reduced BR response, and, therefore, a genome-wide decrease in BR-induced expression in the model plant. The team writes that their study establishes an important role for AtIWS1 in plant steroid-induced gene expression and also suggests the possibility that the protein can be used as a target for pathway-specific activators in Arabidopsis.

In this week's advance online publication of PNAS, California Institute of Technology researchers discuss connections within the neural crest gene regulatory network, specifically the function of Sox10 as one of the earliest neural crest-specifying genes. The team found that Sox10 drives delamination and directly regulates several downstream effectors and differentiation gene batteries. In performing ChIP, DNA pull-down, and gel-shift assay experiments, the team also demonstrates Sox10E2 - the earliest acting neural crest cis-regulatory element-binding to its enhancer in vivo. This cis-regulatory analysis helped the researchers to establish the direct link of upstream effectors to a key neural crest specifier.

Also in PNAS this week, Markus Rinschen and his international colleagues describe their use of mass spectrometry-based quantitative phosphoproteomics to identify signaling pathways involved in the short-term V2-receptor-mediated response in murine renal collecting duct cells. Using the mouse model, Rinschen's team created two treatment groups: one received 0.1 nM dDAVP, the other merely the treatment vehicle. In the quantification of 2884 phosphopeptides, the researchers establish the roles of multiple V2-receptor-dependent signaling pathways in the vasopression signaling network of collecting duct cells.

Money, Mouths, and All That

ScienceInsider looks at the 2011 NIH budget to determine whether Francis Collins is favoring big science over single-investigator grants. Collins is emphasizing his five themes — high-throughput technologies, translational science, health care reform, global health, and reinvigorating biomedical research — and those areas have received large increases in the budget proposal. However, in 2011 NIH will fund 199 fewer research project grants will be funded. The Federation of American Societies for Experimental Biology's Howard Garrison says that change isn't due to policy, but a two percent increase in grant size. "Overall, the number of RPGs is rising, and the amount of money for them—$17.1 billion in 2011—is going up 3.2%, in step with NIH's overall budget," ScienceInsider says.

Looking at Diversity

Researchers are hoping to capture some of the diversity seen in Latin Americans through the new Slim Initiative for Genomic Health between the Broad Institute and Mexico City's Carlos Slim Health Institute, says MIT's Technology Review. That project is still in the planning stages — though it will include gene sequencing and microarray-based studies — but INMEGEN published a Mexican version of the HapMap last year. "We can clearly see different components in the admixture pattern in the Mexican population," says Gerardo Jimenez-Sanchez, former director of INMEGEN. "We can also observe that the Mexican population is a range of admixture from those individuals who are very European to those who are very indigenous." Jimenez-Sanchez adds that "if personalized medicine is going to become a global phenomenon, then scientists need to understand the genomes of all the world's population."

"All the Same"

Coming to televisions near you (or online) this week is a show from Harvard's Henry Louis Gates, Jr. In Faces of America, Gates will use genealogy and genetic tools to look into the family histories of 12 Americans, including Stephen Colbert, Yo-Yo Ma, and Meryl Streep. The series kicks off this Wednesday on PBS at 8 Eastern and will be available on line the following day. "[We] used DNA analysis to look for "deep cousins" — common ancestors among our guests — and we found genetic connections between eleven of our twelve guests. I found that despite all our apparent differences in terms of culture and history, we are all the same," Gates says in a PBS blog post.

This Week in PLoS

In this week's issue of PLoS Genetics, researchers at the University of Georgia report their identification of the DNA-binding domain of a centromere binding protein, CENPC, in maize. They demonstrate that CENPC requires a single-stranded RNA to effectively bind DNA in vitro, and, when absent, the accuracy of CENPC targeting to centromeres is reduced. The authors report that their results support the notion that RNA binding ensures that centromeres are stably inherited, a critical function of the epigenetic determination process.

Also in PLoS Genetics, Neil Morgan and colleagues identify mutations of the gene SLC29A3 as the molecular basis for a familial form of syndromic histiocytosis, confirming a direct link between Faisalabad histiocytosis and Rosai-Dorfman disease, as well as other associated phenotypes. Mutations in SLC29A3, characteristic of these disorders, cause the generation of excessive histiocytes which phagocytose other cells and process antigens. The authors surmise that their discoveries will shed light on the pathophysiology of histiocytic disorders, which have been recognized for nearly a century, but have afforded no disease-specific treatments.

Researchers report a universal trend of reduced mRNA stability near the translation-initiation site in both prokaryotes and eukaryotes in PLoS Computational Biology. Using computational methods to predict the thermodynamic stability of mRNA downstream from the start codon, and information from the complete genomes of 340 species, the team found that, in nearly all species, mRNA stability is reduced near the start codon, and that the reduction of stability correlates with the increasing genomic GC content. While the team did not find a genome-wide trend of reduced mRNA stability near the start codon in birds and mammals, they did find such a reduction in the most GC-rich genes.

Meanwhile, in PLoS One, an international team describes VAV2 and VAV3 as candidate disease genes for spontaneous glaucoma in both mice and humans. VAV2/VAV3-deficient mice show early onset of iridocorneal angle alterations and elevated intraocular pressure with the subsequent loss of retinal gangilion cells and optical nerve head cupping, characteristic of glaucoma, which is the leading cause of blindness in humans. The researchers posit that VAV2/VAV3-deficient mice could serve as a useful model to study the pathogenesis of glaucoma in humans.

Arden Bement to Leave NSF

The National Science Foundation Director Arden Bement will be leaving the agency to lead Purdue University's new Global Policy Research Institute, reports ScienceInsider. Bement was appointed director of NSF in November 2004 by President George W. Bush and during his tenure saw the budget get on track to be doubled as well as oversaw new initiatives, adds an NSF press release. Bement will take the helm of the Purdue institute beginning in June.

It's Going to Get Nippy

To close its $150 million budget gap, Yale University will be cutting staff, freezing salaries, and limiting the number of graduate students, reports the New York Times. A memo from Yale’s president and its provost, Richard Levin and Peter Salovey, said these steps were needed because the school's endowment dropped from $22.9 billion in June 2008 to $16.3 billion in June 2009. The Times adds that the memo did not say how many positions would be cut, though the reduction in gradates students will be between 10 and 15 percent. Also, Yale will be turning its heat down, setting thermostats to 68 degrees.

SACGHS on Gene Patents

The Health and Human Service's Secretary's Advisory Committee on Genetics, Health and Society is expected to release six recommendations concerning gene patents, reports ScienceInsider. One of the recommendations advises that Congress exempt gene patents from infringement liability, which ScienceInsider says would "potentially allowing anyone to use any gene patent" and that has drawn the ire of some industry folks.

At Patent Docs, Donald Zuhn notes that BIO President and CEO Jim Greenwood says that these recommendations "would undermine the U.S. patent system and the Bayh-Dole technology transfer system that have served our nation so well." Former Senator Bayh adds that these changes are trying "to reimpose the failed policies of the past, policies that just didn't work."

This Week in Science

In Science this week, a Japanese research team reports that multiple copies of genes coding for ribosomal RNA helps protect the yeast genome following DNA damage. By comparing four Saccharomyces cerevisiae strains with 20 to 110 copies of rDNA genes, the researchers found that low-copy strains were more sensitive to a DNA damaging chemical or ultraviolet light than high-copy strains. Their experiments indicate that rDNA gene sequences contribute to recombination repair and sister chromatid cohesion. For more information, check out a related news story in our sister publication GenomeWeb Daily News.

A trio of authors from the American Association for the Advancement of Science, the University of California at San Diego, and the World Anti-Doping Agency present an ethics paper on the state of gene doping in sports. Researchers must take care in conducting and presenting gene therapy research, they say, and "be aware that some athletes and coaches will be tempted, prematurely and unwisely, to take advantage of results packaged by some as performance enhancement 'breakthroughs.'" As CBC News reports, WADA is hot on the trail of potential gene dopers and is funding research aimed at uncovering this gene doping in Olympic and other athletes.

National Cancer Institute researcher Tom Misteli and his team describe how histone modifications influence alternative splicing in the early, online edition of the journal. They report that histone modification signatures directly affect human gene splicing patterns by mediating the interactions between splice sites and regulators. "Histone marks affect splicing outcome by directly modulating the recruitment of splicing regulators via a chromatin-binding protein," they write.

In Science Translational Medicine, a pair of researchers from the Cleveland Clinic and Case Western Reserve University address the promise and potential problems associated with direct-to-consumer genetic testing, touching on everything from the reliability of the information that these tests provide to physicians' interpretation of test results. "Despite the many challenges raised by DTC genomic testing, we are reminded that commercial interests have sometimes acted as a disruptive force or a technology that drives non-conventional approaches to difficult problems," they write.