Home » The Daily Scan

Big Data Training

The US National Institutes of Health is seeking comments for its the Big Data to Knowledge initiative, Sally Rockey, the deputy director for extramural research at NIH, writes at her Rock Talk blog. The BD2K initiative, she says, aims to find effective ways to use and manage the large datasets coming out of new biomedical studies.

One part of the initiative is to focus on honing the skills of researchers so that they can work with such data, and that, Rockey says, is what NIH wants to hear about. "NIH asks for your input on both the short and long-term training needs of individuals who work with biomedical data, seeks examples of programs or strategies to cross-train scientists at all career levels, and also requests comments on evaluating workforce skills and knowledge and developing a diverse research workforce," she writes.

The comment period ends March 15.

March 01, 2013

This Week in Science

In Science this week, a multi-institute team of Australian researchers reports on the discovery of a protein found in the female reproductive tract that appears to protect against sexually transmitted diseases. The protein, interferon-epsilon, is expressed by cells that line the ovary, uterus, cervix, and vagina, and mice lacking interferon-epsilon are more susceptible to infection with herpes simplex virus 2 and chlamydia. The regulatory and protective properties of interferon-epsilone may "facilitate the development of new strategies for preventing and treating STIs and, perhaps, other diseases," the researchers say.

Also in Science, a group of Japanese and Australian researchers provide evidence that a family of genes called KNOX2 may be behind the haploid-to-diploid morphological transition found in land plants. "In mosses, the haploid gametophyte generation is dominant, whereas in vascular plants — including ferns, gymnosperms, and angiosperms — the diploid sporophyte generation is dominant," the researchers note. In their study, the scientists found that KNOX2 genes appear to suppress the development of a normal reproductive form of moss during its spore-producing generation, "indicating a critical role for the evolution of KNOX2 in establishing an alternation of generations in land plants."

March 01, 2013

All Sequester's Eve

The showdown in Washington, DC, over the sequester is unlikely to be resolved before the March 1 deadline, Politico reports, predicting that bills aimed at preventing the across-the-board cuts are merely "political cover" and will fail to receive the required number of votes to pass the US Senate.

Funding agencies and research institutes across the US are already planning for dealing with funding cuts.

The National Institutes of Health, the Huffington Post reports, has already scaled back some grants by 10 percent in anticipation of the sequester. The National Science Foundation has said, according to ScienceInsider, that its existing grants won't be affected by sequestration, but the number of new grants that it will fund would drop by about 1,000. If the sequester goes into place, the NIH and NSF budgets both face about a 5 percent cut.

Biomedical research labs rely heavily on federal funding to keep their research programs going. Keith Yamamoto, vice chancellor for research at the University of California, San Francisco, notes that salaries and stipends are the biggest costs for most labs. "There's just no way to escape the impact on employment," he tells HuffPo. Scott Zeger, the vice provost for research at Johns Hopkins University, similarly says that labs would have to become smaller under sequestration cuts.

The Harvard Crimson reports that some labs there have sought to contain costs by cutting staff and spending less on equipment and reagents.

The effect, Marc Kastner, a the dean of the School of Science at MIT, tells Tom Levenson at Scientific American's Guest Blog, will be felt most acutely by smaller labs and by graduate students, postdocs, and people who are supported by soft money. "Is ever Eric Lander going to slow down? He'll find a way," Kastner says, adding that "the rich survive and the poor get devastated. The real question is the next generation."

Research will, of course, continue on, but Zeger tells the Huffington Post that the pace will slow. "America will be a little bit less competitive. We're still going to make these discoveries ultimately. It may take a little longer, people may suffer in the meantime, but we're going to make these discoveries. It's human nature," Zeger says to HuffPo. "The question is, what role does America want to play in the discoveries that will define our future?"

February 28, 2013 / 2 comments

The Ome-Ome

In recent years the "omics" business has begun treading dangerously close to New York Times Styles section territory. Just as three people doing something you've never heard of before is enough to make for a "trend", it seems these days any collection of a dozen or so data points qualifies as an "ome."

There are those (we're looking at you, Jonathan Eisen) who have committed themselves to raging against this state of affairs. And then there are those who have just decided to embrace it.

For instance, Nature, which this week put out an all "omes" crossword puzzle — giving lovers and haters alike something to mull over their morning coffee.

The crossword accompanies an article by Monya Baker on the ongoing proliferation of omes in which she observes that, omics-bashing aside, the construction would appear to be here to stay and might, in fact, even prove worthy.

"Ideally, branding an area as an 'ome helps to encourage big ideas, define research questions and inspire analytical approaches to tackle them," she writes.

"It's the idea of everything, it's the thing we find inspiring," adds Yale University computational biologist Mark Gerstein.

That settled, we've got another question for the scientific community: omics, 'omics, or –omics? Feel free to fight it out in the comments.

February 28, 2013 / 2 comments

Nature Buys a Stake in Open Access

Nature Publishing Group has purchased a majority investment in open-access publisher Frontiers, the Nature News Blog reports. Kamila Markram, a Swiss Federal Institute of Lausanne neuroscientist, co-founded the company in 2007 and it now publishes 14 journals, which put out a total of 5,000 articles last year.

Frontiers uses a cooperative peer-review model in which authors and reviewers discuss the papers in an online forum; reviewers' names, the Nature News Blog adds, are listed on the final paper. "Referees and handling editors are named on published papers, which is very unusual in the life sciences community," says Philip Campbell, the editor-in-chief of Nature, in a statement. "Nature has experimented with open peer review in the past, and we continue to be interested in researchers' attitudes."

Because of this approach, Markram says that the journals only reject between 5 percent and 10 percent of papers submitted.

Going forward, the companies say that they will expand the "Frontiers in…" series and have bilateral links between their websites to ensure that open-access papers are visible at both spots. "Combining NPG's established publishing expertise with Frontiers' innovative solutions for researchers opens up a wealth of opportunities for transforming the landscape of science communication," Markram, who is now the CEO of Frontiers, says in a statement. "Frontiers is not only aiming to innovate in open access, but also to provide a more transparent and constructive peer review process, and offer an ecosystem of tools for scientists to build their academic standing."

February 28, 2013

NIPT Tests Abound

With San Carlos, Calif.-based Natera announcing the launch of its prenatal DNA testing, Nature Medicine's Spoonful of Medicine blog says competition in that area is heating up. Bio-Reference Laboratories announced earlier this week, according to our sister publication GenomeWeb Daily News, that it would offer Natera's test. In addition to Natera's Panorama test that identifies chromosomal abnormalities, Ariosa Diagnostics, Sequenom, and Verinata Health, which was recently purchased by Illumina, offer similar services.

David Ferreiro, an analyst at Oppenheimer & Co, tells a Spoonful of Medicine that the prenatal testing market represents "a billion dollar opportunity," especially as some health insurers are moving to cover the tests.

The costs of the tests, Spoonful of Medicine adds, vary, though some differences may be chalked up to what the various tests can identify. The blog also offers a handy chart comparing the methods the tests use, their prices, and their sensitivity and accuracy.

February 28, 2013

This Week in Nature

In this week's Nature, a team of researchers from the Institute for Research in Biomedicine in Spain report on the role of the RNA-binding protein CPEB1, which controls mRNA translation, in regulating alternative 3'-UTR processing. They found that CPEB1 shuttles to the nucleus, where it co-localizes with splicing factors and mediates shortening of hundreds of mRNA 3' UTRs, modulating their translation efficiency in the cytoplasm. "CPEB1 binding to pre-mRNAs not only directs the use of alternative polyadenylation sites, but also changes alternative splicing by preventing U2AF65 recruitment," they write.

Meanwhile, in Nature Genetics, a multi-institute team reports on the first lamprey whole-genome sequence and assembly, work that was complicated by the high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. An analysis of the assembly indicated that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages, and help "define key evolutionary events within vertebrate lineages, including the origin of myelin associated proteins and the development of appendages," the researchers say.

Our sister publication GenomeWeb Daily News has more on the lamprey genome here.

Also in Nature Genetics, Chinese scientists present the draft genome of the fast-growing, non-timber forest plant moso bamboo. Gene prediction modeling identified 31,987 genes, and analyses of clustered gene families and gene co-linearity show that bamboo underwent whole-genome duplication 7 million to 12 million years ago. Additionally, the identification of gene families key in cell wall biosynthesis suggest that the whole-genome duplication event generated more gene duplicates involved in bamboo shoot development, while RNA sequencing analysis of flowering tissues suggests a connection between drought-responsive and flowering genes.

February 28, 2013

Part of Nature or Not?

In an amicus brief, the Broad Institute's Eric Lander shares his personal view of the ongoing gene patenting case between Myriad Genetics and the American Civil Liberties Union, saying that isolated DNA fragments are products of nature.

The central issue of the case revolves around Myriad's patents on the BRCA1 and BRCA2 genes. In a mixed ruling, the federal appeals court found that while some of the company's methods patents may not be patentable, its BRCA1 and BRCA2 gene patents, as they concern isolated DNA fragments, are patentable items as human intervention is needed to isolate DNA.

Lander argues that that is not true, though, as the Boston Globe points out, his brief was not filed in support of either side. Isolated DNA, he says, happens all the time in nature. "It is well-accepted in the scientific community that (a) chromosomes are constantly being broken into DNA fragments by natural biological processes that break the covalent bonds within DNA chains; (b) these DNA fragments can be routinely found in the human body … and (c) these fragments cover the entire human genome and, in particular, include many of the DNA fragments claimed by Myriad's patents," the brief says.

The US Supreme Court announced in December that it will re-hear the Myriad gene patenting case.

February 27, 2013 / 1 comment

Campus Genetics

More colleges and universities are offering courses that incorporate personal genetic testing, the Associated Press reports. Harvard Medical School and the Stanford University School of Medicine have offered such courses as electives for a few years, but the course the AP highlights is aimed at undergraduates.

The University of Iowa is offering an honors seminar on personal genomics that includes the option to be tested through 23andMe. The AP adds that Duke University, Stanford University, the University of Illinois, and the University of Texas also offer personal genomics courses that take advantage of a 23andMe testing discount.

Jeff Murray, the professor teaching the class, "talked through the pros and cons of testing with students, and spent two class periods examining 23andMe's consent form," the AP says. He also told them to discuss the test with their families. A few students decided not to be tested.

Iowa freshman Bakir Hajdarevic tells the AP that he was nervous that he might find out about something deleterious in his DNA, but that he was also curious to learn more — and that his curiosity won out. Hajdarevic learned that he's at increased risk for being lactose intolerant and a carrier for Alpha 1-antitrypsin deficiency.

"I was kind of scared going in, like, 'Oh my God, I might have a high risk factor for some kind of cancer'," he tells the AP. "But knock on wood, according to the test, I don't really have much to worry about."

February 27, 2013

This Week in Cell

A Harvard University and Broad Institute-led team tapped genome sequence data generated through the 1000 Genomes Project in its search for variants involved in recent human adaptations. As they write in Cell, the researchers used a genome-wide version of their "composite of multiple signals," or CMS method to help find regions of the genome suspected of being subject to selection. From there, they fine mapped more than 400 candidate regions, uncovering potential causal SNPs in recent human adaptation. Along with several SNPs contributing to infectious disease response, for instance, the team tracked down almost three-dozen non-synonymous variants and 59 SNPs that appear to influence the expression of nearby RNA or protein-coding sequences.

Using whole-exome sequence data, researchers from the Broad Institute, Massachusetts General Hospital, Brigham and Women's Hospital, and elsewhere identified mutations within different tumor sub-populations in chronic lymphocytic leukemia — information that proved useful for tracking clonal evolution within the cancer. By using a sensitive mutation caller to consider exome sequence data for matched tumor and normal samples from 149 individuals with CLL, they say, the researchers saw that apparent driver mutations tended to turn up in tumor clones or sub-clones. Meanwhile, data from 18 individuals whose CLL tumors sampled more than once indicated that driver mutation-containing sub-clones can expand with time, fueling CLL progression.

Finally, an international team led by investigators at the University of California, San Francisco, describes a two-stage method for exploring biological pathways behind various processes or diseases using genetic interaction maps of mammalian cells. In that study, researchers demonstrated the feasibility of the approach — which relies on genome-wide RNA interference screening followed by genetic interaction analyses using double short hairpin libraries — by mapping genetic interactions related to ricin susceptibility. In addition to genes already known for bumping the toxin's effects up or down, the investigators saw previously unappreciated contributors to the process. And, they say, the genetic interaction mapping strategy itself "provides a potentially transformative tool for defining gene function and designing combination therapies based on synergistic pairs."

February 27, 2013

To the Highest Bidder: One Nobel Medal

Francis Crick's family is auctioning off the Nobel Prize medal and diploma that he won in 1962 for discovering the structure of DNA.

Heritage Auctions, the auction house handling the sale, estimates the value of the 23 carat medal to be around $500,000. Heritage describes it as "housed in an elegant, yet simple, red leather case with Crick's initials giltstamped on the top, surrounded by a decorative border, also in gilt."

The auction, scheduled for April 10-11, will also include Crick's award check, his lab coat, his gardening logs, nautical journals, and books.

In a separate auction, the family is selling a letter that Crick wrote in 1953 to his son Michael, describing "a most important discovery" that he made with James Watson. The New York Times reports that Christie's is handling that sale. The auction house values the letter to be worth between $1 million and $2 million.

Kindra Crick, Francis Crick's granddaughter, tells LiveScience that the Nobel medal "was locked in a room with her grandfather's other awards and other family heirlooms after he moved to California at the age of 60" and later placed in a safe deposit box.

"My grandfather was not the type of personality to show off," she says. "His conversation tended to be on what's next as opposed to reminiscing about the past … I guess he always thought there was more to come."

LiveScience reports that the Crick family hopes to see the medal displayed publicly after its sale and that the family and Heritage Auctions plan to donate a portion of the proceeds from the sale of the medal and the other items to the Francis Crick Institute, which is scheduled to open in London in 2015.

A portion of the proceeds from the sale of the letter to Michael Crick will benefit the Salk Institute, where Francis Crick held a post after retiring from the UK's Medical Research Council.

February 26, 2013

A Little Look

While this year's Advances in Genome Biology and Technology, held last week in Marco Island, Fla., didn't have as many big splashes as years past — a complaint noted by Keith Robison at Omics! Omics! — attendees were able to get a look at Nabsys' semiconductor-based sequencing system.

Our sister publication In Sequence reported back in January that Nabsys is planning to launch its sequencing system in the second half of this year, at a cost of around $50,000 for the machine. Further, Stan Rose, the company's chief commercial officer, told In Sequence that the turnaround time from samples to results will be less than a day.

Over at Omics! Omics!, Robison has posted pictures of the system from AGBT, which he said "happily whirred away" in the hotel suite during the presentation. He adds that the "exhibited instrument consists of a liquid handling robot with eight stations for the Nabsys devices."

Robison also notes that "Nabsys played it safe with their samples; one was phage lambda DNA and the other a synthetic 20kb standard, and each had a small number of binding sites for Nabsys' proprietary probes." He adds that while this approach allowed "them to demonstrate generating highly precise consensus maps of the probes, with resolutions approaching 20 bp," the conditions are "highly artificial test environments which don't really represent actual use cases."

Susan Young at MIT's Technology Review adds that the Nabsys machine, since it is a so-called positional sequencer, may be well placed to handle oncological samples. "In a tumor, you need to characterize the mixture of [genetic variation] in your sample at different length scales," company CEO Barrett Bready tells her.

February 26, 2013

New Sequester Deadline Looms

The sequester, which is set to go into effect at the end of this week if US lawmakers don't come to an agreement to avoid the cuts, will lead to a 5.1 percent, or $1.6 billion, decrease to the National Institutes of Health budget. New grants, USA Today reports, would be particularly affected by the cuts. ScienceInsider reports that grant success rates could fall from 17 percent or 18 percent — which is already lower that success rates seen in years past — to 15 percent.

"I worry desperately this means we will lose a generation of young scientists," says NIH Director Francis Collins, according to USA Today.

Former NIH Director Elias Zerhouni concurs that young investigators will be the most affected by the sequestration, should it go into effect. He tells the Washington Post's Wonk Blog that "the most impacted are the young, new investigator scientists, who are coming into science, and will now abandon the field of science. There will be a generational gap created."

Further, Zerhouni, who now is the director of research and development at Sanofi, says that "the suddenness of [the sequester] and the depth of it would be a disaster for research, which is not an activity that you can turn on and off from year to year. It's an activity that takes time."

Indeed, USA Today's Dan Vergano notes, delays in grant funding may lead to labs closing their doors. "The sequester is going to be a huge mess for basic research, but I'm not sure if folks really appreciate what this means for the average Joe academic scientists," New Mexico State University's Brad Schuster tells him. "There are no furloughs in academic science. If funding runs out, that's it, everyone's out on the street."

February 26, 2013