Abe's Old Hat

US President Abraham Lincoln is known for his stovepipe hat, and some people who oversee the Abraham Lincoln Presidential Library and Museum want to make sure that the hat they have on display is the real deal through DNA testing, the Chicago Sun-Times reports.

Some members of the panel overseeing the museum say that there is a "credibility gap" surrounding the origin of the hat, which is worth an estimated $6.5 million. The museum says that Lincoln gave the hat to a farmer in Illinois following his debate with Stephen Douglas, but, as the Sun-Times reports, ones of the farmer's descendents said in an affidavit in 1958 that the farmer received the hat while in Washington, DC, during the Civil War. The museum curator, however, says that it is a "dead" issue, according to the Huffington Post.

In any event, DNA testing may not be possible, the Sun-Times adds, as the hat does not appear to contain hair or other DNA sources, Lincoln does not have any living descendants, and any samples of his blood or tissue are small and might be harmed by sampling.

Sara Will Crews Finley Dies

Sara Will Crews Finley, a geneticist at the University of Alabama at Birmingham, has died, according to the school. She was 82. Finley and her husband, Wayne, founded the medical genetics program at UAB, the first in the southeast US. She joined the medical faculty in 1960 — the school was then called Medical College of Alabama — and co-directed UAB's medical genetics lab for 30 years.

"Sara Finley was a true pioneer in medicine," Bruce Korf, the chair of the UAB genetics department, says in a statement. "She and her husband, Wayne, were among the first physicians to recognize the importance of the new field of medical genetics, and they were among the first to implement new technologies for culturing cells and analyzing chromosomes. These technologies helped untold numbers of families by providing new approaches to the diagnosis and classification of birth defects and genetic disorders, as well as enabling genetic counseling for families."

This Week in Science

In Science this week, a Cornell University team reports on the results of a study using a precision nuclear run-on and sequencing assay to map the genome-wide distribution of transcriptionally engaged Pol II at base-pair resolution. They found that Pol II accumulates immediately downstream of promoters, at intron-exon junctions that are efficiently used for splicing and over 3′ polyadenylation sites. "Focused analyses of promoters reveal that pausing is not fixed relative to initiation sites, nor is it specified directly by the position of a particular core promoter element or the first nucleosome," the researchers write. Meantime, core promoter elements function "beyond initiation, and when optimally positioned they act collectively to dictate the position and strength of pausing," they add.

Also in Science, a group of National Institutes of Health researchers detail a framework for making decisions about future research with highly pathogenic avian influenza H5N1 viruses. They review two reports from mid-2012 showing that the viruses could be rendered transmissible by respiratory droplets among ferrets, and discuss international talks that led to the creation of the new framework, which calls for any research proposals involving the transmission of HPAI H5N1 among mammals by respiratory droplets to undergo additional review.

Finally in Science, a group of investigators from the University of Basel and from the Institute of Molecular Systems Biology described a new role for the Ser-Thr kinase mammalian target of rapamycin, or mTOR, which controls cell growth and metabolism by stimulating glycolysis, as well as protein and lipid synthesis. They used quantitative phosphoproteomics to identify substrates or downstream effectors of the two mTOR complexes and found that mTOR controlled the phosphorylation of 335 proteins including CAD, which catalyzes the first three steps in de novo pyrimidine synthesis. Further, mTORC1 indirectly phosphorylated CAD-S1859 through S6 kinase, and CAD-S1859 phosphorylation promoted CAD oligomerization and thereby stimulated de novo synthesis of pyrimidines and progression through S phase of the cell cycle in mammalian cells. "Thus, mTORC1 also stimulates the synthesis of nucleotides to control cell proliferation."

For the Cause

DNA sequencing is increasingly becoming the go-to test to uncover the causes of rare genetic disorders, writes Gina Kolata at the New York Times. While parents seeking such a test for their children have high expectations, experts note that genetic mutations are only found in about a quarter of cases, and the test leads to better treatment plans in only about 3 percent of cases and improvement in about 1 percent of cases. "We give the impression that we can do these things because we only publish our successes," William Gahl from the National Institutes of Health says. He adds that, when seeing patients, "we try to make expectations realistic."

"It seems this is a floor in terms of the results outcome for these children, as some of them may receive better or more effective treatments in the future, because the specific nature of their disease is already known," Razib Khan at the Gene Expression blog notes. "Since most medical treatments today are marginal in effect these outcomes don't surprise or depress me, and the price point is sure to come down."

Kolata also points out that having a diagnosis can also help patients and their families access special education services as well as ease the medical claims process.

Rethinking Grant Reviews

Advisers to the National Institutes of Health have suggested a change to its grant review process that could boost its success rate, ScienceInsider reports.

The advisers recommend that "instead of allowing researchers one more shot if a proposal is rejected, NIH would give them unlimited chances to resubmit, but consider all applications to be new," ScienceInsider writes. They also suggest conducting a pilot study during which investigators would be allowed "an unlimited number of resubmissions but no more than two applications over 12 months."

According to the article, the idea is one of five that came out of the December meeting of the advisory council for NIH's Center for Scientific Review. It was originally suggested in a 2008 report that recommended an overhaul of the NIH's peer review system and an end to "the practice of allowing two resubmissions for a grant."

ScienceInsider adds that research community appears to be "divided" on the plan's merits.

Database Access

Private companies may be able to purchase access to medical and genetic data, and possibly to personal data, housed in databases of the UK's National Health Service, the Observer's Jamie Doward reports. Last December, David Cameron announced a £100 million ($160.9 million) plan to sequence 100,000 people to study cancer and other diseases as well as bolster the NHS data infrastructure.

But, this "revelation, which contradicts government claims that such material would be completely anonymous, has raised fears that pharmaceutical firms and insurance companies will be able to determine the identities of people susceptible to particular diseases," Doward says.

Doward notes that details obtained under the Freedom of Information Act indicate that the data provided will initially be anonymized, but that companies can appeal to receive data that includes ages and postcodes. Further, while people will be able to request that their genetic data not be shared, it might not always be possible.

"While most researchers will only want access to effectively anonymized data, legal authority to access identifiable information may be provided through the consent of the citizens concerned or through legislation, such as section 251 of the NHS Act 2006," the Department of Health says, according to Doward. That section, the health department adds, says that approval may be given in cases wherre "it is very difficult to contact patients to seek their consent, or where it is vital that the data is identifiable."

Sally Davies, the chief medical officer, adds that "the privacy and confidentiality of NHS patients will be paramount at every stage of fulfilling the government's commitment to sequence 100,000 whole genomes."

Chameau to Lead KAUST

Jean-Lou Chameau, the president of Caltech, will be leaving sometime later this year to take over the helm of the King Abdullah University of Science and Technology in Saudi Arabia, the Nature News Blog reports. Chameau, a trained engineer, has supported multidisciplinary research at Caltech, and has raised about $1 billion in funding for the school since his arrival there in 2006, the Nature News Blog adds.

In a note, Chameau says that he had envisioned retiring in Pasadena, where Caltech is located, but could not pass up the "unique and life-changing opportunity" to lead KAUST. Chameau will take over the KAUST top spot from Choon Fong Shih who has led the school since its founding in 2009.

This Week in Nature

In Nature this week, a team of German researchers report on the discovery that microRNA-34a is induced in the aging heart, and that in vivo silencing or genetic deletion of the small, non-coding RNA reduces age-related cardiomyocyte cell death. Additionally, inhibition of the miRNA reduces cell death and fibrosis following heart attack and improves recovery. The team also reports on a novel direct target of the miRNA, which reduces telomere shortening, DNA damage responses, and cardiomyocyte apoptosis, as well as improves functional recovery after acute myocardial infarction.

In Nature Biotechnology, a multi-institute team of Korean researchers publishes a genome-scale collection of transcription activator-like effector nucleases, or TALENs, which can be engineered to bind specific genomic loci and enable the introduction of precise genetic modifications in human cells. The scientists selected target sites that did not have highly similar sequences elsewhere in the genome to avoid off-target mutations and assembled TALEN plasmids for 18,740 protein-coding genes. They used the library to generate single- and double-gene-knockout cells in which NF-kappa B signaling pathways were disrupted, and found that these cells "showed unambiguous suppression of signal transduction" compared with ones treated with short interfering RNAs.

Meanwhile, in Nature Cell Biology, a team led by Max Planck Institute investigators report on the development of a genomic toolkit enabling the examination of kinesin and myosin motor functions in cells. They generated of a library of 243 amino- and carboxy-terminally tagged mouse and human bacterial artificial chromosome transgenes to establish 227 stably transfected HeLa cell lines, 15 mouse embryonic stem cell lines, and 1 transgenic mouse line. "The cells were characterized by expression and localization analyses and further investigated by affinity-purification mass spectrometry, identifying 191 candidate protein-protein interactions." The result is a set of validated resources and candidate molecular pathways for investigating motor protein function across cell lineages.

DNA Testing for Food

In the wake of the horse meat scandal, European authorities are asking for meat samples to undergo DNA testing to detect any contamination, but, as the Wall Street Journal reports, testing may not prevent another incident. Testing, it adds, may not catch all contaminants, and it is expensive.

"If a sample is mixed (contains DNA from more than one species) then sequencing for the unknown is not possible," Angela Bromley, the general manager of Genon Laboratories, which performs meat testing, says.

And, the Journal adds, broadening the scope of testing becomes expensive — each test, it says, costs about €400, or approximately $535. "You have to concentrate your resources where the intelligence is, and right now the problem is pork and horse," spokesperson from the UK's Food Standards Authority says.

Old Techs, New Tricks

Researchers and clinicians are justifiably excited about methods like LC-MS/MS and next-generation sequencing making their way into their labs, but, asks Christine Snozek, director of clinical chemistry at the Mayo Clinical Arizona, what about the technicians?

Beyond simply worrying about technical validation of new platforms, lab leaders also need to make sure these new technologies are embraced by their employees, Snozek writes this week on the blog of the National Academy of Clinical Biochemistry.

Otherwise, she says, that shiny new mass spec could end up just "a dusty, expensive box sitting idle in the corner."

"Introducing any form of change is challenging," Snozek writes. "Humans are change-resistant by nature, and this is even more true for those individuals whose personalities are well-suited for the clinical laboratory with its stringent regulations and SOP-driven nature."

Education is key, she says. For instance, technicians might not be excited to switch from a fully-automated platform to LC-MS/MS detection using manual extraction. But if supervisors explain the benefits of the extra work — eliminating metabolite cross-reactivity, for example — their team will probably be more willing to come onboard.

Taking a page from the military, Snozek recommends after-action reviews to help implement new technologies. "As laboratorians, it's easy to forget about the human side of the process," she says, but with a host of new omics platforms making their way to the clinic, it's an important consideration.

Notes for NGS Newbies

Before diving in with both feet, next-generation sequencing neophytes might want to take a gander at a post by Dan Koboldt at MassGenomics where he describes his 10 commandments for good next-gen sequencing.

In his post, Koboldt breaks up his instructions into four categories: analysis, publications, data sharing and submissions, and research ethics and cost.

His list includes some oft repeated warnings. For example, he cautions against reinventing the wheel when it comes to developing analysis software, and, for pity's sake, don't invent any more words that end in "ome" or "omics."

Some other no-no's, according to Koboldt, include publishing results before they've been vetted properly, testing new methods on simulated data only, and taking "unfair advantage of submitted data."

He also admonishes newcomers to think a little bit about the cost of analysis without which "your sequencing data, your $1,000 genome, is about as useful as a chocolate teapot," and to have a care for the privacy of their study participants' samples and data.

The 'Breakthrough' Prize

A new Breakthrough Prize in Life Sciences has been awarded to 11 scientists, according to a press release from the Milner Foundation. The prize is sponsored by Genetech's Art Levinson, Google's Sergey Brin, Anne Wojcicki from 23andMe, Facebook's Mark Zuckerberg and Priscilla Chan, and Yuri Milner, the founder of Mail.ru Group.

Eleven researchers have been named this year's recipients of the award and its $3 million prize. Those researchers are: Rockefeller University's Cornelia Bargmann, David Botstein at Princeton University, Lewis Cantley from Weill Cornell Medical College, the Hubrecht Institute's Hans Clevers, Napoleone Ferrara at the University of California, San Diego, Titia de Lange, also at Rockefeller, the Broad Institute's Eric Lander, Memorial Sloan-Kettering Cancer Center's Charles Sawyers, Bert Vogelstein at Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, MIT's Robert Weinberg, and Shinya Yamanaka from Kyoto University.

Each year's winners will also serve on the selection committee.

"I believe this new prize will shine a light on the extraordinary achievements of the outstanding minds in the field of life sciences, enhance medical innovation, and ultimately become a platform for recognizing future discoveries," Levinson says in a statement.

This Week in Genome Research

The University of Washington's Jay Shendure and colleagues describe an approach for finding low frequency variants, while reining in sequence errors. This "single molecule molecular inversion probe," or smMIP, assay combines single molecule tagging with molecular inversion probe-based multiplexed targeted capture, they say. In their Genome Research study, for instance, investigators used smMIP on eight cell lines and 45 clinical cancer samples, targeting 33 clinically informative genes apiece. The approach picked up mutations at down to the 1 percent frequency level with 83 percent sensitivity, prompting those involved to argue that "smMIP will be broadly adoptable as a practical and effective method for accurately detecting low frequency mutations in both research and clinical settings."

For more on the method, check out the latest issue of our sister publication, In Sequence.

Complex breakpoints are common in cancer genomes, according to a study by researchers at the University of Virginia and elsewhere. Using a paired-end mapping algorithm called HYDRA-MULTI, the team tallied up breakpoints in 64 cancer samples using matched tumor and normal sequence data generated for The Cancer Genome Atlas. From mapping patterns for nearly 6,200 somatic structural variant breakpoints, the investigators determined that three-quarters of the tumor genomes housed one or more complex clusters of breakpoints. Their subsequent analyses suggest that many of the complex rearrangements found in the cancer genomes appeared through lone mutational events — apparently involving a combination of double-strand breaks and non-homologous repair.

Researchers from the Massachusetts General Hospital and Harvard Medical School performed deep sequencing on small RNAs from Caenorhabditis elegans and a few nematode worms from the same genus to explore the evolutionary history of small regulatory RNAs. When it sifted through microRNA, small interfering RNA, and piwi-interacting RNA profiles in the worms, the team saw relatively little conservation at specific siRNAs or piRNAs. On the other hand, C. elegans and the three other worms shared conservation across dozens of miRNA families and in broader features of the siRNA and piRNA pathways.