AACR Throws a Birthday Party for James Watson

The American Association for Cancer Research honored James Watson's 85th birthday at its annual meeting this weekend with a special session that included a round of "Happy Birthday to You" and a birthday cake.

After blowing out his candles, Watson spoke about his recent work investigating the hypothesis that antioxidants play a role in cancer. He published a paper earlier this year in Open Biology outlining his views on the subject, but apparently that journal wasn't his first choice.

He said during his talk on Saturday that he initially submitted the paper – his first since 1972 – to the New England Journal of Medicine, but was rejected because, he said he was told, NEJM "doesn't publish ideas, only facts." Several other journals also turned him down.

This experience, he said, led him to believe that journal publishers see it as their mission to reject papers rather than publish them. "I hate the editors of these journals more than I hate Republicans," he said. "They're anti-science."

He wrapped up by calling for a more concerted research effort into the role that antioxidants play in cancer, noting that the cancer research community can make faster progress if it considers new ideas. "We can do it if we don't spend all our money investigating RAS," he said.

Cost Conscious

With sequestration-driven budget cuts and waning bipartisan support, the environment for medical research funding in the US is looking bleak and could turn bleaker still unless researchers work to turn things around, the University of Pennsylvania's Ezekiel Emanuel writes in a commentary published this week in the Journal of the American Medical Association. (Emanuel is the brother of Rahm Emanuel, the Chicago mayor and former chief of staff for President Barack Obama.)

Emanuel attributes this fall-off in support for medical research to four factors: the increased politicization of science; the current lack of strong Congressional champions for agencies like the National Institutes of Health; the increased scrutiny large NIH budgets have drawn; and, in an irony worthy of Alanis Morissette herself, the role of medical advances have played in increasing healthcare costs.

Of that last factor, Emanuel writes that roughly half the increase in healthcare costs can be attributed to "technology, that is, advances in biomedical science."

"And a main source — if not the main source — of advances in biomedical technology is the NIH," he notes.

So what's a person to do? Go back to bleeding patients with leeches?

Well, no. But, Emanuel says, NIH and the larger medical research community would be well served by focusing more seriously on developing "technologies that are not just 'incredibly exciting' but also cost lowering and value enhancing."

"Focusing research on cost-lowering, quality-improving interventions has not been an NIH priority," he writes. "This change in focus is vital to the future of both the country and the NIH."

Which Is It?

Big science can lead to big reactions, and Greg Miller at Wired has put together a poll comparing reactions to the announcement of the Human Genome project to those in response to the new brain mapping initiative, conveniently called BRAIN.

"Today [the Human Genome Project] is widely viewed as a success, but in the early days it too was controversial," Miller writes. "Just because the critics of the genome project got it wrong doesn’t mean that the critics of the brain project aren't raising good points, but there's a similar ring to many of the arguments for and against the two projects."

For example, respondents to the poll split 48 to 52 that this phrase referred to the brain project or the genome project: "Arguments are made that the ... project will give birth to a new generation of technologies. What good will that do in the absence of individuals trained and capable of applying these technologies?"

For the answer, and more comparisons, take Miller's poll.

LncRNA, the Place to Be

The field of long non-coding RNAs is moving from the fringe into mainstream research, bringing a number of young researchers with it, writes Amy Maxmen at Nature. While there is enthusiasm for the field, she adds, lncRNA studies can still be difficult to tackle. "There are no optimized experimental protocols and few clues to the habits of individual lncRNAs, so experiments often fail," she says. "And when they do work, investigators need to go the extra mile to convince reviewers that their results are real."

"I have had so many conversations where people think I'm just full of crap," Kevin Morris, from the Scripps Research Institute tells Nature. "You need a thick skin to be in this field. You need to do it because you love it."

And researchers who are taking on the problem are in demand, Maxmen says. Case Western Reserve University's Saba Valadkhan "was consumed with curiosity about the possibility that long RNA sequences that do not encode proteins nevertheless have a function — enhancing or suppressing gene expression," and more senior researchers noticed. Valadkhan says that before she even began to look for a job, she was hearing about job openings.

Further, there are funding opportunities for lncRNA studies. Maxmen notes that 28 grant applications for lncRNA studies were approved in 2012, and that more a announcements are specifically targeted at lncRNA studies.

Deep in the Navel

There are parts of the body that people tend to scrub well and others that may only get a passing wash. The belly button, Rob Dunn from North Carolina State University tells NPR's Talk of the Nation, might not be the cleanest spot, but it is home to tens of bacterial species in the average person, though across the population the navel is home to thousands of species.

"They're kind of a nature reserve when it comes to our body," says Dunn, who leads the Belly Button Biodiversity Project. "And so I think that the better indication of, you know, what our body is like in terms of microbes and those places we don't scrub all the time."

Dunn and his colleagues recently reported in PLOS One that, within a group of 60 volunteers, they uncovered more than 2,000 types of bacteria and archaea, with each person harboring an average of 67 different bacteria, through sequencing of 16S rDNA libraries.

"We're finding not only whole new species in belly buttons but whole new lineages …," Dunn tells NPR. "You know, they don't have names — even their families often don't have names. And so it's really a pretty amazing time."

This Week in Science

In Science this week, researchers from the University of Massachusetts and the University of Oxford report on the discovery that transposons are more mobile in certain neurons than others in the Drosophila brain. Fly cells typically use the piwi-interacting proteins Aubergine and Argonaute 3 to suppress transposable elements. However, in mushroom body neurons, where transposon expression is more abundant, these two proteins are less abundant. The team suggests that the greater level of transposons in this part of the brain helps ensure genomic heterogeneity.

Also in Science, investigators from the UK's Medical Research Council present a paper indicating that translational inhibition is the primary event required for microRNA-mediated mRNA degradation, and that the process relies on impairing the function of the eIF4F initiation complex. Additionally, the scientists report a "correlation between the presence of miRNA target sites in the 3' untranslated region of mRNAs and secondary structure in the 5' UTR and show that mRNAs with unstructured 5' UTRs are refractory to miRNA repression."

Not Yet Perfection

As non-invasive prenatal tests for genetic abnormalities are adopted in the clinic, the Wall Street Journal says that there may be confusion among doctors and patients regarding what the results of those tests mean. In fact, the Journal points out, the American College of Genetics and Genomics is working on a statement urging such tests to be called "screens" to emphasize that they predict risk rather than give definitive results. Four US companies, Ariosa Diagnostics, Natera, Sequenom, and Verinata Health, which is part of llumina, offer such tests.

Non-invasive screens appeal to many pregnant women as they avoid the small miscarriage risk associated with amniocentesis. Jeff Chapa, the head of obstetrics and maternal-fetal medicine at the Cleveland Clinic, tells the Journal that doctors there perform half as many invasive tests.

"All patients want to hear that you don't need to have something invasive," says Laura Limone, genetic-counseling supervisor New Jersey Perinatal Associates in Livingston and a member of Sequenom's speakers bureau. "Those who understand the technology find it very promising, but we also know it isn't perfect yet."

Indeed, the screens can yield false-positive or false-negative results, and positive results should be followed up on with invasive procedures, the Journal says. Athena Cherry, who heads the cytogenetics lab at Stanford University Medical Center, tells the Journal that case studies like one of a patient who terminated a pregnancy after only the screening — and the fetus was subsequently found to be normal — indicate that the message to follow up on positive results may not be "driven home enough."

False-negative results also may occur, as one instance was recounted at the ACMG annual meeting last month, as our sister publication GenomeWeb Daily News reported. The test, from Verinata, indicated that the fetus did not have Down syndrome but an amniocentesis performed after unusual ultrasound findings found that the fetus did have Down syndrome — the company's test had boasted a 100 percent sensitivity for detecting the syndrome; it now indicates a sensitivity greater than 99.9 percent, the Journal adds.

"Noninvasive prenatal [testing] as a whole has the potential to someday replace invasive procedures," says Jonathan Sheena, Natera's chief technology, adding that "the field has taken a giant leap forward … but we believe it is important to understand they don't replace invasive tests yet."

Sequester Pain Hits Genome Research, Cancer Clinics

Pains wrought by the sequestration of the US federal budget have already begun to put the hurt on biomedical and genomics research communities, as had been predicted, but also it is directly affecting cancer clinics and patients, which was not expected.

It was expected, predicted, and widely announced that the 5 percent hunk that has been hewn from the National Institutes of Health budget would have a swift impact on biomedical research, and that appears to be happening now, according to the Huffington Post's Howard Fineman.

It is particularly ironic that the budget cuts are hitting human genomics research, a rapidly growing field that was largely launched with the NIH's Human Genome Project, Fineman writes.

Academic research centers that are some of the biggest drivers of genome science may lose "a big chunk" of their funding, including Harvard University, Johns Hopkins University, the University of Pennsylvania, and Washington University in St. Louis, he notes.

According to Fineman, Washington University, which houses the Genome Institute at Washington University, could lose about $40 million in funding over the next eight months.

"Our genomics progress will be substantially slowed," Larry Shapiro, dean of the medical school there, tells the Huffington Post.

"Shapiro and others worry about any pause in their drive to attract top scientists, researchers and entrepreneurs to one of the most advanced programs of its kind in the world," Fineman writes.

According to Washington Post Wonkblog reporter Sarah Kliff, US cancer clinics have been forced to turn away thousands of Medicare patients, because the sequester has triggered a two percent slash in the amount the program provides to doctors . Although relatively small, that cut has hit private cancer clinics uniquely hard, because of the way Medicare pays oncologists for cancer drugs.

While most meds for seniors generally fall under the optional Medicare Part D, which was excluded from the sequester cut, cancer drugs must be administered by doctors and therefore are under Part B, which covers doctor visits and was subject to the cut, Kliff notes.

This 2 percent slice is magnified because it is being cut from the 6 percent reimbursement oncologists receive for storing and administering medications, she writes.

"If we treated the patients receiving the most expensive drugs, we'd be out of business in six months to a year," Jeff Vacirca, chief executive of North Shore Hematology Oncology Associates in New York, tells the Washington Post.

"The drugs we're going to lose money on we're not going to administer right now."

Central Draw

PubMed Central draws readers away from scientific journals, weakening community ties, says Philip Davis, from Phil Davis Consulting based in Ithaca, NY, in a forum article in The FASEB Journal. Davis examined 13,223 articles published in 14 research journals — spanning the fields of nutrition, experimental biology, physiology, and radiology — published by academic societies between February 2008 and January 2011. The articles were available only to subscribers for a year, and then they were available to all at the journals' websites. Forty-five percent of the articles were funded in part by the US National Institutes of Health, and they were, as policy requires, also deposited into PubMed Central after a year.

Davis found that there is 21.4 percent decline in HTML downloads and 13.8 percent decrease in PDF downloads of articles from the journals' websites after the articles become available at PubMed Central, as compared to articles that were not deposited into PMC. "Whereas PMC may be providing access to readers traditionally underserved by scientific journals, the loss of readership from journal websites may have negative consequences for readers," Davis argues. "As PMC draws readership away from the journal, the journal editor loses the opportunity to direct readers to related articles, editorials, letters and commentary surrounding the article of interest."

"Traditionally, scientific societies published the scholarly research of their members in their own journals. This collegial nexus has been extended — some say disrupted — by the centralization of research reports in PubMed Central," says Gerald Weissmann, the editor in chief of The FASEB Journal, according to Science 2.0.

On the Radar

This post has been updated to reflect that the flu virus is an RNA, not DNA, virus.

Flu researchers are examining the genes of the new bird flu strain that has sickened a handful of people in China, Reuters reports. The new flu strain, H7N9, has infected nine people in China, killing three of them. While Reuters notes that the flu does not appear to be able to pass from person to person, flu researchers are examining its genes, obtained from patient samples, to gauge its potential as a threat. The flu virus is an RNA virus.

"The virus has to a certain extent already adapted to mammalian species and to humans, so from that point of view it's worrisome," Ab Osterhaus, from the Erasmus Medical Centre in The Netherlands, tells Reuters. "Really we should keep a very close eye on this."

This Week in Nature

In this week's Nature Genetics, a team from Washington University publishes the sequence and analysis of the platyfish genome, representing the first genome sequence of a poeciliid fish. The researchers found that genes associated with viviparity show signatures of positive selection, "identifying new putative functional domains and rare cases of parallel evolution." They also discovered that genes implicated in cognition show an "unexpectedly high rate of duplicate gene retention after the teleost genome duplication event, suggesting a hypothesis for the evolution of the behavioral complexity in fish, which exceeds that found in amphibians and reptiles."

Daily Scan sister publication GenomeWeb Daily News has more on the platyfish here.

Meanwhile, in Nature Methods, a team from the J. Craig Venter Institute describe a new method for the transfer of genomes into yeast, a process that aids genome engineering for genetically intractable organisms, but that has been hampered by need to isolate intact genomes before transfer. The new process allows involves direct cell-to-cell transfer of bacterial genomes as large as 1.8 megabases into yeast under conditions that promote cell fusion. Removal of restriction endonucleases from donor bacteria was also found to enhance genome transfer.

A Conversation Piece at the Least

A Dutch design studio is putting on an exhibition of DNA-inspired furniture and jewelry, Wired reports. The studio, called Tjep., is working in conjunction with Eric Wolthuis at DutchDNA to obtain genetic profiles which they then map using 3D imaging and turn into a furniture design that "literally capture a person's essence and stand as unique pieces of art," Wired says.

Frank Tjepkema from Tjep. starts with saliva sample that is analyzed at 16 variable markers that he feeds into a design program he created to develop a visual depiction of the DNA pattern, Wired writes. Both a 3D and 2D image of the DNA is used to inform his design of the piece.

"When I was asked to work with an abstract series of numbers I was thrown back into a world without cultural references and this was actually quite liberating," Tjepkema tells Wired. "I had an excuse to make something abstract within a given conceptual framework. The resulting designs are either completely abstract, in which case the data itself was source of inspiration or a combination of a symbolic reference."

NPR's The Two-Way adds that Tjep. is to exhibit this line in Milan, Italy, later this month and after then, it will be taking commissioned projects. "[I]f Ikea isn't cutting it and you want a genetically inspired bed, table or desk, this is your chance," NPR adds. Prices, it notes, have not been set.

'Muzzled' Science

The Canadian federal information commissioner is investigating complaints that media access to government scientists has been restricted, reports the Vancouver Sun. Both the University of Victoria Environmental Law Clinic and Democracy Watch, a non-profit organization, filed a complaint with Suzanne Legault, the information commissioner, arguing that government media policies violated the Access to Information Act, the Nature News Blog adds.

"There are few issues more fundamental to democracy than the ability of the public to access scientific information produced by government scientists … Yet the attached report shows that the federal government is preventing the media and the Canadian public from speaking to government scientists for news stories," the groups say in their letter, referencing a report they generated called "Muzzling Civil Servants: A Threat to Democracy?" The letter adds that the "muzzling" especially affects researchers whose work "runs counter to current Government policies on matters such as environmental protection, oil sands development, and climate change."

The office of the information commissioner has notified seven agencies that it plans to investigate such complaints, the Vancouver Sun adds.