Shaking Signs for Science

In Washington, DC, yesterday thousands of protestors from the biomedical and patient activists communities drew attention to the stagnation of funding for biomedical research and the negative impact of the sequester, and urged that money that has been lost over the last decade be restored to the National Institutes of Health.

"Funding medical research is a no-brainer when it comes to our national interests," said Rep. Chris Van Hollen, (D - Md.) according to an article posted in USA Today. "Let's make sure we have more progress, more hope and more lives."

The event's organizers said they are seeking at least $32 billion for NIH in next year's budget, which would be an increase of around $1.3 billion over this year's funding. They also said that the automatic sequestration cuts have whacked the NIH budget down from the initial $31 billion to around $29 billion, according to the USA Today item.

The Hill also covered the rally, and aims its focus on the statements of Van Hollen and Rep. Rosa DeLauro (D - Conn.).

"We need to make it clear to my colleagues exactly what these cuts mean for the health of America's families," DeLauro said in her statements to the crowd, The Hill reports. "When they see a grassroots movement rising up, from doctors, from scientists, from advocates and patients, you are impossible to ignore … You need to overwhelm the institution with your voices."

Science's Jocelyn Kaiser notes that NIH Director Francis Collins had been billed to speak at the event but was a no-show. She pointed out that while "federal employees cannot participate in lobbying activities, Collins was initially going to speak as a private citizen, according to sources, but ultimately cancelled."

She also cites American Association for Cancer Research CEO Margaret Foti as saying that for a while during the event tweets with the hash tag #RallyMedRes were rated second only to tweets about former UK Prime Minister Margaret Thatcher's death.

The Dark Side of Open-Access Journals

A growing number of open-access journals of questionable reputation are offering to publish "seemingly anything" for a fee and are preying on researchers to lend them credibility, The New York Times reports today.

One doctor who submitted two articles to The Journal of Clinical Case Reports was billed $2,900 for their publication, a fee he had not been told about. When he tried to withdraw the papers, they were published anyway, and his fee was waived after a year of back-and-forth.

A plant pathologist at Rutgers University agreed to join the editorial board of another journal, Plant Pathology & Microbiology, only to find himself listed by the publisher as an organizer and speaker for a conference called Entomology-2013."I am not even an entomologist," he told the Times. The conference is trying to mimic a well-known meeting called Entomology 2013.

Up to 4,000 such "predatory journals" exist today – at least a quarter of all open-access journals – according to Jeffrey Beall, a research librarian at the University of Colorado, who keeps a blacklist of them called "Beall's list."

The Long-Read Game

Long-reads sequencing is once again at the forefront, writes Michael Eisenstein at Nature Biotechnology. A few years ago, Pacific Biosciences made a splash at the 2010 Advances in Genome Biology and Technology meeting with its RS machine, which it said at the time could produce sequences as long as 20,000 bases. However, as Eisenstein notes, the approach was limited by a low throughput and high error rate.

The company, though, has improved its machine, and other companies are hot in pursuit. Talks at AGBT this year, Eisenstein says, showed that a PacBio approach could be applied to de novo sequence assembly of repetitive genomes as well as to elucidate structural variations. "In the past year, the read lengths have improved by a factor of four," Michael Schatz from Cold Spring Harbor Laboratory tells Nature Biotechnology. "If this were Apple, they would have branded it as a new model — it really feels like a new instrument."

At the same time, Illumina and Nabsys are developing long-read sequencing capabilities. Illumina acquired Moleculo earlier this year, and that technology is slated to launch this summer. It, too, has been used to sequence a de novo, repetitive plant genome, Eisenstein notes. While it has its drawbacks in dealing with GC regions, CSHL's Schatz notes that there is time for improvement before its launch. And Nabsys says that its semiconductor-based system will allow for fast and precise sequencing.

DNA as Search and Seizure

The US Supreme Court recently heard arguments in Maryland v. King concerning whether obtaining DNA samples from people as they are arrested violates Fourth Amendment protections against unreasonable searches and seizures. In The Nation, Jason Silverstein writes that a factor beyond privacy comes into play with the collection of DNA samples upon a person's arrest. "Because people of color are disproportionately stopped, searched and arrested, they will disproportionately bear the burden of this genetic dragnet," he writes. "And because DNA samples can be used to establish family relationships, it has the potential to widen the surveillance to entire communities."

Indeed, the Los Angeles Police Department has said that it was able to make an arrest in the 'Grim Sleeper' serial killer case because of a familial search. Christopher Franklin was arrested in conjunction with a weapons charge and his DNA test showed a similarity to samples from the serial killer case; his father Lonnie Franklin, Jr., was subsequently arrested and charged in the Grim Sleeper case.

However, Silverstein notes that such police DNA databases likely contain a significant portion of samples from people who were never convicted or sometimes even charged with a crime. The American Civil Liberties Union estimates that about 19 percent of people arrested in California for a felony were never charged with a crime, Silverstein writes. Getting removed from the database is also difficult, with the procedures differing from state to state.

The Court is expected to rule on the case this summer. How the Court votes, Silverstein says, may be unusual. "When Maryland's chief deputy attorney general, Katherine Winfree, recited the number of convictions won through DNA matches, Justice Antonin Scalia fired back, 'If you conducted a lot of unreasonable searches and seizures, you'd get more convictions, too. That proves absolutely nothing.'" On the other hand, Justice Stephen Breyer pushed back against King's attorney, saying DNA tests are "no more intrusive" than fingerprints but "much more accurate."

This Week in PLOS

A PLOS One study by Swiss researchers suggests individuals may have distinct and distinguishable metabolite profiles in their breath. The research team used real-time mass spectrometry to assess exhaled compounds in breath samples from six men and five women. Analyses of the samples — taken at multiple times per day for each individual over nine days — revealed consistent core metabolite "breathprints" that were specific to each individual and remained stable over time. "Consistent with previous metabolomic studies based on urine," authors of the study explain, "we conclude that individual signatures of breath composition exist."

Members of the Gentrepreneur Consortium brought together genotyping and employment data for more than 50,000 European individuals as part of a meta-analysis looking for genetic contributors to entrepreneurial personality traits. As they report in PLOS One, the researchers did not find individual SNPs of significant effect, though their findings hint that common genetic variants spread across many genes may explain a considerable proportion of self-employment heritability (as estimated using twin data). "Although self-employment is a multi-faceted, heavily environmentally influenced, and biologically distal trait," study authors note, "our results are similar to those for other genetically complex and biologically more proximate outcomes, such as height, intelligence, personality, and several diseases."

A PLOS Genetics study by the Uppsala University's Siv Andersson and colleagues from Sweden, Greece, and Austria outlines a multiple displacement amplification-based scheme for sequencing the genomes of bacterial endosymbionts that can't be cultured in the lab. The group sequenced representatives from two strains of Wolbachia (an intracellular symbiont) that seem to co-infect the Drosophila simulans fly. Comparative genomic analyses of these so-called wHa and wNo strains revealed that the strains are not only genetically distinct Wolbachia clades, but also that they can co-exist in the same host without mixing.

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."