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Possible STEM Visa Changes

Lawmakers in the US have made a bipartisan proposal to change the nation's immigration laws, including rules governing visas for skilled scientific workers, The New York Times reports. One bill, which was introduced in the Senate earlier this week by Orrin Hatch (R-Utah), would increase the number of temporary and permanent resident visas available for such immigrants. Specifically, the Nature News blog adds, it would increase the number of H-1B visas that can be issued each year by 50,000, and it would change the employment-based visa caps so that people who received a degree from a US institution in science, technology, engineering, and mathematics would not be subject to them.

"This bill is a common sense approach to ensuring that those who have come here to be educated in high-tech fields have the ability to stay here," Hatch says. "It's good for workers, good for businesses trying to grow, and good for our economy."

Another group of senators led by Charles Schumer (D-NY) and John McCain (R-Ariz.) also presented an immigration reform bill, the Times adds, but that one did not include specifics on what changes would be made with regard to highly skilled immigrants.

January 31, 2013

Sudden Impact

Every journal editor likes their publication to have a high impact factor, but things might be getting out of hand, writes publishing consultant Phil Davis at the academic publishing blog The Scholarly Kitchen.

Impact factor is a measure of a journal's influence devised and tracked by Thompson Reuters, and among the metrics including in calculating impact factor is the number of times a journal's articles are cited by other papers.

Perhaps unsurprisingly, this has led some journal editors to try to goose their stats by publishing editorials citing a raft of papers from their own publication.

In his post, Davis highlights as one particularly flagrant example a recent editorial published in the Netherlands Heart Journal by its editor E.E. Van der Wall. That piece, Davis writes, "contains 25 self-citations to the NHJ, 24 of which cite articles written between 2010 and 2011 — the window from which the journal's next impact factor will be calculated."

More striking than the editorial itself, though, is the nakedness of its author's intentions, Davis says.

"The editor of the NHJ doesn't attempt to hide his intentions, which is, without remorse, to increase his journal's impact factor. Having analyzed what gets cited in his journal, Van der Wall is direct and forthcoming about his editorial intentions."

Davis doesn't entirely blame editors like Van der Wall, however. "Through selfless self-citation, editors are merely exploiting a loophole in the metrics system much like corporations exploit loopholes in the taxation system," he writes.

Or, as rapper Ice-T once put it: Don't hate the player, hate the game.

January 31, 2013

The Malnourished Microbiome

The gut microbiome may be a causal factor of kwashiorkor, a form of severe malnutrition, researchers from Washington University in St. Louis report in Science. WashU's Jeffrey Gordon and his colleagues studied the gut microbiomes of 317 Malawian twin pairs until they turned three. They then focused on nine, well-nourished, same-gender twin pairs and 13 same-gender twin pairs in which one twin developed kwashiorkor. The microbiomes of the healthy twins became more diverse, but as Ed Yong at Not Exactly Rocket Science puts it, "the bacteria of kwashiorkor children stagnated."

The discordant twin pairs were fed a ready-to-use therapeutic food, and the researchers found that their gut bacteria began to mature, but then reverted when the children returned to their traditional diet.

The researchers alsotransplanted the gut microbiomes from three discordant twin pairs into gnotobiotic mice. The mice that received the kwashiorkor microbiomes and that were fed a Malawian-style diet lost weight. "The combination of Malawian diet and kwashiorkor microbiome produced marked weight loss in recipient mice, accompanied by perturbations in amino acid, carbohydrate, and intermediary metabolism that were only transiently ameliorated with RUTF," Gordon and his colleagues write, referring to the ready-to-use therapeutic food.

As Yong notes, though, "the microbes aren't the whole story," but he adds that diet also isn't the whole story — they likely work in conjunction to bring about kwashiorkor. One possibility is that, together, they limit the amount of sulfur in the children's diet. Sulfur, Yong writes is common in animal and cereal proteins, but the Malawian diet is low in those types of protein. Further, Biophilia wadsworthia, which is more common in the microbiomes of children with kwashiorkor, may absorb what little sulfur there is. Further, Yong adds that there is evidence that the kwashiorkor microbiome also interferes with the citric acid cycle.

January 31, 2013

Darwin Day, It's Almost Official

A resolution introduced in the US House of Representatives would designate Feb. 12, 2013, the anniversary of Charles Darwin's birth, as Darwin Day in recognition of Darwin as "a worthy symbol on which to celebrate the achievements of reason, science, and the advancement of human knowledge."

Introduced on Jan. 22 by Rush Holt (D-NJ), the resolution has been referred to the House Committee on Science, Space, and Technology. Five representatives have signed on as co-sponsors.

The American Humanist Association, which manages the International Darwin Day Foundation, worked with Holt on the bill and is asking its members to contact their representatives and ask them to co-sponsor the legislation, H Res 41.

"Without Charles Darwin, our modern understandings of biology, ecology, genetics, and medicine would be utterly impossible, and our comprehension of the world around us would be vastly poorer," Holt says in an AHA press release. "By recognizing Darwin Day, we can honor the importance of scientific thinking in our lives, and we can celebrate one of our greatest thinkers."

As the National Center for Science Education points out, the language of H. Res. 41 is identical to H. Res. 81, introduced in 2011 by Pete Stark (D-Calif.).

"Like H. Res. 41, H. Res. 81 was referred to the House Committee on Science, Space, and Technology. From there, it proceeded to the Subcommittee on Research and Science Education, where it eventually died," NCSE says.

Even if the new resolution meets a similar fate, that doesn't mean you can't celebrate. The International Darwin Day Foundation offers a comprehensive list of upcoming events in honor of the big day, including the Bake a Cake for Darwin Contest in Vancouver, BC; the Darwin Day Chili Cook Off in Pensacola, Fl.; the Darwin Day Bagel Brunch in Albany, Calif.; and more.

January 31, 2013 / 1 comment

This Week in Nature

In Nature Biotechnology this week, a multi-national team of researchers publish the draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety containing an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identified targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits were also highlighted.

Our sister publication GenomeWeb Daily News has more on this new sequence here.

Meanwhile, in Nature Methods, a team of scientists led by researchers from Indiana University and Miami University report the results of the first large-scale community-based critical assessment of protein function annotation experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. The investigators found that the best protein function algorithms were substantially better widely used first-generation methods, with “large gains on all types of targets." Still, they say, there is "considerable need" to improve currently available tools.

January 31, 2013

Suggestions, Right?

The unwillingness on the part of some researchers to deposit data may be associated with low quality of that data, writes Johns Hopkins University School of Medicine's Kenneth Witwer in Clinical Chemistry.

Witwer examined 127 microarray-based articles published between July 2011 and April 2012 in journals such as PLOS One, the Journal of Biological Chemistry, Blood, and Oncogene to determine whether they complied with the Minimum Information About a Microarray Experiment, or MIAME, guidelines. Those guidelines, published in Nature Genetics in 2001, aimed to establish standards for reporting gene expression data derived from microarray experiments, and were subsequently adopted by many journals.

Witwer reviewed the articles and assigned them a quality score. "Overall, data submission was reported at publication for [less than] 40% of all articles, and almost 75% of articles were MIAME noncompliant," he writes.

Ivan Oransky at Retraction Watch notes that "perhaps not surprisingly, papers whose authors did submit such data scored higher on a quality scale than those whose authors didn't deposit their data."

Oransky also points out that Witwer's findings led to a retraction of a 2011 PLOS One study on host cell response to HIV infection.

January 30, 2013 / 2 comments

Gene Silencing Drug Wins Approval

The US Food and Drug Administration has approved Kynamro, a gene silencing drug from Isis Pharmaceuticals, to treat homozygous familial hypercholesterolemia, The New York Times reports. The drug will be marketed by Sanofi's Genzyme division.

Kynamro, or mipomersen, inhibits the apolipoprotein B gene, whose gene product is involved in carrying cholesterol in the blood, working to lower levels of LDL cholesterol. In a trial, the drug decreased mean LDL levels by 24.7 percent, as compared with a 3.3 percent decrease in people who received a placebo, the Times says. The drug will, though, come with a warning about the risk of liver damage.

Homozygous familial hypercholesterolemia affects a small number of people, and the drug is unlikely, the Times notes, to be a blockbuster, especially as it can have some serious side effects. "Still, Kynamro could become the first commercial success for the gene silencing technique, which is known as antisense, and which some experts say is finally poised to fulfill its promise after over two decades of research and numerous disappointments," the Times adds.

Our sister publication Gene Silencing News has more on this here.

January 30, 2013 / 1 comment

The New Tang Prize

Samuel Yin, a Taiwanese businessman who made his fortune by investing in real estate, finance, and retail, has established a new research prize called the Tang Prize, ScienceInsider reports. The Tang Prize, named after China's Tang Dynasty, which Yin says was a golden age for China, is to recognize research in the fields of biopharmaceuticals, law, sinology, and sustainable, ScienceInsider adds.

The prize is to come with a $1.36 million award as well as $341,000 in funding for five years to support further research by prize recipients. The cumulative $1.7 million, ScienceInsider notes, is more than what the Nobel Prize comes with, which was about $1.2 million in 2012. Yin has endowed the Tang Prize Foundation with $102 million.

The prize is to be awarded biennially.

January 30, 2013

Using the Cloud to Improve Access to HIV Testing

A blog post at Nature Medicine's Spoonful of Medicine blog this week describes a prototype of newly developed HIV test chip — a little bigger than a credit card — that analyzes blood samples in minutes and sends its results to doctors via the cloud, making it possible to diagnose HIV-infected people living in remote areas.

According to Spoonful of Medicine blog, the device, dubbed mChip, was developed by a team led by Samuel Sia, a biomedical engineer at New York's Columbia University.

The post says that the device collects blood from a finger prick, loads the sample onto a small fluidics chip that contains the antibodies and reagents needed to perform an enzyme-linked immunosorbent assay, or ELISA. It returns results in just 15 minutes.

These results are then sent via cell phone networks and satellite connections to a database of medical records which doctors can access, the post states.

In a recent study, the team tested the device on serum, plasma, and blood samples from more than 200 HIV-infected individuals in Rwanda. More details are available in a paper published in Clinical Chemistry.

January 30, 2013

This Week in Cell

Researchers with Harvard University's FAS Center for Systems Biology report on changes to the human gut microbiome associated with the use of xenobiotics. The team followed human gut microbiomes in three individuals taking xenobiotic compounds over nine months, using a combination of 16S ribosomal RNA sequencing, microbial community gene expression experiments, and flow cytometry to test the individuals' fecal samples. The analyses revealed shifts in the gut microbiome composition, physiological features, and gene expression profiles, even after fairly brief xenobiotic exposures, with drug-exposed gut bugs showing elevated expression of resistance, stress response, and drug metabolism-related genes. "These results demonstrate the power of moving beyond surveys of microbial diversity to better understand metabolic activity, highlight the unintended consequences of xenobiotics," researchers write, "and suggest that attempts at personalized medicine should consider inter-individual variations in the active human gut microbiome."

Our sister publication GenomeWeb Daily News has more on this study here.

In another Cell study, the National Cancer Institute's André Nussenzweig and colleagues from the US and Spain describe sites in the genome that are particularly prone to DNA damage in replicating B cells. The group identified these recurrent sites — dubbed "early replication fragile sites," or ERFSs — through a series of ChIP-seq, Repli-seq, RNA-seq, and other experiments in mouse B cells. Their subsequent experiments suggest that the ERFSs overlap with sites with pronounced gene expression or elevated repetitive element contents. But they also seem to coincide with many places in the human genome where recurrent amplifications or deletions have been documented in diffuse large B-cell lymphoma, prompting speculation that the sites are a key player in lymphomagenesis-related rearrangements in mammalian cells.

An American-led team takes a look at chromatin organization across the genome in a set of assorted human tissue types and stem cell lines. The researchers turned to ChIP-seq to map genome-wide chromatin patterns, defining the position of various histone modifications in 29 tissue or cell types. Together, the information offers clues to the chromatin state transitions and regulatory features characterizing cells from various lineages, developmental phases, or cellular contexts. The study also considers chromatin organization relative to other features in the cell, including nuclear architecture.

January 30, 2013

A Patch to Deliver Vaccine

Patches made up of microneedles may be an effective way to deliver, or 'tattoo', DNA vaccines, researchers led by the Massachusetts Institute of Technology's Darrell Irvine report in Nature Materials. In their paper, they present "an approach for rapid implantation of vaccine-loaded polymer films carrying DNA, immune-stimulatory RNA, and biodegradable polycations into the immune-cell-rich epidermis, using microneedles coated with releasable polyelectrolyte multilayers."

TechNewsDaily notes that rhesus monkeys given a patch of microneedles coated with a DNA vaccine had a 140-fold higher gene expression response than monkeys that received the vaccine though an injection.

"We have very direct control over how the vaccine is delivered, and the prolonged exposure to the vaccine that is possible with this system can really enhance immunity," MIT's Peter DeMuth, the paper's first author, tells TechNewsDaily. He adds that the patch feels a bit like a cat's tongue.

Additionally, the microneedle patches may be stored at room temperature for weeks.

January 29, 2013

Hopkins to Hire with Bloomberg Money

New York City Mayor Michael Bloomberg has given his alma mater, Johns Hopkins University, a $250 million gift that the school plans to use to hire 50 scientists, ScienceInsider reports. Another $100 million will go toward need-based financial aid for undergraduate students. Bloomberg received an engineering degree from Hopkins in 1964, for which, CNN notes, he had to take out loans. Bloomberg's overall donations to the school total $1 billion.

The Bloomberg Distinguished Professors, ScienceInsider adds, will focus on big-picture, interdisciplinary problems, such as "clean water, individualized health care, urban revitalization, and the science of learning."

"These professors will be the focal points for efforts to tackle complex problems from multiple disciplinary perspectives," Dennis O'Shea, executive director of media relations, tells ScienceInsider. O'Shea adds that the first professors will be hired in the spring.

January 29, 2013

Motor City to Biotech City?

Detroit is seeing a growth of biotech companies, both established and newer firms, reports The Huffington Post's David Sands. He adds that Detroit has a city plan called "Eds and Meds" to encourage growth in education and medicine as the city's economic base.

"[Biotech] has seen growth in Michigan, and particularly in Detroit, even when the economy was going downhill. The R&D/testing sector of the industry was doing quite well here," Stephen Rapundalo, president and CEO of the Michigan biosciences trade association, MichBio, tells Sands.

For example, Sands writes that Detroit is home to genetic testing company Genesis Genetics as well as MitoStem, which focuses on regenerative medicine. MitoStem, in particular, he says, has benefited from a business incubator called TechTown that is associated with Wayne State University and from a ballot measure that loosened stem cell research restrictions.

January 29, 2013 / 1 comment