Home

This Week in PNAS

In the early, online edition of the Proceedings of the National Academy of Sciences, an international team led by investigators in New Zealand presents findings from metagenomics-based functional analyses of soil and rock samples from an ice-free area in the Antarctic. The researchers used GeoChip — an array targeting variants in genes from hundreds of functional categories — in their assessment of samples from McKelvey Valley, one of the Antarctic's so-called McMurdo Dry Valleys. Results of these experiments highlight key functional pathways in the samples, which varied depending on the substrate considered. The search also uncovered pathways related to temperature, osmotic, and nutrient related stressors, study authors say, "offering tangible clues to the mechanisms behind the enduring success of microorganisms in this seemingly inhospitable terrain."

Major depressive disorder corresponds with changes in circadian rhythm-related gene expression in the human brain, according to work by researchers at the University of Michigan, the University of California, and elsewhere. The team performed array-based gene expression analyses on post-mortem brain samples from nearly three dozen individuals with MDD and 55 unaffected controls, incorporating information related to each individual's time of death. From this data, investigators were able to track down hundreds of transcripts with expression profiles that vary over the span of a day in various brain regions. These expression cycles appeared to askance in samples from individuals with MDD, they found, with expression peaks that were less pronounced and had somewhat different timing.

Exposure to warm temperatures can allow the expression of certain genes that would otherwise remain silent in Arabidopsis, researchers from China, the US, and France found. Using deep sequencing and other experiments, the team determined that Arabidopsis plants grown at warmer temperatures tend to have lower levels of post-transcriptional gene silencing — an apparent consequence of epigenetic changes that alter expression of the suppressor of gene silencing 3, or SGS3, protein and lead to a dip in the production of small, interfering RNAs. The epigenetic factors affecting this process are apparently inherited across Arabidopsis generations, researchers note, pointing to a "previously undescribed association between warming temperatures, an epigenetic system, and siRNA biogenesis."

May 14, 2013

The Science Halftime Show

A group of US lawmakers are calling for the creation of a 'science laureate' post, ScienceInsider reports. Senators Mazie Hirono (D-Hawaii) and Roger Wicker (R-Miss.) along with Representatives Lamar Smith (R-Texas) and Zoe Lofgren (D-Calif.) have introduced a bill that would enable the president to choose an expert from a list developed by the National Academy of Sciences who would "travel around the country to inspire future scientists." The honorary position would last one to two years and would be similar to that of the poet laureate.

"At a time when our students are falling behind other countries in the scientific subjects, scientists should be engaged to help remedy that wrong for the good of the country," says Ryan Taylor, Sen. Wicker's communications director, according to Wired. Taylor adds that as this is a bipartisan bill, it may move quickly through the legislative process.

Mike Brown, an astronomer from Caltech, says, though, that such an expert should take on more high-profile tasks than speaking at schools. "You want the person with that national forum to be on The Daily Show ... or halftime of the Super Bowl," he tells NPR's Weekend Edition Saturday. "The goal would be to encourage the public to think about science and to understand science."

A few names are already being batted around, such as astronomer Neil deGrasse Tyson, physicist Brian Greene, or Brown himself.

Daily Scan, though, is partial to Dr. Bunsen Honeydew.

May 13, 2013 / 4 comments

Using Names

US Department of Health and Human Services attorney Dean Landis has sent a letter to the managing editor of OMICSonline, Venkatesh Yanamadala, alleging that the company has infringed HHS trademarks, ScienceInsider reports.

According to the letter obtained by ScienceInsider, HHS says the Omics website uses the National Institute of Health, PubMed, and other HHS names in "an erroneous and/or misleading manner." For example, Landis writes that a FAQ at the site says that articles published in Omics journals will be submitted to PubMed, while PubMed does not accept any articles from that publishing company. (A previous exchange from the fall indicated that the National Library of Medicine has "serious concerns" about Omics' publishing practices.) In addition, the letter alleges that the company improperly uses the names of some NIH and former NIH employees.

Landis asks for those and other mentions of NIH and PubMed to be removed.

ScienceInsider adds that Omics has made changes to its website, and that it forwarded emails showing thatsome of the employees agreed to be Omics editors. One, Raymond Dionne, is identified as Omics' current editor-in-chief, though Dionne says that he agreed to be an editor when he retired from NIH in a few weeks and that his NIH affiliation was not to be used.

May 13, 2013 / 1 comment

This Week in PLOS

In PLOS Biology, University of California, Davis, researchers Peter Ralph and Graham Coop present results from a population genomics study of almost 2,300 individuals from Europe. With data collected from individuals in 40 populations for the Population Reference Sample effort, the pair looked for long shared stretches of sequence suspected of being inherited from shared ancestors in different individuals — known as identity-by-descent, or IBD, blocks — in an effort to start untangling relationships between populations in Europe during the past 3,000 years or so. Findings from the analysis reinforced the notion that European populations tend to share ancestry over the past couple thousand years, though the researchers also refined some relationships between these groups.

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

Variants on chromosome 27 can contribute to a canine version of the skin condition atopic dermatitis, according to a study in PLOS Genetics by researchers at Uppsala University, the Broad Institute, the Swedish University of Agricultural Sciences, and elsewhere. Along with ELISA analyses revealing lower-than-usual IgA levels in pooches with canine atopic dermatitis, the team performed a genome-wide association study involving 179 German shepherds — a breed known to be especially prone to the allergic skin condition. When they compared genotyping patterns in German shepherds from Sweden with or without canine atopic dermatitis, the investigators found a particularly suspicious set of SNPs in and around eight genes on chromosome 27. Through targeted sequencing and genotyping analyses in additional dogs, they narrowed the locus down to a stretch of sequence containing the plakophilin 2 gene PKP2.

A proteomics-based analysis in PLOS One indicates that the proteins produced by mitochondria in placental tissue shift during the development of the pregnancy complication pre-eclampsia. Researchers from Nanjing Medical University profiled mitochondrial proteins in placental tissue from four women with pre-eclampsia and four women without using a peptide-labling approach called iTRAQ, coupled with liquid chromatography-tandem mass spectrometry. The search unearthed four proteins with higher-than-usual expression in the pre-eclampsia samples, along with almost two-dozen more proteins whose expression was dialed down during pre-eclampsia.

May 13, 2013 / 1 comment

Tweeting Sequestration

As recent chatter and anecdotal evidence has begun to suggest that budget pains from the US federal budget sequester may be beginning to set in at universities and institutes around the country, National Institutes of Health Director Francis Collins is encouraging scientists to take to Twitter to describe how the 5 percent whack to the budget has impacted them.

"I want to hear how the #sequester is affecting your biomedical research right now," Collins tweeted on May 7.

Many of the response tweets reflect a research community in exasperation:

"I am no longer encouraging undergraduates to consider graduate school. No future in it."

"The [NIH sequester] makes me think, 'that's what doing science in Britain has been like for years.' Still very sad to hear, though."

"I am leaving the US to start a lab. Basic research can't be held hostage to short-term political games."

"I had to refuse to take a once-in-a-decade student this year due to the [sequester]. This one really hurt."

"Layoffs in companies that supply consumables and equipment in biomedical research labs [because the money] for supplies is gone."

"My former collaborator shut down his lab at HMS; 30+ years of research program came to a screeching halt."

The day after Collins launched the Twitter thread, NIH issued a notice officially recognizing that the sequester will cut around 5 percent of the agency's budget this fiscal year, compared with fiscal year 2013, to $29.15 billion. NIH also reiterated that most non-competing grants, many of which were funded at only 90 percent of the actual award level, are unlikely to see their full funding restored, and that it will probably make fewer competing awards this year than in fiscal 2012.

Writing in Science Insider, Jocelyn Kaiser noted that the sequester will result in a drop of around 703 competing research grants this year, and a fall of around 1357 total grants funded this year when the grants that are ending are included.

May 10, 2013 / 1 comment

Opening Government

President Barack Obama yesterday signed an executive order to make it the default policy of his administration to make government information open and available in a machine readable format.

With the order, the president took "historic steps to make government-held data more accessible to the public and to entrepreneurs and others as fuel for innovation and economic growth," the White House said yesterday.

The order declares that information is a valuable resource and a national strategic asset, and that newly generated government data will be more accessible and useful – ensuring for privacy and security

"Openness in government strengthens our democracy, promotes the delivery of efficient and effective services to the public, and contributes to economic growth," the order reads.

According to the statement, one of the principles guiding the policy is the notion that "making information resources easy to find, accessible, and usable can fuel entrepreneurship, innovation, and scientific discovery that improves Americans' lives and contributes significantly to job creation."

Decades ago, the order notes, the government made weather data and Global Positioning System information freely available, and since then American entrepreneurs and innovators have used these data to create navigation systems, weather newscasts and warning systems, and new applications and tools for farming and location systems, the White House explained.

Under the new Open Data Policy, within 30 days the chief information officer and chief technology officer will publish an online repository of tools and best practices to help agencies integrate the new policy into their operations; within 90 days several government councils and executives will initiate measures to support the integration of the new policy and to establish a cross-agency effort to track the policy's implementation; and within 180 days agencies are expected to start reporting their progress on putting the new policy in place.

May 10, 2013

DNA-based Art

In a new art project that is likely to stir up queezy worries that a Gattaca-like science fiction future is swiftly becoming reality, a New York artist has been plucking up bits of DNA from strangers on city streets and creating 3-D printed images of what their faces might look like.

Smithsonian covers the art of Heather Dewey-Hagborg, an electronic arts PhD student at Rensselaer Polytechnic Institute, who has been snagging up bits of hair, chewing gum, pieces of fingernails, and cigarette butts left behind by unknown people

Dewey-Hagborg, who received some training in DNA extraction using PCR from the Brooklyn do-it-yourself molecular biology lab Genspace, has been putting together a series of these 3-D printed faces called Stranger Visions.

She then has the samples sequenced and analyzed for certain SNPS, and then plugs information from around 400 based pairs into a computer program she wrote that allows her to generate a mask-like portrait. These visages should be rough approximations of the individual who unknowingly left the sample behind, based on the SNPs for certain traits that she found.

"For example gender, ancestry, eye color, hair color, freckles, lighter or darker skin, and certain facial features like nose width and distance between eyes are some of the features I am in the process of studying," she says.

She also can add some finishing touches and then uses a Zcorp printer that spits out the 3-D image in full color.

May 10, 2013

This Week's Science

In Science this week, researchers from McGill University reported new details about the activation of Parkin, a gene that, when mutated, is responsible for an autosomal recessive form of Parkinson’s disease. Using x-ray scattering, the team determined the crystal structure of the full-length parkin protein in rat tissue. The protein is ordinarily inactive, but they found that mutations that the disrupted two inhibitory binding interactions activated it. The findings may offer insights into enhancing parkin’s neuroprotective activity.

Also in Science, investigators from the Massachusetts Institute of Technology published new data detailing how changes in certain protein-protein have contributed to species diversity. The scientists examined the basic region-leucine zipper, or bZIP, transcription factors and quantified bZIP dimerization networks for five metazoan and two single-cell species, measuring interactions in vitro for 2,891 protein pairs.
They found that metazoan bZIP interactomes have “broadly similar structures,” yet there has been “extensive rewiring of connections compared to the last common ancestor.” At the same time, each species network is highly distinct, and many metazoan bZIP orthologs and paralogs display “strikingly different” interaction specificities.”

Overall, the data suggest that the changes in biochemical functions related to signaling and gene expression had a major impact on the rise of different species.

May 10, 2013

This Week's Nature

In this week’s Nature Genetics, a group of Harvard University researchers report the sequences of the genomes of a collection of Streptococcus pneumonia, the pathogen responsible for pneumonia, bacteraemia, and meningitis. The scientists sequenced the whole genomes of 616 asymptomatically carried pneumococci, obtained from children living in Massachusetts between 2000 and 2007, and found that the pneumococcal population was disrupted by the introduction of the 7-valent pneumococcal conjugate vaccine and that changes in pneumococcal serotype are largely responsible for the decline in invasive pneumococcal disease afterwards.

Also in Nature Genetics, a Stanford University team published the results of a proteomic and bioinformatics analysis of SWI/SNF complexes, known to be tumor suppressors, uncovering greater than expected roles in human malignancies. A proteomic analysis of endogenous mammalian SWI/SNF complexes revealed several new dedicated, stable subunits not found in yeast SWI/SNF complexes. The investigators also found that mammalian SWI/SNF subunits are mutated in 19.6 percent of all human tumors reported in 44 studies, suggesting that specific subunits protect against cancer in specific tissues. They also discovered that mutations affecting more than one subunit are “prevalent in certain cancers.” Taken together, the data indicate that proper functioning of polymorphic SWI/SNF complexes may constitute a “major mechanism of tumor suppression.”

May 09, 2013

Visions of Treelight

A group of synthetic biology do-it-yourself researchers want to develop and sell glow-in-the-dark plants that could be used as decoration or, in the case of trees, to light streets, Andrew Pollack writes in the New York Times.

The plan is to work out of the BioCurious hacker lab space in Silicon Valley to initially splice DNA from a luminous organism like a jellyfish or marine bacterium into an Arabidopsis mustard plant and to move on to other plants later.\

The partners, including San Francisco tech entrepreneur Antony Evans and Omri Amirav-Drory, who runs a firm called Genome Compiler, also hope that their project will inspire others to pursue independent biology engineering, Pollack writes.

To fund the effort, the partners have raised $250,000 from around 4,500 Kickstarter donors in around two weeks, the Times reports.

“We hope to have a plant which you can visibly see in the dark (like glow-in-the-dark paint), but don’t expect to replace your light bulbs with version 1.0,” according to the project's Kickstarter page.

Not surprisingly, the plan has drawn concerned criticism from environmental groups, including Friends of the Earth and the ETC Group, who have asked Kickstarter to remove the project from its website and have asked the US Department of Agriculture to take some action, according to the Times.

The environmental groups said that the glowing mustard plant project will lead to the "widespread and uncontrolled release of bioengineered seeds and plants through the controversial and risky techniques of synthetic biology," Pollack notes.

So far, Kickstarter has told the critics to talk to the project's partners, and USDA has not responded to the letter, according to the Times.

May 09, 2013

Not So Anonymous

Participants in human genomics studies are typically guaranteed anonymity, a practice intended to safeguard against use of an individual's data by outside parties like insurers or employers.

Just how anonymous, though, is this anonymous data?
This week in Nature, Erica Check Hayden profiles Whitehead Institute researcher Yaniv Erlich, a computational biologist who is applying lessons learned from his days as a hacker to investigate the security of genomic study data. And this data, it turns out, isn't all that secure.

For instance, Check Hayden reports, in a paper published in Science this January, Erlich's lab demonstrated they could identify participants in genetic research studies by cross-referencing their genetic data with publicly available information like age and place of residence.

Using a software program he and an undergraduate student had developed for profiling short tandem repeats, Erlich identified nearly 50 supposedly anonymous participants from the 1000 Genomes project.

As Check Hayden observes, this wasn't the first time someone had demonstrated that it was possible to identify study participants based on their data. Those past efforts, though, had relied on other sources of research data.

"Erlich's study," she writes, "upped the stakes, because it showed that it was possible to identify people from their genetic data by linking not to other sources of research data, but to information freely available on the Internet."

How, exactly, the community can and will address this issue isn't entirely clear, but regardless, Check Hayden says, Erlich has helped move the problem into the spotlight.

May 09, 2013

747 Complexity

Even 'intelligent design' proponents need evolution for their ideas to work, Gerhard Adam writes in Science 2.0.

The common critique that advocates of 'intelligent design' level against evolutionary biology is that there are instances of complexity in the natural world that cannot have evolved, and must have had a designer.

But Adam says that even the examples and analogies they provide for evidence of a designer have required evolution to become what they are.

Take a look at the example of the 747 jumbo jet, which has been used as an analogy to biological phenomena that intelligent design advocates see as being far too complex to have arisen through randomness, Adam says.

Leaving aside the "complete misunderstanding about randomness," Adam notes: where did the design for the 747 come from?

"We can immediately see that it didn't occur directly, but rather was the result of an evolutionary process beginning with the Wright Brothers [and even previous unsuccessful attempts at flight]," he says.

The same holds for finely crafted and complex watches, or any other complex objects that are proposed as too complex.

"Rather the object in question is invariably the result of design, evolution, and selection. At each design step, the characteristics that work best get selected for incorporation in future versions of the object. There are simply no exceptions," Adam adds.

Any such object that exhibits design also "exhibits evolution and selection," he says, pointing out that it is "what we call progress."

May 09, 2013 / 8 comments

This Week in Genome Biology

Queen Mary University of London's Pedro Cutillas and colleagues from the UK describe phosphoproteomic analyses of cancer cell lines and potential applications of this information in the early, online edition of Genome Biology. When the researchers used mass spectrometry to assess phosphorylation levels at some 2,000 sites in nine cancer cell lines — three representatives apiece from acute myeloid leukemia, lymphoma, and multiple myeloma — they found that cell lines tended to cluster by cancer type. And the team's more in-depth analysis of seven AML lines suggested phosphoproteomics can provide clues to which tumor samples are more or less apt to respond to compounds that inhibit kinase enzymes.

A Wellcome Trust Sanger Institute team outlines a new computational method for surmising the sorts of mutational processes at play in cancer genomes. After applying this probabilistic inference approach, called Emu, to simulated data, the researchers used it to scour sequences from 21 previously sequenced breast cancer samples. Those tumors harbored signs of four main mutational processes, study authors explained. And in conjunction with known functional annotations in the genome, the nature of the mutations and their locations offered clues to some of the biological processes going awry in the tumors.

The human microbiome is home to a range of mobile genetic elements that provide insights into the viral pathogens or plasmids that microbiome members have encountered in the past, according to another Genome Biology study. Researchers from Indiana University and the Roswell Park Cancer Institute sifted through metagenomic sequence data, focusing on spacer sequences at the so-called CRISPR locus, a site in the genome where sequences from potential genetic interlopers are integrated as part of the CRISPR-CAS system used in the bacterial and archaeal immune system. Using data from 95,000 contigs — corresponding to sequences potentially targeted by CRISPR spacers in the metagenomic data — the group was able to tally up and compare the apparent mobile genetic element networks found in the human mouth and gut microbiomes.

May 08, 2013