In the early, online edition of Genome Research, a group from the US, UK, and Colombia describes findings from a comparative genomics-based study on a form of adaptive variation in butterflies known as mimetic wing coloring. By sequencing co-mimicking Heliconius butterflies from two species and a handful of hybrid zones, researchers narrowed in on a color pattern-associated site near a gene already implicated in red color variation — an apparent regulatory region suspected of evolving by convergence in the two species distantly related species. "Using a combination of next-generation sequencing analyses, we have refined our understanding of the genetic architecture of wing pattern variation in Heliconius," they write, "and gained important insights into the evolution of novel adaptive phenotypes in natural populations."

Eusocial insects tend to share regulatory features suspected of contributing to sociality despite rapid changes to other regulatory regions and gene-coding sequences, according to a study by Arizona State University's Jürgen Gadau and colleagues. Using genome sequence data for eight eusocial insects — the honeybee and seven ant species — and 22 solitary insect representatives, the team looked at coding and regulatory patterns within each lineage and in relation to insects' sociality. In the seven ant species, representing four lineages, investigators identified a slew of novel genes. But just a few dozen genes were conserved across species, and divergence was often rampant in non-coding regions of the genomes, too, though eusocial species tended to have similar sequences within certain gene promoter regions.

Researchers from Japan and the US present evidence suggesting classical inbred mouse strains carry sequences passed down from the ancestor of "fancy" mouse species from Japan. The team re-sequenced the genomes of mice from two inbred strains developed using the Japanese mouse sub-species Mus musculus molossinus. When they compared the genomes with sequences from the mouse reference strain and other re-sequenced inbred lines, the investigators saw signs of introgression from the Japanese wild mouse lineage into the M. m. domesticus sub-species, ultimately contributing to the mosaic genomes of inbred mice, according to study authors.

The makeup of the gut microbiome has been thought to influence weight and obesity, and researchers from the Catholic University of Louvain found that one member of the gut microbiota, Akkermansia muciniphila, appears to be inversely related to obesity and metabolic disorders in rodents.

The researchers, led by Patrice Cani, fed live or heat-killed A. muciniphila to mice given a high-fat diet and subsequently examined their gut barriers, glucose homeostasis, and adipose tissue metabolism. As they report in the Proceedings of the National Academy of Sciences, mice given live A. muciniphila gain less weight on the high-fat diet than mice given dead bacteria and had a better metabolic profile.

Further, the researchers note that there is likely cross-talk between A. muciniphila and its host. As Ed Yong writes at Not Exactly Rocket Science, A. muciniphila eats the mucus layer coating the intestines and prevents that layer from becoming smaller, as it usually does in mice as they gain weight. "By shoring up the mucus, it could prevent other microbes from inflaming the gut and triggering other changes that cause disease," Yong writes.

"Akkermansia might eventually help us to control our weight or reduce the risk of diabetes, but that will take a lot more research. This study was done in mice, and Cani wants to check that the same relationships happen in the human gut," he adds.

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."

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.

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.

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.