The US Fish and Wildlife Service is seeking to label all chimpanzees as endangered, the Nature News Blog reports. Such a move could, as the New York Times says, enact a "major barrier to conducting invasive medical research on the animals for human diseases."

Currently, the US considers only wild chimps to be endangered, and this change would expand the coverage of the Endangered Species Act to all captive chimps, including ones in zoos, private homes, and research centers.

According to the Nature News Blog, primatologist Jane Goodall, speaking on the behalf of a number of animal welfare groups that had petitioned for the change, says it is "an important step toward saving our closest living relatives from extinction."

The Federation of American Societies for Experimental Biology says, however, that changing the status of chimpanzees "would make biomedical research using chimpanzees difficult" and "[we] believe the status change will negatively affect the health of both humans and great apes."

Under this rule, to study chimpanzees, researchers would need to establish that their research would contribute to their conservation and receive a permit, the Times adds.

In January, the National Institutes of Health announced that it planned to retire most of its research chimpanzees. The 60-day comment period on that plan recently ended, and the Times notes that the final decision has not yet been released.

The US Fish and Wildlife Service recommendation is open for its own 60-day comment period.

Using array comparative genomic hybridization data for 21,470 individuals, Baylor College of Medicine's James Lupski and colleagues considered the frequency with which deletions or other disruptive copy number variants appear in genes known for roles in recessive disease. As they report in Genome Research, the investigators unearthed more than 3,200 instances in which deletions affected one allele of a recessive disease gene, affecting 419 different recessive disease genes in all. The CNVs — which render individuals potential carriers of recessive disease — tended to occur in long genes and genes falling far from those contributing to dominant disease risk, study authors note. Based on their findings, they argue that "a complete recessive carrier screening method or diagnostic test should detect CNV alleles."

Pancreatic beta cells — insulin-secreting cells best known for their role in type 1 and type 2 diabetes — share certain expression profiles with neurons, another Genome Research study finds. A Swiss team assessed beta cell transcriptomics through deep RNA sequencing on purified beta cells from 11 individuals. Analysis of the sequences, which included comparisons with neighboring islet cells, helped the group unearth expression and splicing signatures distinct to beta cells as well as variants suspected of regulating beta cell expression patterns. Consistent with past reports, the study's authors saw that at least some genes showing enhanced expression in pancreatic beta cells overlapped with those believed to contribute to neuronal activity.

A Vanderbilt University-led group describes genetic changes to EGFR mutant lung cancers that may help render the cancers resistant to tyrosine kinase inhibitors that target EGFR alterations. By sequencing and comparing five drug-resistant EGFR mutated lung cancer cell lines and four sensitive lines, researchers uncovered known contributors to TKI treatment resistance, including MET gene amplifications or secondary mutations to the EGFR gene. They also saw several new variants — along with an over-representation of copy number changes — in the resistant lines. "These results demonstrate a framework for studying the evolution of drug-related genetic variants over time," the team writes, "and provide the first genome-wide spectrum of mutations associated with the development of cellular drug resistance in an oncogene-addicted cancer."

Researchers from the University of Adelaide's Australian Centre for Ancient DNA and Environment Institute have developed a genetic test that identifies kangaroo species from their droppings.

The PCR-based test categorizes the marsupials based on species-specific DNA fragmentation patterns. These patterns were obtained from DNA extracted from hundreds of samples collected across northeastern Australia.

The developers say they've already used the test to identify a number of kangaroo species that occur well outside their known range, which has important implication for population management and conservation.

"The more information on the distribution of species, the better management decisions can be made, particularly in gauging potential land-use and climate change impacts on biodiversity," says Jessica Wadley, PhD student and lead author of paper published in Wildlife Research that describes the test, in a statement.

For example, it could be used "to rapidly and cheaply identify the source of kangaroo meat and products to detect illegal hunting of protected species," adds Jeremy Austin, ACAD's deputy director and co-author of the study.

In the early, online edition of the Proceedings of the National Academy of Sciences, researchers from France, the US, and the Netherlands report on findings from a sequencing study of the algae-infecting virus PgV-16T — the most massive DNA virus found in eukaryotes so far. Using sequence reads from PgV-16T grown in the phytoplankton species Phaeocystis globosa, the group pieced together a nearly 460,000 base genome assembly de novo. In addition to characterizing the protein-coding content of the genome itself, the researchers went on to look at PgV-16T's place in a viral phylogenetic tree, determining that it's more closely related to a clade of hefty viruses known as Megaviridae than it is to other microalgae-infecting viruses.

Another PNAS study uses transcriptome sequence data from horses, donkeys, and crosses between the two to look at gene expression patterns and imprinting in the placenta. The study, done by a Cornell University team, revealed preferential expression of paternal alleles for numerous genes in trophoblast tissue from the placenta. That was particularly true for a set of 15 ancient imprinted genes, 10 of which showed signs of paternal expression in the study. Imprinting status was somewhat more tenuous across a group of 78 candidate imprinted genes that the study's authors identified — variability that appears to set the stage for inter-individual differences in the uterine environment — though paternal expression still tended to predominate.

Investigators with the J. Craig Venter Institute and other centers in the US and Russia describe the "mini-metagenome" approach they used sequence the genome sequence of a representative from the uncultivated bacterial phylum dubbed TM6. From swab samples collected from a biofilm in the sink of a hospital's public restroom, the team narrowed in on individual bacterial cells using fluorescence activated cell sorting and other techniques. After amplifying and sequencing DNA in individual bacteria cells, investigators put together an assembly comprised of reads from cells with shared 16S ribosomal RNA sequences, covering around 90 percent of the genome for a TM6 bug called TM6SC1.

A number of organizations across the world announced last week that they were working to form an alliance to develop standards so researchers would be able to share genomic and clinical data. "The idea is to focus not on the creation of individual data sets but to focus on the standards and shared principles and ethics that would make it possible for many people to build things that would be individually innovative and yet collectively could learn from each other," the Broad Institute's David Altshuler tells ScienceInsider in a Q&A.

Altshuler notes that it is "an ambitious proposal" and that working groups will be set up later this year to begin discussing technical standards, ethics, and more. He says they hope to come up with standards so researchers can share information, but also so that participants can determine how their data is used.

"We're going to try to come together and work together and develop a menu of options and technical standards to implement them so that people can make decisions," he says, adding that "[i]f it turns out there's a set of data that, because of permissions, can only be used for certain purposes, then that's exactly what should happen."

Individuals with chronic periodontitis tend to have distinct microbial communities in deep pockets around their teeth compared to those at healthier sites closer to the surface, according to a PLOS One study by Virginia Commonwealth University researchers. The team used 16S ribosomal RNA gene sequencing to characterize paired shallow and deep oral microbiome samples from 88 individuals with chronic periodontal disease. Along with microbiome shifts between the shallow and deep dental pocket sites in each person — which varied with factors such as smoking status or race — the analysis pointed to possible differences between the collections of bugs contributing to cavities and those linked to periodontal disease.

A PLOS Genetics study looks at genetic variants influencing traits such as height, weight, body fat, or waist and hip measurements that differ between men and women. Members of the international Genetic Investigation of Anthropometric Traits, or GIANT, consortium drew on data for 133,723 individuals for a meta-analysis aimed at finding sexually dimorphic genetic contributors to these and other anthropometric traits. That analysis, followed by a validation study involving more than 137,000 other individuals, led to variants at seven loci showing significant ties to waist-related traits in women but not men.

In PLOS Neglected Tropical Diseases, French researchers take a look at genetic patterns found in Madagascar's black rats — an animal reservoir for the plague-causing pathogen Yersinia pestis. The team used microsatellite markers to gauge genetic structure and diversity in nearly 1,300 animals in four black rat populations sampled in mountainous or flat parts of the island, looking at how these profiles corresponded to the serotype of Y. pestis detected in the rats when the pathogen was present. Genetic structure was highest for rats living in mountainous regions of Madagascar, study authors note, though more research is needed to understand genetics in the plague reservoir animals relates to the pathogen's presence and spread.