A University of California-led team sequenced the genomes of dozens of Batrachochytrium dendrobatidis isolates in an effort to understand the evolutionary history of the fungus — an amphibian pathogen that's had particularly detrimental effects on amphibian populations in the Americas. As they report in the early, online edition of the Proceedings of the National Academy of Sciences, the researchers found a great deal of genetic diversity amongst 29 B. dendrobatidis isolates collected from sites around the world, consistent with a complex evolutionary history for the fungus. They also saw signs of selective pressure on genes coding for protease enzymes, suggesting these processes are prone to shifts during evolutionary transitions.

Mutations to the RASA1 gene can cause conditions involving abnormalities to the lymphatic fluid-carrying vasculature, according to a study by researchers from Texas and Michigan. The group unearthed frame-shift mutations in RASA1 when they did whole-exome sequencing on a 20-year-old individual with a lymphatic condition called Parkes-Weber syndrome and his unaffected parents. Together with analyses of the affected individual's vasculature, the findings suggest RASA1 mutations may lead to unusual lymphatic vascular architecture, study authors say — a notion supported by experiments in mice missing the RASA1 gene. Even so, RASA1 mutations seem to have variable expressivity since the unaffected father in the exome-sequenced trio carried the same RASA1 alteration found in his Parkes-Weber syndrome-affected son.

For another study slated to appear online this week in PNAS, Cornell University researchers relied on data from the Drosophila Genetic Reference Panel to tally up natural genetic variation in the fruit fly — information that they used to help find new players in endoplasmic reticulum stress response pathways. The team treated flies from 114 sequenced DGRP lines with an ER stress-inducing compound called tunicamycin. By following flies' survival times and looking at how they corresponded with both array-based gene expression profiles and SNP patterns, the investigators identified 25 candidate ER stress response genes. Their follow-up functional experiments suggested that at least 17 of the genes could be plausible ER stress response pathway participants.

The American College of Medical Genetics and Genomics, which recently issued guidelines regarding the return of incidental findings, has published a clarification regarding that statement.

The guidelines, released during the ACMG annual meeting in Phoenix in March, recommended that certain genetic findings uncovered by a lab during whole-exome or whole-genome sequencing of a patient be reported back to the physician and patient, even if those findings were unrelated to why the patient was undergoing testing. For example, if the patient is being tested for mutations linked to heart disease, but sequencing turns up a mutation in, say BRCA1 that predisposes that patient to cancer, that finding should be reported.

After the statement was released, some critics said the report was "too conservative" while others said it overlooked patient autonomy, among other issues.

In its clarification, the ACMG reiterates its thoughts on patient autonomy, reporting findings from children, laboratory policies, communicating results, and predicting disease likelihood.

For example, in addressing patient autonomy, the group says its reason for advising returning results was because its list of mutations and conditions only included pathogenic variants that had a high likelihood of leading to disease. "The rationale for our recommendations was that not reporting a laboratory test result that conveys a near certainty of an adverse yet potentially preventable medical outcome would be unethical," it adds.

In a blog post at the Huffington Post, guideline author Robert Green adds that "autonomy is not removed, but shifted to a more appropriate place" under these guidelines. "[O]rdering physicians should receive a report that includes the potentially dangerous incidental mutation, and thus informed, the physician and patient together can choose to learn more about the illness that it implicates. … Absent the knowledge that such a mutation exists, patients will not have any authentic opportunity to inform themselves or exert any choice over this danger," he adds.

Relaxation practices such as yoga, meditation, and repetitive prayer are associated with shifts in the expression of metabolic, immune, and stress response pathways genes, according to a study in PLOS One. A Massachusetts-led team did array-based gene expression analyses on blood samples from 26 healthy individuals over eight weeks, as each embarked on a relaxation response program. This gene expression data, coupled with a systems biology network analysis, suggest that both short and longer term relaxation practices can produce a dip in the stress response and inflammation-related gene expression, along with a boost in the expression of certain metabolic, insulin, and mitochondrial genes.

Researchers from Brazil and France looked at the relationship between a Chagas disease-causing parasite and its insect host for another PLOS One study. The team developed complementary DNA libraries with RNA from the guts of Triatoma infestans insects that did or did not carry the Chagas disease parasite, Trypanosoma cruzi. The resulting expressed sequence tag data revealed genes with an uptick or decline in expression in the infected insects. The study's authors also saw metabolic- and immune-related transcripts with similar expression profiles under both conditions. "[T]his work provides the first global analysis of expression profiles from the midgut of a Chagas disease vector under T. cruzi infection," they write, "with a resulting repertoire of transcripts that are important in the elucidation of metabolic processes in T. infestans."

In PLOS Genetics, researchers from Canada and the US describe the approach they used to look at the interplay between nucleosome architecture and transcriptional regulation. The team tracked nucleosome position patterns in dozens of yeast strains carrying loss-of-function deletions or conditional mutations to genes influencing histone, chromatin, or transcription-related processes. Together with information on yeast strains treated with compounds known to alter some of the same pathways, findings from the experiment "confirm and extend the roles of chromatin remodelers and chaperones as major determinants of genic nucleosome positioning," the researchers write, "and these data provide a valuable resource for future studies."

New efforts in by Republicans in Congress to require that the National Science Foundation ensure that the studies it funds meet certain criteria that lawmakers would judge have stirred up questions about whether any science may be safe from grant-level oversight by lawmakers.

LiveScience contributor Wynne Parry writes that the efforts by Representative Lamar Smith (R-Texas) and Senator Tom Coburn (R-Okla.) have created "a battle over science" by trying to make NSF justify to Congress the value to society of the research projects that it funds.

Writing in Science today, Columbia University Professor Kenneth Prewitt says that Coburn's recent success in forcing NSF to certify that any political science projects it funds are promoting the national security and economic interests of the US could open the door to even broader efforts to meddle in the scientific enterprise.

"Every scientific discipline has a stake in undoing the damage inflicted on political science, and, in fact, to the national interest, by the Coburn criteria," Prewitt says, adding that scientists "should vigorously contest any effort to apply those criteria more broadly."

This week, Smith proposed legislation that would expand on Coburn's political science clause and require that NSF certify that all of its research advances "the national health, prosperity, and welfare" of the US.

Prewitt says there are there are three major problems with these sorts of rules, which enable lawmakers to "micromanage" science funding.

Rules like these favor research with near-term benefits, but overlook the long-term potential of lines of inquiry that may pay off in unknown ways. He says that Congress has a history of supporting both present and future-oriented research, the likes of which led to the development of the Internet.

"Today, we cannot know how and when the science of the Higgs boson subatomic particle will prove useful. But conditions will change; the knowledge will be used," Prewitt writes.

Criteria like that in Coburn's amendment also "weaken the way science builds theories," and miss the larger point that "science is an interconnected enterprise."

Lastly, the peer review process will be hurt by such rules, Prewitt argues, because "Congressional intimidation" will lead scientists to pursue the kinds of projects that lawmakers want, and avoiding those that some do not want, such as research that hits political hot-buttons, like studies involving climate change, stem cells, and evolution.

Harvard University researchers were able to correctly identify between 84 percent and 97 percent of Personal Genome Project participants through demographic information they provided.

The Personal Genome Project, led by George Church at Harvard Medical School, began about a half dozen years ago to examine the interactions among genotype, the environment, and phenotype. Project participants provide genomic information as well as health information and some other personal data. The project notes that privacy cannot be guaranteed, though the online profiles do not include names or addresses.

Latanya Sweeney and her colleagues write in a paper, available at the arXiv preprint server, that they matched demographic data— such as ZIP code, age, and gender — from 579 of 1,130 public PGP profiles to data housed in voter or other public records. From this, they received 241 unique matches.

The researchers shared their findings with the PGP to determine the accuracy of their matches. According to the response from the PGP, 84 percent of Sweeney and her team's matches were correct, and, the researchers note, if nicknames were taken into consideration, that proportion of correct matches increases to 97 percent. "Our ability to learn their names is based on their demographics, not their DNA, thereby revisiting an old vulnerability that could be easily thwarted with minimal loss of research value," they write.

Sweeney and her colleagues add that by making age and location data a bit fuzzier, PGP participants would be able to protect themselves from identification. They note that they developed a tool to help PGP participants make such changes.

"That should make the Personal Genome Project significantly more private for those who choose this option. It should also serve as a warning for future projects involving personal data that privacy isn't always as easy to protect as it might at first seem," the Physics arXiv blog adds.

File this under "sentences we never thought we'd type:" If you haven't checked out the "YoMammasGenomeSoFat" hashtag on Twitter, you should really stop whatever you're doing right now and take a look.

Yes, the life sciences community is trying its collective hand at "Yo Momma" jokes, and, what do you know, it turns out applying genomics geekery to insult comedy is a lot of fun.

For instance, from @pdoofus: "#YoMammasGenomeSoFat her introns don't get spliced…they get bariatric surgery."

And then you have your more inside baseball jokers like @evolvability, who mixes in a little sequencing platform humor: "#YoMammasGenomeSoFat it makes PacBio look like short read technology" and @Graham_Coop, who can't resist taking a swipe at the scientific press's coverage of the ENCODE project: "#YoMammasGenomeSoFat even encode press coverage thinks it can't all be functional ;-)"

Good times.