Sequester spending cuts could delay scientific research for two years, US President Barack Obama said in a speech to the National Academy of Sciences yesterday, the New York Times reports. The academy was celebrating its 150th anniversary.

"Instead of racing ahead on the next cutting-edge discovery, our scientists are left wondering if they'll get to start any new projects, any new research projects at all over the next few years," Obama said, "which means that we could lose a year, two years of scientific research as a practical matter because of misguided priorities here in [Washington, DC]."

The sequester imposes about a 5 percent cut to both the National Institutes of Health and the National Science Foundation budgets.

Those cuts, Obama said, according to LiveScience, are "misguided" and harm the US competitive edge in science."What we produce here ends up having benefits worldwide," he said. "We should be reaching for a level of private and public research and development investment that we haven't seen since the height of the space race, that's my goal."

In the early, online version of the Proceedings of the National Academy of Sciences, a group from Germany and the US looks at whether post-traumatic stress disorder stemming from childhood events coincides with distinct gene expression and epigenetic profiles in individuals' blood samples. When they compared array-based gene expression and DNA methylation patterns in samples from 61 individuals with PTSD, the investigators found different expression patterns in those who had experienced childhood abuse relative to those who had not — changes that often corresponded to methylation shifts in the childhood trauma group. Expression signatures differed yet again when the team considered blood samples from 108 individuals with a traumatic past but no signs of PTSD.

The transcription factor-coding gene MYBL1 is prone to recurrent, truncating rearrangements in at least one diffuse pediatric low-grade glioma sub-category, according to another study in PNAS. Researchers from the Dana-Farber Cancer Institute and elsewhere performed copy number analyses on 44 formalin-fixed, paraffin-embedded samples, representing tumors from several histologically defined diffuse pediatric low-grade glioma sub-categories. Together with whole-genome sequencing on a tumor from the diffuse astrocytoma grade II, or DA2, sub-category, the copy number data pointed to a key alteration in the DA2 tumors: a partial duplication of MYBL1 and truncation of the gene's regulatory domain-coding sequence. The team also saw two tumors in another histological sub-group that harbored truncations to a related gene — MYB — hinting at a role for the transcription factor family in low-grade glioma risk.

An international team led by investigators in the US and Australia describes a high-throughput array for finding stretches of the wheat genome under selection during crop improvement. After selecting target SNPs from transcriptome sequence data on more than two-dozen wheat accessions, the researchers used this chip to put together a genetic diversity map representing nearly 3,000 wheat accessions. Their data highlighted sites of differentiation between populations, for instance, as well as regions of the genome that have undergone selective sweeps as part of the crop improvement processes. For more on this study, check out a related news story in our sister publication GenomeWeb Daily News.

With more and more cancers being parsed by their genetic mutations, even oncologists can have a hard time keeping up with the variants and which treatments go with them, the New York Times writes.

"There are so many genes and so many mutations," William Pao from Vanderbilt University tells the Times. "The human brain can't memorize all those permutations." He and some colleagues developed a website called My Cancer Genome to keep all those mutations and drugs straight for doctors and patients. For example, clinicians can search the database, which is maintained by a team of more than 50 people from 20 different institutions, for different cancers and mutations and then for related treatments or drug trials.

As the Times points out, to get to the stage of being able to search for treatments for a specific genetic mutation, that mutation first has to be uncovered, and there are more and more tools to do that, it adds. It highlights Foundation Medicine's $5,800 FoundationOne test that profiles tumor genomes.

Fadi Braiteh at the Comprehensive Cancer Centers of Nevada in Las Vegas tells the Times that he has used that test and, while it wasn't helpful for every patient, it did point to a new therapy for a lung cancer patient who was not responding to chemotherapy. "It gave me some guidance," Braiteh said. "We were able to give a drug we've never used before for this mutation."

In PLOS Genetics, the University of Edinburgh's Pamela Wiener and colleagues from the UK and the Netherlands look at genetic signatures coinciding with diversifying selection in European pigs. The team used a pig-specific Porcine60K chip to assess SNP patterns in the genomes of pigs from 13 European breeds and their wild boar cousins. Using data from between two dozen and nearly three dozen pigs per breed, investigators tracked down genetic signatures and/or expression quantitative trait loci corresponding to several breed-specific traits — from color and ear shape to growth patterns and pork production-related features such as fat deposition. The data also revealed signs of past genetic mixing with pigs from Asian breeds, researchers note, study authors note, and point to places in the genome where the European breeds differ from wild boars.

A team from the Universities of Toronto and Minneapolis took a comparative proteomics approach to profiling intrinsically disordered regions in human proteins and their relationships to splicing and protein function. As they report in PLOS Computational Biology, the researchers focused on protein regions known for flexible or constrained disorder. While both types of conserved disorder tend to appear in parts of proteins that are prone to tissue-specific splicing, for instance, they found differences in disorder enrichment depending on the nature, location, and function of the protein-coding exons involved.

Exposure to aerosol forms of the hemorrhagic fever-causing Lassa virus prompts changes in immune gene expression that ultimately compromise effective adaptive immune response to the virus, according to a study in PLOS Neglected Tropical Diseases. Researchers from Boston University and elsewhere did array-based gene expression profiling on white blood cells from four non-human primates exposed to Lassa virus aerosols over the two weeks or so before each died from the disease. Based on the sorts of genes showing higher or lower expression at each stage of infection, the study's authors determined that Lassa virus spurs a strong innate immune reaction. But adaptive immune gene response apparently lagged, they note, perhaps due to negative regulation by the virus itself.

The human body is teeming with microorganisms. "John Donne said 'no man is an island,' and Jefferson Airplane said 'He’s a peninsula,' but it now looks like he's actually a metropolis," writes Richard Conniff at Smithsonian magazine.

Conniff notes that recent technological advances have allowed researchers, through initiatives like the Human Microbiome Project, to get a glimpse of 10,000 or so species that call the human body home. Link between changes in the microbiome and disease, Conniff adds, are tantalizing researchers, some clinicians, and even venture capitalists. The public, too, he says, has been drawn in, especially intrigued by links made between the microbiome and obesity.

However, as Conniff writes, too much emphasis is sometimes placed on the role of the microbiome in health and disease with not enough evidence. "I believe the community of microbes that live in and on us is going to be shown to have major influences," Jonathan Eisen from the University of California, Davis, tells him, but Eisen adds that that “is different from actually showing it, and showing it doesn’t mean that we have any idea what to do to treat it."

Still, procedures like fecal transplants are increasingly being used to treat Clostridium difficile infections, and clinical trials of such treatments are underway.

"Coming to understand our microbes not as enemies, but as intimate partners could change our lives at least as dramatically, with time and proper testing," Conniff adds.

HT: Jonathan Eisen at the Tree of Life

Nature Publishing Group has announced a new initiative aimed at improving the reproducibility of research published in articles appearing across its spectrum of journals.

To help with the issue of reproducibility, the publishing company says in a press release it has developed a checklist to help researchers report the details of their methodologies. The checklist "focuses on a small number of often-incompletely reported elements of experimental and analytical design that are crucial to the interpretation of research results; it also consolidates several existing policies about data deposition and presentation," the statement adds.

Nature adds that it will also be changing some of its in-house practices, eliminating length restrictions on methods sections, and may consult with statisticians on certain papers.

It notes in an editorial, though, that this is but a "small step" toward solving the issue of reproducibility. "Tackling these issues is a long-term endeavour that will require the commitment of funders, institutions, researchers and publishers. …. We urge others to take note of these and of our initiatives, and do whatever they can to improve research reproducibility," the editorial adds.