A news article in Nature looks into the problems inherited by the new FDA commissioner Margaret Hamburg: "The FDA, once globally revered as the gold standard in regulation of food and medical-product safety, has lapsed repeatedly in recent years under a string of different leaders and a long stretch without any permanent chief," the article says. As part of re-establishing FDA as that high standard, Hamburg plans to increase the agency's budget and increase its enforcement of fraudulent companies and companies whose manufacturing specs aren't up to snuff.

Another feature explores the work of Jasmin Fischer at Microsoft Research in Cambridge, UK. Fischer is interested in what she calls "executable biology," a new approach to biological modeling that may simulations of cells easier to do, understand, as well as confirm in the lab. "Ultimately, she says, this kind of software should develop to a point at which researchers can draw a hypothetical pathway or interaction on the screen in exactly the way they're already used to doing, and have the computer automatically convert their drawing into a working simulation," the article adds.

Dmitriy Krepkiy and Mihaela Mihailescua are first authors on a paper showing that alpha helices can be quite happy in a hydrophobic lipid bilayer. Using neutron diffraction, solid-state nuclear magnetic resonance spectroscopy and molecular dynamics simulations, they and their colleagues looked at the structure and hydrophobicty of S1-S4 voltage sensing domains and found that the voltage sensors "adopt transmembrane orientations and cause a modest reshaping of the surrounding lipid bilayer." A News and Views article gives a bit more background here.

The title of Derek Lowe's blog post is "Applied Organic Synthesis: Chocolate Pecan Pie" and to us that sounded like a great way to put chemistry to use. Just follow his protocol to get some tasty pecan pie. He's helpfully converted the measurements into the metric system for non-US readers, but you can also pretend you're still at the bench. "Note that this product has an extremely high energy density — it's not shock-sensitive or anything, but make the slices fairly small," Lowe adds.

Writedit points out a notice issued by NIH that lists the changes for submissions being made January 25^th or later. She says the most important reminder relates to online submissions. The notice says:

Writedit's post also contains links to a sample biosketch and other useful information.

In the Proceedings of the National Academy of Sciences this week, scientists at Rockefeller University studied how stress affects histone marks in the hippocampus in mice. Previous work has associated histone H3 methylation at lysines 4, 9, and 27 with transcription, heterochromatin formation, and lowered transcription, respectively. Using antibodies to these marks, they found that "acute stress increased the levels of H3K9 tri-methylation (H3K9me3) in the dentate gyrus and CA1, while it reduced levels of H3K9 mono-methylation (H3K9me1) and H3K27 tri-methylation (H3K27me3) in the same regions, and had no effect on levels of H3K4 tri-methylation (H3K4me3)." The results, they write in the paper, "show a pattern of changes remarkable for their rapidity, magnitude, and regional specificity."

Harvard Medical School's Norbert Perrimon and Laurence Rahme are lead authors on work that shows that a genetic variant can help bacterial infections lead to stem-cell mediated intestinal cancer. Using Drosophila as a model, they discovered that infection by Pseudomonas aeruginosa ultimately leads to apoptosis of enterocytes, the largest class of differentiated intestinal cells, they say. This in turn makes stem cells and stem cell progenitors proliferate. "However, we find that this homeostatic mechanism can lead to massive over-proliferation of intestinal cells when infection occurs in animals with a latent oncogenic form of the Ras1 oncogene."

Researchers at the Max Planck Institute for Molecular Genetics and the Institute Gustave-Roussy have used next-gen sequencing to study mutations in E. coli. Sequencing several E. coli genomes from colonies of cells subjected to chemical mutagenesis, they saw a "strikingly nonrandom distribution" of mutations. The results, they say, show how "analysis of the molecular records left in the genomes of the descendants of an individual mutagenized cell allows for genome-scale observations of fixation and segregation of mutations, as well as recombination events, in the single genome of their progenitor."

Wayne State University scientists led phylogenetic analysis of human, elephant, tenrec, and mouse genomes to look for patterns of adaptive evolution in aerobic energy metabolism genes. Scanning substitution rates for about 6,000 genes, they found that elephant and human showed much slower nucleotide substitution rates than tenrec and mouse, but more adaptively evolved genes. Taking into account absolute brain size and brain oxygen consumption, they saw that "adaptively evolved aerobic energy metabolism genes were most evident in the elephant lineage and next most evident in the human lineage."

A group of German researchers led by Pawel Smialowski and Philipp Pagel created a database, called the Negatome, of protein interactions that are unlikely to occur. As the report in Nucleic Acids Research, they scoured the literature for evidence against physical interactions of proteins and also analyzed protein complexes deposited in the Protein Data Bank to come up with their database, which may be found here. They report on 1,892 non-interacting proteins and predict a further 979 non-interacting domain pairs.
"The negatome is well on the way to become a 'gold-standard' dataset for training predictors of protein–protein interaction, thus proving that negative results are still results," adds Dr Jim at Mental Indigestion.

Just watch out for Jonathan Eisen's Worst New Omics Award.

HT: Effect Measure