University of Massachusetts researcher Albertha Walhout and colleagues describe diet-related gene expression networks delineated multiple genetic screening methods. The group used a mutagenesis screen, RNA interference, and other approaches to track down a gene network involved in dietary response when Caenorhabditis elegans worms munch on Comamonas bacteria rather than their standard Escherichia coli fare. Through analyses of this set of 146 apparent activators and 38 repressors, the study authors unearthed "a transcriptional response system that is poised to sense dietary cues and metabolic imbalances, illustrating extensive communication between metabolic networks in the mitochondria and gene regulatory networks in the nucleus."

German researchers report on findings from an RNA interference-based search for genetic factors involved in liver regeneration. The team used small hairpin RNAs to systematically knock down genes in a mouse model of liver regeneration, looking for targets that enhanced or suppressed this liver regeneration. The search led them to a kinase-coding gene called MKK4 that seems to have a central regulatory role in liver regeneration. This process got a boost in mouse models when the gene is silenced, researchers found, even when underlying acute or chronic liver disease was present.

The succession of players that come together in protein complexes appears to be under evolutionary selection, according to a UK team, suggesting this assembly order contributes to biological function. The researchers considered protein assembly in general and in the context of proteins produced from fused genes. With the help of genome sequence data, for example, they found evidence that protein assembly pathways tend to be conserved in the face of gene fusion events. These and other data "reveal the intimate relationships among protein assembly, quaternary structure, and evolution," study authors say, "and demonstrate on a genome-wide scale the biological importance of ordered assembly pathways."

By adding genes from a variety sources — including other microorganisms and the camphor tree — researchers have coaxed Escherichia coli to produce diesel, Scientific American's David Biello reports.

As John Love from University of Exeter and his colleagues write in the Proceedings of the National Academy of Sciences, they engineered E. coli to metabolize fatty acids into different hydrocarbons by inserting a Photorhabdus luminescens fatty acid reductase complex along with aldehyde decarbonylase from Nostoc punctiforme, a thioesterase from Cinnamomum camphora, and the branched-chain α-keto acid dehydrogenase complex and β-keto acyl-acyl carrier protein synthase III from Bacillus subtilis.

The E. coli were fed sugar and yeast extract and could produce diesel, which it appears to be able to expel from the cell through an unknown mechanism.

"We wanted to make biofuels that could be used directly with existing engines to completely replace fossil fuels," Love tells Biello. "Our next step will be to try to develop a bacterium that could be deployed industrially."

Columbia University's Ian Lipkin led an international team that unearthed dozens of hepaciviruses and pegiviruses in bats. As they report in the early, online edition of the Proceedings of the National Academy of Sciences, the researchers started with an RNA sequencing-based look at viral diversity in blood samples from more than 400 African and Central American bats. When they tossed out host sequences and compared the remaining reads with RNA and amino acid databases, investigators identified various viral representatives from the Flaviridae family. Among them: representatives from the Hepacivirus and Pegivirus genera that contain hepatitis C and related GB viruses, respectively. Follow-up experiments in more than 1,200 samples from bats in seven countries indicated that a significant proportion of bats — almost 5 percent of those tested — carried hepaciviruses and/or pegiviruses.

An international team led by investigators at the University of California, Davis, describes a new four billion base physical map for Aegilops tauschii — a diploid plant with a genome that's thought to correspond to the hexaploid wheat plant's "D genome." Using an Ae. tauschii SNP array and contigs assembled from fingerprinting information on hundreds of thousands of bacterial artificial chromosomes, researchers put together a 4.03 billion base physical map for Ae. tauschii. Through comparisons with sequenced plants, authors of that study gained insights into gene density, disease resistance gene profiles, recombination, chromosome structure, and other features related to grass plant evolution.

Finally, for another study slated to come out online this week in PNAS, researchers from Cornell University outline a single-molecule analysis strategy that they are using to tally up multiple epigenetic marks in combination with one another. The "single chromatin molecule analysis in nanochannels," or SCAN, approach centers on a nanofluidic manipulation of bits of chromatin with fluorescent labels recognizing methylated DNA and other epigenetic marks, study authors explain. In the new study, for example, they demonstrated that this method could assess combinations of epigenetic marks in both normal and cancerous cell lines.

BMC Genomics has issued an expression of concern regarding a 2011 article on an adaptive role for subfunctionalization in modulating the effect of gene dosage, Retraction Watch reports. According to a statement from the journal, one of the institutions to which first author Ariel Fernandez was affiliated found that the data he generated was not reproducible while a second institution he was associated with did not find anything wrong with the methods or data. "Given the conflicting conclusions of these investigations, the Editors advise the readers to interpret the data with due caution," the statement says.

Retraction Watch notes that Fernandez was affiliated with the National Research Council of Argentina, the University of Chicago, and the Morgridge Institute for Research in Wisconsin.

A University of California, San Francisco-led team interrogated SNPs in 17 candidate genes as part of its search for genetic and other factors contributing to lymphedema risk in women treated for breast cancer. As they report in PLOS One, the researchers unearthed lymphedema-associated variants in four lymphatic and/or blood vessel formation-related genes after testing more than 150 breast cancer patients with lymphedema and 387 breast cancer patients without the lymphatic blockage condition. Along with the apparent risk variants, the team notes that women with more lymph nodes removed during treatment appeared to be at higher-than-usual lymphedema risk. So, too, were those who were heavier and/or had later stage breast cancers.

In PLOS Genetics, researchers from Ireland, the UK, Canada, and France describe findings from a genome sequencing-based analysis of Salmonella enterica. By sequencing 73 isolates of a S. enterica serovar called Agona — collected during five foodborne infection outbreaks, from individuals or animals with sporadic infections, or from environmental sources — the team delved into details of past outbreaks and tallied up genetic diversity in the gastroenteritis-causing bug. For instance, their results suggest the outbreaks considered in the current study involved genetically different versions of S. enterica. Even so, outbreak strain diversity appeared to be lower than that predicted by pulsed-field gel electrophoresis, which seems to pick up variation in the bug's accessory genome rather than from core sequences containing outbreak-related determinants.

The simian Treponema strain Fribourg-Blanc is most genetically similarly to the T. pallidum sub-species that causes yaws in humans, according to a study in PLOS Neglected Tropical Diseases. Investigators from Masaryk University in the Czech Republic and Washington University School of Medicine generated a high-quality genome sequence for the Fribourg-Blanc strain. When they compared the genome sequences for representatives from the T. pallidum sub-species that cause syphilis (pallidum) or yaws (pertenue), researchers found that the Fribourg-Blanc strain clustered most closely with the yaws-causing pertenue sub-species. "[W]e propose to rename the unclassified simian isolate to T. pallidum ssp. pertenue strain Fribourg-Blanc," authors of the study say, noting that "non-human primates could serve as possible reservoirs of [yaws-causing] strains."

With all the licking and petting, dogs and their owners share microorganisms. Dog ownership, writes Lisa Raffensperger at D-brief, may be a main factor influencing what microbes live on a person's skin.

In a new study, researchers led by the University of Colorado's Rob Knight examined the fecal, oral, and skin microbiota of 60 families with and without children or dogs. As they report in eLife, cohabitating partners shared many microbes, especially Prevotella and Veillonella, but people also had similar microbial communities as their dogs. Dogs, Raffensperger notes, harbor Methylophilaceae bacteria in their mouths that appear to make their way to dog owners' skin.

"It is intriguing to consider that who we cohabit with, including companion animals, may alter our physiological properties by influencing the consortia of microbial symbionts that we harbor in and on our various body habitats, and in particular, our skin habitats," Knight and his colleagues write.