Editor's Note: Some of the articles described below are not yet available at the PNAS site but are scheduled to be posted this week.
A team from Yamaguchi University, the National Institute of Infectious Diseases in Tokyo, and the Tokai University School of Medicine investigate a domestic cat restriction factor known as Refrex-1 that combats both a feline leukemia virus and an endogenous retrovirus. With a series of cell line experiments, RNA sequencing analyses, and other approaches, the investigators flagged a copper transport protein used as a receptor for these and other viruses, while demonstrating that Refrex-1 or similar structures may have antiviral activity in other animals, including primates, as a result of convergent evolution. "Refrex-1 is encoded by a subset of [domestic cat endogenous retrovirus] loci with truncated envelope [env] genes and secreted from cells as a soluble protein," the authors say, noting that the new work "provides a mechanistic finding that soluble ENV proteins broadly suppress retroviruses from different host species through binding interactions with a common entry receptor."
For another paper slated to appear in PNAS this week, researchers at the University of Bonn, Bayer, and the University of Exeter turn to phylogenomics to tally cytochrome P450 enzymes involved in detoxifying insecticides in bees. The team highlighted more than 100 potential functional orthologs for a CYP9Q subfamily enzymes, previously linked to insecticide susceptibility in the honeybee Apis mellifera. The suspected ortholog set turned up in 75 different bee species spanning the main bee families, the authors note, and their subsequent functional experiments on a subset of 26 P450 orthologs pointed to conserved detoxification capacities for the enzymes across pollinator bee families. "[O]ur results reveal an evolutionary conserved capacity to metabolize certain insecticides across all major bee families, while identifying a small number of bee species where this function may have been lost," they write, adding that the toxicogenomics strategy used in the study "has the potential to inform pesticide risk assessment for non-managed bee species that are not accessible for acute toxicity testing."
A team from Canada, France, and the US describes a neural network strategy used to assess gap gene patterning-related gene expression dynamics over the course of development in a Drosophila fly embryo model — an approach that dialed down the dimensionality associated with this system, compressing the gap gene network into two dimensions. "The resulting 2D dynamics suggests an almost linear model, with a small bare set of essential interactions," the researchers report, arguing that "optimization of small neural networks on medium-sized biological datasets is sufficiently informative to capture essential underlying mechanisms of network function.