This week in PLoS Computational Biology, the University of Copenhagen's Jan Gorodkin and Ivo Hofacker discuss the "basic principles of RNA folding" as well as how genomic screens for de novo RNA structures have been used to interrogate regulatory RNA structure on mRNAS and novel non-coding RNA genes, among other things.
Over in PLoS Genetics, Hirosaki University's Akiko Kashiwagi and Osaka University's Tetsuya Yomo report on the genomic and phenotypic changes they observed in an experimental coevolution study on the lytic RNA bacteriophage Qβ and E. coli. Kashiwagi and Yomo say that their "observations suggest that the virus and its host can coexist in an evolutionary arms race, despite a difference in genome mutability … of approximately one to three orders of magnitude."
Elsewhere in the journal, a team led by researchers at Medical Center Groningen and the University of Groningen suggest that trans-expression quantitative trait loci "could well represent some of the intermediate genes that connect genetic variants with their eventual complex phenotypic outcomes." In its study to assess the effects of 1,167 published trait- or disease-associated SNPs on trans-gene expression in whole peripheral blood samples from 1,469 unrelated individuals, the team found that "HLA [human leukocyte antigen] SNPs were 10-fold enriched for trans-eQTLs," and further, that "48 percent of the trans-acting SNPs map within the HLA."
And in PLoS One this week, Imperial College London's Daniel Henk and Matthew Fisher discuss "genetic diversity, recombination, and divergence in animal associated-Penicillium dipodomyis" — the asexual fungus that grows at 37°C, produces no toxins, and is "thought to be ... associated with kangaroo rats." By analyzing sequence data for five protein-coding P. dopodymis genes, Henk and Fisher found evidence to suggest that "recombination occurs … on a small spatial scale" within the species, and that "the P. dipodomyis lineage diverged from closely related species also found in cheek pouches of kangaroo rats and their stored seeds about 11 million years ago."