Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.
In the early, online edition of the Proceedings of the National Academy of Sciences, a team from the University of Pennsylvania and the University of Missouri present a catalog of gene expression patterns coinciding with 24-hour circadian cycles in a dozen different mouse organs. Based on their RNA sequencing and DNA array data, the researchers saw organ-specific oscillations in the way genes were expressed over time, though nearly half of the genes and many of the non-coding RNAs identified displayed circadian shifts in at least one of the organs tested. In general, the analysis pointed to clustering and orchestrated pathway patterns amongst genes with circadian expression cycles, which also tended to be longer and more splice-prone.
Another PNAS paper describes new viruses detected in frozen caribou feces from Canada's Northwest Territories. For that study, researchers from the University of California, San Francisco, and other centers used metagenomic sequencing of genetic material from ice core samples containing caribou poo between 700 years and 3,230 years old. In the 700-year-old caribou droppings, the team saw two new viruses. The first, a small, circular DNA virus dubbed the "ancient caribou feces associated virus," or aCFV, appears to be distantly related to modern-day viruses that infect plants and fungi. The second, represented by a partial RNA sequence, was called the "ancient Northwest Territories cripavirus," or aNCV, and resembled contemporary insect-infecting viruses. "We hypothesize that these viruses originate from plant material ingested by caribou or from flying insects," the researchers note, "and that their preservation can be attribute to protection within viral capsids maintained at cold temperatures."
An international team led by investigators in the US and Canada did transcriptome sequencing on streptophyte algae from 92 taxa in an effort to better understand phylogenetic relationships between algae and land plants. After adding in published genome sequence data for 11 more plants, the researchers performed a series of phylogenetic analyses based on as many as 852 nuclear genes, revealing a sister group relationship between green algae known as Zygnematophyceae and land plants as well as the presence of a previously undescribed phylogenetic clade containing both mosses and liverwort plants. "Results support some generally accepted phylogenetic hypotheses, while rejecting others," the study's authors say, arguing that the paper "provides a new framework for studies of land plant evolution."