In the latest issue of Nucleic Acids Research, researchers from San Diego State University, Argonne National Laboratory, and Cairo University report on a new computational method for fishing out viral sequences tucked away in bacterial genomes. The weighted phase detection algorithm, dubbed PhiSpy, relies on sequence similarity, prophage traits such as protein lengths and phage insertion sites, and nucleotide composition cues to root out these prophages. In their own analyses, for instance, the study's authors managed to find 94 percent of prophages present in the 50 bacterial genomes they considered using PhiSpy. There, the false negative rate was 6 percent and the false positive rate was lower than 1 percent. By combining similarity- and composition-based analyses, the researchers say, it was possible to put together "an automated application that can identify prophages with or without the homology to known phage genes."
A paper in the early, online version of the journal describes a microRNA profile associated with prion infection of neuronal cells. University of Melbourne biochemistry and molecular biology researcher Andrew Hill and his colleagues focused on very small vesicles called exosomes that are released from some cell types. Using deep sequencing, they compared the small RNA patterns in exosomes produced by mouse neuronal cells with or without prion infection. The analysis uncovered a shift in the small RNA content of the exosomes released by prion-infected cells, including a handful of miRNAs with enhanced or muted expression. "Overall," the team notes, "these results demonstrate that circulating exosomes released during prion infection have a distinct miRNA signature that can be utilized for diagnosis and understanding pathogenic mechanisms in prion disease."
Finally, researchers from China's Peking University introduce a new online resource for those involved in monkey-related research: a rhesus macaque genomics database called RhesusBase. Based on more than one billion strand-specific RNA sequence reads generated through the group's own studies of 10 rhesus macaque tissues, it re-annotated nearly 29 percent of the macaque transcripts that had been described previously. In addition to presenting these revised gene models on the RhesusBase site, the researchers incorporated functional information from dozens of other resource sites, producing what they called a "'one-stop' resource for the monkey research community."