Skip to main content
Premium Trial:

Request an Annual Quote

This Week in Nucleic Acids Research: Apr 4, 2013

In the advance access edition of Nucleic Acids Research, National Institutes of Health researchers summarize findings from genomic studies on archaea and bacteria, focusing in particular on defense strategies uncovered in the prokaryotic microbes via comparative genomics. Such data have helped in delineating the types of defense systems that are sprinkled across the archaeal and bacterial phylogenies, the team says, highlighting the propensity for defense genes to cluster, for instance, and revealing ties between genes contributing to immune system function and those in place to prompt dormancy or cell suicide.

A Japanese team presents a new statistical method for calling somatic mutations in cancer genomes using high-throughput sequence data. The strategy — known as empirical Bayesian mutation calling, or EBCall — relies on a Bayesian statistical model to help find situations in which allele frequencies don't match patterns predicted from known sequencing error profiles, the researchers say. In addition to describing the rationale behind their approach, authors of the study demonstrate the utility of EBCall, using whole-exome sequence data on paired tumor-normal samples to call mutations stretching into the low frequency range in coding regions of the tumors.

A study by researchers from Wayne State University and elsewhere highlights the variety of RNA molecules found in sperm cells and that apparently contribute to the function of these reproductive cells. The group used RNA sequencing to follow shifts in coding and non-coding RNA representatives present in human sperm during development, looking also at factors influencing this collection. The population of RNA in sperm as revealed by RNA-seq provides a window into the developmental history, functional viability, and potential elements present by sperm that may serve a role in the final stages of spermiogenesis or at fertilization," the study authors say.