In a paper appearing this week in PLoS Computational Biology, Forest Rohwer at San Diego State University and colleagues have published software for comparing metagenomic sequence data. Genome relative Abundance and Average Size is "a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats," they say in the abstract. Using it to conduct a meta-analysis of microbial and viral average genome lengths in 169 metagenomes from four biomes, they found that there is both significant size differences between genomes from different biomes and big differences within biomes.
Scientists led by Cold Spring Harbor Lab's Greg Hannon and the Carnegie Institution of Washington's Alex Bortvin have studied the localization of piRNAs in fetal mice cells. Using a "combination of genetic, molecular, and cell biological approaches," they show that in mouse germ cells that lack Maelstrom, a protein involved in transposon silencing, key proteins involved in the genesis of small RNAs, MILI and MIWI2, occupy specific domains within the cytoplasm of germ cells, they say. "Surprisingly, MIWI2 shares its domain with proteins known to degrade RNAs and repress synthesis of cellular proteins, thus raising a possibility of cooperation of the two mechanisms in transposon defense." The study appears in PLoS Genetics this week, and a perspective elaborates on their findings.
Patrick Schloss at the University of Michigan, Ann Arbor, presents a sequence aligner for microbial genomes that "operates in linear time, requires a small memory footprint, and generates a high quality alignment." The aligner, he says, will enable scientists to "rapidly generate robust multiple sequences alignments that are implicitly based upon the predicted secondary structure of the 16S rRNA molecule." His work was published this week in PLoS One.
Also in PLoS One, scientists have looked for genetic clues to longevity. Results from the New England Centenarian Study revealed 18 SNPs in the RNA editing genes ADARB1 and ADARB2 to be associated with extreme old age, and replication studies in Italian, Ashkenazi Jewish, and Japanese populations came up with the same genes. In C. elegans they showed that by silencing their orthologs, median survival was reduced by 50 percent but by silencing the RNAi regulatory argonaute gene, rde-1, lifespan was restored to normal levels. The results suggest that "RNA editors may be an important regulator of aging in humans and that, when evaluated in C. elegans, this pathway may interact with the RNA interference machinery to regulate lifespan."