In Genome Biology this week, researchers in France report their investigation of the diversity of bacterial genomes at the species level via a systematic analysis of the variable segments detected by multiple whole genome alignments of Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes. Three to six percent of all genes harbor microdiversity, the team writes, and "microdiversity loci are particularly abundance in genes encoding membrane proteins." The team suggests that their study "uncovers the importance of this small-sized genome diversity."
Researchers in Indiana and Texas report the role of DNA transposon families and recombination in mutation accumulation in Daphnia pulex — the recently sequenced aquatic microcrustacean. The team identified and characterized 55 families belonging to 10 of the known DNA transposon superfamilies in the D. pulex genome. The authors suggest the duality of sex is a mechanism for both the dispersal and elimination if transposons across the genome and that " independent assortment of chromosomes leads to significant copy loss in lineages undergoing sex" in D. pulex.
Investigators in Poland identify "molecules of drug-induced genes that share functional relationships," which "may play a critical role in the early stages of addition" in Genome Biology this week. The team compared the effects of several drugs on gene expression profiles in the mouse striatum using whole-genome microarray profiling to determine transcriptome alterations over set timespans. "Using pharmacological tools, we were able to inhibit the induction of particular modules of drug-related genomic profiles," the authors write.
In a Genome Biology review, Lincoln Stein at the Ontario Institute for Cancer Research in Toronto suggests that "with DNA sequencing now getting cheaper more quickly than data storage or computation, the time may have come for genome informatics to migrate to the cloud." Stein discusses the economics and practicalities of cloud computing for genomic data. "For genomics, the biggest obstacle to moving to the cloud may well be network bandwidth," he writes. "If cloud computing is to work for genomics, the service providers will have to offer some flexibility in how large datasets get into the system."