In this week's PNAS Early Edition, investigators at the University of Iowa Carver College of Medicine report their use of exome sequencing "to identify a homozygous Alu insertion in exon 9 of male germ cell-associated kinase as the cause of disease in an isolated individual with RP," or retinitis pigmentosa. The Iowa team screened 1,798 additional, unrelated RP patients and found 20 others who, like the proband, were homozygous for this insertion. Based on the "algorithmic and molecular obstacles to the discovery of pathogenic insertions" the team faced in its study, the authors suggest "specific changes in strategy … can be implemented to more fully harness the power of sequencing technologies."
A trio of researchers at the University of California, Berkeley, shows that in Drosophila "every gap gene contains multiple enhancers with overlapping activities to produce authentic patterns of gene expression." The team says that the observed fidelity of expression programs in the fruit fly may be governed by one or more "different models for 'enhancer synergy,' whereby two enhancers with overlapping activities produce authentic patterns of gene expression," which the researchers outline in their paper.
Elsewhere in the PNAS Early Edition, the National Human Genome Research Institute's Julie Segre and her colleagues report their genomic investigation of a polyclonal outbreak of multidrug-resistant A. baumannii that occurred at the National Institutes of Health's Clinical Center. "Comparing the complete genome sequences of the three dominant outbreak strain types enabled us to conclude that, despite all belonging to the same epidemic lineage, the three strains diverged before their arrival at the NIH," Segre et al. write, adding that "the simultaneous presence of three divergent strains from this lineage supports its increasing prevalence in international hospitals and suggests an ongoing adaptation to the hospital environment." When inspecting the recombinant regions among A. baumannii strain genomes, the team identified "several regions [that] were associated with either the loss or swapping out of genes encoding proteins that are exposed to the cell surface or that synthesize cell-surface molecules." Segre and her colleagues say that their genomic epidemiology analysis has "immediate implications in surveillance, prevention, and treatment of A. baumannii infections."
A team led by investigators at the University of New South Wales proposes generating bacterial community assemblies "based on functional genes rather than species" in a paper published online in advance in PNAS this week. Using metagenomic sequence analysis, the team investigated the link between community structure and function in communities associated with the green macroalga Ulva australis. "This observation of similarity in … functional genes, but not species, together with the relative ease with which bacteria share genetic material, suggests that the key level at which to address the assembly and structure of bacterial communities may not be 'species' (by means of rRNA taxonomy), but rather the more functional level of genes," the authors write.