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This Week in PLOS : Aug 13, 2012

This week in PLOS One, investigators from the Australian Collaborating Centre for Enterococcus and Staphylococcus Species Typing and Research and their colleagues in Germany and the US discuss the molecular epidemiology of the highly virulent, PVL-positive ST93-IV [2B] S. aureus strain, which is colloquially known as "Queensland CA-MRSA." The team used a variety of molecular methods — from pulsed-field gel electrophoresis to MLST — in an effort "to determine if the increased prevalence of ST93-IV [2B] is due to the widespread transmission of a single strain of ST93-IV [2B]" by examining the genetic relatedness of 58 S. aureus ST93 samples that were isolated throughout Australia over time. "Although multiple ST93-MRSA strains were characterised, little genetic diversity was identified for most isolates, with PVL-positive ST93-IVa [2B]-t202-dt10 predominant across Australia," the authors write. "Whether ST93-IVa [2B] t202-dt10 arose from one PVL-positive ST93-MSSA-t202, or by independent acquisitions of SCCmec-IVa [2B]-dt10 into multiple PVL-positive ST93-MSSA-t202 strains is not known."

Elsewhere in the journal, researchers at Radboud University Medical Center in The Netherlands and their colleagues present a new Web-based software tool for the rapid analysis of high-throughput transposon-insertion sequencing data. The tool, which the researchers have dubbed Essentials, "accurately predicts (conditionally) essential genes and offers the flexibility of using different sample normalization methods, genomic location bias correction, data preprocessing steps, appropriate statistical tests and various visualizations to examine the results, while requiring only a minimum of input and hands-on work from the researcher," they write.

Over in PLOS Genetics, investigators from the University of California, San Diego, and the National Health Research Institutes in Miaoli, Taiwan, report having analyzed genome-wide transcription start site profiles that they generated for E. coli and Klebsiella pneumoniae using a modified 5' RACE approach, followed by deep sequencing of primary mRNA. Next, the researchers used the transcription start sites they had determined to define promoter regions and 5' untranslated regions upstream of coding genes. "Comparative analysis of these regulatory elements revealed the use of multiple TSSs, identical sequence motifs of promoter and Shine-Dalgarno sequence, reflecting conserved gene expression apparatuses between the two species," the authors write, later adding that their results "reveal a new dimension of comparative genomics such that a comparison of two genomes needs to be comprehensive over all levels of genome organization."

And in PLOS Computational Biology, Iga Korneta from the International Institute of Molecular and Cell Biology in Warsaw, and Janusz Bujnicki from the Adam Mickiewicz University in Poznan, both in Poland, discuss "intrinsic disorder in the human spliceosomal proteome," and its functional impacts. "In particular, proteins involved in the secondary functions of the spliceosome, such as mRNA recognition, intron/exon definition and spliceosomal assembly and dynamics, are more disordered than proteins directly involved in assisting splicing catalysis," Korneta and Bujnicki write.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.