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This Week in PLoS: Oct 11, 2010

In PLoS Genetics this week, researchers in France describe "alternative splicing at a NAGNAG acceptor site as a novel phenotype modifier." Upon their identification of a mild to asymptomatic phenotype in cystic fibrosis patients homozygous for the E831X mutation in CFTR, the team performed in silico analyses and determined that there is "an indel of a stop codon by alternative splicing at a NAGNAG acceptor site," which contributes to "proteome plasticity" and confers the ability to "remove a disease-causing UAG stop codon."

An international research team led by investigators at Stanford University reports its use of a tagged transposon mutant collection to annotate genes and identify drug targets in Candida albicans in PLoS Pathogens this week. Using their library of 3633 tagged heterozygous transposon disruption mutants in a competitive growth assay, the team "identified 269 genes that were haploinsufficient in four growth conditions, the majority of which were condition-specific," as well as "two new genes necessary for filamentous growth as well as ten genes that function in essential processes" in C. albicans. In addition, the Stanford-led team identified Tfp1p as a specific target for the synthetic compound 0136-0228 in the pathogen.

In a paper published online in PLoS One this week, researchers at the University of New Mexico in Albuquerque and their collaborators propose genetic and epigenetic markers that influence population structure. More specifically, Vince Calhoun et al. "assessed the impact of population diversity on genome-wide single nucleotide polymorphisms and DNA methylation levels in 196 participants from five ethnic groups, using principle and independent component analyses," and identified three population stratification factors that account for six percent of total variance. The primary SNP-population stratification factor "consists of 8 SNPs from three genes, SLC45A2, HERC2 and CTNNA2, known to encode skin/hair/eye color," the authors write, while the main methylation-PSF "includes 48 methylated sites in 44 genes coding for basic molecular functions, including transcription regulation, DNA binding, cytokine, and transferase activity."

And over in PLoS Neglected Tropical Diseases, investigators at the Scripps Research Institute in La Jolla, Calif., detail their "metabolomics-based discovery of diagnostic biomarkers for onchocerciasis." Liquid chromatography-mass spec, the team writes, is a "powerful approach" for biomarker detection based on its sensitivity and specificity. Using LC-MS, the Scripps group analyzed 73 serum and plasma samples and identified "14 biomarkers that showed excellent discrimination between Onchocerca volvulus–positive and negative individuals by multivariate statistical analysis."

The Scan

Follow-Up Data Requests to Biobank Participants Ineffective, Study Finds

An effort to recontact biobank enrollees for additional information reports low participation in a new BMJ Open study.

Study Finds Widespread Transmission of Resistant Bacteria in Vietnam Hospitals

A sequencing study in The Lancet Microbe finds widespread transmission of drug-resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii in two Vietnam ICUs.

Novel Brain Cell Organoids Show Promise for Autism Research

University of Utah researchers report in Nature Communications on their development of brain cell organoids to study SHANK3-related autism.

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.