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This Week in PLoS: Nov 25, 2008

In PLoS Medicine, UCSF researchers discuss selective reporting of drug trials in the literature. In this observational study, researchers looked at efficacy trials from approved NDAs from 2001 and 2002, and published clinical trials that correspond to those NDA trials. Trials with favorable outcomes were more likely to be published. In the NDAs, there were 43 outcomes that were not favorable and 20 of those were not included in the published papers and, in the NDAs and papers, there were 99 conclusions made and nine of those changed from the NDA to the paper, all to favor the drug. "The information that is readily available in the scientific literature to health care professionals is incomplete and potentially biased," they conclude.

Yoav Gilad and his colleague report on their genome-wide scan for genes whose regulation evolved under natural selection. They used a multi-species microarray and measured gene expression levels in the hearts, kidneys, and livers of chimpanzees, rhesus macaques, and people to identify genes and pathways whose expression patterns indicate a stabilization or selection of regulation. Some metabolic pathway genes, they say, evolved specific to certain tissues.

A group of researchers used short tags from the 16S hypervariable regions to identify microbial taxa. They say that this tagging method is equivalent to using full rRNA sequences and that greater sampling depth of tag pyrosequencing can also uncover more rare microbial species that capillary sequencing of the full rRNA. (This technique was used in a PLoS Biology paper published last week).

RIKEN scientists developed an NMR methodology for stable isotope-labeling, of living animals and plants, identifying the metabolites through HSQC-based metabolite chemical shift database, and visualizing them using a coarse-grained view. "This method can thus be used to screen physiological changes in organisms by using coarse-grained views of metabolic pathways in which it would be useful to have an overview of several specific metabolic states," the researchers write.

Berkeley researchers developed a quantitative PCR assay to measure Schistosoma japonicum cercariae concentration in water. Schistosomiasis affects humans and animals in China, the Philippines, and Indonesia; the current method of detecting the parasite uses sentinel mice. For this assay, they used sequences from a conserved region of the S. japonicum genome that encodes a putative deoxyribodipyrimidine photo-lyase.

This past week, PLoS Pathogens included an article reporting on a newly discovered Ebola virus, called Bundibugyo ebolavirus, behind the recent outbreaks of hemorrhagic fever in Uganda. Using random-primed pyrosequencing, the researchers determined about 70 percent of the viral genome and developed an assay to be used in the field. The genome was then completed using primer-walking methods.


The Scan

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.