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This Week in PLoS: Aug 22, 2011

In PLoS One this week, researchers at the World Health Organization's Collaborating Center for Reference and Research on Influenza report their development of a pyrosequencing assay "for the rapid identification and subtyping of potential human influenza A virus reassortants based on all eight gene segments of the virus," which they say could enhance flu surveillance. "This method was shown to be capable of detecting reassortant viruses by correctly identifying the source of all eight gene segments from three vaccine production reassortant viruses and three H1N2 viruses," the authors say. They add that pyrosequencing is a "sensitive and specific procedure for screening large numbers of viruses for reassortment events amongst the commonly circulating human influenza A viruses."

Elsewhere in PLoS One, investigators in Denmark and the Netherlands report their use of pyrosequencing to comparatively analyze bacterial communities in a potato field. By analyzing the rhizospheres of six cultivars at three growth stages, along with their corresponding bulk soils, the team obtained around 350,000 bacterial sequences. "Across all samples, rank abundance distributions best fitted the power law model, which indicates a community composed of a few highly dominant species next to numerous rare species," the authors report. Overall, the researchers found that, across all cultivars, "the young plant stages revealed cultivar-dependent bacterial community structures, which disappeared in the flowering and senescence stages."

Researchers at Germany's University of Cologne and Wageningen University in the Netherlands discuss the theoretical evolutionary accessibility of mutational pathways. "We define a mutational pathway to be accessible if it contains the minimal number of mutations required to reach the target genotype, and if fitness increases in each mutational step," Cologne's Jasper Franke et al. write in their PLoS Computational Biology paper. In assessing this definition and its resulting model predictions on an empirical eight-locus fitness landscape for the filamentous fungus Aspergillus niger, the team found that "the globally optimal configuration should be accessible to genome-wide evolution, but the repeatability of evolutionary trajectories is limited owing to the presence of a large number of alternative mutational pathways."

Over in PLoS Pathogens, a pair of researchers at GlaxoSmithKline discuss its use of phenotypic screens and chemical genomics to identify antimalarial compounds as potential treatments. "From a chemical standpoint, some hits may look like bona fide drug leads while others more like chemical probes for target identification," the GSK duo writes. In reviewing such screening initiatives, the researchers suggest room for improvement. "Sets of whole-cell hits should be re-screened for specific modes of action. Even with the small numbers of compounds in such sets, single target screens are probably not practical given the effort required to validate individual targets and develop robust assays," the authors write, later adding that "most of those assays are complex and not amenable to high throughput screening." Further, the GSK researchers say that "it may not be possible to assign individual targets to all compounds, particularly to those hitting more than one target, but validating a given pathway or cellular process as amenable to pharmacological intervention will still be useful."

The Scan

Vaccine Update Recommended

A US Food and Drug Administration panel recommends booster vaccines be updated to target Omicron, CNBC reports.

US to Make More Vaccines for Monkeypox Available

The US is to make nearly 300,000 vaccine doses available in the coming weeks to stem the spread of human monkeypox virus, according to NPR.

Sentence Appealed

The Associated Press reports that Swedish prosecutors are appealing the sentence given to a surgeon once lauded for transplanting synthetic tracheas but then convicted of causing bodily harm.

Genome Biology Papers on COVID-19 Effector Genes, Virtual ChIP-seq, scDART

In Genome Biology this week: proposed COVID-19 effector genes, method to predict transcription factor binding patterns, and more.