Skip to main content
Premium Trial:

Request an Annual Quote

This Week in PLOS: May 13, 2019

For a paper PLOS Pathogens, a team from Denmark and Belgium profile a yeast species called Saccharomycopsis schoenii that is known for infecting Candida auris and other clinically relevant Candida species. In addition to doing de novo genome sequencing, assembly, and annotation, the researchers incorporated RNA sequencing, liquid chromatography-tandem mass spectrometry-based proteomic analyses, and microscopy to characterize the mycoparasite.  To get a look at its predation of other fungi, meanwhile, they followed S. schoenii in a range of nutritional conditions in a Saccharomyces cerevisiae yeast prey model. For example, the authors saw an uptick in cell wall-busting aspartic protease enzymes as S. schoenii attacked the yeast. "With these fundamental insights into the predatory behavior of S. schoenii, we open up for further exploitation of this yeast as a biocontrol yeast and/or source for novel antifungal agents," they write.

In PLOS Genetics, researchers from the University of Pittsburgh, Indiana University, and the University of Puerto Rico present an approach for integrating genomic, epigenomic, and transcriptomic datasets to explore the biology behind complex diseases. The team's modified Fisher's computational method, dubbed the Omnibus-Fisher statistic, brought together p-values generated for association tests done using each type of data. When they applied this approach to array-based genotyping, white blood cell DNA methylation profiles, and white blood cell RNA sequences data for more than 1,100 children from Connecticut and Puerto Rico with childhood asthma, the authors replicated a known asthma association and identified a handful of new loci with potential ties to the disease.

An international team led by investigators in Brazil and South Africa introduce a software tool called ArboTyping for classifying mosquito-transmitted dengue virus (DENV), Chikungunya virus (CHIKV), and Zika virus (ZIKV) species, serotypes, or genotypes. "To assign the genotypes uploaded by the user, the tool analyzes the sequences one by one," the authors say, and "genotypes through identification, alignment, and phylogenetic reconstruction." As they report in PLOS Neglected Tropical Diseases, the investigators developed the bioinformatics tool with the help of phylogenetics and 4,118 DENV, 653 CHIKV, and 413 ZIKV sequences from GenBank, which spanned a range of serotypes and/or genotypes. From there, they validated the ArboTyping tool with whole-genome or partial-genome sequences, demonstrating that the computational approach compared favorably with manual classification of the arboviruses.