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This Week in PLOS: Jun 18, 2018

Ghent University researchers examined how well a dozen commercial bisulfite kits fared for DNA fragmentation and DNA recovery. As they report in PLOS One, they assessed the performance of the kits by coupling them with gel electrophoresis, qPCR and digital PCR, and next-generation sequencing to find clear differences between the kits. The kit with the best recovery was Zymo Research's EZ DNA Methylation Gold Kit, while the ones with least fragmentation were Qiagen's Epitect Bisulfite Kit and Merck Millipore's CpGenome Turbo Bisulfite Modification Kit. Which kit is best, though, varies by study goal, the researchers say, as, for instance, studies with limited amounts of DNA may value kits with high recovery, while ones interested in examining long stretches of DNA would prefer low fragmentation.

Also in PLOS One, a pair of researchers from Shaanxi Normal University presents a new approach to predict which proteins might be essential. To do this, the approach relies on a new measure of centrality called Participation degree of a protein in protein Complexes and Subgraph Density, or PCSD. When the researchers applied their approach to Saccharomyces cerevisiae protein data, they found it could better predict essential proteins, as compared to other methods.

Researchers from the University of California, Berkeley, report in PLOS Genetics that similar changes in gene expression are behind the convergent evolution in two high-toothed stickleback populations. They compared transcriptome data from an ancestral low-toothed stickleback population and two high-toothed stickleback populations to find that the high-toothed populations had significantly shared gene expression changes that convergently evolved. They further noted that the similar gene expression changes are largely due to shared alterations to the trans regulatory environment, while cis regulatory changes were most population specific. This, they write, indicates that shared transcriptome changes may evolve even when there are genetic differences.