In PLoS One this week, a study looks at retrogene evolution in mammals. In scrutinizing patterns of retrogene distribution in eight mammalian genomes and four non-mammalian genomes, researchers found that there has been a burst of young retrogenes in mammals and that in these shared retrofamilies, 14 to 18 percent of functional retrogenes may have originated independently in multiple mammalian species. "Retroposition continues to be an important active process in shaping the dynamics of mammalian genomes, as compared to being rather inert in non-mammals," they write.
Also in PLoS One, scientists used a proteomics approach to identify exon skipping events, the most common form of alternative splicing. Screening their database of computationally derived peptide splice variants against tandem mass spec data, they were able to verify novel splice isoforms of ITGA2, NPEPPS, and FH. They say that their method is applicable to all new or existing MS/MS datasets.
Sean Eddy has written a book review for PLoS Biology of Opening Up Education, a collection of essays edited by Toru Iiyoshi and M.S. Vijay Kumar that details the open education movement. While the essays are informative, Eddy says, time is money and ideals of open access eventually need to face the fact that intellectual work needs to be paid for in one way or another. "A more utopian 'open' advocacy simply denies this real-world tension," he writes. "Information wants to be free; corporations are evil; people will make great stuff for love not money; free stuff will save the developing world; we'll pay for it with taxes and charity. You don't have to subscribe to Ayn Rand's brand of laissez-faire capitalism to have serious problems with this."
Two studies in PLoS Genetics explore epigenetics. In one, scientists take on repetitive DNA elements and heterochromatin; after cytological and genetic analyses, they found that in Drosophila, loss of methylation of histone H3 at lysine 9 leads to increased spontaneous DNA damage and activation of DNA repair cell cycle checkpoints. In another study, researchers used bisulfite sequencing to analyze DNA methylation patterns of 190 gene promoter regions on chromosome 21 in five human cell types. They found that among other things, DNA methylation acts in a switch-like manner and that DNA methylation in promoter regions is correlated with the absence of gene expression and low levels of activating H3K4 methylation and H3K9 and K14 acetylation.