In PLoS One this week, research led in part by Harvard's Martha Bulyk found that short-term calorie restriction in male mice alters global gene expression patterns, making them more like those of female mice. Comparing gene expression data from the livers of male mice fed high calorie or calorie-restricted diets -- known to extend lifespan -- they found that a CR diet changes the expression of more than 3,000 genes, suggesting that a CR diet "feminizes" gene expression. Among the genes showing the largest and most statistically significant CR-induced expression differences are Ddit4, a key regulator of the TOR pathway, and Nnmt, a regulator of lifespan linked to the sirtuin pathway, they write in the abstract.
Using a variety of systems biology techniques, including Blast searching and phylogenetic and global transcription analysis, researchers pinpointed two proteins, PfSir2A and PfSir2B, that can silence the expression of var genes in Plasmodium falciparum-infected erythrocytes. There are 60 var genes that code for different antigens of the P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) molecules, which are expressed on the surface of these cells and cause them to stick to brain, organ, and peripheral microvasculature. This antigenic variation, they say in work published in PLoS Biology, is controlled epigenetically.
Bioinformaticists at the University of Oxford have demonstrated what researchers can do with semantic enhancements by creating a journal article with all of them. Taking a recent PLoS Neglected Tropical Diseases article, they've included along with the text, among other things: live DOIs and hyperlinks; semantic markup of textual terms with links to third-party resources; interactive figures; a study summary, a tag cloud and a citation analysis; and a Supporting Claims Tooltip to permit "Citations in Context" and Tag Trees that bring together semantically related terms. "The enhanced article presents a compelling existence proof of the possibilities of semantic publication," they say in a paper published in PLoS Computational Biology.
Researchers at Texas Tech looked at miRNA-related antisense transcription in Arabidopsis. Using whole genome tiling array transcriptome and small RNA deep sequencing data, they found more antisense transcription signatures and small RNAs for miRNA targets than for paralogous genes with no miRNA cleavage site. "This suggests that miRNA-associated 'transitivity' (production of small interfering RNAs through antisense transcription) is more common than previously reported." Their work was published this week in PLoS Genetics.