Researchers at the University of Michigan present in PLOS One this week new software to analyze aptamer-free SELEX-seq data, which they have dubbed TFAST. "TFAST is designed with a simple graphical interface so that it can be installed and executed without extensive expertise in bioinformatics," the team writes, adding that it "completes analysis within minutes on most personal computers."
Over in PLOS Biology, an international team led by investigators at the Hebrew University in Jerusalem reports on its systematic study of effects of 83 histone mutants and 119 gene-deletion mutants on the induction/repression dynamics of 170 transcripts in response to diamide stress in yeast. "Importantly, we find that chromatin regulators play far more pronounced roles during gene induction/repression than they do in steady-state expression," the authors write.
And in a PLOS Genetics paper, an international team led by scientists at China Agricultural University in Beijing compares the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae. "Each genome contains thousands of loci of transposon-like elements, but less than 30 percent of them are conserved among different isolates, suggesting active transposition events in M. oryzae," the team writes. Later, it adds: "Our results indicate that gain or loss of unique genes, DNA duplication, gene family expansion, and frequent translocation of transposon-like elements are important factors in genome variation of the rice blast fungus."
Elsewhere in the journal, researchers at the University of Minnesota report on their sequencing-based investigation of genomic diversity at the nucleotide level among 12 Sinorhizobium medicae and 32 S. meliloti strains. "Although these species are closely related and share host plants, based on the ratio of shared polymorphisms to fixed differences we found that horizontal gene transfer between these species was confined almost exclusively to plasmid genes," the researchers write in PLOS Genetics this week.