In the PNAS Early Edition this week, an international research team presents "an allele-specific copy number analysis of the in vivo breast cancer genome" and describe allele-specific copy number analysis of tumors — or ASCAT — a novel bioinformatics approach that allows users to "accurately dissect the allele-specific copy number of solid tumors, [while] simultaneously estimating and adjusting for both tumor ploidy and non-aberrant cell admixture." ASCAT profiles, the authors suggest, allow for the calculations of gains, losses, and copy-number neutral events genome-wide. Using ASCAT, they created a map of "allelic skewness in breast cancer," which may influence disease development.
Investigators in Israel this week describe a "binary search approach to whole-genome data analysis," a protocol which allows users to detect the margins of long and short genome fragments enriched by upregulated signals. The authors suggest that the method is a powerful tool for "identifying both the short up-regulated fragments (such as exons and transcription factor binding sites) and the long — even moderately up-regulated zones — at their precise genome margins."
Also in PNAS this week, researchers at the Mount Sinai School of Medicine in New York, along with their colleagues at the University of Kansas Medical Center, describe the design of chimeric peptide nucleic acids capable of entering a cell's nucleus, binding its target, and reactivating gene expression in both adult transgenic mouse bone marrow and human primary peripheral blood cells. The team used in vitro and in vivo DNA-binding assays and live cell imaging to design the chimeric PNAs capable of gene activation. "Our final molecule contains a specific γ-promoter-binding PNA sequence embedded within two amino acid motifs: one leads to efficient cell/nuclear entry, and the other generates transcriptional reactivation of the target," the authors write.
A pair of researchers in Israel describe their use of RNAi-mediated gene silencing to deduce the "functional significance of pheromone biosynthesis activating neuropeptide receptor in a male moth." PBAN, the duo suggests, may aid in the regulation of free fatty-acid and alcohol components in male complexes. Rachel Bobera and Ada Rafaelib performed knockdown of PBAN-R and found that "injections of PBAN-R dsRNA into the male hemocoel significantly inhibited levels of the various male components."