In this week's PNAS Early Edition, an international research team reports the interactions between the Jumonji C domain-containing hydroxylase JMJD6 and single-stranded RNA. Based on its molecular morphology, the investigators found that JMJD6 binds to single-stranded RNA, but not single-stranded DNA, double-stranded RNA, or double-stranded DNA, suggesting that the molecule is more likely to bind and modify single-strand RNA "rather than the previously reported peptide substrates."
In another paper published online in advance, researchers in Korea report their flux-balance analysis of a genome-scale metabolic model using a strategy that incorporates "systematic and condition-independent constraints that restrict the achievable flux ranges of grouped reactions by genomic context and flux-converging pattern analyses." The team's "analyses of three types of genomic contexts, conserved genomic neighborhood, gene fusion events, and co-occurrence of genes across multiple organisms" suggested that a group of fluxes are "likely on or off simultaneously." The authors suggest that their "strategy will be useful for accurately predicting the intracellular fluxes of large metabolic networks when their experimental determination is difficult."
Researchers at the University of Massachusetts Medical School and their colleagues in Japan and Korea this week report that "heterodimers of NF-κB transcription factors DIF and Relish regulate antimicrobial peptide genes in Drosophila," which they've deduced via examinations of the dimerization tendencies of these molecules using transgenic assays. "The formation of the DIF-Relish heterodimer is particularly interesting because it may mediate signaling for the seemingly independent Toll and IMD pathways," the authors write, adding that the complex is "detectable in whole animal extracts," suggesting that it is functional in vivo.
A Memorial Sloan-Kettering Cancer Center team shows in PNAS this week that the histone deacetylase inhibitor vorinostat induces DNA double-strand breaks in both normal and cancer cell lines. Normal cells can repair this damage, while transformed cells cannot, the authors write. They also found that vorinostat "suppressed DNA DSB repair proteins," like RAD50 and MRE11, in cancer but not normal cells. "These findings can explain, in part, the selectivity of vorinostat in causing cancer cell death at concentrations that cause little or no normal cell death," the authors conclude.