In the PNAS Early Edition this week, a public-private research collaboration among academicians and investigators at array technology vendors reports its development of a 6.9 million-feature oligonucleotide "human transcriptome array for high-throughput clinical studies." When compared to that of RNA-seq, the team says, this transcriptome array "allows comprehensive examination of gene expression and genome-wide identification of alternative splicing as well as detection of coding SNPs and non-coding transcripts," and it is "highly reproducible in estimating gene and exon abundance."
A team led by investigators at the University of Chicago reports on two cardiac-specific transcription factor genes, Smad4 and Gata4, that "cooperatively regulate cardiac valve development," online in PNAS this week. In their in vivo analysis, the team found that the genes interact — their endothelial-specific compound haploinsufficiency causes atrioventricular septal defects and Smad4 knockout causes "an absense of valve-forming activity" altogether. "We suggest that one determinant of the phenotypic spectrum caused by human GATA4 mutations is differential effects on GATA4/SMAD4 interactions required for endocardial cushion development," the authors write.
Researchers at the Marine Biology Laboratory in Woods Hole, Mass., led a team that reports "a combinatorial labeling strategy coupled with spectral image acquisition and analysis that greatly expands the number of fluorescent signatures distinguishable in a single image," which it used to differentiate 15 phylotypes in an E. coli community. This Combinatorial Labeling and Spectral Imaging FISH, or CLASI-FISH, approach uses "genus- and family-specific probes to differentiate phylotypes" in both lab-grown microbes and natural communities. Using CLASI-FISH, the team also reports "an initial systems-level structural analysis of biofilm organization."
Investigators at the University of Tokyo describe in PNAS the "structural basis for non-ribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog." More specifically, the team reports the crystal structures of "Bacillus licheniformis CDPS YvmC-Blic, in the apo form and complexed with substrate mimics," as well as its mutational and biochemical analyses, in which the researchers identified residues important to cyclodileucine formation and that "YvmC-Blic binds tRNA and generates cyclodileucine as a monomer."