RNA-Seq is not required to determine stable reference genes for qPCR normalization

Assessment of differential gene expression by qPCR is heavily influenced by the choice of reference genes. Although numerous statistical approaches have been proposed to determine the best reference genes, they can give rise to conflicting results depending on experimental conditions. Hence, recent studies propose the use of RNA-Seq to identify stable genes followed by the application of different statistical approaches to determine the best set of reference genes for qPCR data normalization. In this study, however, we demonstrate that the statistical approach to determine the best reference genes from commonly used conventional candidates is more important than the preselection of ‘stable’ candidates from RNA-Seq data. Using a qPCR data normalization workflow that we have previously established; we show that qPCR data normalization using conventional reference genes render the same results as stable reference genes selected from RNA-Seq data. We validated these observations in two distinct cross-sectional experimental conditions involving human iPSC derived microglial cells and mouse sciatic nerves. These results taken together show that given a robust statistical approach for reference gene selection, stable genes selected from RNA-Seq data do not offer any significant advantage over commonly used reference genes for normalizing qPCR assays.     

Natural mycosis of mango leafhoppers (Cicadellidae: Hemiptera) by Fusarium sp.

Mango leafhoppers that feed on inflorescences and young shoots of mango (Mangifera indica L.) were found mycotized under natural conditions in Bangalore, India. Isolation and characterisation of the etiological agents by sequencing of the Translation Elongation Factor-1α gene, revealed 99% identity with the plant pathogenic fungus Fusarium proliferatum. This is an early report on the Fusarium associated entomopathogenicity in different mango leafhopper species.     

Effect of DL alpha-lipoic acid on some carbohydrate metabolising enzymes in stone forming rats.

DL alpha-lipoic acid has been shown to prevent the induced precipitation of calcium oxalate crystals in the renal tissues of laboratory animals. The acid seems to have a profound influence on carbohydrate metabolism in diabetic rats. Here the effect of alpha-lipoic acid was studied on certain key carbohydrate metabolising enzymes in the tissues of calcium oxalate stone forming rats administered with glycollate as oxalate precursor. There was augmentation of glycolysis in the renal tissues of stone forming as well as lipoate administered rats. The two major gluconeogenic enzymes, glucose-6-phosphatase (G6P) and fructose-1, 6 diphosphatase (FDP) were significantly inhibited in tissues of calculogenic rats. Lipoic acid also reduced the enzyme activities significantly. The citric acid cycle enzymes were not influenced to an appreciable extent. The observed alterations are likely to be due to the regulatory effects of oxalate and lipoate on the enzyme systems.     

Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata

The nuclear pore complex (NPC), embedded in the nuclear envelope, is a large, dynamic molecular assembly that facilitates exchange of macromolecules between the nucleus and the cytoplasm. The yeast NPC is an eightfold symmetric annular structure composed of ～456 polypeptide chains contributed by ～30 distinct proteins termed nucleoporins. Nup116, identified only in fungi, plays a central role in both protein import and mRNA export through the NPC. Nup116 is a modular protein with N‐terminal “FG” repeats containing a Gle2p‐binding sequence motif and a NPC targeting domain at its C‐terminus. We report the crystal structure of the NPC targeting domain of Candida glabrata Nup116, consisting of residues 882–1034 [CgNup116(882–1034)], at 1.94 Å resolution. The X‐ray structure of CgNup116(882–1034) is consistent with the molecular envelope determined in solution by small‐angle X‐ray scattering. Structural similarities of CgNup116(882–1034) with homologous domains from Saccharomyces cerevisiae Nup116, S. cerevisiae Nup145N, and human Nup98 are discussed. Proteins 2012; © 2012 Wiley Periodicals, Inc.