MICA: desktop software for comprehensive searching of DNA databases

Background  

Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays) that allows large DNA databases to be searched efficiently using very little memory.     

Pathway of cholesterol biosynthesis in the brain of the neonatal rat

Suckling rats were killed at various intervals after intraperitoneal injection of acetate-1-(14)C and their brain sterols were analyzed by column, thin-layer, paper, and gas-liquid chromatography. The crude sterol (to which carrier zymosterol was added) was separated by column chromatography into cholesterol, desmosterol, and zymosterol fractions, and the specific activities of the recovered digitonides were determined. The zymosterol fraction, mainly carrier, was not uniformly labeled, in that the trailing half of the peak had a higher specific activity than the leading half. Evidence obtained suggests that this carbon activity was present in one or more sterols resembling zymosterol (Delta(8,24)-cholestadienol), Delta(7,24)-cholestadienol, and Delta(7,5.24)-cholestatrienol. The desmosterol and cholesterol were also carbon-labeled. The time course of the distribution of carbon activity among the above fractions indicated that the zymosterol fraction is a precursor of the desmosterol and that the desmosterol is, in turn, a precursor of the cholesterol. The data suggest that, in the developing brain of the rat, the course of the transformation of cholesterol precursors into cholesterol is influenced by the presence of at least two slow steps, one involving the conversion of Delta(7)- and Delta(8)-compounds to Delta(5)-compounds and the other, the reduction of the Delta(24)-unsaturation.     

Association of a P2RX7 gene missense variant with brachycephalic dog breeds

Missense variants are associated with various phenotypic traits and disorders in dogs. The canine P2RX7 gene, coding the ATP-gated P2X7 receptor ion channel, contains four known missense variants. The current study aimed to examine the presence of these variants in a random sample of pedigree and mixed-pedigree dogs. Exons 3, 8, 11 and 13 of the P2RX7 gene, encoding these four respective variants, in 65 dogs were assessed by Sanger sequencing and combined with existing sequencing data from another 69 dogs. The distribution of these variants was then evaluated in all 134 dogs combined and separately within individual breeds including 35 different pure breeds. The rs23314713 (p.Phe103Leu) and rs23315462 (p.Pro452Ser) variants were present in 47 and 40% of all dogs studied respectively, with the rs23314713 variant associated with brachycephalic breeds. Among pedigree dogs, the rs23314713 and rs23315462 variants were associated with brachycephalic and non-brachycephalic breeds respectively. The rs851148233 (p.Arg270Cys) and rs850760787 (p.Arg365Gln) variants were present only in dogs of Cocker Spaniel and Labrador Retriever pedigrees respectively. No other missense variants were found in exons 3, 8, 11 and 13 of the P2RX7 gene within the dogs. In conclusion, the rs23314713 and rs23315462 missense variants of the P2RX7 gene are present in a large proportion of dogs, with the rs23314713 variant associated with a number of brachycephalic breeds. However, the association of this variant with dogs of bulldog ancestry, not brachycephaly per se, cannot be excluded.     

Two-pore channel 1 interacts with citron kinase,regulating completion of cytokinesis

Two-pore channels (TPC1, 2, and 3) are recently identified endolysosmal ion channels, but remain poorly characterized. In this study, we show for the first time a role for TPC1 in cytokinesis, the final step in cell division. HEK 293 T-REx cells inducibly overexpressing TPC1 demonstrated a lack of proliferation accompanied by multinucleation and an increase in G2/M cycling cells. Increased TPC1 was associated with a concomitant accumulation of active RhoGTP and a decrease in phosphorylated myosin light chain (MLC). Finally, we demonstrated a novel interaction between TPC1 and citron kinase (CIT). These results identify TPC1 as a central component of cytokinetic control, specifically during abscission, and introduce a means by which the endolysosomal system may play an active role in this process.