NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels

Typically, next-generation resequencing projects produce large lists of variants. NovelSNPer is a software tool that permits fast and efficient processing of such output lists. In a first step, NovelSNPer determines if a variant represents a known variant or a previously unknown variant. In a second step, each variant is classified into one of 15 SNP classes or 19 InDel classes. Beside the classes used by Ensembl, we introduce POTENTIAL_START_GAINED and START_LOST as new functional classes and present a classification scheme for InDels. NovelSNPer is based upon the gene structure information stored in Ensembl. It processes two million SNPs in six hours. The tool can be used online or downloaded

Feeding of the probiotic bacterium <it>Enterococcus faecium</it> NCIMB 10415 differentially affects shedding of enteric viruses in pigs

Abstract Effects of probiotic bacteria on viral infections have been described previously. Here, two groups of sows and their piglets were fed with or without feed supplementation of the probiotic bacterium Enterococcus faecium NCIMB 10415. Shedding of enteric viruses naturally occurring in these pigs was analyzed by quantitative real-time RT-PCR. No differences between the groups were recorded for hepatitis E virus, encephalomyocarditis virus and norovirus. In contrast, astrovirus was exclusively detected in the non-supplemented control group. Rotavirus was shedded later and with lower amounts in the probiotic piglet group (p p p p p p < 0.1) B cell populations. The results indicate that probiotic bacteria could have effects on virus shedding in naturally infected pigs, which depend on the virus type. These effects seem to be caused by immunological changes; however, the distinct mechanism of action remains to be elucidated.</p

Track analysis of the species of Agrodes and Plochionocerus (Coleoptera: Staphylinidae)

The geographical distributions of 2 species of Agrodes and 13 species of Plochionocerus were analyzed using a panbiogeographic approach to identify their biogeographic patterns. Nine species have been recorded as being exclusively freom South America, 2 exclusively freom Central America, and 4 are shared between both areas. Two species of Agrodes and 3 of Plochionocerus are widely distributed in 2 or more subregions of the Neotropical region, and 6 species of Plochionocerus have more restricted distributions, basically ranging in a single subregion, and 4 species are restricted to a small number of localities. Three generalized tracks were identified in the Mesoamerican dominion of the Caribbean subregion, in the northwestern South American dominion of the Caribbean subregion, and in the Amazonian subregion. Species of other staphylinid genera provide additional support to these tracks