Identification and analysis of integrons and cassette arrays in bacterial genomes

Integrons recombine gene arrays and favor the spread of antibiotic resistance. Their broader roles in bacterial adaptation remain mysterious, partly due to lack of computational tools. We made a program – IntegronFinder – to identify integrons with high accuracy and sensitivity. IntegronFinder is available as a standalone program and as a web application. It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching. We searched for integrons, integron-integrases lacking attC sites, and clusters of attC sites lacking a neighboring integron-integrase in bacterial genomes. All these elements are especially frequent in genomes of intermediate size. They are missing in some key phyla, such as α-Proteobacteria, which might reflect selection against cell lineages that acquire integrons. The similarity between attC sites is proportional to the number of cassettes in the integron, and is particularly low in clusters of attC sites lacking integron-integrases. The latter are unexpectedly abundant in genomes lacking integron-integrases or their remains, and have a large novel pool of cassettes lacking homologs in the databases. They might represent an evolutionary step between the acquisition of genes within integrons and their stabilization in the new genome.     

Monitoring age‐related trends in genomic diversity of Australian lungfish

An important challenge for conservation science is to detect declines in intraspecific diversity so that management action can be guided towards populations or species at risk. The lifespan of Australian lungfish (Neoceratodus forsteri) exceeds 80 years, and human impacts on breeding habitat over the last half century may have impeded recruitment, leaving populations dominated by old postreproductive individuals, potentially resulting in a small and declining breeding population. Here, we conduct a “single‐sample” evaluation of genetic erosion within contemporary populations of the Australian lungfish. Genetic erosion is a temporal decline in intraspecific diversity due to factors such as reduced population size and inbreeding. We examined whether young individuals showed signs of reduced genetic diversity and/or inbreeding using a novel bomb radiocarbon dating method to age lungfish nonlethally, based on ¹⁴C ratios of scales. A total of 15,201 single nucleotide polymorphic (SNP) loci were genotyped in 92 individuals ranging in age from 2 to 77 years old. Standardized individual heterozygosity and individual inbreeding coefficients varied widely within and between riverine populations, but neither was associated with age, so perceived problems with recruitment have not translated into genetic erosion that could be considered a proximate threat to lungfish populations. Conservation concern has surrounded Australian lungfish for over a century. However, our results suggest that long‐lived threatened species can maintain stable levels of intraspecific variability when sufficient reproductive opportunities exist over the course of a long lifespan.     

Identification of a yeast ribonuclease H as an Sm antigen

We have isolated a 55-kDa enzyme from Saccharomyces cerevisiae on the basis of its ability to hydrolyze specifically the RNA moiety of RNA/DNA hybrids [RNase H(55)]. Remarkably, monospecific anti-[RNase H(55)] antibodies revealed that the protein associates with several small RNAs, including some of the essential yeast spliceosomal snRNAs. Moreover, immunoprecipitation as well as immunoblotting experiments demonstrated that the yeast enzyme reacts (a) with human anti-Sm autoantisera, (b) with a monoclonal antibody specific for the human snRNP proteins B/B', but (c) not with U1-ribonucleoprotein-specific autoantibodies. These results disclosed a hitherto unexpected degree of evolutionary conservation in snRNP protein structure between yeast and man. Additionally, our findings suggested a re-evaluation of the enzymatic mechanism of RNases H which recognize both RNA and RNA/DNA hybrids.     

Determinants of participation restriction among community dwelling stroke survivors: A path analysis

Background  

Apart from promoting physical recovery and assisting in activities of daily living, a major challenge in stroke rehabilitation is to minimize psychosocial morbidity and to promote the reintegration of stroke survivors into their family and community. The identification of key factors influencing long-term outcome are essential in developing more effective rehabilitation measures for reducing stroke-related morbidity. The aim of this study was to test a theoretical model of predictors of participation restriction which included the direct and indirect effects between psychosocial outcomes, physical outcome, and socio-demographic variables at 12 months after stroke.