Development of a panel of recombinase polymerase amplification assays for detection of common bacterial urinary tract infection pathogens

Aims: To develop and evaluate the performance of a panel of isothermal real?time recombinase polymerase amplification (RPA) assays for detection of common bacterial urinary tract infection (UTI) pathogens. Methods and Results: The panel included RPAs for Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa and Enterococcus faecalis. All five RPAs required reaction times of under 12 min to reach their lower limit of detection of 100 genomes per reaction or less, and did not cross?react with high concentrations of nontarget bacterial genomic DNA. In a 50?sample retrospective clinical study, the five?RPA assay panel was found to have a specificity of 100% (95% CI, 78�0%) and a sensitivity of 89% (95% CI, 75�%) for UTI detection. Conclusions:The analytical and clinical validity of RPA for the rapid and sensitive detection of common UTI pathogens was established. Significance and Impact of the Study: Rapid identification of the causative pathogens of UTIs can be valuable in preventing serious complications by helping avoid the empirical treatment necessitated by traditional urine culture's 48�?h turnaround time. The routine and widespread use of RPA to supplement or replace culture?based methods could profoundly impact UTI management and the emergence of multidrug?resistant pathogens

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Structural dynamics of the RNA dependent RNA polymerase of H1N1 strain affecting humans: a bioinformatics approach

The Influenza flu is a pandemic disease that renders the highest risk factor to the society due to its efficient ability of airborne transmission. Studies on the H1N1 strain gained significant focus, since its pandemic outbreak in 2009 and particularly the computational studies on its structural elements significantly aided in revealing their functional uniqueness. Among the 10 structural proteins of H1N1, the RNA-dependent RNA polymerase (RdRp) heterotrimeric protein complex, which is responsible for the synthesis of viral RNA (vRNA) from the negative-sense RNA genome of the virus, is the focus of the present study. This study aimed to investigate the structural dynamics of the RdRp complex with particular emphasis on the reported 17 mutations. The mutant strain is more stabilized by strong concerted residue-residue interactions at both intra- and inter- monomeric levels. In comparison, the mutant strain is structurally flexible with enhanced stabilizing interactions. The structural dynamics of RdRp are significantly governed by the dynamics of the (i) endonuclease domain of PA, (ii) RNA-entry region of PB1 and (iii) cap-binding region of PB2. Explicitly, the cap binding region of PB2 expresses (i) a concerted motion with the RNA-entry region, along with (ii) an anti-correlated motion with the endonuclease domain of the PA subunit, which further supports the stable dynamics of cap-binding towards RNA binding. These findings contribute to the understanding of the structural dynamics associated with the pandemic and mutant structures of RdRp and render a basic knowledge for further development of novel inhibitors towards influenza flu affected humans. Communicated by Ramaswamy H. Sarma</p

Revascularization in ischemic heart failure with preserved ejection fraction: a nationwide cohort study

No abstract available