Kaplanballe6432

We speculate that the inosine-ribonuclease activity of EndoV is disabled in vivo, but RNA binding allowed to promote stabilization of transcripts or recruitment of proteins to fine-tune gene expression. The EndoV-/- tumor suppressive phenotype calls for related studies in human HCC. © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.The structure of the 68 nt sequence with G-quadruplex forming potential within the hTERT promoter is disputed. One model features a structure with three stacked parallel G-quadruplex units, while another features an unusual duplex hairpin structure adjoined to two stacked parallel and antiparallel quadruplexes. We report here the results of an integrated structural biology study designed to distinguish between these possibilities. As part of our study, we designed a sequence with an optimized hairpin structure and show that its biophysical and biochemical properties are inconsistent with the structure formed by the hTERT wild-type sequence. By using circular dichroism, thermal denaturation, nuclear magnetic resonance spectroscopy, analytical ultracentrifugation, small-angle X-ray scattering, molecular dynamics simulations and a DNase I cleavage assay we found that the wild type hTERT core promoter folds into a stacked, three-parallel G-quadruplex structure. The hairpin structure is inconsistent with all of our experimental data obtained with the wild-type sequence. All-atom models for both structures were constructed using molecular dynamics simulations. These models accurately predicted the experimental hydrodynamic properties measured for each structure. We found with certainty that the wild-type hTERT promoter sequence does not form a hairpin structure in solution, but rather folds into a compact stacked three-G-quadruplex conformation. © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.OBJECTIVES In lung transplantation (LT), femoral venoarterial extracorporeal membrane oxygenation (VA-ECMO) usually requires an open approach that may be associated with severe groin wound infection. In endovascular aortic procedures, preclosing of the femoral artery (PFA) with vascular closure devices allows the percutaneous insertion and withdrawal of large-bore cannulae. We sought to evaluate whether this innovative technique could be applied in the specific setting of LT to achieve total percutaneous VA-ECMO and decrease groin wound infection. METHODS We conducted a retrospective study of a prospective database including patients who underwent LT in our centre from January 2011 to December 2017. Patients who underwent peripheral VA-ECMO using the PFA technique after January 2014 (PFA group, n = 106) were compared to those who underwent peripheral VA-ECMO using open cannulation and/or decannulation before January 2014 (non-PFA group, n = 48). The primary end point was the rate of technical success defined as total percutaneous VA-ECMO. Secondary end points included groin wound infections and delayed vascular complications. RESULTS The PFA technique was technically successful in 98 patients (92.5%). As compared with the non-PFA group, the PFA group was characterized by a similar rate of vascular complications (16.6% vs 11.3%, P = 0.360) and a decreased rate of groin wound infection (18.9% vs 0%, P  less then  0.001). In multivariate analysis, risk factors associated with vascular complications following PFA included female sex, peripheral arterial disease and ECMO duration. CONCLUSIONS In LT patients, PFA is associated with a high rate of total percutaneous VA-ECMO, thus preventing the occurrence of groin wound infection. © The Author(s) 2020. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.STUDY OBJECTIVES Traffic noise has been associated with poor sleep quality and short sleep duration. This study investigates the association between nighttime road traffic noise at the least and most exposed façade of the residence, and redemption of sleep medication. METHODS In a cohort of 44,438 Danes, aged 50-64 at baseline (1993-97), we identified all addresses from 1987-2015 from a national registry, and calculated nighttime road traffic noise at the most and least exposed façades. Using Cox Proportional Hazard Models we investigated the association between residential traffic noise over 1, 5 and 10 years before redemption of the first sleep medication prescription in the Danish National Prescription Registry. During a median follow-up time of 18.5 years, 13,114 persons redeemed a prescription. RESULTS We found that 10-year average nighttime exposure to road traffic noise at most exposed façade was associated with a hazard ratio (HR) of 1.05, 95 % confidence interval (CI) (1.00-1.10) for Ln >55 as compared to ≤ 45 dB, which when stratified by sex was confined to men (HR 1.16, 95 % CI 1.08-1.25). For the least exposed façade the HR for Ln > 45 vs. ≤ 35 dB was 1.00, 95 % CI (0.95-1.05). For the most exposed façade, the overall association was strongest in smokers and physically inactive. CONCLUSION Long-term residential nighttime noise exposure at the most exposed façade may be associated with a higher likelihood of redeeming prescriptions for sleep medication, especially among men, smokers, and physically inactive. © Sleep Research Society 2020. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.DNA methyltransferases are primary enzymes for cytosine methylation at CpG sites of epigenetic gene regulation in mammals. De novo methyltransferases DNMT3A and DNMT3B create DNA methylation patterns during development, but how they differentially implement genomic DNA methylation patterns is poorly understood. Here, we report crystal structures of the catalytic domain of human DNMT3B-3L complex, noncovalently bound with and without DNA of different sequences. Human DNMT3B uses two flexible loops to enclose DNA and employs its catalytic loop to flip out the cytosine base. As opposed to DNMT3A, DNMT3B specifically recognizes DNA with CpGpG sites via residues Asn779 and Lys777 in its more stable and well-ordered target recognition domain loop to facilitate processive methylation of tandemly repeated CpG sites. We also identify a proton wire water channel for the final deprotonation step, revealing the complete working mechanism for cytosine methylation by DNMT3B and providing the structural basis for DNMT3B mutation-induced hypomethylation in immunodeficiency, centromere instability and facial anomalies syndrome. © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.Mixotrophy, the combination of heterotrophic and autotrophic nutrition modes, is emerging as the rule rather than the exception in marine photosynthetic plankton. Trichodesmium, a prominent diazotroph ubiquitous in the (sub)tropical oceans, is generally considered to obtain energy via autotrophy. While the ability of Trichodesmium to use dissolved organic phosphorus when deprived of inorganic phosphorus sources is well known, the extent to which this important cyanobacterium may benefit from other dissolved organic matter (DOM) sources is unknown. Here we provide evidence of carbon-, nitrogen- and phosphorus-rich DOM molecules enhancing N2 fixation rates and nifH gene expression in natural Trichodesmium colonies collected at two stations in the western tropical South Pacific. Sampling at a third station located in the oligotrophic South Pacific Gyre revealed no Trichodesmium but showed presence of UCYN-B, although no nifH expression was detected. Our results suggest that Trichodesmium may behave mixotrophically in response to certain environmental conditions, providing them with metabolic plasticity and adding up to the view that mixotrophy is widespread among marine microbes. © FEMS 2020.Current study aims to characterize the influence of sub-minimum inhibitory concentration (sub-MIC) of ciprofloxacin on Salmonella intracellular survival and host virulence. Selleck Ionomycin Herein, Salmonella resistance patterns to various antibiotics were in agreement with those reported in previous studies. Moreover, intracellular survival of both ciprofloxacin-sensitive and -resistant Salmonella was markedly reduced upon treatment with sub-MIC of ciprofloxacin as determined by gentamicin protection assay. These findings were further confirmed using immunostaining indicating an inhibitory effect of sub-MIC of ciprofloxacin on Salmonella intracellular survival. RT-qPCR revealed that expression of genes encoding Salmonella type three secretion system (TTSS) decreased upon bacterial exposure to sub-MIC of ciprofloxacin. Furthermore, bacterial exposure to sub-MIC of ciprofloxacin significantly reduced expression of both sifA and sifB, which are important for Salmonella filaments formation within the host. Treatment of Salmonella with sub-MIC of ciprofloxacin reduced bacterial capacity to kill mice infection models. A lower mortality rate was observed in mice injected with Salmonella treated with sub-MIC of ciprofloxacin as compared with mice inoculated with untreated bacteria. Collectively, current findings indicate that, in addition to its bactericidal potential, sub-MIC of ciprofloxacin could inhibit Salmonella intracellular survival, virulence genes expression as well as host pathogenesis, providing another mechanism for ciprofloxacin in limiting Salmonella host infection. © FEMS 2020.Measuring minimal residual disease in cancer has applications for prognosis, monitoring treatment and detection of recurrence. Simple sequence-based methods to detect nucleotide substitution variants have error rates (about 10-3) that limit sensitive detection. We developed and characterized the performance of MASQ (multiplex accurate sensitive quantitation), a method with an error rate below 10-6. MASQ counts variant templates accurately in the presence of millions of host genomes by using tags to identify each template and demanding consensus over multiple reads. Since the MASQ protocol multiplexes 50 target loci, we can both integrate signal from multiple variants and capture subclonal response to treatment. Compared to existing methods for variant detection, MASQ achieves an excellent combination of sensitivity, specificity and yield. We tested MASQ in a pilot study in acute myeloid leukemia (AML) patients who entered complete remission. We detect leukemic variants in the blood and bone marrow samples of all five patients, after induction therapy, at levels ranging from 10-2 to nearly 10-6. We observe evidence of sub-clonal structure and find higher target variant frequencies in patients who go on to relapse, demonstrating the potential for MASQ to quantify residual disease in AML. © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.OBJECTIVES The combination of cefepime and the novel β-lactam enhancer zidebactam (WCK 5222) is under development for the treatment of difficult-to-treat Gram-negative infections. Against MBL-producing pathogens, cefepime and zidebactam induce cell elongation and spheroplast formation, indicating PBP3 and PBP2 dysfunction, respectively, having a potent bactericidal effect as a combination. The objective of the present study was to determine the mechanistic basis of the bactericidal effect of cefepime/zidebactam on MBL-expressing pathogens. METHODS Pseudomonal PBP-binding affinities of cefepime, zidebactam and imipenem were assessed at different timepoints and also in the presence of purified VIM-1 using a Bocillin FL competition assay. The antibacterial activity of cefepime/zidebactam against three VIM-expressing Pseudomonas aeruginosa isolates was assessed by time-kill and neutropenic mouse lung/thigh infection studies. RESULTS Amidst cefepime-hydrolysing concentrations of VIM-1, substantial cefepime binding to target PBPs was observed.