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Probing Differential Binding Mechanisms of Phenylalanine-Glycine-Rich Nucleoporins by Single-Molecule FRET
2018
Abstract Phenylalanine-glycine-rich nucleoporins (FG-Nups) are intrinsically disordered proteins, constituting the selective barrier of the nuclear pore complex. They are highly dynamic under physiological conditions and studying their interaction with nuclear transport receptors (NTRs) is key to understanding the molecular mechanism of nucleocytoplasmic transport. Distinct conformational features of FG-Nups interacting with diverse NTRs can be detected by multiparameter single-molecule fluorescence energy transfer (smFRET), which is a powerful technique for studying the dynamics and interactions of biomolecules in solution. Here we provide a detailed protocol utilizing smFRET to reveal dif…
Two differential binding mechanisms of FG-nucleoporins and nuclear transport receptors
2018
Summary Phenylalanine-glycine-rich nucleoporins (FG-Nups) are intrinsically disordered proteins, constituting the selective barrier of the nuclear pore complex (NPC). Previous studies showed that nuclear transport receptors (NTRs) were found to interact with FG-Nups by forming an “archetypal-fuzzy” complex through the rapid formation and breakage of interactions with many individual FG motifs. Here, we use single-molecule studies combined with atomistic simulations to show that, in sharp contrast, FG-Nup214 undergoes a coupled reconfiguration-binding mechanism when interacting with the export receptor CRM1. Association and dissociation rate constants are more than an order of magnitude lowe…
Comparative evaluation of shear bond strength of universal dental adhesives : an in vitro study
2017
Background Patient demand for tooth colored restorations and desire for minimally invasive restorations have made composites an indispensable part of the restorative process. An important factor affecting the intra-oral performance of composite restorations is bonding. Material and methods Ninty six freshly extracted molar teeth were collected and occlusal 3mm is removed using a diamond disc to expose dentine. Following with samples were divided in to two main groups (self-etch & total etch). Each main group is again sub divided in to three groups each according to bonding agent used (Tetric N- Bond Universal, Single Bond Universal, Tetric N Bond Total etch in total etch group and Clear Fil…
DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning
2020
Genome-wide association studies (GWAS) identify genetic variants associated with traits or diseases. GWAS never directly link variants to regulatory mechanisms. Instead, the functional annotation of variants is typically inferred by post hoc analyses. A specific class of deep learning-based methods allows for the prediction of regulatory effects per variant on several cell type-specific chromatin features. We here describe “DeepWAS”, a new approach that integrates these regulatory effect predictions of single variants into a multivariate GWAS setting. Thereby, single variants associated with a trait or disease are directly coupled to their impact on a chromatin feature in a cell type. Up to…
Identifying Prognostic SNPs in Clinical Cohorts: Complementing Univariate Analyses by Resampling and Multivariable Modeling
2016
Clinical cohorts with time-to-event endpoints are increasingly characterized by measurements of a number of single nucleotide polymorphisms that is by a magnitude larger than the number of measurements typically considered at the gene level. At the same time, the size of clinical cohorts often is still limited, calling for novel analysis strategies for identifying potentially prognostic SNPs that can help to better characterize disease processes. We propose such a strategy, drawing on univariate testing ideas from epidemiological case-controls studies on the one hand, and multivariable regression techniques as developed for gene expression data on the other hand. In particular, we focus on …
Effect of graphene substrate type on formation of Bi2Se3 nanoplates
2019
AbstractKnowledge of nucleation and further growth of Bi2Se3 nanoplates on different substrates is crucial for obtaining ultrathin nanostructures and films of this material by physical vapour deposition technique. In this work, Bi2Se3 nanoplates were deposited under the same experimental conditions on different types of graphene substrates (as-transferred and post-annealed chemical vapour deposition grown monolayer graphene, monolayer graphene grown on silicon carbide substrate). Dimensions of the nanoplates deposited on graphene substrates were compared with the dimensions of the nanoplates deposited on mechanically exfoliated mica and highly ordered pyrolytic graphite flakes used as refer…
Meta-analysis of exome array data identifies six novel genetic loci for lung function
2018
Background: Over 90 regions of the genome have been associated with lung function to date, many of which have also been implicated in chronic obstructive pulmonary disease. Methods: We carried out meta-analyses of exome array data and three lung function measures: forced expiratory volume in one second (FEV1), forced vital capacity (FVC) and the ratio of FEV1 to FVC (FEV1/FVC). These analyses by the SpiroMeta and CHARGE consortia included 60,749 individuals of European ancestry from 23 studies, and 7,721 individuals of African Ancestry from 5 studies in the discovery stage, with follow-up in up to 111,556 independent individuals. Results: We identified significant (P<2·8x10-7) associatio…
mRCC Outcome in the Treatment of Metastatic Renal Cell Carcinoma - A German Single-center Real-world Experience.
2018
Background/Aim: Since the advent of targeted therapeutics, paradigms in metastatic renal cell carcinoma (mRCC) treatment have changed. We investigated if efficacy and safety data from randomized controlled trials can be transferred into real-world settings. Patients and Methods: All patients with mRCC treated from 2006-2015 at the Department of Urology (Marburg-Germany) were retrospectively analyzed. Collected data include: Patient demographics, tumor characteristics, efficacy, safety, and used therapy sequences. Results: In total, 197 patients with mRCC were identified. About one third of patients reached third-line therapy. Median overall survival in real-world amounted to 25.8 months wit…
Impact of novel polymorphisms related to cytotoxicity of cytarabine in the induction treatment of acute myeloid leukemia.
2017
Several novel single nucleotide polymorphisms (SNPs) involved in cytarabine cytotoxicity and related to clinical outcomes have been reported recently in a series of 232 pediatric patients with acute myeloid leukemia (AML). We report the first adult AML cohort in which the influence of these SNPs in cytarabine efficacy and toxicity was analyzed. Six of polymorphisms with clinical significance in the previous study [rs12036333, rs10758713, rs9883101, rs6550826, IRX2: rs2897047, mutated in colorectal cancers (MCC): rs7729269] were analyzed in a cohort of 225 adult patients at initial diagnosis of AML treated with an induction scheme of idarubicin plus cytarabine. The variant alleles of rs12036…
Genetically elevated gamma-glutamyltransferase and Alzheimer's disease
2018
Observational epidemiological evidence supports a linear and independent association between serum gamma-glutamyltransferase (GGT) concentrations and the risk of Alzheimer's disease (AD). However, the causality of this association has not been previously investigated. We sought to assess the causal nature of this association using a Mendelian randomization (MR) approach. Using inverse-variance weighted MR analysis, we assessed the association between GGT and AD using summary statistics for single nucleotide polymorphism (SNP)-AD associations obtained from the International Genomics of Alzheimer's Project of 17,008 individuals with AD and 37,154 controls. We used 26 SNPs significantly associ…