In vitro synthesis of uniform poly(dG)–poly(dC) by Klenow exo(−) fragment of polymerase I

In this paper, we describe a production procedure of the one-to-one double helical complex of poly(dG)–poly(dC), characterized by a well-defined length (up to 10 kb) and narrow size distribution of molecules. Direct evidence of strands slippage during poly(dG)–poly(dC) synthesis by Klenow exo(−) fragment of polymerase I is obtained by fluorescence resonance energy transfer (FRET). We show that the polymer extension results in an increase in the separation distance between fluorescent dyes attached to 5′ ends of the strands in time and, as a result, losing communication between the dyes via FRET. Analysis of the products of the early steps of the synthesis by high-performance liquid chromatography and mass spectroscopy suggest that only one nucleotide is added to each of the strand composing poly(dG)–poly(dC) in the elementary step of the polymer extension. We show that proper pairing of a base at the 3′ end of the primer strand with a base in sequence of the template strand is required for initiation of the synthesis. If the 3′ end nucleotide in either poly(dG) or poly(dC) strand is substituted for A, the polymer does not grow. Introduction of the T-nucleotide into the complementary strand to permit pairing with A-nucleotide results in the restoration of the synthesis. The data reported here correspond with a slippage model of replication, which includes the formation of loops on the 3′ ends of both strands composing poly(dG)–poly(dC) and their migration over long-molecular distances (μm) to 5′ ends of the strands

Use Of Computational Fluid Dynamics And Scale Model Component Testing For A Large FCC Prototype Air Compressor

LecturePg. 69-76The purpose of this paper is to describe the use of computational fluid dynamics (CFD) and scale model testing techniques that were used accurately predict and confirm the performance of a large centrifugal air compressor. Compressor performance was later verified by a field performance test

Effects of Very Low Nicotine Content Cigarettes on Smoking Behavior and Biomarkers of Exposure in Menthol and Non-menthol Smokers.

IntroductionBecause 30% of cigarettes sold in the United States are characterized as menthol cigarettes, it is important to understand how menthol preference may affect the impact of a nicotine reduction policy.MethodsIn a recent trial, non-treatment-seeking smokers were randomly assigned to receive very low nicotine cigarettes (VLNC; 0.4 mg nicotine/g tobacco) or normal nicotine cigarettes (NNC; 15.5 mg/g) for 20 weeks. On the basis of preference, participants received menthol or non-menthol cigarettes. We conducted multivariable regression analyses to examine whether menthol preference moderated the effects of nicotine content on cigarettes per day (CPD), breath carbon monoxide (CO), urinary total nicotine equivalents (TNE), urinary 2-cyanoethylmercapturic acid (CEMA), and abstinence.ResultsAt baseline, menthol smokers (n = 346) reported smoking fewer CPD (14.9 vs. 19.2) and had lower TNE (52.8 vs. 71.6 nmol/mg) and CO (17.7 vs. 20.5 ppm) levels than non-menthol smokers (n = 406; ps < .05). At week 20, significant interactions indicated that menthol smokers had smaller treatment effects than non-menthol smokers for CPD (-6.4 vs. -9.3), TNE (ratio of geometric means, 0.22 vs. 0.10) and CEMA (ratio, 0.56 vs. 0.37; ps < .05), and trended toward a smaller treatment effect for CO (-4.5 vs. -7.3 ppm; p = .06). Odds ratios for abstinence at week 20 were 1.88 (95% confidence interval [CI] = 0.8 to 4.4) for menthol and 9.11 (95% CI = 3.3 to 25.2) for non-menthol VLNC smokers (p = .02) relative to the NNC condition.ConclusionsAlthough menthol smokers experienced reductions in smoking, toxicant exposure, and increases in quitting when using VLNC cigarettes, the magnitude of change was smaller than that observed for non-menthol smokers.ImplicationsResults of this analysis suggest that smokers of menthol cigarettes may respond to a nicotine reduction policy with smaller reductions in smoking rates and toxicant exposure than would smokers of non-menthol cigarettes

Drugst.One -- A plug-and-play solution for online systems medicine and network-based drug repurposing

In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network medicine tools have emerged to identify potential drug repurposing candidates. However, these tools often require complex installation and lack intuitive visual network mining capabilities. To tackle these challenges, we introduce Drugst.One, a platform that assists specialized computational medicine tools in becoming user-friendly, web-based utilities for drug repurposing. With just three lines of code, Drugst.One turns any systems biology software into an interactive web tool for modeling and analyzing complex protein-drug-disease networks. Demonstrating its broad adaptability, Drugst.One has been successfully integrated with 21 computational systems medicine tools. Available at https://drugst.one, Drugst.One has significant potential for streamlining the drug discovery process, allowing researchers to focus on essential aspects of pharmaceutical treatment research.Comment: 45 pages, 6 figures, 7 table

A Unifying Mechanism for Mitochondrial Superoxide Production during Ischemia-Reperfusion Injury.

Ischemia-reperfusion (IR) injury occurs when blood supply to an organ is disrupted--ischemia--and then restored--reperfusion--leading to a burst of reactive oxygen species (ROS) from mitochondria. It has been tacitly assumed that ROS production during IR is a non-specific consequence of oxygen interacting with dysfunctional mitochondria upon reperfusion. Recently, this view has changed, suggesting that ROS production during IR occurs by a defined mechanism. Here we survey the metabolic factors underlying IR injury and propose a unifying mechanism for its causes that makes sense of the huge amount of disparate data in this area and provides testable hypotheses and new directions for therapies.Work in our laboratories is supported by the Medical Research Council (UK) and the British Heart Foundation. E.T.C. is supported by a Human Frontiers Science Program fellowship.This is the author accepted manuscript. The final version is available from Cell Press via http://dx.doi.org/10.1016/j.cmet.2015.12.00

Systematic protein-protein interaction mapping for clinically relevant human GPCRs

G‐protein‐coupled receptors (GPCRs) are the largest family of integral membrane receptors with key roles in regulating signaling pathways targeted by therapeutics, but are difficult to study using existing proteomics technologies due to their complex biochemical features. To obtain a global view of GPCR‐mediated signaling and to identify novel components of their pathways, we used a modified membrane yeast two‐hybrid (MYTH) approach and identified interacting partners for 48 selected full‐length human ligand‐unoccupied GPCRs in their native membrane environment. The resulting GPCR interactome connects 686 proteins by 987 unique interactions, including 299 membrane proteins involved in a diverse range of cellular functions. To demonstrate the biological relevance of the GPCR interactome, we validated novel interactions of the GPR37, serotonin 5‐HT4d, and adenosine ADORA2A receptors. Our data represent the first large‐scale interactome mapping for human GPCRs and provide a valuable resource for the analysis of signaling pathways involving this druggable family of integral membrane proteins

Riociguat treatment in patients with chronic thromboembolic pulmonary hypertension: Final safety data from the EXPERT registry

Objective: The soluble guanylate cyclase stimulator riociguat is approved for the treatment of adult patients with pulmonary arterial hypertension (PAH) and inoperable or persistent/recurrent chronic thromboembolic pulmonary hypertension (CTEPH) following Phase

Prognostic Role of miR-21, miR-126 and miR-221 in Clear Cell Renal Cell Carcinoma with Tumor Thrombus of the Inferior Vena Cava

Im Rahmen der Progression des klarzelligen Nierenzellkarzinoms kann es zur Invasion der Vena cava durch einen Tumorthrombus (ccRCC/TT) kommen. Allerdings besteht auch in diesem fortgeschrittenen Stadium eine deutliche Heterogenität bezüglich des klinischen Verlaufs. Während sich mit bekannten Verfahren die Prognose bislang unzureichend vorhersagen ließ, gelang es in Vorarbeiten mittels im Tumorgewebe erfasster miRNA-Expressionen, ein Überlebensklassifikationsmodell auf Basis eines Kombinierten Risikoscores (miR-21, miR-126, miR-221) zu konzipieren. Hierdurch konnte das postoperative Überleben von ccRCC/TT Patienten des Würzburger Universitätsklinikums retrospektiv vorhergesagt werden. In der vorliegenden Arbeit war es möglich, mit Hilfe molekularbiologischer und biostatistischer Methoden das vorbeschriebene Modell erfolgreich an einem unabhängigen, größeren Regensburger ccRCC/TT Patientenkollektiv zu validieren. Am Tumor verstorbene Patienten konnten erneut einer klinisch relevanten High-Risk-Gruppe bzw. einer prognostisch günstigeren Gruppe zugeordnet werden. MiR-21 und miR-126 waren erneut statistisch signifikant mit der Fernmetastasierung und dem tumorbedingten Versterben assoziiert. MiR-21 präsentierte sich sowohl in der am Tumor verstorbenen als auch in der fernmetastasierten Patientengruppe deutlich überexprimiert, während die Expression von miR-126 stark vermindert war. Die neu untersuchte miR-205 zeigte sich in der fernmetastasierten sowie nodal positiven Patientengruppe hochreguliert, ein geringer Zusammengang mit dem tumorbedingten Versterben konnte hergestellt werden. Im zweiten Ansatz gelang es relevante miRNA-Expressionsunterschiede zwischen Seren Würzburger ccRCC-Patienten mit und ohne Invasion des Gefäßsystems sowie tumorfreien Kontrollen zu identifizieren. Die langfristige Herausforderung besteht darin, das validierte Überlebensklassifikationsmodell derart weiterzuentwickeln, dass es supportive klinische Anwendung in der Therapieplanung finden kann.Advanced clear cell renal cell carcinoma extending into the inferior vena cava (ccRCC/TT) represents a clinical high-risk setting. However, there is substantial heterogeneity within this high-risk patient subgroup regarding the survival outcomes. Previously, members of our group developed a combined risk score (CRS) – containing tumor tissue miR-21, miR-126 and miR-221 expression – which allowed the retrospective prediction of postoperative cancer-specific survival (CSS) in ccRCC/TT patients. In the present study, we successfully validated the CRS within an independent, larger cohort of ccRCC/TT patients from Regensburg. The combined risk score significantly stratified the ccRCC/TT cohort according to CSS. MiR-21 and miR-126 expression were significantly associated with the development of distant metastasis during follow-up, lymphonodal status at the time of surgery and cancer-related death. The newly investigated miR-205 showed an upregulation in the subgroup with distant metastasis and lymph node involvement and was associated to cancer-related mortality. In a second approach we measured the expression levels of serum-miR-21, miR-126, miR-145 and miR-221 using qRT-PCR in a ccRCC patient cohort from Würzburg. In this examination significant relative expression differences were identified between sera of ccRCC patients with and without vascular invasion, as well as controls. Conclusion: In our retrospective analysis, we successfully validated the CRS within an independent ccRCC/TT cohort

Determining Amazon's Mechanical Turk's Survey Response Consistency: A UROP Project

This research was supported by the Undergraduate Research Opportunities Program (UROP)