Gentrepid V2.0: a web server for candidate disease gene prediction

Contains fulltext : 124935.pdf (publisher's version ) (Open Access)BACKGROUND: Candidate disease gene prediction is a rapidly developing area of bioinformatics research with the potential to deliver great benefits to human health. As experimental studies detecting associations between genetic intervals and disease proliferate, better bioinformatic techniques that can expand and exploit the data are required. DESCRIPTION: Gentrepid is a web resource which predicts and prioritizes candidate disease genes for both Mendelian and complex diseases. The system can take input from linkage analysis of single genetic intervals or multiple marker loci from genome-wide association studies. The underlying database of the Gentrepid tool sources data from numerous gene and protein resources, taking advantage of the wealth of biological information available. Using known disease gene information from OMIM, the system predicts and prioritizes disease gene candidates that participate in the same protein pathways or share similar protein domains. Alternatively, using an ab initio approach, the system can detect enrichment of these protein annotations without prior knowledge of the phenotype. CONCLUSIONS: The system aims to integrate the wealth of protein information currently available with known and novel phenotype/genotype information to acquire knowledge of biological mechanisms underpinning disease. We have updated the system to facilitate analysis of GWAS data and the study of complex diseases. Application of the system to GWAS data on hypertension using the ICBP data is provided as an example. An interesting prediction is a ZIP transporter additional to the one found by the ICBP analysis. The webserver URL is https://www.gentrepid.org/

Identification of urgent gaps in public and policymaker knowledge of heart failure: results of a global survey

Background: Despite advances in the treatment of heart failure (HF) with reduced ejection fraction, people with HF continue to have a high risk of mortality and hospitalisation. Patients also suffer from poor quality of life, with reduced societal and economic participation. The burden of HF on patients and healthcare systems is extraordinary, yet awareness remains low. This survey was conducted to identify gaps in general public and policymaker knowledge around HF. Methods: A closed-question web-based survey of the general public and policymakers was conducted between February and October 2020. Study outcomes assessed the participants’ awareness and understanding of HF symptoms, risk factors and mortality, and views around hospital admissions in their country. Responses were collected using multiple-choice questions. Results: The survey was completed by 26,272 general public respondents in 13 countries and 281 government and public sector policymakers in nine countries. While 99% of general public respondents had heard of HF, their understanding of the condition and its symptoms was poor, and only 6% identified that shortness of breath, fatigue, and leg swelling were the main symptoms of HF. Of policymaker respondents, 14% identified HF as the leading cause of avoidable hospitalisations, and only 4% recognised that ~ 87% of government spending on HF is related to hospitalisations. Conclusions: Major gaps were identified in the understanding of HF and the burden it places on patients and their caregivers, healthcare systems and society. This study confirms an ongoing need for national policy strategies and investment to raise awareness of the importance of HF prevention, early diagnosis, and implementation of effective treatments to reduce hospitalisations and death

The Changing Landscape for Stroke\ua0Prevention in AF: Findings From the GLORIA-AF Registry Phase 2

Background GLORIA-AF (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients with Atrial Fibrillation) is a prospective, global registry program describing antithrombotic treatment patterns in patients with newly diagnosed nonvalvular atrial fibrillation at risk of stroke. Phase 2 began when dabigatran, the first non\u2013vitamin K antagonist oral anticoagulant (NOAC), became available. Objectives This study sought to describe phase 2 baseline data and compare these with the pre-NOAC era collected during phase 1. Methods During phase 2, 15,641 consenting patients were enrolled (November 2011 to December 2014); 15,092 were eligible. This pre-specified cross-sectional analysis describes eligible patients\u2019 baseline characteristics. Atrial fibrillation disease characteristics, medical outcomes, and concomitant diseases and medications were collected. Data were analyzed using descriptive statistics. Results Of the total patients, 45.5% were female; median age was 71 (interquartile range: 64, 78) years. Patients were from Europe (47.1%), North America (22.5%), Asia (20.3%), Latin America (6.0%), and the Middle East/Africa (4.0%). Most had high stroke risk (CHA2DS2-VASc [Congestive heart failure, Hypertension, Age  6575 years, Diabetes mellitus, previous Stroke, Vascular disease, Age 65 to 74 years, Sex category] score  652; 86.1%); 13.9% had moderate risk (CHA2DS2-VASc = 1). Overall, 79.9% received oral anticoagulants, of whom 47.6% received NOAC and 32.3% vitamin K antagonists (VKA); 12.1% received antiplatelet agents; 7.8% received no antithrombotic treatment. For comparison, the proportion of phase 1 patients (of N = 1,063 all eligible) prescribed VKA was 32.8%, acetylsalicylic acid 41.7%, and no therapy 20.2%. In Europe in phase 2, treatment with NOAC was more common than VKA (52.3% and 37.8%, respectively); 6.0% of patients received antiplatelet treatment; and 3.8% received no antithrombotic treatment. In North America, 52.1%, 26.2%, and 14.0% of patients received NOAC, VKA, and antiplatelet drugs, respectively; 7.5% received no antithrombotic treatment. NOAC use was less common in Asia (27.7%), where 27.5% of patients received VKA, 25.0% antiplatelet drugs, and 19.8% no antithrombotic treatment. Conclusions The baseline data from GLORIA-AF phase 2 demonstrate that in newly diagnosed nonvalvular atrial fibrillation patients, NOAC have been highly adopted into practice, becoming more frequently prescribed than VKA in Europe and North America. Worldwide, however, a large proportion of patients remain undertreated, particularly in Asia and North America. (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients With Atrial Fibrillation [GLORIA-AF]; NCT01468701

Effect of oxic/anoxic conditions on the removal of organic micropollutants in the activated sludge process

Among the emerging issues in the field of wastewater treatments, reducing energy consumption and removal of new organic pollutants have become of primary concern. With respect to the first goal, alternating oxic/anoxic conditions in the bioreactor has demonstrated to be a feasible way to ensure the required efficiency of carbon and nitrogen removal along with energy saving. The aim of the present study was to investigate if these alternating oxic/anoxic conditions are also capable of boosting organic micropollutants degradation, by stimulating the appropriate enzymes. Three different aeration frequencies were tested in a laboratory scale activated sludge reactor and the effects evaluated in terms of removal of carbon, nitrogen and a mixture of OMPs (Sulfamethoxazole, Sulfadiazine, Lincomycin, Carbamazepine, Pyrazole, Naproxen, Atrazine and Sucralose). It was also evaluated if these aeration strategies could change the microbial community composition with respect to the control test conducted under continuous air supply. Among the tested strategies, the longest and shortest durations of anoxic conditions promoted the best removal for the majority of OMPs. This enhancement was statistically well correlated to the activity increase of Lignin Peroxidase and Cellulase enzymes whereas the microbial speciation did not change statistically. The same durations were also capable of maintaining high carbon and nitrogen removal rates within the same biological reactor

Controlling leucine zipper specificity with interfacial hydrophobic residues

Dimerisation of leucine zippers results from the parallel association of alpha-helices to form a coiled coil. Coiled coils comprise a heptad repeat, denoted as (abcdefg)(n), where residues at positions a and d are hydrophobic and constitute the core of the dimer interface. Charged amino acids at the e and g positions of the coiled coil are thought to be the major influence on dimerisation specificity through the formation of attractive and repulsive interhelical electrostatic interactions. However, the variability of a-position residues in leucine zipper transcription factors prompted us to investigate their influence on dimerisation specificity. We demonstrate that mutation of a single interfacial a-position Ala residue to either Val, Ile or Leu significantly alters the homo- and heterodimerisation specificities of the leucine zipper domain from the c-Jun transcription factor. These results illustrate the importance of a-position residues in controlling leucine zipper dimerisation specificity in addition to providing substantial contributions to dimer stability

Induction of Microbial Oxidative Stress as a New Strategy to Enhance the Enzymatic Degradation of Organic Micropollutants in Synthetic Wastewater

Organic micropollutants (OMPs) are pervasive anthropogenic contaminants of receiving waters where they can induce various adverse effects to aquatic life. Their ubiquitous environmental occurrence is primarily attributed to discharge from wastewater treatment plants due to incomplete removal by common biological wastewater treatment processes. Here, we assess a new strategy for promoting the degradation of six representative OMPs (i.e. sulfamethoxazole, carbamazepine, tylosin, atrazine, naproxen and ibuprofen) by intentionally stimulating the production of microbial oxidoreductases to counter oxidative stress caused by oxygen perturbations. Mixed microbial cultures from a dairy farm wastewater were subjected to cyclic perturbations of dissolved oxygen (DO). A distance-based redundancy analysis was used to show that DO perturbations correlate with the abundance of Pseudomonadaceae and Rhodocyclaceae families, activities of peroxidases and cytochromes, and the degradation of OMPs. DO perturbation of 0.25 and 0.5 cycles/hr led to most abundance of Pseudomonadaceae and Rhodocyclaceae families, showed higher activity of peroxidase and cytochrome, and gave largest removal of OMPs (removal of 92±3% for sulfamethoxazole, 84±3% for naproxen, 82±3% for ibuprofen, 66±2% for carbamazepine, 57±15% for tylosin, and 88±1% for atrazine)

Mapping the phosphoinositide-binding site on chick cofilin explains how PIP2 regulates the cofilin-actin interaction

Cofilin plays a key role in the choreography of actin dynamics via its ability to sever actin filaments and increase the rate of monomer dissociation from pointed ends. The exact manner by which phosphoinositides bind to cofilin and inhibit its interaction with actin has proven difficult to ascertain. We determined the structure of chick cofilin and used NMR chemical shift mapping and structure-directed mutagenesis to unambiguously locate its recognition site for phosphoinositides (Pis). This structurally unique recognition site requires both the acyl chain and head group of the PI for a productive interaction, and it is not inhibited by phosphorylation of cofilin. We propose that the interaction of cofilin with membrane-bound Pis abrogates its binding to both actin and actin-interacting protein 1, and facilitates spatiotemporal regulation of cofilin activity