ARTICLE Download: 14| View: 128| Comments: 0 | doi:10.20944/preprints201907.0222.v1
Subject: Life Sciences, Microbiology Keywords: antimicrobial resistance; biocuration; microbial nomenclature; molecular epidemiology
Online: 19 July 2019 (08:23:38 CEST)
With the increasing use of genome sequencing as a surveillance tool for molecular epidemiology of antimicrobial resistance, we are seeing an increased intersection of genomics, microbiology, and clinical epidemiology. Clear nomenclature for AMR gene families and pathogens is critical for communication. For CARD release version 3.0.3 (July 2019), we updated the entire CARD database to reflect the latest pathogen names. In total, we detected 48 name changes or updates, some of which reflect major changes in familiar names.
ARTICLE Download: 10| View: 82| Comments: 0 | doi:10.20944/preprints201907.0219.v1
Subject: Life Sciences, Molecular Biology Keywords: circRNA; reproducible analysis; pipeline, Docker images
Online: 19 July 2019 (05:05:35 CEST)
Recently the increased cost-effectiveness of high-throughput technologies has made available a large number of RNA sequencing datasets to identify circular RNAs (circRNAs). However, despite many computational tools were developed to predict circRNAs, a limited number of workflows exists to predict and to characterize circRNAs. Moreover, to the best of our knowledge, these available workflows do not ensure computational reproducibility and require advanced bash scripting skills to be correctly installed and used. To cope with these critical aspects we present Docker4Circ, a new computational framework designed for a comprehensive analysis of circRNAs composed of: circRNAs prediction, classification and annotation using public databases, the back-splicing sequence reconstruction; the internal alternative splicing of circularizing exons; the alignment-free circRNAs quantification from RNA-Seq reads, and, finally, their differential expression analysis. Docker4Circ was specifically designed for making easier and more accessible circRNAs analysis thanks to the following features: (i) its R interface; (ii) the encapsulation of its computational tasks into a docker image; (iii) an available user-friendly Java GUI Interface. Furthermore, Docker4Circ ensures a reproducible analysis because all its tasks were embedded into a docker image following the guidelines provided by Reproducible Bioinformatics Project (RBP, http://reproducible-bioinformatics.org/). The effectiveness of Docker4Circ was demonstrated on a real case study whose goal is to characterize the circRNAs predicted in colorectal cancer cell lines and quantified in public RNA-Seq experiments performed on primary tumor tissues. In conclusion, we propose Docker4Circ as a framework for reproducible and comprehensive analyses of circRNAs to efficiently exploit their biological role.
Tue, 16 July 2019
REVIEW Download: 16| View: 151| Comments: 0 | doi:10.20944/preprints201907.0188.v1
Subject: Life Sciences, Other Keywords: polybrominated diphenyl ethers; PBDE; neurodevelopment; epigenetics; DNA methylation; chromatin remodeling; environmental toxins; toxicity
Online: 16 July 2019 (07:25:37 CEST)
Disruption of epigenetic regulation by environmental toxins is an emerging point of focus for understanding the latter’s impact on human health. Polybrominated diphenyl ethers (PBDEs), one such toxin, are an environmentally pervasive class of brominated flame retardants that have been extensively used as coatings on a wide range of consumer products. Their environmental stability, propensity for bioaccumulation, and known links to adverse health effects have evoked extensive research to characterize underlying biological mechanisms of toxicity. Of particular concern is the growing body of evidence correlating human exposure levels to behavioral deficits related to neurodevelopmental disorders. The developing nervous system is particularly sensitive to influence by environmental signals, including dysregulation by toxins. Several major modes of actions have been identified, but a clear understanding of how observed effects relate to negative impacts on human health has not been established. Here we review the growing body of evidence for epigenetic disruptions induced by PBDEs, including DNA methylation, chromatin dynamics, and non-coding RNA expression while discussing potential relationship between PBDEs and neurodevelopmental disorders.
Mon, 15 July 2019
ARTICLE Download: 16| View: 125| Comments: 0 | doi:10.20944/preprints201907.0180.v1
Subject: Life Sciences, Other Keywords: GPETAFLR peptide; protein hydrolysate; liver; hepatic steatosis; high-fat diet
Online: 15 July 2019 (06:09:04 CEST)
Bioactive peptides are related to the prevention and treatment of many diseases. GPETAFLR is an octapeptide which was isolated from lupine (Lupinus angustifolius L.) and showed anti-inflammatory properties. The aim of this study was to evaluate the potential activity of GPETAFLR to prevent non-alcoholic fatty liver disease (NAFLD) in high-fat diet (HFD)-induced obese mice. C57BL/6J mice were fed a standard diet or an HFD. Two of the groups fed the HFD diet were treated with GPETAFLR in their drinking water at 0,5 mg/kg/d or 1 mg/kg/d. To determine the ability of GPETAFLR to improve the onset and progression of NAFLD, histological studies, hepatic enzyme profile, inflammatory cytokine and lipid metabolism-related genes and proteins were analyzed. Our results suggest that HFD-induced inflammatory metabolic disorders were alleviated by treatment with GPETAFLR. In conclusion, dietary lupine consumption could repair HFD-induced hepatic damage, possibly via modifications in the liver’s lipid signalling pathways.