Search results for "GENOMICS"
showing 10 items of 1255 documents
General Principles for the Detection of Modified Nucleotides in RNA by Specific Reagents.
2021
Epitranscriptomics heavily rely on chemical reagents for the detection, quantification, and localization of modified nucleotides in transcriptomes. Recent years have seen a surge in mapping methods that use innovative and rediscovered organic chemistry in high throughput approaches. While this has brought about a leap of progress in this young field, it has also become clear that the different chemistries feature variegated specificity and selectivity. The associated error rates, e.g., in terms of false positives and false negatives, are in large part inherent to the chemistry employed. This means that even assuming technically perfect execution, the interpretation of mapping results issuin…
Interactions between dietary n-3 fatty acids and genetic variants and risk of disease
2012
Nutritional genomics has undergone rapid development and the concept is now very popular with the general public. Therefore, there is increasing demand for knowledge on adapting dietary composition to the genome. Our aim has been to undertake a systematic review so as to find out the level of evidence existing on whether the effects of n-3 fatty acids on health can be modulated by genetic variation. A systematic literature search was conducted on studies that jointly analyse the effect of one or more genetic variants in candidate genes and n-3 fatty acids. Both observational and experimental studies were included. Results are classified in accordance with whether the study was undertaken on…
A multi-layer method to study genome-scale positions of nucleosomes
2009
AbstractThe basic unit of eukaryotic chromatin is the nucleosome, consisting of about 150 bp of DNA wrapped around a protein core made of histone proteins. Nucleosomes position is modulated in vivo to regulate fundamental nuclear processes. To measure nucleosome positions on a genomic scale both theoretical and experimental approaches have been recently reported. We have developed a new method, Multi-Layer Model (MLM), for the analysis of nucleosome position data obtained with microarray-based approach. The MLM is a feature extraction method in which the input data is processed by a classifier to distinguish between several kinds of patterns. We applied our method to simulated-synthetic and…
The Epistemics of “Personalized Medicine”. Rebranding Pharmacogenetics
2015
Whereas chapter 4 focuses on uses and normative claims of the rhetorical frame “Personalized Medicine” in medical and popular writings, chapter 5 analyzes the intellectual formation of pharmacogenetic, -genomics as a disciplinary field. It explores when, how, and why the leading journals in the field present themselves as part of the overall phenomenon labelled “Personalized Medicine”. Pharmacogenetic journals founded at the beginning of the twenty-first century, not only adopted the rhetorical framing of PM, but also branded pharmacogenomics as a milestone in medical history. Their vision extended to a large societal context that included not only pharmacology and genetics, but also broad …
Insects’ potential: Understanding the functional role of their gut microbiome
2021
The study of insect-associated microbial communities is a field of great importance in agriculture, principally because of the role insects play as pests. In addition, there is a recent focus on the potential of the insect gut microbiome in areas such as biotechnology, given some microorganisms produce molecules with biotechnological and industrial applications, and also in biomedicine, since some bacteria and fungi are a reservoir of antibiotic resistance genes (ARGs). To date, most studies aiming to characterize the role of the gut microbiome of insects have been based on high-throughput sequencing of the 16S rRNA gene and/or metagenomics. However, recently functional approaches such as m…
Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples
2021
AbstractMetagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories.MethodsMetagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analysed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The…
Paradigm of tunable clustering using Binarization of Consensus Partition Matrices (Bi-CoPaM) for gene discovery
2013
Copyright @ 2013 Abu-Jamous et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Clustering analysis has a growing role in the study of co-expressed genes for gene discovery. Conventional binary and fuzzy clustering do not embrace the biological reality that some genes may be irrelevant for a problem and not be assigned to a cluster, while other genes may participate in several biological functions and should simultaneously belong to multiple clusters. Also, these algorithms cannot generate tight cluster…
Importance of denitrifiers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil
2010
Analyses of the complete genomes of sequenced denitrifying bacteria revealed that approximately 1/3 have a truncated denitrification pathway, lacking the nosZ gene encoding the nitrous oxide reductase. We investigated whether the number of denitrifiers lacking the genetic ability to synthesize the nitrous oxide reductase in soils is important for the proportion of N2O emitted by denitrification. Serial dilutions of the denitrifying strain Agrobacterium tumefaciens C58 lacking the nosZ gene were inoculated into three different soils to modify the proportion of denitrifiers having the nitrous oxide reductase genes. The potential denitrification and N2O emissions increased when the size of ino…
Promoter-Targeted Histone Acetylation of Chromatinized Parvoviral Genome Is Essential for the Progress of Infection
2015
ABSTRACT The association of host histones with parvoviral DNA is poorly understood. We analyzed the chromatinization and histone acetylation of canine parvovirus DNA during infection by confocal imaging and in situ proximity ligation assay combined with chromatin immunoprecipitation and high-throughput sequencing. We found that during late infection, parvovirus replication bodies were rich in histones bearing modifications characteristic of transcriptionally active chromatin, i.e., histone H3 lysine 27 acetylation (H3K27ac). H3K27ac, in particular, was located in close proximity to the viral DNA-binding protein NS1. Importantly, our results show for the first time that in the chromatinized …
Epigenetic modifiers are necessary but not sufficient for reprogramming non-myelinating cells into myelin gene-expressing cells.
2010
Background Modifications on specific histone residues and DNA methylation play an essential role in lineage choice and cellular reprogramming. We have previously shown that histone modifications or combinatorial codes of transcription factors (TFs) are critical for the differentiation of multipotential progenitors into myelinating oligodendrocytes. In this study we asked whether combining global manipulation of DNA methylation and histone acetylation together with the expression of oligodendrocyte- specific TFs, was sufficient to switch the identity of fibroblasts into myelin gene-expressing cells. Methodology/Principal Findings Transfection of six oligodendrocyte-specific TFs (Olig1, Olig2…