Search results for "Genome"
showing 10 items of 1913 documents
Oxidative DNA Damage Profiles in Mammalian Cells
1997
Reactive oxygen species (ROS) are formed inside cells not only under the influence of exogenous agents (visible light, ionizing radiation, and many oxidants such as peroxides or quinones), but also under normal (physiological) conditions as byproducts of oxygen metabolism and other cellular redox reactions (Pryor 1986; Halliwell and Gutteridge 1986; Sies 1986; Clayson et al. 1994). ROS such as hydroxyl radicals and singlet oxygen are a serious threat to the integrity of the cellular genome, since they efficiently react with DNA to generate many types of DNA modifications, at least some of which are pre- mutagenic (Breimer 1990; Halliwell and Aruoma 1991; Epe 1991; Feig et al. 1994). Steady-…
Icosahedral dsDNA Bacterial Viruses with an Internal Membrane
2008
The icosahedral double-stranded DNA bacteriophages containing an internal membrane belong to two families, the Tectiviridae and the Corticoviridae. Members of the Tectiviridae have a linear dsDNA genome (e.g., PRD1) and those of the Corticoviridae have a circular genome (the only example being PM2). The DNA is covered by a membrane which is in turn covered by a protein capsid. The infection cycle begins when spikes on the capsid recognize the host cell receptor and the virus starts the delivery of the genome into the cell cytoplasm. The replication of the virus genome occurs in the cytoplasm. The members of the Tectiviridae may be virulent or temperate; PM2 is virulent. Virulent bacteriopha…
PUNAS: A Parallel Ungapped-Alignment-Featured Seed Verification Algorithm for Next-Generation Sequencing Read Alignment
2017
The progress of next-generation sequencing has a major impact on medical and genomic research. This technology can now produce billions of short DNA fragments (reads) in a single run. One of the most demanding computational problems used by almost every sequencing pipeline is short-read alignment; i.e. determining where each fragment originated from in the original genome. Most current solutions are based on a seed-and-extend approach, where promising candidate regions (seeds) are first identified and subsequently extended in order to verify whether a full high-scoring alignment actually exists in the vicinity of each seed. Seed verification is the main bottleneck in many state-of-the-art a…
Structure and dynamics of RNA guanine quadruplexes in SARS-CoV-2 genome. Original strategies against emerging viruses
2021
Guanine quadruplexes (G4) structures in viral genome have a key role in modulating viruses’ biological activity. While several DNA G4 structures have been experimentally resolved, RNA G4s are definitely less explored. We report the first calculated G4 structure of the RG-1 RNA sequence of SARS-CoV-2 genome, obtained by using a multiscale approach combining quantum and classical molecular modelling and corroborated by the excellent agreement between the corresponding calculated and experimental circular dichroism spectra. We prove the stability of RG-1 G4 arrangement as well as its interaction with G4 ligands potentially inhibiting viral protein translation.
Genome-wide detection of copy-number variations in local cattle breeds
2019
The aim of the present study was to identify copy-number variations (CNVs) in Cinisara (CIN) and Modicana (MOD) cattle breeds on the basis of signal intensity (logR ratio) and B allele frequency of each marker, using Illumina’s BovineSNP50K Genotyping BeadChip. The CNVs were detected with the PennCNV and SVS 8.7.0 software and were aggregated into CNV regions (CNVRs). PennCNV identified 487 CNVs in CIN that aggregated into 86 CNVRs, and 424 CNVs in MOD that aggregated into 81 CNVRs. SVS identified a total of 207 CNVs in CIN that aggregated into 39 CNVRs, and 181 CNVs in MOD that aggregated into 41 CNVRs. The CNVRs identified with the two softwares contained 29 common CNVRs in CIN and 17 co…
Taxonomical and Functional Assessment of the Endometrial Microbiota in A Context of Recurrent Reproductive Failure: A Case Report
2019
Investigation of the microbial community in the female reproductive tract has revealed that the replacement of a community dominated by Lactobacillus with pathogenic bacteria may be associated with implantation failure or early spontaneous abortion in patients undergoing assisted reproductive technology (ART) treatment. Herein we describe taxonomically and functionally the endometrial microbiome of an infertile patient with repeated reproductive failures (involving an ectopic pregnancy and two clinical miscarriages). The microbiological follow-up is presented over 18-month in which the microbiota was evaluated in six endometrial fluid samples. The microbial profile of 16S rRNA gene sequenci…
The ATXN1 and TRIM31 genes are related to intelligence in an ADHD background: evidence from a large collaborative study totaling 4,963 subjects
2010
Contains fulltext : 96400.pdf (Publisher’s version ) (Closed access) Intelligence is a highly heritable trait for which it has proven difficult to identify the actual genes. In the past decade, five whole-genome linkage scans have suggested genomic regions important to human intelligence; however, so far none of the responsible genes or variants in those regions have been identified. Apart from these regions, a handful of candidate genes have been identified, although most of these are in need of replication. The recent growth in publicly available data sets that contain both whole genome association data and a wealth of phenotypic data, serves as an excellent resource for fine mapping and …
Polygenic association between attention-deficit/hyperactivity disorder liability and cognitive impairments.
2022
AbstractBackgroundA recent genome-wide association study (GWAS) identified 12 independent loci significantly associated with attention-deficit/hyperactivity disorder (ADHD). Polygenic risk scores (PRS), derived from the GWAS, can be used to assess genetic overlap between ADHD and other traits. Using ADHD samples from several international sites, we derived PRS for ADHD from the recent GWAS to test whether genetic variants that contribute to ADHD also influence two cognitive functions that show strong association with ADHD: attention regulation and response inhibition, captured by reaction time variability (RTV) and commission errors (CE).MethodsThe discovery GWAS included 19 099 ADHD cases …
La genètica de les migracions humanes: Seguint el rastre de les migracions a través del nostre genoma
2014
La reconstruccio de les migracions humanes es possible gracies a la informacio aportada per diverses disciplines. L’estudi de la diversitat genetica de les poblacions humanes actuals ens revela quins han estat els esdeveniments demografics i moviments migratoris passats que han deixat una empremta en el nostre genoma. El coneixement dels moviments migratoris en temps prehistorics ens permet comprovar hipotesis proposades des d’altres disciplines cientifiques. De la mateixa manera, la distribucio de la diversitat genetica en el futur dependra, en gran part, de les intenses migracions humanes actuals facilitades pels avencos tecnologics.
CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content
2020
Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, fro…