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Fast and accurate imputation of genotypes from noisy low-coverage sequencing data in bi-parental populations.
PLoS One
January 2025
DIADE, IRD, Cirad, University of Montpellier, Montpellier, France.
Motivation: Genotyping of bi-parental populations can be performed with low-coverage next-generation sequencing (LC-NGS). This allows the creation of highly saturated genetic maps at reasonable cost, precisely localized recombination breakpoints (i.e.
View Article and Find Full Text PDFGenetic diversity and selection signatures in sheep breeds.
J Appl Genet
January 2025
Departamento de Ciências Exatas, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil.
Natural and artificial selection in domesticated animals can cause specific changes in genomic regions known as selection signatures. Our study used the integrated haplotype score (iHS) and Tajima's D tests within non-overlapping windows of 100 kb to identify selection signatures, in addition to genetic diversity and linkage disequilibrium estimates in 9498 sheep from breeds in Ireland (Belclare, Charollais, Suffolk, Texel, and Vendeen). The mean observed and expected heterozygosity for all the sheep breeds were 0.
View Article and Find Full Text PDFMultiplex Nontargeted Framework Enables Tracking Metabolic Profile of Oxymetholone and Methasterone In Vivo at Nanogram Level by GC-Orbitrap-HRMS for Antidoping Purpose.
Anal Chem
January 2025
Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
Oxymetholone and methasterone are anabolic androgenic steroids prohibited by the World Anti-Doping Agency (WADA) for both in-competition and out-of-competition use. Detecting metabolites of exogenous steroids is crucial for establishing doping violations, making the study of these metabolites essential in antidoping efforts. This study investigated the urinary metabolic profiles of oxymetholone and methasterone using gas chromatography-orbitrap high-resolution mass spectrometry (GC-Orbitrap-HRMS) in nanogram level by utilizing a novel multiplex nontargeted framework protocol.
View Article and Find Full Text PDFMicrobiome characterization of two fresh pork cuts during production in a pork fabrication facility.
Microbiol Spectr
January 2025
Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA.
The goal of this study was to characterize the microbial profile of two different fresh pork cuts, bootjack (BJ) trim and tenderloin (TL), through a 16S rRNA sequencing workflow developed specifically for investigating low-biomass fresh meat within a commercial production schedule. Additionally, this study aimed to determine a baseline prevalence and enumeration profile across these two fresh pork cuts. Results showed that microbiome diversity was different between the BJ and TL, and also differed significantly by processing date.
View Article and Find Full Text PDFWildfire Smoke Contributions to Polycyclic Aromatic Hydrocarbon Loadings in Western Canadian Urban Surface Grime.
Environ Sci Technol
January 2025
Department of Chemistry & Chemical Biology, McMaster University, Hamilton L8S 4L8, Canada.
Wildfires emit large amounts of polycyclic aromatic hydrocarbons (PAHs) into the atmosphere. As PAHs emitted from anthropogenic sources are known to accumulate in urban surface grime present on building exteriors and windows, we hypothesized that PAH-containing wildfire smoke plumes could similarly increase PAH grime loadings. To explore this hypothesis, we coupled analysis of PAHs in grime samples collected from August to November 2021 in two historically smoke-affected Canadian cities, Calgary and Kamloops, with contemporaneous field- and model-based indicators of wildfire influence.
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