Emily K. Herman
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View article: Respiratory Bacteria and Antimicrobial Resistance Genes Detected by Long-Read Metagenomic Sequencing Following Feedlot Arrival, Subsequent Treatment Risk and Phenotypic Resistance in Feedlot Calves
Respiratory Bacteria and Antimicrobial Resistance Genes Detected by Long-Read Metagenomic Sequencing Following Feedlot Arrival, Subsequent Treatment Risk and Phenotypic Resistance in Feedlot Calves Open
Background/Objectives: Long-read metagenomic sequencing can assign antimicrobial resistance genes (ARGs) to speciated bacterial reads. This study evaluated whether metagenomic data from respiratory bacteria derived from feedlot calves samp…
View article: How a paramyxovirus fusion/entry complex adapts to escape a neutralizing antibody
How a paramyxovirus fusion/entry complex adapts to escape a neutralizing antibody Open
View article: A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application
A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application Open
View article: Bacterial enrichment prior to third-generation metagenomic sequencing improves detection of BRD pathogens and genetic determinants of antimicrobial resistance in feedlot cattle
Bacterial enrichment prior to third-generation metagenomic sequencing improves detection of BRD pathogens and genetic determinants of antimicrobial resistance in feedlot cattle Open
Introduction Bovine respiratory disease (BRD) is one of the most important animal health problems in the beef industry. While bacterial culture and antimicrobial susceptibility testing have been used for diagnostic testing, the common prac…
View article: Proksee: in-depth characterization and visualization of bacterial genomes
Proksee: in-depth characterization and visualization of bacterial genomes Open
Proksee (https://proksee.ca) provides users with a powerful, easy-to-use, and feature-rich system for assembling, annotating, analysing, and visualizing bacterial genomes. Proksee accepts Illumina sequence reads as compressed FASTQ files o…
View article: Endosomal vesicle fusion machinery is involved with the contractile vacuole in <i>Dictyostelium discoideum</i>
Endosomal vesicle fusion machinery is involved with the contractile vacuole in <i>Dictyostelium discoideum</i> Open
Contractile vacuoles (CVs), enigmatic osmoregulatory organelles, share common characteristics, such as a requirement for RAB11 and high levels of V-ATPase. These commonalities suggest a conserved evolutionary origin for the CVs with implic…
View article: Characterisation of eight cattle with Swyer syndrome by whole‐genome sequencing
Characterisation of eight cattle with Swyer syndrome by whole‐genome sequencing Open
Swyer syndrome is where an individual has the karyotype of a typical male yet is phenotypically a female. The lack of a (functional) SRY gene located on the Y‐chromosome is implicated in some cases of the Swyer syndrome, although many Swye…
View article: Correction to: Evolution of factors shaping the endoplasmic reticulum
Correction to: Evolution of factors shaping the endoplasmic reticulum Open
View article: Sharing of either phenotypes or genetic variants can increase the accuracy of genomic prediction of feed efficiency
Sharing of either phenotypes or genetic variants can increase the accuracy of genomic prediction of feed efficiency Open
Background Sharing individual phenotype and genotype data between countries is complex and fraught with potential errors, while sharing summary statistics of genome-wide association studies (GWAS) is relatively straightforward, and thus wo…
View article: Evolution of factors shaping the endoplasmic reticulum
Evolution of factors shaping the endoplasmic reticulum Open
Endomembrane system compartments are significant elements in virtually all eukaryotic cells, supporting functions including protein synthesis, post‐translational modifications and protein/lipid targeting. In terms of membrane area the endo…
View article: Evaluating the potential of third generation metagenomic sequencing for the detection of BRD pathogens and genetic determinants of antimicrobial resistance in chronically ill feedlot cattle
Evaluating the potential of third generation metagenomic sequencing for the detection of BRD pathogens and genetic determinants of antimicrobial resistance in chronically ill feedlot cattle Open
Background Bovine respiratory disease (BRD) is an important cause of morbidity and mortality and is responsible for most of the injectable antimicrobial use in the feedlot industry. Traditional bacterial culture can be used to diagnose BRD…
View article: EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotes
EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotes Open
Version 3 (22 November, 2021) See https://doi.org/10.24072/pcjournal.173 for a detailed description of the database. See http://evocellbio.com/eukprot/ for a BLAST database, interactive plots of BUSCO scores and ‘The Comp…
View article: Additional file 2 of Sharing of either phenotypes or genetic variants can increase the accuracy of genomic prediction of feed efficiency
Additional file 2 of Sharing of either phenotypes or genetic variants can increase the accuracy of genomic prediction of feed efficiency Open
Additional file 2: Table S1. Number of filtered polymorphic variants (Minimac R2 > 0.4) per chromosome in the imputed WGS for the overseas cows.
View article: Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri
Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri Open
View article: Mechanism and evolution of the Zn-fingernail required for interaction of VARP with VPS29
Mechanism and evolution of the Zn-fingernail required for interaction of VARP with VPS29 Open
VARP and TBC1D5 are accessory/regulatory proteins of retromer-mediated retrograde trafficking from endosomes. Using an NMR/X-ray approach, we determined the structure of the complex between retromer subunit VPS29 and a 12 residue, four-cys…
View article: The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion
The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion Open
The discovery that the protist Monocercomonoides exilis completely lacks mitochondria demonstrates that these organelles are not absolutely essential to eukaryotic cells. However, the degree to which the metabolism and cellular systems of …
View article: Regulation of early endosomes across eukaryotes: Evolution and functional homology of Vps9 proteins
Regulation of early endosomes across eukaryotes: Evolution and functional homology of Vps9 proteins Open
Endocytosis is a crucial process in eukaryotic cells. The GTPases Rab 5, 21 and 22 that mediate endocytosis are ancient eukaryotic features and all available evidence suggests retained conserved function. In animals and fungi, these GTPase…
View article: Membrane Trafficking Modulation during Entamoeba Encystation
Membrane Trafficking Modulation during Entamoeba Encystation Open
View article: Resolving the homology—function relationship through comparative genomics of membrane-trafficking machinery and parasite cell biology
Resolving the homology—function relationship through comparative genomics of membrane-trafficking machinery and parasite cell biology Open
View article: A Eukaryote without a Mitochondrial Organelle
A Eukaryote without a Mitochondrial Organelle Open
View article: The high complexity and dynamic evolution of the Ras superfamily of GTPases in Naegleria
The high complexity and dynamic evolution of the Ras superfamily of GTPases in Naegleria Open