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In Europe, Maedi-Visna disease has high prevalence rates at the individual and flock levels, respectively, and is regarded as one of the most significant infectious disease in sheep. The lack of treatment or a commercial …
Read PDFAvian aspergillosis, caused by <i>Aspergillus fumigatus</i> (<i>Af</i>), lacks sensitive antemortem diagnostics. Existing microbial cell-free DNA (cfDNA) tests are prone to contamination and require a high pathogen load. We hypothesized that infection-induced tissue damage in chickens …
Read PDFBACKGROUND: This study provides an in-depth genomic and functional characterization of Lactiplantibacillus pentosus LP309, a strain isolated from table olive fermentations. The microorganism was sequenced using three next‑generation sequencing platforms—Illumina, PacBio, and Oxford Nanopore Technologies …
Read PDFAntimicrobial resistance (AMR) poses a significant threat to public health. Rapid and accurate antimicrobial sensitivity testing is essential to guide effective treatment. Here, we present "simplified 5PSeq" (s5PSeq), a streamlined protocol for profiling 5' monophosphorylated …
Read PDFThis study examined the relationships among seminal bacterial composition, oxidative status, and semen quality in Thai native, crossbred, and commercial roosters. Fresh ejaculates (<i>n</i> = 10 per group) were evaluated for semen quality parameters-mass motility, …
Read PDFThe respiratory microbiome plays a crucial role in health and disease, necessitating accurate characterization through high-throughput sequencing technologies. This study provides a comparative analysis of Illumina NextSeq and Oxford Nanopore Technologies (ONT) sequencing platforms for …
Read PDFGuyuan cattle, a transitional breed between northern and central Chinese cattle, are known for their climbing ability and disease resistance. However, the genomic resources of indigenous Chinese cattle breeds, including Guyuan cattle, remain largely unexplored. …
Read PDFNanopore-based sequencing has emerged as a revolutionary tool for animal pathogen genomics, offering capabilities unattainable with Sanger and next-generation sequencing (NGS). Despite rapid technical progress, routine veterinary deployment still faces uncertainty in study design, sample …
Read PDFGenomic surveillance of respiratory syncytial virus (RSV) enables detecting and monitoring of circulating lineages and the emergence of amino acid substitutions affecting transmission, severity, and treatment. We present a comprehensive workflow for RSV whole-genome sequencing, …
Read PDFSynthetic combinatorial DNA libraries are widely used to produce protein variants, optimize binders, and for high-throughput studies of protein-DNA interactions. The libraries can be made by researchers or vendors, and high-throughput sequencing is used for …
Read PDFWhole-genome sequencing (WGS) is a comprehensive approach for the genomic evaluation of acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). We recently described a streamlined tumor-only WGS assay (ChromoSeq) that uses Illumina short-read sequencing with …
Read PDFThird-generation long-read sequencing technologies, significantly improve metagenome assemblies. Highly accurate PacBio HiFi reads can yield hundreds of near-complete metagenome-assembled genomes (MAGs) from a single sample. Recently, the accuracy of the more cost-effective Oxford Nanopore Technologies …
Read PDF<h4>Motivation</h4>Untargeted, also known as metagenomic, nanopore sequencing is a powerful tool for virus genomic surveillance, particularly in resource-limited settings and when paired with the portability of the MinION device (Oxford Nanopore Technologies, ONT). However, a …
Read PDF<h4>Introduction</h4>Early and accurate diagnosis of drug-resistant tuberculosis (DR-TB) is essential for improving treatment outcomes. Phenotypic drug susceptibility testing (pDST) is comprehensive but slow, while rapid molecular assays provide resistance information for a limited number of …
Read PDF<h4>Motivation</h4>Recent advancements in long-read single-cell RNA sequencing (scRNA-seq) have facilitated the quantification of full-length transcripts and isoforms at the single-cell level. Historically, long-read data would need to be complemented with short-read single-cell data in order …
Read PDFBloodstream infections (BSIs) pose a significant global health challenge, particularly due to the increasing prevalence of antimicrobial resistance (AMR). Timely and accurate identification of pathogens and resistance determinants is critical for guiding appropriate therapy and …
Read PDF<h4>Background</h4>Endometrial cancer (EC) is the most common gynaecological malignancy globally, with rising incidence and notable disparities in outcomes. In New Zealand, EC rates have increased significantly, particularly among Māori and Pacific women, who face higher …
Read PDFWe present the genome sequence of <i>Ceratocystis huliohia</i>, one of two fungal pathogens causing the Rapid 'Ōhi'a Death disease of the native 'ōhi'a tree in Hawai'i. This assembly was generated using long-read Nanopore sequencing of …
Read PDFTick-borne encephalitis virus (TBEV) is primarily transmitted by <i>Ixodes</i> spp. and poses significant health risks, leading to morbidity and mortality in humans. Two of the five subtypes, Siberian and Far Eastern are known to circulate …
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