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<h4>Background</h4>Species-level resolution is essential to understand gastric microbiome recovery after Helicobacter pylori eradication, yet short-read 16 S rRNA approaches often obscure clinically relevant changes.<h4>Methods</h4>Gastric biopsies from 121 adults in Bayan-Ölgii, Mongolia (71 H. pylori-positive, 50 …
Read PDFTelomeres cap the extremities of linear chromosomes and prevent their detection as DNA damage. Telomere uncapping poses a profound threat to genome integrity, yet the immediate consequences of transient uncapping remain unclear. In Saccharomyces cerevisiae, …
Read PDFProtein-DNA interactions can be manipulated in vitro by changing buffer conditions. Here, we develop a methodology to map the cleavage preferences of chimeric gene editors that are fusions of the I-TevI nuclease domain to CRIPSR …
Read PDFSanger sequencing of the first ~500 bp of the 16S rRNA gene is frequently used to identify bacterial pathogens that have ambiguous biochemical profiles or proteomic mass spectra. When diversity does not occur within that …
Read PDFThis study investigates the optimisation of poly(3-hydroxybutyrate) (PHB) production by Mycolicibacterium smegmatis using sugarcane bagasse (SCB) hydrolysate as a low-cost, renewable carbon source. Key fermentation parameters including temperature, pH, agitation, inoculum size and nitrogen supplementation …
Read PDFLong-read metagenomic sequencing allows for the rapid, culture-independent, and accurate identification of causative pathogens and antimicrobial resistance (AMR) profiles, supporting precise antibiotic use and reducing the spread of resistance. However, its application to mastitis milk …
Read PDFMOTIVATION: Facioscapulohumeral Muscular Dystrophy (FSHD) is an autosomal dominant form of muscular dystrophy caused by genetic or epigenetic changes within the D4Z4-repeat at the DUX4-gene, on chromosome 4q. Genetic analysis is challenging due to a …
Read PDFBACKGROUND: Direct whole genome sequencing of Capripox virus genomes from diagnostic samples is not always straightforward. Low viral content in a sample, biased sequencing and subsequent assembly and mapping methods may all influence the outcome. …
Read PDFPaenibacillus sp. TAB_01, an isolate recovered from cotton tissue culture plates and a potential novel species within the genus Paenibacillus was sequenced using Oxford Nanopore technology. The genome was 7.46 Mb with a G + …
Read PDFAdvances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals and plants. However, ongoing development is needed to improve accessibility, affordability, and assembly quality …
Read PDFZoysia macrostachya Franch. & Sav. is a halophytic perennial turfgrass in the Poaceae family, commonly found in the coastal regions of Korea, Japan, and East Asia. Z. macrostachya thrives in high-salinity environments, making it an …
Read PDFThe longhorn beetle Arhopalus rusticus (Coleoptera: Cerambycidae) is a widely distributed wood-boring pest of conifers. Here, we assembled a chromosome-level genome of A. rusticus using Illumina, Oxford Nanopore, and Hi-C sequencing technologies. The assembled genome …
Read PDFBalancing replication fork progression and origin usage is essential to maintain genome stability, but measuring replication fork progression rates and origin usage throughout the genome has been challenging. Here, we use nanopore sequencing combined with …
Read PDF<h4>Introduction</h4>Accessing samples from mediastinal and hilar lymph nodes is considerably more difficult, rendering the diagnosis of tuberculous mediastinal and hilar lymphadenopathy particularly challenging. Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive interventional technique …
Read PDFThe global spread of SARS-CoV-2 was significantly impacted by the emergence of Variants of Concern (VOC), with Pakistan experiencing similar trends to other countries. To gain a comprehensive understanding of the genomic epidemiology of SARS-CoV-2 …
Read PDFWe report complete circular genomes of five <i>Janthinobacterium lividum</i> strains isolated from Austrian freshwater sources. Genomes (6.3-6.6 Mbp, >99% complete) were assembled using Oxford Nanopore sequencing. Each encodes a full violacein biosynthesis pathway. Phylogenomic analysis …
Read PDFAlaska has the highest incidence of tuberculosis (TB) in the United States, with 8% mortality while undergoing TB treatment. With a quarter of TB cases lacking sputum culture to enable drug resistance testing, FreezeTB aimed …
Read PDFThe Korean cattle breed, Hanwoo, has been selected as a meat cattle breed since the late 1980s in Korea, but has suffered from reduced genetic diversity due to repeated selection within a single population. In …
Read PDFFermented shrimp paste (Kapi) is a culturally significant condiment valued for its flavor and nutritional value. However, inconsistent production practices may lead to microbial contamination and histamine accumulation, posing health risks. Understanding microbial diversity, salt-tolerant …
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