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The methylation of CpG sites with 5mC mark is a dynamic epigenetic modification. However, the relationship between the methylation and the surrounding genomic sequence context remains poorly explored. Investigation of the allele methylation provides an …
Read PDFThe exploration of microbial genomes through next-generation sequencing (NGS) and genome mining has transformed the discovery of natural products, revealing an immense reservoir of previously untapped chemical diversity. Bacteria remain a prolific source of specialized …
Read PDFThe bacterial microbiome in aquaria plays an essential role in system stability by metabolizing toxic compounds like ammonia. This study monitored microbiome changes in seven zoo aquatic systems during their first year to assess responses …
Read PDFDiscovery of disease-related bacterial biomarkers could be a useful approach for early prevention or diagnosis of various afflictions, such as colorectal cancer. This typically involves analyzing small regions of the 16S rRNA gene (e.g. V3V4) …
Read PDF<h4>Background</h4>The RNA bacteriophage MS2 is an RNA phage that infects the bacterium E. coli and is one of the most studied and prototypical model phages in molecular biology and microbiology. Previous research revealed complex translational …
Read PDF<h4>Key message</h4>The first genome-wide evidence of 6 mA methylation in the organellar genomes of Riccia fluitans was provided by this study, with methylation patterns being shown to differ between aquatic and terrestrial forms, suggesting that …
Read PDFFoodborne enteric infections are a major public health and economical burden, yet their surveillance often relies on latent indicators that delay containment efforts by several days and weeks. Conversely, whole metagenome shotgun sequencing of communal …
Read PDFBACKGROUND: Hemophilia A (HA) is an X-linked recessive bleeding disorder caused by pathogenic variants in the F8 gene, resulting in deficient coagulation factor VIII activity. Although intron 22 and intron 1 inversions (Inv22 and Inv1) …
Read PDF<h4>Background</h4>Ongoing antimalarial drug resistance surveillance is essential to guide effective treatment strategies. Historically, resistance to chloroquine and sulfadoxine-pyrimethamine (SP) has been associated with well-characterized mutations in the chloroquine resistance transporter (Pfcrt; K76T) and antifolate pathway …
Read PDFLong-read single-cell RNA sequencing provides an opportunity to understand human health and disease at a level difficult to resolve with bulk or short-read methods. This approach enables isoform-level investigation of cellular diversity and disease mechanisms …
Read PDFA fully phased, chromosome-level reference genome assembly for an IUCN-declared critically endangered and paleo-endemic tree, Eidothea hardeniana (Nightcap Oak) was assembled de novo using long-read PacBio HiFi, Oxford Nanopore (ONT) and Hi-C sequencing technologies. Consensus …
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Read PDFWheat Snow Mold (WSM), caused by Microdochium species, poses a serious threat to global wheat production. Despite its importance, the genetic and molecular mechanisms of Microdochium remain poorly understood. In particular, genome-wide differences between M. …
Read PDF<b>Background/Objectives</b>: Short-read-sequencing (SRS) is currently the standard for genetic testing in inherited human diseases. Intrinsic limitations include PCR dependency, restricted read length, and challenges in identifying structural variants (SVs), copy number variations (CNVs), and intronic …
Read PDFDNA methylation has been proposed as an epigenetic driver of phenotypic plasticity in social insects, yet experimental evidence remains limited. Even less is known about the role of epigenetic mechanisms underlying behavioural and social polymorphism. …
Read PDFAlthough full-length 16S rRNA gene sequencing has substantially improved taxonomic resolution compared to short-read approaches, a high proportion of unclassified taxa are reported in rumen microbiome studies. This limitation is largely driven by platform-specific analytical …
Read PDFContinuous emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants may influence viral transmission dynamics and alter interactions with the respiratory microbiota, potentially increasing the risks of reinfection. This study investigated cases of …
Read PDFShort-read assembly of the African swine fever virus (ASFV) genome is challenging due to the presence of inverted terminal repeat (ITR) and hairpin loop sequences, which often cause ambiguity in contig reconstruction. In this study, …
Read PDF<h4>Purpose</h4>Cell-free DNA (cfDNA) fragmentation patterns carry biological information beyond fragment length, revealing nuclease activity, chromatin organization, and tissue of origin. Fragmentomics has emerged as a powerful approach to improve circulating tumor DNA (ctDNA) detection, particularly …
Read PDF<b>Background:</b> Long-read, single-CpG-resolution sequencing is redefining the information-to-depth ratio in epigenomics. While conventional methylome analysis often requires high coverage, we propose a scalable pipeline designed to extract high-density regulatory logic from shallow sequencing data. <b>Methods:</b> …
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