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As nanopore sequencing has been widely adopted, data accumulation has surged, resulting in over 700,000 public datasets. While these data hold immense potential for advancing genomic research, their utility is compromised by the absence of …
Read PDFLocal protein synthesis in neurons is vital for synaptic maintenance and plasticity, yet the regulatory mechanisms, particularly cytoplasmic polyadenylation, are not fully understood. This study used nanopore sequencing to examine transcriptomic responses and 3'-end dynamics …
Read PDFA unique feature of Oxford Nanopore Technologies sequencers, adaptive sampling, allows precise DNA molecule selection from sequencing libraries. Here, we present enhancements to our tool, readfish, enabling all features for the industrial scale PromethION sequencer, …
Read PDF<h4>Background</h4>Culturing of fungi is labor-intensive and reveals limited diversity, while high-throughput sequencing of barcodes (i.e., metabarcoding) enables a simultaneous detection of fungi from multiple environmental samples. Metabarcoding using short-read sequencers, such as Illumina platforms, provides …
Read PDFMore than 60 human disorders are caused by unstable expansion of short tandem repeat (STR) tracts. These can exhibit cell-type-specific mosaicism in several repeat expansion disorders and remain difficult to characterize due to technical challenges …
Read PDF<h4>Background</h4>Mycena is a widespread genus of mushroom capable of decomposing various dead plant substrates. Gastrodia elata is a fully mycoheterotrophic orchid whose seed germination depends on specific Mycena strains. However, only a few Mycena species …
Read PDFSarcandra glabra (Thunb.) Nakai, a member of the family Chloranthaceae, has a rich history of use in traditional Chinese medicine. To date, >400 compounds have been isolated and characterized from this plant. Studying the genome …
Read PDFBACKGROUND: After the first case of COVID-19 was reported in Côte d’Ivoire in March 2020, the virus spread significantly, with several epidemic waves. During a carriage study conducted from November 2020 to April 2021 to …
Read PDFBACKGROUND: Since 2019, Cameroon has reported a high number of seasonal influenza cases caused by the A(H1N1)pdm09 subtype, which remained the predominant global strain as of 2024. METHODS: To characterize the evolutionary dynamics of circulating …
Read PDFPorcine biomedical models have emerged as valuable tools in biomedical research due to their physiological, anatomical, metabolic, immunological, and genetic similarities to humans. As a result, they offer greater relevance for translational studies than rodent …
Read PDFCarbapenemase-producing Enterobacterales (CPE) are a major public health concern. Within the <i>Enterobacter cloacae</i> complex (ECC), the <i>bla</i><sub>VIM-1</sub> carbapenemase gene is frequently plasmid-borne, enabling inter-clonal and inter-species spread that complicates the detection and control of carbapenemase …
Read PDFLong COVID or Post-Acute Sequelae of SARS-CoV-2 Infection (PASC), marked by persistent symptoms lasting weeks to months after acute SARS-CoV-2 infection, affects multiple organ systems including the respiratory, cardiovascular, neurological, gastrointestinal, and renal systems. These …
Read PDFHere, we report the resequencing, assembly, and annotation of two actinomycete genomes containing abyssomicin gene clusters. <i>Kutzneria buriramensis</i> DSM 45791 with a circular chromosome of 11,681,598 bp and 4 circular plasmids (14,175-207,548 bp) and <i>Streptomyces</i> …
Read PDFMulti-kilobase knock-ins (KIs) are a necessary, yet challenging type of genome editing to create and characterize in cell lines and animals. The combination of rAAV donor transduction and electroporation of single-cell mouse embryos with Cas9/gRNA …
Read PDFReconstructing exact haplotypes is important when sequencing a mixture of similar sequences. Long-read sequencing can connect distant alleles to disentangle similar haplotypes, but handling sequencing errors requires specialized techniques. Here, we present <i>devider</i>, an algorithm …
Read PDF<h4>Background</h4>Hao-Fountain syndrome (HAFOUS) is a rare neurodevelopmental disorder caused by pathogenic variants in the <i>USP7</i> gene. This condition is associated with a distinct DNA methylation episignature that aids its diagnosis. While microarray-based methods have traditionally …
Read PDFThe assembly of insect mitochondrial genomes remains challenging in certain taxa due to extreme AT biases and long repetitive regions. The family Diaspididae (Hemiptera: Coccomorpha) exemplifies this difficulty; despite more than 2,700 described species worldwide, …
Read PDFAs a protandrous hermaphroditic fish species with natural sex change from male to female, Asian seabass (Lates calcarifer) represents an attractive model for studying sequential hermaphroditism. In this study, we constructed the first telomere-to-telomere (T2T) …
Read PDFShort-read metabarcoding analysis is the gold standard for accessing partial 16S and ITS genes with high read quality. With the advent of long-read sequencing, the amplification of full-length target genes is possible, but with low …
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