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Evaluation of long-read sequencing for Ostreid herpesvirus type 1 genome characterization from infected tissues.
Microbiol Spectr
January 2025
Ifremer, ASIM, La Tremblade, France.
Since the 1990s, the Pacific oyster has faced significant mortality, which has been associated with the detection of the Ostreid Herpesvirus type 1 (OsHV-1). Due to the complex genomic architecture and the presence of multiple genomic isomers, short-read sequencing using Illumina method struggles to accurately assemble tandem and repeat regions and to identify and characterize large structural variations in the OsHV-1 genome. Third-generation sequencing technologies, as long-read real-time nanopore sequencing from Oxford Nanopore Technologies (ONT), offer new possibilities for OsHV-1 whole-genome analysis.
View Article and Find Full Text PDFUltra pure high molecular weight DNA from soil for Nanopore shotgun metagenomics and metabarcoding sequencing.
MethodsX
June 2025
IRD, UMR Eco&Sols, INRAE, CIRAD, Institut Agro, Université Montpellier, Montpellier, France.
Soil microbes are among the most abundant and diverse organisms on Earth but remain poorly characterized. New technologies have made possible to sequence the DNA of uncultivated microorganisms in soil and other complex ecosystems. Genome assembly is crucial for understanding their functional potential.
View Article and Find Full Text PDFWintering loons in South Korea face an ongoing threat from polycyclic aromatic hydrocarbons: Shifting sources and potential DNA damage.
Environ Pollut
January 2025
Department of Biological Sciences, College of Natural Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, Republic of Korea. Electronic address:
Diving birds, particularly those sharing coastal habitats with fishing grounds, are at risk from oil pollution. Despite documented cases of bird mortality, the specific role of oil pollution in these death remains unclear. To address this knowledge gap, this study examined polycyclic aromatic hydrocarbon (PAH) contamination, its sources, and its impact on loon health.
View Article and Find Full Text PDFPRDX5 and PRDX6 translocation and oligomerization in bull sperm: a response to cryopreservation-induced oxidative stress.
Cell Commun Signal
January 2025
Institute of Animal Reproduction and Food Research, Olsztyn, Poland.
Cryopreservation of bull sperm, crucial for breeding and assisted reproduction, often reduces sperm quality due to oxidative stress. This study examines how oxidative stress during cryopreservation affects peroxiredoxin 5 (PRDX5) and peroxiredoxin 6 (PRDX6) proteins, leading to their translocation and oligomerization in bull sperm. Increased reactive oxygen species (ROS) and nitric oxide (NO) levels were linked to reduced mitochondrial potential, higher DNA fragmentation, and increased membrane fluidity, prompting PRDX5 to move intracellularly and PRDX6 to the cell membrane.
View Article and Find Full Text PDFThe effect of commonly employed forensic DNA extraction protocols on ssDNA/dsDNA proportion and DNA integrity.
Forensic Sci Int Genet
December 2024
Estonian Forensic Science Institute, Tallinn, Estonia.
The utilisation of massively parallel sequencing (MPS) in forensic DNA analysis is on the rise, driven by the expansion of targeted MPS panels in the market and the introduction of forensic investigative genetic genealogy. The MPS library preparation process, integral to both whole-genome sequencing (WGS) and targeted MPS panel data generation, is largely based on converting double-stranded DNA (dsDNA) into sequencing libraries. In the current study, we examined the effect of seven routinely used forensic DNA extraction methods on the strandedness (single-stranded or double-stranded) and the fragment size of the DNA extracted from buccal swab, blood, bone and tooth samples.
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