Denaturing gradient gel electrophoresis (DGGE) has proven to be a powerful pre-screening method for the detection of DNA variants. If such variants occur, however, in DNA fragments that are very rich in G and C, they may escape detection. To overcome this limitation, we tested a novel gel system which combines DGGE and constant denaturant gel electrophoresis (CDGE), as it might have the advantages of both methods. Indeed, this combination had the advantages of both methods, good separation of hetero-duplex molecules and prevention of total strand dissociation, and it proved successful in the detection of DNA variants in several GC-rich fragments.
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http://dx.doi.org/10.1093/nar/27.15.e9 | DOI Listing |
Anal Bioanal Chem
January 2025
Statistical Engineering Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899-8980, USA.
Closely related species of Salmonidae, including Pacific and Atlantic salmon, can be distinguished from one another based on nucleotide sequences from the cytochrome c oxidase sub-unit 1 mitochondrial gene (COI), using ensembles of fragments aligned to genetic barcodes that serve as digital proxies for the relevant species. This is accomplished by exploiting both the nucleotide sequences and their quality scores recorded in a FASTQ file obtained via Next Generation (NextGen) Sequencing of mitochondrial DNA extracted from Coho salmon caught with hook and line in the Gulf of Alaska. The alignment is done using MUSCLE (Muscle 5.
View Article and Find Full Text PDFCryobiology
January 2025
Laboratorio de Biotecnología de la Reproducción Animal, Facultad de Ciencias Agropecuarias, Universidad de Cuenca, EC010205, Cuenca, Ecuador.
This study evaluated the effectiveness of Percoll® density gradient centrifugation (Percoll-DGC) for selecting bull epididymal sperm prior to conventional slow (CS) or ultra-rapid (UR) freezing and its effects on sperm quality. Fifteen pooled samples from 30 epididymides (2 different samples/pool) of 15 bulls were split into two aliquots assigned to either CS or UR freezing. Samples were either selected using Percoll-DGC (40/80 %) or left non-selected (control), resulting in four pre-freezing treatments: Percoll-CS, Control-CS, Percoll-UR, and Control-UR.
View Article and Find Full Text PDFMol Cell
January 2025
Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA. Electronic address:
DNA replication, a fundamental process in all living organisms, proceeds with continuous synthesis of the leading strand by DNA polymerase ε (Pol ε) and discontinuous synthesis of the lagging strand by polymerase δ (Pol δ). This inherent asymmetry at each replication fork necessitates the development of methods to distinguish between these two nascent strands in vivo. Over the past decade, strand-specific sequencing strategies, such as enrichment and sequencing of protein-associated nascent DNA (eSPAN) and Okazaki fragment sequencing (OK-seq), have become essential tools for studying chromatin replication in eukaryotic cells.
View Article and Find Full Text PDFEcotoxicol Environ Saf
January 2025
Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, PR China. Electronic address:
Cigarette smoke (CS) has detrimental effects on placental growth and embryo development, but the underlying mechanisms remain unclear. This study aims to investigate the impact of CS on trophoblast cell proliferation and regulated cell death (RCD) by examining its interference with iron-sulfur cluster (ISC) proteins and the CIA pathway. Exposure to CS disrupted the cytosolic ISC assembly (CIA) pathway, downregulated ISC proteins, and decreased ISC maturation in the placenta of rats exposed to passive smoking.
View Article and Find Full Text PDFMicrosc Res Tech
January 2025
Molecular Biology and Genetics Department, Faculty of Engineering and Natural Sciences, Uşak University, Uşak, Turkey.
Sulfoxaflor (SFX) is an insecticide that is commonly used for the control of sap-feeding insects. Since SFX is extensively applied globally, it has been implicated in the substantial induction of environmental toxicity. Therefore, in this study, Allium cepa roots have been employed to elucidate the potential cytogenotoxic effects of SFX in non-target cells by examination of mitotic index (MI), chromosomal aberrations (CAs), and DNA damage.
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