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Identification of G-quadruplex nucleic acid structures by high-throughput sequencing: A review.
Int J Biol Macromol
January 2025
School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China; Smart Medical Innovation Technology Center, Guangdong University of Technology, Guangzhou 510006, China. Electronic address:
G-quadruplexes (G4s) are non-canonical nucleic acid secondary structures formed by guanine-rich DNA or RNA sequences. These structures play pivotal roles in cellular processes, including DNA replication, transcription, RNA splicing, and protein translation. High-throughput sequencing has significantly advanced the study of G4s by enabling genome-wide mapping and detailed characterization.
View Article and Find Full Text PDFThe pivotal role of CRIHSP sequences in orchestrating antigen receptor diversity and genomic stability within antigen receptor germline genes.
Int J Biol Macromol
January 2025
Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, Henan, China; School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, Henan, China. Electronic address:
The mechanisms underlying antigen receptor germline gene diversification have always been a topic of intensive study. Here, we discovered that the frequency of stem-loop sequences in the antigen receptor germline gene region is remarkably higher than the genomic background. By analyzing these stem-loop sequences' similarity and distribution patterns, we found that clustered regularly interspaced homologous stem-loop pairs (CRIHSP) are widely present on the germline genes of antigen receptors in different species.
View Article and Find Full Text PDFThe Clinical Utility of Incorporating Next-Generation Sequencing Results in the Management Algorithm of Pancreatic Cysts.
Gastrointest Endosc
January 2025
Division of Digestive and Liver Diseases, University of Texas Southwestern Medical Center, Dallas, TX. Electronic address:
Background & Aims: Pancreatic cysts often pose challenges in predicting malignant progression. Next-generation sequencing has become an appealing ancillary diagnostic test. The diagnostic performance is well characterized, but the impact on clinical management remains unclear.
View Article and Find Full Text PDFOutbreak of carbapenem resistant Klebsiella pneumoniae in a neurorehabilitation unit: genomic epidemiology reveals complex transmission pattern in a tertiary care hospital.
J Glob Antimicrob Resist
January 2025
Microbiology Unit, Clinical Pathology Department, Piacenza General Hospital, Piacenza, Italy; Medicine and Surgery Department, University of Parma, Parma, Italy.
Objectives: Infections by Carbapenem-Resistant Enterobacterales in hospitals represent a severe threat but little is known on outbreaks in rehabilitation wards caused by Klebsiella pneumoniae producing Klebsiella pneumoniae Carbapenemase (KPC-Kp). We report an outbreak by KPC-Kp, in a Neurorehabilitation Unit in Italy, analysed through Whole-Genome Sequencing (WGS) for transmission routes reconstruction to improve management of KPC-Kp infections in rehabilitation units.
Methods: We investigated cases and KPC-Kp isolates collected from February to October 2022 from hospital surveillance.
OLAgen: A Software Tool for Reagent Design to Expand Access to Single Nucleotide Variant Detection by the Oligonucleotide Ligation Assay.
J Mol Diagn
January 2025
Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, United States. Electronic address:
Single nucleotide variations (SNVs) and polymorphisms (SNPs) are characteristic biomarkers in various biological contexts, including pathogen drug resistances and human diseases. Tools that lower the implementation barrier of molecular SNV detection methods would provide greater leverage of the expanding SNP/SNV database. The oligonucleotide ligation assay (OLA) is a highly specific means for detection of known SNVs and is especially powerful when coupled with polymerase chain reaction (PCR).
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