The ribose of RNA nucleotides can be 2'-O-methylated (Nm). Despite advances in high-throughput detection, the inert chemical nature of Nm still limits sensitivity and precludes mapping in mRNA. We leveraged the differential reactivity of 2'-O-methylated and 2'-hydroxylated nucleosides to periodate oxidation to develop Nm-seq, a sensitive method for transcriptome-wide mapping of Nm with base precision. Nm-seq uncovered thousands of Nm sites in human mRNA with features suggesting functional roles.
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http://dx.doi.org/10.1038/nmeth.4294 | DOI Listing |
iScience
January 2025
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
The regulation of gene expression relies on the coordinated action of transcription factors (TFs) at enhancers, including both activator and repressor TFs. We employed deep learning (DL) to dissect HepG2 enhancers into positive (PAR), negative (NAR), and neutral activity regions. Sharpr-MPRA and STARR-seq highlight the dichotomy impact of NARs and PARs on modulating and catalyzing the activity of enhancers, respectively.
View Article and Find Full Text PDFiScience
January 2025
Department of Biology, New Mexico State University, Las Cruces, NM, USA.
Forest edges, where humans, mosquitoes, and wildlife interact, may serve as a nexus for zoonotic arbovirus exchange. Although often treated as uniform interfaces, the landscape context of edge habitats can greatly impact ecological interactions. Here, we investigated how the landscape context of forest edges shapes mosquito community structure in an Amazon rainforest reserve near the city of Manaus, Brazil, using hand-nets to sample mosquitoes at three distinct forest edge types.
View Article and Find Full Text PDFJ Clin Exp Hepatol
December 2024
Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute, Giza, Egypt.
Background: Liver fibrosis is a serious global health issue, but current treatment options are limited due to a lack of approved therapies capable of preventing or reversing established fibrosis.
Aim: This study investigated the antifibrotic effects of a synthetic peptide derived from α-lactalbumin in a mouse model of thioacetamide (TAA)-induced liver fibrosis.
Methods: analyses were conducted to assess the physicochemical properties, pharmacophore features, and docking interactions of the peptide.
Cureus
December 2024
Pediatric Infectious Diseases, Armed Forces Hospital Southern Region, Khamis Mushait, SAU.
Basidiobolomycosis, a rare fungal infection seen in immunocompetent patients, is a chronic granulomatous infection affecting the skin and subcutaneous tissue. It is caused by the fungus . Gastrointestinal basidiobolomycosis usually has non-specific clinical manifestations, and its diagnosis requires a high index of suspicion.
View Article and Find Full Text PDFCureus
December 2024
Orthopedics and Rehabilitation, Yale University, New Haven, USA.
Purpose The purpose of this study was to evaluate the ability of a Chat Generative Pre-trained Transformer (ChatGPT) to provide academic answers to frequently asked questions using a comparison with Google web search FAQs and answers. This study attempted to determine what patients ask on Google and ChatGPT and whether ChatGPT and Google provide factual information for patients about arthroscopic meniscus repair. Method A cleanly installed Google Chrome browser and ChatGPT were used to ensure no individual cookies, browsing history, other side data, or sponsored sites.
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