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High-recombining genomic regions affect demography inference based on ancestral recombination graphs.
Genetics
January 2025
Max Planck Research Group Behavioural Genomics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany.
Multiple methods of demography inference are based on the ancestral recombination graph. This powerful approach uses observed mutations to model local genealogies changing along chromosomes by historical recombination events. However, inference of underlying genealogies is difficult in regions with high recombination rate relative to mutation rate due to the lack of mutations representing genealogies.
View Article and Find Full Text PDFAMPed up immunity: 418 whole genomes reveal intraspecific diversity of koala antimicrobial peptides.
Immunogenetics
January 2025
School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
Characterising functional diversity is a vital element to understanding a species' immune function, yet many immunogenetic studies in non-model organisms tend to focus on only one or two gene families such as the major histocompatibility complex (MHC) or toll-like receptors (TLR). Another interesting component of the eukaryotic innate immune system is the antimicrobial peptides (AMPs). The two major groups of mammalian AMPs are cathelicidins and defensins, with the former having undergone species-specific expansions in marsupials.
View Article and Find Full Text PDFRuvbl1 silencing affects reproduction of the corn planthopper, Peregrinus maidis.
PLoS One
January 2025
Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America.
Ruvbl1 (also known as TIP49, Pontin) encodes an ATPase of the AAA+ protein superfamily involved in several cellular functions, including chromatin remodeling, control of transcription, and cellular development (motility, growth, and proliferation). While its role has been well established in model organisms including vertebrates and invertebrates (e.g.
View Article and Find Full Text PDFTrAnnoScope: A Modular Snakemake Pipeline for Full-Length Transcriptome Analysis and Functional Annotation.
Genes (Basel)
November 2024
Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark.
: Transcriptome assembly and functional annotation are essential in understanding gene expression and biological function. Nevertheless, many existing pipelines lack the flexibility to integrate both short- and long-read sequencing data or fail to provide a complete, customizable workflow for transcriptome analysis, particularly for non-model organisms. : We present TrAnnoScope, a transcriptome analysis pipeline designed to process Illumina short-read and PacBio long-read data.
View Article and Find Full Text PDFCurrent Knowledge on CRISPR Strategies Against Antimicrobial-Resistant Bacteria.
Antibiotics (Basel)
November 2024
Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Paseo Prado de la Magdalena 3-5, 47011 Valladolid, Spain.
CRISPR/Cas systems have emerged as valuable tools to approach the problem of antimicrobial resistance by either sensitizing or lysing resistant bacteria or by aiding in antibiotic development, with successful applications across diverse organisms, including bacteria and fungi. CRISPR/Cas systems can target plasmids or the bacterial chromosome of AMR-bacteria, and it is especially necessary to have an efficient entry into the target cells, which can be achieved through nanoparticles or bacteriophages. Regarding antibiotic development and production, though the use of CRISPR/Cas in this field is still modest, there is an untapped reservoir of bacterial and fungal natural products, with over 95% yet to be characterized.
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