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A comprehensive benchmarking for evaluating TCR embeddings in modeling TCR-epitope interactions.
Brief Bioinform
November 2024
Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, 999077, China.
The complexity of T cell receptor (TCR) sequences, particularly within the complementarity-determining region 3 (CDR3), requires efficient embedding methods for applying machine learning to immunology. While various TCR CDR3 embedding strategies have been proposed, the absence of their systematic evaluations created perplexity in the community. Here, we extracted CDR3 embedding models from 19 existing methods and benchmarked these models with four curated datasets by accessing their impact on the performance of TCR downstream tasks, including TCR-epitope binding affinity prediction, epitope-specific TCR identification, TCR clustering, and visualization analysis.
View Article and Find Full Text PDFRejection of the concept of hemiurid genus Pulmovermis (Digenea: Hemiuridae) and other taxonomic propositions: new morphological and molecular data regarding Lecithochirium cyanovitellosum (Coil and Kuntz, 1960) Urabe and Sokolov, comb. nov. (formerly Pulmovermis cyanovitellosus).
Syst Parasitol
January 2025
A.N. Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia.
Pulmovermis cyanovitellosus Coil and Kuntz, 1960 is a species of hemiurid trematode that localizes in the lung of sea snakes, an unusual trait for this group of parasites. Recent molecular phylogenetic studies based on 28S rRNA gene sequences have shown that this species is closely related to members of the genus Lecithochirium Lühe, 1901. This finding is unexpected given that Pulmovermis Coil and Kuntz, 1960 and Lecithochirium are currently classified in different subfamilies of Hemiuridae (Pulmoverminae Sandars, 1961 vs.
View Article and Find Full Text PDFInfluence of Ty3/gypsy and Ty1/copia LTR-retrotransposons on the large genomes of Alstroemeriaceae: genome landscape of Bomarea edulis (Tussac) Herb.
Protoplasma
January 2025
Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil.
Repetitive elements are the main components of many plant genomes and play a crucial role in the variation of genome size and structure, ultimately impacting species diversification and adaptation. Alstroemeriaceae exhibits species with large genomes, not attributed to polyploidy. In this study, we analysed the repetitive fraction of the genome of Bomarea edulis through low-coverage sequencing and in silico characterization, and compared it to the repeats of Alstroemeria longistaminea, a species from a sister genus that has been previously characterized.
View Article and Find Full Text PDFA high-resolution view of RNA endonuclease cleavage in Bacillus subtilis.
Nucleic Acids Res
January 2025
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
RNA endonucleases are the rate-limiting initiator of decay for many bacterial mRNAs. However, the positions of cleavage and their sequence determinants remain elusive even for the well-studied Bacillus subtilis. Here we present two complementary approaches-transcriptome-wide mapping of endoribonucleolytic activity and deep mutational scanning of RNA cleavage sites-that reveal distinct rules governing the specificity among B.
View Article and Find Full Text PDFMicrobiome characterization of two fresh pork cuts during production in a pork fabrication facility.
Microbiol Spectr
January 2025
Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA.
The goal of this study was to characterize the microbial profile of two different fresh pork cuts, bootjack (BJ) trim and tenderloin (TL), through a 16S rRNA sequencing workflow developed specifically for investigating low-biomass fresh meat within a commercial production schedule. Additionally, this study aimed to determine a baseline prevalence and enumeration profile across these two fresh pork cuts. Results showed that microbiome diversity was different between the BJ and TL, and also differed significantly by processing date.
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