Summary: We present Systematic ProtEin AnnotatoR (SPEAR), a lightweight and rapid SARS-CoV-2 variant annotation and scoring tool, for identifying mutations contributing to potential immune escape and transmissibility (ACE2 binding) at point of sequencing. SPEAR can be used in the field to evaluate genomic surveillance results in real time and features a powerful interactive data visualization report.
Availability And Implementation: SPEAR and documentation are freely available on GitHub: https://github.com/m-crown/SPEAR and are implemented in Python and installable via Conda environment.
Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btac391 | DOI Listing |
BMC Cancer
January 2025
Department of Pathology, Faculty of Medicine, Shahed University, Tehran, Iran.
Background: Cytokeratins are intracellular proteins known as diagnostic biomarkers or prognostic factors for certain cancers. Cytokeratin 19 (CK-19) expression has been proven to have prognostic value for some cancers, but its relationship with others, such as prostate cancer (PCa), remains unclear. This systematic review article aimed to examine the relationship between CK-19 expression and prostate adenocarcinoma (PAC).
View Article and Find Full Text PDFJ Cell Mol Med
January 2025
Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China.
This study aims to elucidate the potential genetic commonalities between metabolic syndrome (MetS) and rheumatic diseases through a disease interactome network, according to publicly available large-scale genome-wide association studies (GWAS). The analysis included linkage disequilibrium score regression analysis, cross trait meta-analysis and colocalisation analysis to identify common genetic overlap. Using modular partitioning, the network-based association between the two disease proteins in the protein-protein interaction set was divided and quantified.
View Article and Find Full Text PDFNat Struct Mol Biol
January 2025
Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
Many protein complexes are highly dynamic in cells; thus, characterizing their conformational changes in cells is crucial for unraveling their functions. Here, using cryo-electron microscopy, 451,700 ribosome particles from Saccharomyces cerevisiae cell lamellae were obtained to solve the 60S region to 2.9-Å resolution by in situ single-particle analysis.
View Article and Find Full Text PDFCurr Microbiol
January 2025
Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si, Chungnam, 31151, Republic of Korea.
Lactic acid bacteria (LAB), traditionally consumed as fermented foods, are now being applied to the medical field beyond health-functional food as probiotics. Therefore, it is necessary to continuously discover and evaluate new strains with suitable probiotic characteristics, mainly focusing on safety. In this study, we isolated eight new strains from postmenopausal vaginal fluid using culturomics approaches, an emerging area of interest.
View Article and Find Full Text PDFSci Rep
January 2025
College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010018, Inner Mongolia, China.
Pugionium cornutum (L.) Gaertn (P. cornutum) has strong tolerance to drought, salt and disease, but the tolerance mechanisms for such stresses in P.
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