The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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http://dx.doi.org/10.1093/molbev/msy096 | DOI Listing |
Introduction: China implemented a dynamic zero-COVID strategy to curb viral transmission in response to the coronavirus disease 2019 (COVID-19) pandemic. This strategy was designed to inhibit mutation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19. This study explores the dynamics of viral evolution under stringent non-pharmaceutical interventions (NPIs) through real-world observations.
View Article and Find Full Text PDFJ Immunother Cancer
January 2025
Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
Evidence has shown that T-cell receptors (TCRs) that recognize the same epitopes may not be the exact TCR clonotypes but have slightly different TCR sequences. However, the changes in the genomic and transcriptomic signatures of these highly homologous T cells during immunotherapy remain unknown. Here, we examined the evolutionary features in circulating TCR clonotypes observed in tumors (tumor-infiltrating lymphocyte (TIL)-TCRs) by combining single-cell RNA/TCR sequencing of longitudinal blood samples and TCR sequencing of tumor tissue from a patient treated with anti-cytotoxic T-lymphocyte-associated protein 4/programmed cell death protein-1 therapy.
View Article and Find Full Text PDFGenomics
January 2025
State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, China. Electronic address:
Gleditsia sinensis Lam. (G. sinensis) as an important species within the Leguminosae family, has been utilized in Chinese medicine for centuries, and its thorns serve as a chief medicinal ingredient.
View Article and Find Full Text PDFCell Genom
January 2025
Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia. Electronic address:
Understanding the evolution of human traits is a fundamental yet challenging question. In a recent Cell Genomics article, Kun et al. integrate large-scale genomic and phenotypic data, including deep-learning-derived imaging phenotypes, with temporal annotations to estimate the timing of evolutionary changes that led to differences in traits between modern humans and primates or hominin ancestors.
View Article and Find Full Text PDFCell
January 2025
Program in Bioinformatics, Boston University, Boston, MA 02215, USA; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Center for Network Systems Biology, Boston University, Boston, MA 02218, USA; Department of Chemistry, Boston University, Boston, MA 02215, USA; Department of Chemical Physiology and Biochemistry, Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA. Electronic address:
Knowledge of protein-metabolite interactions can enhance mechanistic understanding and chemical probing of biochemical processes, but the discovery of endogenous ligands remains challenging. Here, we combined rapid affinity purification with precision mass spectrometry and high-resolution molecular docking to precisely map the physical associations of 296 chemically diverse small-molecule metabolite ligands with 69 distinct essential enzymes and 45 transcription factors in the gram-negative bacterium Escherichia coli. We then conducted systematic metabolic pathway integration, pan-microbial evolutionary projections, and independent in-depth biophysical characterization experiments to define the functional significance of ligand interfaces.
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