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Web Visualization for Spatiotemporal Genomic Epidemiology, Annotation, and Mutation Dynamics of Orthohantavirus hantanense Using Nextstrain.
Am J Trop Med Hyg
January 2025
Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea.
The phylogeographic inference approach aims to connect genomic data with epidemiology to understand the spread and evolution of pathogens using visualization of spatiotemporal reconstructions. Orthohantavirus hantanense (HTNV), the causative agent of hemorrhagic fever with renal syndrome (HFRS), represents a significant global public health concern. Here, we introduce a localized Nextstrain platform for HTNV, offering a comprehensive resource for facilitating spatiotemporal genomic surveillance and the study of evolutionary dynamics of viral genomes.
View Article and Find Full Text PDFExamining the Biophysical Properties of the Inner Membrane of Gram-Negative ESKAPE Pathogens.
J Chem Inf Model
January 2025
Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador A1C 5S7, Canada.
The World Health Organization has identified multidrug-resistant bacteria as a serious global health threat. Gram-negative bacteria are particularly prone to antibiotic resistance, and their high rate of antibiotic resistance has been suggested to be related to the complex structure of their cell membrane. The outer membrane of Gram-negative bacteria contains lipopolysaccharides that protect the bacteria against threats such as antibiotics, while the inner membrane houses 20-30% of the bacterial cellular proteins.
View Article and Find Full Text PDFDirected Evolution's Selective Use of Quantum Tunneling in Designed Enzymes─A Combined Theoretical and Experimental Study.
J Phys Chem B
January 2025
Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States.
Natural enzymes are powerful catalysts, reducing the apparent activation energy for reactions and enabling chemistry to proceed as much as 10 times faster than the corresponding solution reaction. It has been suggested for some time that, in some cases, quantum tunneling can contribute to this rate enhancement by offering pathways through a barrier inaccessible to activated events. A central question of interest to both physical chemists and biochemists is the extent to which evolution introduces mechanisms below the barrier, or tunneling mechanisms.
View Article and Find Full Text PDFInvestigating Pb2 CAP-binding domain inhibitors from marine bacteria for targeting the influenza A H5N1.
PLoS One
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Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
The ongoing increase in the prevalence and mutation rate of the influenza virus remains a critical global health issue. A promising strategy for antiviral drug development involves targeting the RNA-dependent RNA polymerase, specifically the PB2-cap binding domain of Influenza A H5N1. This study employs an in-silico approach to inhibit this domain, crucial for viral replication, using potential inhibitors derived from marine bacterial compounds.
View Article and Find Full Text PDFImproving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation.
J Chem Inf Model
January 2025
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.
In the field of computational chemistry, predicting bond dissociation energies (BDEs) presents well-known challenges, particularly due to the multireference character of reactive systems. Many chemical reactions involve configurations where single-reference methods fall short, as the electronic structure can significantly change during bond breaking. As generating training data for partially broken bonds is a challenging task, even state-of-the-art reactive machine learning interatomic potentials (MLIPs) often fail to predict reliable BDEs and smooth dissociation curves.
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