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Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data.
G3 (Bethesda)
January 2025
School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ 85281, USA.
The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection.
View Article and Find Full Text PDFQuantum chemical studies of carbon-based graphene-like nanostructures: from benzene to coronene.
J Mol Model
January 2025
Department of Chemistry, Federal Institute of Education, Science and Technology of Espírito Santo, Av. Min. Salgado Filho, Vila Velha, 29106-010, Espírito Santo, Brazil.
Context: This study presents quantum chemical analysis of 14 distinct carbon-based nanostructures (CBN), ranging from simple molecules, like benzene, to more complex structures, such as coronene, which serves as an exemplary graphene-like model. The investigation focuses on elucidating the relationships between molecular orbital (MO) energies, the energy band gaps, electron occupation numbers (eON), electronic conduction, and the compound topologies, seeking to find the one that approaches most of a graphene-like structure for in silico studies. Through detailed examination of molecular properties including chemical hardness and chemical potential, we demonstrate that the electronic exchange between orbitals is directly influenced by the structural topology of the carbon-based nanostructures, as the electron occupation numbers and the molecular orbital energies.
View Article and Find Full Text PDFSite-Selective and High-Density Gold Nanoparticle Photodeposition on the Edges of ZnO Nanowires.
J Phys Chem Lett
January 2025
Graduate School of Science and Engineering, Kindai University, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan.
Selective modification of chemically active sites on supports, such as steps, edges, and corners, with metal nanoparticles (NPs) is a challenging topic in the fields of catalysis and photocatalysis. However, the formation of site-selective, high-density metal NPs on a support has not yet been achieved. Radial ZnO mesocrystals composed of hexagonal nanowires (NWs) with {101̅0} sidewalls were synthesized by a simple solution-phase method.
View Article and Find Full Text PDFA simple cavity-enhanced laser-based heater for reflective samples.
Rev Sci Instrum
January 2025
Institute for Physical Chemistry, University of Göttingen, 37077 Göttingen, Germany.
Surface science instruments require excellent vacuum to ensure surface cleanliness; they also require control of sample temperature, both to clean the surface of contaminants and to control reaction rates at the surface, for example, for molecular beam epitaxy and studies of heterogeneous catalysis. Standard approaches to sample heating within high vacuum chambers involve passing current through filaments of refractory metals, which then heat the sample by convective, radiative, or electron bombardment induced heat transfer. Such hot filament methods lead to outgassing of molecules from neighboring materials that are inadvertently heated; they also produce electrons and ions that may interfere with other aspects of the surface science experiment.
View Article and Find Full Text PDFProximity proteomics provides a new resource for exploring the function of Afadin and the complexity of cell-cell adherens junctions.
Biol Open
February 2025
Department of Biology, University of North Carolina at Chapel Hill, CB#3280, Chapel Hill, NC 27599-3280, USA.
The network of proteins at the interface between cell-cell adherens junctions and the actomyosin cytoskeleton provides robust yet dynamic connections that facilitate cell shape change and motility. While this was initially thought to be a simple linear connection via classic cadherins and their associated catenins, we now have come to appreciate that many more proteins are involved, providing robustness and mechanosensitivity. Defining the full set of proteins in this network remains a key objective in our field.
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