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| http://dx.doi.org/10.1073/pnas.2216444119 | DOI Listing |
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Integrating Protein Language Model and Molecular Dynamics Simulations to Discover Antibiofouling Peptides.
Langmuir
January 2025
Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States.
Antibiofouling peptide materials prevent the nonspecific adsorption of proteins on devices, enabling them to perform their designed functions as desired in complex biological environments. Due to their importance, research on antibiofouling peptide materials has been one of the central subjects of interfacial engineering. However, only a few antibiofouling peptide sequences have been developed.
View Article and Find Full Text PDFEnvironmental Variation Influences Genome Evolution in Hispaniolan Trunk Anoles (Anolis distichus).
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Department of Ecology and Evolutionary Biology, Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA.
Environmental variation often drives evolutionary processes like population differentiation, local adaptation and speciation. We used genome-scale data to investigate the contribution of environmental variation to evolution of the North Caribbean bark anole (Anolis distichus), a widespread common lizard that exhibits impressive phenotypic variation across varying habitats on the island of Hispaniola. We obtained new double-digest restriction-associated DNA sequence data (ddRADseq) from nearly 200 individuals and used 53 GIS data layers representing a range of environmental variables.
View Article and Find Full Text PDFThe complete mitochondrial genome of Gyrodactylus pseudorasborae (Platyhelminthes: Monogenea) with a phylogeny of Gyrodactylidae parasites.
BMC Genomics
January 2025
College of Basic Medicine, Guilin Medical University, Guilin, 541199, P.R. China.
Background: Gyrodactylus von Nordmann, 1832, a genus of viviparous parasites within the family Gyrodactylidae, contains one of the largest nominal species in the world. Gyrodactylus pseudorasborae Ondračková, Seifertová & Tkachenko, 2023 widely distributed in Europe and China, although its mitochondrial genome remains unclear. This study aims to sequence the mitogenome of G.
View Article and Find Full Text PDFOptimizing the NGS-based discrimination of multiple lung cancers from the perspective of evolution.
NPJ Precis Oncol
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Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
Next-generation sequencing (NGS) offers a promising approach for differentiating multiple primary lung cancers (MPLC) from intrapulmonary metastasis (IPM), though panel selection and clonal interpretation remain challenging. Whole-exome sequencing (WES) data from 80 lung cancer samples were utilized to simulate MPLC and IPM, with various sequenced panels constructed through gene subsampling. Two clonal interpretation approaches primarily applied in clinical practice, MoleA (based on shared mutation comparison) and MoleB (based on probability calculation), were subsequently evaluated.
View Article and Find Full Text PDFCryo-EM structure and evolutionary history of the conjugation surface exclusion protein TraT.
Nat Commun
January 2025
Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
Conjugation plays a major role in dissemination of antimicrobial resistance genes. Following transfer of IncF-like plasmids, recipients become refractory to a second wave of conjugation with the same plasmid via entry (TraS) and surface (TraT) exclusion mechanisms. Here, we show that TraT from the pKpQIL and F plasmids (TraT and TraT) exhibits plasmid surface exclusion specificity.
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