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Simulating large molecular systems over long timescales requires force fields that are both accurate and efficient. In recent years, E(3) equivariant neural networks have lifted the tension between computational efficiency and accuracy of force fields, but they are still several orders of magnitude more expensive than established molecular mechanics (MM) force fields. Here, we propose Grappa, a machine learning framework to predict MM parameters from the molecular graph, employing a graph attentional neural network and a transformer with symmetry-preserving positional encoding.
View Article and Find Full Text PDFEnhancing quality and yield of recombinant secretory IgA antibodies in Nicotiana benthamiana by endoplasmic reticulum engineering.
Plant Biotechnol J
January 2025
Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
The production of complex multimeric secretory immunoglobulins (SIgA) in Nicotiana benthamiana leaves is challenging, with significant reductions in complete protein assembly and consequently yield, being the most important difficulties. Expanding the physical dimensions of the ER to mimic professional antibody-secreting cells can help to increase yields and promote protein folding and assembly. Here, we expanded the ER in N.
View Article and Find Full Text PDFDietary flaxseed: Cardiometabolic benefits and its role in promoting healthy aging.
Geroscience
January 2025
Institute of Preventive Medicine and Public Health, Semmelweis University, Budapest, Hungary.
Flaxseed, a rich source of omega-3 polyunsaturated fatty acid alpha-linolenic acid (ALA), lignans, and soluble fiber, has attracted attention for its potential to improve multiple cardiometabolic risk factors. While its benefits are well-recognized, comprehensive evaluations of its direct impact on clinical outcomes, such as the prevention or progression of cardiometabolic diseases, remain limited. Additionally, its potential to support healthy aging and longevity through fundamental biological mechanisms has not been fully elucidated.
View Article and Find Full Text PDFNovel T Cell reactivities to Hybrid Insulin Peptides in Islet Autoantibody-Positive At-Risk Subjects.
Diabetes
January 2025
Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado.
Type 1 Diabetes (T1D) is an autoimmune disease mediated by autoreactive T cells. Our studies indicate that CD4 T cells reactive to Hybrid Insulin Peptides (HIPs) play a critical role in T cell-mediated beta-cell destruction. We have shown that HIPs form in human islets between fragments of the C-peptide and cleavage products of secretory granule proteins.
View Article and Find Full Text PDFEmergence of antibiotic-specific phenotypes during prolonged treatment of mice.
Antimicrob Agents Chemother
January 2025
Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA.
A major challenge in tuberculosis (TB) therapeutics is that antibiotic exposure leads to changes in the physiology of (), which may enable the pathogen to withstand treatment. While antibiotic-treated has been evaluated in experiments it is unclear if and how long-term treatment with diverse antibiotics with varying treatment-shortening activity (sterilizing activity) affects physiologic processes differently. Here, we used SEARCH-TB, a pathogen-targeted RNA-sequencing platform, to characterize the transcriptome in the BALB/c high-dose aerosol infection mouse model following 4 weeks of treatment with three sterilizing and three non-sterilizing antibiotics.
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