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Pediatric Patient Referred for an Optic Nerve Mass.
JAMA Ophthalmol
January 2025
Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland.
GEMLI: Gene Expression Memory-Based Lineage Inference from Single-Cell RNA-Sequencing Datasets.
Methods Mol Biol
January 2025
Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Institute of Bioengineering, Lausanne, Switzerland.
Gene expression memory-based lineage inference (GEMLI) is a computational tool allowing to predict cell lineages solely from single-cell RNA-sequencing (scRNA-seq) datasets and is publicly available as an R package on GitHub. GEMLI is based on the occurrence of gene expression memory, i.e.
View Article and Find Full Text PDFLineage Tracing by Light-Sheet Microscopy and Computational Reconstruction.
Methods Mol Biol
January 2025
Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete, Greece.
Lineage tracing based on modern live imaging approaches enables to visualize, reconstruct, and analyze the developmental history, fate, and dynamic behaviors of cells in vivo in a direct, comprehensive, and quantitative manner. Light-sheet fluorescence microscopy (LSFM) has greatly boosted lineage tracing efforts, because fluorescently labeled specimens can be imaged in their entirety, over long periods of time, with high spatiotemporal resolution and minimal photodamage. In addition, an increasing arsenal of commercial and open-source software solutions for cell and nuclei segmentation and tracking can be employed to convert data from pixel-based to object-based representations, and to reconstruct the lineages of cells in their native context as they organize in tissues, organs, and whole organisms.
View Article and Find Full Text PDFInduction of PD-1 and CD44 in CD4 T cells by circulatory extracellular vesicles from severe dengue patients drives endothelial damage via the NF-kB signaling pathway.
J Virol
December 2024
Laboratory of Virology, Regional Centre for Biotechnology, National Capital Region Biotechnology Science Cluster, Faridabad, Haryana, India.
Extracellular vesicles (EVs) emerged as critical contributors to the pathogenesis of vascular endothelial barrier dysfunction during the inflammatory response to infection. However, the contribution of circulating EVs to modifying endothelial function during dengue virus infection remains unclear. In this study, we showed that severe dengue patients' plasma-derived EV (SD-EV) were found to carry elevated levels of different protein cargos, e.
View Article and Find Full Text PDFDiscovery of small molecules against porcine reproductive and respiratory syndrome virus replication by targeting NendoU activity.
J Virol
December 2024
Department of Animal Science, Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA.
Unlabelled: Porcine reproductive and respiratory syndrome (PRRS) remains a major threat to animal health and causes substantial economic losses worldwide. The nonstructural protein 11 (NSP11) of the causative agent, PRRS virus (PRRSV), contains a highly conserved nidoviral uridylate-specific endoribonuclease (NendoU) domain essential for viral replication and immune evasion. Targeting NSP11 offers a novel approach to antiviral intervention.
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