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Regboost: Enhancing mouse brain image registration using geometric priors and Laplacian interpolation.
Neuroimage
December 2024
Department of Computer Science, University of California, Irvine, CA 92617, USA. Electronic address:
We show in this work that incorporating geometric features and geometry processing algorithms for mouse brain image registration broadens the applicability of registration algorithms and improves the registration accuracy of existing methods. We introduce the preprocessing and postprocessing steps in our proposed framework as RegBoost. We develop a method to align the axis of 3D image stacks by detecting the central planes that pass symmetrically through the image volumes.
View Article and Find Full Text PDFThe PA-X host shutoff site 100 V exerts a contrary effect on viral fitness of the highly pathogenic H7N9 influenza A virus in mice and chickens.
Virulence
December 2025
Key Laboratory of Avian Bioproducts Development, Ministry of Agriculture and Rural Affairs, Yangzhou, China.
Several viruses, including influenza A virus (IAV), encode viral factors to hijack cellular RNA biogenesis processes to direct the degradation of host mRNAs, termed "host shutoff." Host shutoff enables viruses to simultaneously reduce antiviral responses and provides preferential access for viral mRNAs to cellular translation machinery. IAV PA-X is one of these factors that selectively shuts off the global host genes.
View Article and Find Full Text PDFAs the number and variety of assembled genomes continues to grow, the number of annotated genomes is falling behind, particularly for eukaryotes. DNA-based mapping tools help to address this challenge, but they are only able to transfer annotation between closely-related species. Here we introduce LiftOn, a homology-based software tool that integrates DNA and protein alignments to enhance the accuracy of genome-scale annotation and to allow mapping between relatively distant species.
View Article and Find Full Text PDFSingle-cell analysis of bidirectional reprogramming between early embryonic states identify mechanisms of differential lineage plasticities in mice.
Dev Cell
December 2024
Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA. Electronic address:
Two distinct lineages, pluripotent epiblast (EPI) and primitive (extra-embryonic) endoderm (PrE), arise from common inner cell mass (ICM) progenitors in mammalian embryos. To study how these sister identities are forged, we leveraged mouse embryonic stem (ES) cells and extra-embryonic endoderm (XEN) stem cells-in vitro counterparts of the EPI and PrE. Bidirectional reprogramming between ES and XEN coupled with single-cell RNA and ATAC-seq analyses showed distinct rates, efficiencies, and trajectories of state conversions, identifying drivers and roadblocks of reciprocal conversions.
View Article and Find Full Text PDFOptimized MALDI2-Mass Spectrometry Imaging for Stable Isotope Tracing of Tissue-Specific Metabolic Pathways in Mice.
Anal Chem
December 2024
State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR 999077, China.
Spatial stable isotope tracing metabolic imaging is a cutting-edge technique designed to investigate tissue-specific metabolic functions and heterogeneity. Traditional matrix-assisted laser desorption ionization-mass spectrometry imaging (MALDI-MSI) techniques often struggle with low coverage of low-molecular-weight (LMW) metabolites, which are often crucial for spatial metabolic studies. To address this, we developed a high-coverage spatial isotope tracing metabolic method that incorporates optimized matrix selection, sample preparation protocols, and enhanced post-ionization (MALDI2) techniques.
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