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Abdellah M, Foni A, Cantero JJG, Guerrero NR, Boci E, Fleury A, Coggan JS, Keller D, Planas J, Courcol JD, Khazen G. Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling. Brief Bioinform 2024; 25:bbae393. [PMID: 39129363 PMCID: PMC11317524 DOI: 10.1093/bib/bbae393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/06/2024] [Accepted: 07/29/2024] [Indexed: 08/13/2024] Open
Abstract
Understanding the intracellular dynamics of brain cells entails performing three-dimensional molecular simulations incorporating ultrastructural models that can capture cellular membrane geometries at nanometer scales. While there is an abundance of neuronal morphologies available online, e.g. from NeuroMorpho.Org, converting those fairly abstract point-and-diameter representations into geometrically realistic and simulation-ready, i.e. watertight, manifolds is challenging. Many neuronal mesh reconstruction methods have been proposed; however, their resulting meshes are either biologically unplausible or non-watertight. We present an effective and unconditionally robust method capable of generating geometrically realistic and watertight surface manifolds of spiny cortical neurons from their morphological descriptions. The robustness of our method is assessed based on a mixed dataset of cortical neurons with a wide variety of morphological classes. The implementation is seamlessly extended and applied to synthetic astrocytic morphologies that are also plausibly biological in detail. Resulting meshes are ultimately used to create volumetric meshes with tetrahedral domains to perform scalable in silico reaction-diffusion simulations for revealing cellular structure-function relationships. Availability and implementation: Our method is implemented in NeuroMorphoVis, a neuroscience-specific open source Blender add-on, making it freely accessible for neuroscience researchers.
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Affiliation(s)
- Marwan Abdellah
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Alessandro Foni
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Juan José García Cantero
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Nadir Román Guerrero
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Elvis Boci
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Adrien Fleury
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Jay S Coggan
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Daniel Keller
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Judit Planas
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Jean-Denis Courcol
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Georges Khazen
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
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Herron JC, Hu S, Watanabe T, Nogueira AT, Liu B, Kern ME, Aaron J, Taylor A, Pablo M, Chew TL, Elston TC, Hahn KM. Actin nano-architecture of phagocytic podosomes. Nat Commun 2022; 13:4363. [PMID: 35896550 PMCID: PMC9329332 DOI: 10.1038/s41467-022-32038-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/13/2022] [Indexed: 11/09/2022] Open
Abstract
Podosomes are actin-enriched adhesion structures important for multiple cellular processes, including migration, bone remodeling, and phagocytosis. Here, we characterize the structure and organization of phagocytic podosomes using interferometric photoactivated localization microscopy, a super-resolution microscopy technique capable of 15-20 nm resolution, together with structured illumination microscopy and localization-based super-resolution microscopy. Phagocytic podosomes are observed during frustrated phagocytosis, a model in which cells attempt to engulf micropatterned IgG antibodies. For circular patterns, this results in regular arrays of podosomes with well-defined geometry. Using persistent homology, we develop a pipeline for semi-automatic identification and measurement of podosome features. These studies reveal an hourglass shape of the podosome actin core, a protruding knob at the bottom of the core, and two actin networks extending from the core. Additionally, the distributions of paxillin, talin, myosin II, α-actinin, cortactin, and microtubules relative to actin are characterized.
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Affiliation(s)
- J Cody Herron
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shiqiong Hu
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Takashi Watanabe
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Gene Regulation, Cancer Center, Fujita Health University, Toyoake, Aichi, Japan
| | - Ana T Nogueira
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bei Liu
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Megan E Kern
- Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jesse Aaron
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, USA
| | - Aaron Taylor
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, USA
| | - Michael Pablo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Program in Molecular and Cellular Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, USA
| | - Timothy C Elston
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Klaus M Hahn
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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