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Schiøtz OH, Kaiser CJO, Klumpe S, Morado DR, Poege M, Schneider J, Beck F, Klebl DP, Thompson C, Plitzko JM. Serial Lift-Out: sampling the molecular anatomy of whole organisms. Nat Methods 2024; 21:1684-1692. [PMID: 38110637 PMCID: PMC11399102 DOI: 10.1038/s41592-023-02113-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 10/25/2023] [Indexed: 12/20/2023]
Abstract
Cryo-focused ion beam milling of frozen-hydrated cells and subsequent cryo-electron tomography (cryo-ET) has enabled the structural elucidation of macromolecular complexes directly inside cells. Application of the technique to multicellular organisms and tissues, however, is still limited by sample preparation. While high-pressure freezing enables the vitrification of thicker samples, it prolongs subsequent preparation due to increased thinning times and the need for extraction procedures. Additionally, thinning removes large portions of the specimen, restricting the imageable volume to the thickness of the final lamella, typically <300 nm. Here we introduce Serial Lift-Out, an enhanced lift-out technique that increases throughput and obtainable contextual information by preparing multiple sections from single transfers. We apply Serial Lift-Out to Caenorhabditis elegans L1 larvae, yielding a cryo-ET dataset sampling the worm's anterior-posterior axis, and resolve its ribosome structure to 7 Å and a subregion of the 11-protofilament microtubule to 13 Å, illustrating how Serial Lift-Out enables the study of multicellular molecular anatomy.
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Affiliation(s)
- Oda Helene Schiøtz
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christoph J O Kaiser
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sven Klumpe
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Dustin R Morado
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department for Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Matthias Poege
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jonathan Schneider
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Beck
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David P Klebl
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christopher Thompson
- Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Jürgen M Plitzko
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany.
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2
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Struckman HL, Moise N, Vanslembrouck B, Rothacker N, Chen Z, van Hengel J, Weinberg SH, Veeraraghavan R. Indirect Correlative Light and Electron Microscopy (iCLEM): A Novel Pipeline for Multiscale Quantification of Structure From Molecules to Organs. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2024; 30:318-333. [PMID: 38525890 PMCID: PMC11057817 DOI: 10.1093/mam/ozae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/09/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024]
Abstract
Correlative light and electron microscopy (CLEM) methods are powerful methods that combine molecular organization (from light microscopy) with ultrastructure (from electron microscopy). However, CLEM methods pose high cost/difficulty barriers to entry and have very low experimental throughput. Therefore, we have developed an indirect correlative light and electron microscopy (iCLEM) pipeline to sidestep the rate-limiting steps of CLEM (i.e., preparing and imaging the same samples on multiple microscopes) and correlate multiscale structural data gleaned from separate samples imaged using different modalities by exploiting biological structures identifiable by both light and electron microscopy as intrinsic fiducials. We demonstrate here an application of iCLEM, where we utilized gap junctions and mechanical junctions between muscle cells in the heart as intrinsic fiducials to correlate ultrastructural measurements from transmission electron microscopy (TEM), and focused ion beam scanning electron microscopy (FIB-SEM) with molecular organization from confocal microscopy and single molecule localization microscopy (SMLM). We further demonstrate how iCLEM can be integrated with computational modeling to discover structure-function relationships. Thus, we present iCLEM as a novel approach that complements existing CLEM methods and provides a generalizable framework that can be applied to any set of imaging modalities, provided suitable intrinsic fiducials can be identified.
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Affiliation(s)
- Heather L Struckman
- Department of Biomedical Engineering, College of Engineering, 2124 Fontana Labs, 140 W. 19th Ave, The Ohio State University, Columbus, OH 43210, USA
- The Frick Center for Heart Failure and Arrhythmia, Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, 2255 Kenny Rd, Rm 5189, Pelotonia Research Center, Columbus, OH 43210, USA
| | - Nicolae Moise
- The Frick Center for Heart Failure and Arrhythmia, Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, 2255 Kenny Rd, Rm 5189, Pelotonia Research Center, Columbus, OH 43210, USA
| | - Bieke Vanslembrouck
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, Building B, Entrance 36, 9000 Ghent, Belgium
| | - Nathan Rothacker
- Department of Biomedical Engineering, College of Engineering, 2124 Fontana Labs, 140 W. 19th Ave, The Ohio State University, Columbus, OH 43210, USA
- The Frick Center for Heart Failure and Arrhythmia, Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, 2255 Kenny Rd, Rm 5189, Pelotonia Research Center, Columbus, OH 43210, USA
| | - Zhenhui Chen
- Krannert Cardiovascular Research Center, Department of Medicine, Indiana University, Room E400, 1801 N. Senate Blvd., Suite E400, Indianapolis, IN 46202, USA
| | - Jolanda van Hengel
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, Building B, Entrance 36, 9000 Ghent, Belgium
| | - Seth H Weinberg
- Department of Biomedical Engineering, College of Engineering, 2124 Fontana Labs, 140 W. 19th Ave, The Ohio State University, Columbus, OH 43210, USA
- The Frick Center for Heart Failure and Arrhythmia, Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, 2255 Kenny Rd, Rm 5189, Pelotonia Research Center, Columbus, OH 43210, USA
| | - Rengasayee Veeraraghavan
- Department of Biomedical Engineering, College of Engineering, 2124 Fontana Labs, 140 W. 19th Ave, The Ohio State University, Columbus, OH 43210, USA
- The Frick Center for Heart Failure and Arrhythmia, Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, 2255 Kenny Rd, Rm 5189, Pelotonia Research Center, Columbus, OH 43210, USA
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3
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Zobaroğlu-Özer P, Bora-Akoğlu G. Split but merge: Golgi fragmentation in physiological and pathological conditions. Mol Biol Rep 2024; 51:214. [PMID: 38280063 DOI: 10.1007/s11033-023-09153-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 12/12/2023] [Indexed: 01/29/2024]
Abstract
The Golgi complex is a highly dynamic and tightly regulated cellular organelle with essential roles in the processing as well as the sorting of proteins and lipids. Its structure undergoes rapid disassembly and reassembly during normal physiological processes, including cell division, migration, polarization, differentiation, and cell death. Golgi dispersal or fragmentation also occurs in pathological conditions, such as neurodegenerative diseases, infectious diseases, congenital disorders of glycosylation diseases, and cancer. In this review, current knowledge about both structural organization and morphological alterations in the Golgi in physiological and pathological conditions is summarized together with the methodologies that help to reveal its structure.
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Affiliation(s)
- Pelin Zobaroğlu-Özer
- Faculty of Medicine, Department of Medical Biology, Hacettepe University, Ankara, Turkey
- Faculty of Medicine, Department of Medical Biology, Niğde Ömer Halisdemir University, Niğde, Turkey
| | - Gamze Bora-Akoğlu
- Faculty of Medicine, Department of Medical Biology, Hacettepe University, Ankara, Turkey.
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4
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Hacker C, Sendra K, Keisham P, Filipescu T, Lucocq J, Salimi F, Ferguson S, Bhella D, MacNeill SA, Embley M, Lucocq J. Biogenesis, inheritance, and 3D ultrastructure of the microsporidian mitosome. Life Sci Alliance 2024; 7:e202201635. [PMID: 37903625 PMCID: PMC10618108 DOI: 10.26508/lsa.202201635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 11/01/2023] Open
Abstract
During the reductive evolution of obligate intracellular parasites called microsporidia, a tiny remnant mitochondrion (mitosome) lost its typical cristae, organellar genome, and most canonical functions. Here, we combine electron tomography, stereology, immunofluorescence microscopy, and bioinformatics to characterise mechanisms of growth, division, and inheritance of this minimal mitochondrion in two microsporidia species (grown within a mammalian RK13 culture-cell host). Mitosomes of Encephalitozoon cuniculi (2-12/cell) and Trachipleistophora hominis (14-18/nucleus) displayed incremental/non-phasic growth and division and were closely associated with an organelle identified as equivalent to the fungal microtubule-organising centre (microsporidian spindle pole body; mSPB). The mitosome-mSPB association was resistant to treatment with microtubule-depolymerising drugs nocodazole and albendazole. Dynamin inhibitors (dynasore and Mdivi-1) arrested mitosome division but not growth, whereas bioinformatics revealed putative dynamins Drp-1 and Vps-1, of which, Vps-1 rescued mitochondrial constriction in dynamin-deficient yeast (Schizosaccharomyces pombe). Thus, microsporidian mitosomes undergo incremental growth and dynamin-mediated division and are maintained through ordered inheritance, likely mediated via binding to the microsporidian centrosome (mSPB).
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Affiliation(s)
| | - Kacper Sendra
- Biosciences Institute, The Medical School, Catherine Cookson Building, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - James Lucocq
- Department of Surgery, Dundee Medical School Ninewells Hospital, Dundee, UK
| | - Fatemeh Salimi
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Sophie Ferguson
- School of Medicine, University of St Andrews, St Andrews, UK
| | - David Bhella
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Martin Embley
- Biosciences Institute, Centre for Bacterial Cell Biology, Baddiley-Clark Building, Newcastle University, Newcastle upon Tyne, UK
| | - John Lucocq
- School of Medicine, University of St Andrews, St Andrews, UK
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5
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Serra Lleti JM, Steyer AM, Schieber NL, Neumann B, Tischer C, Hilsenstein V, Holtstrom M, Unrau D, Kirmse R, Lucocq JM, Pepperkok R, Schwab Y. CLEMSite, a software for automated phenotypic screens using light microscopy and FIB-SEM. J Cell Biol 2022; 222:213779. [PMID: 36562752 PMCID: PMC9802685 DOI: 10.1083/jcb.202209127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
In recent years, Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) has emerged as a flexible method that enables semi-automated volume ultrastructural imaging. We present a toolset for adherent cells that enables tracking and finding cells, previously identified in light microscopy (LM), in the FIB-SEM, along with the automatic acquisition of high-resolution volume datasets. We detect the underlying grid pattern in both modalities (LM and EM), to identify common reference points. A combination of computer vision techniques enables complete automation of the workflow. This includes setting the coincidence point of both ion and electron beams, automated evaluation of the image quality and constantly tracking the sample position with the microscope's field of view reducing or even eliminating operator supervision. We show the ability to target the regions of interest in EM within 5 µm accuracy while iterating between different targets and implementing unattended data acquisition. Our results demonstrate that executing volume acquisition in multiple locations autonomously is possible in EM.
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Affiliation(s)
- José M. Serra Lleti
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anna M. Steyer
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Anna M. Steyer:
| | - Nicole L. Schieber
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Beate Neumann
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christian Tischer
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Volker Hilsenstein
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | | | - John M. Lucocq
- Medical and Biological Sciences, Schools of Medicine and Biology, University of St. Andrews, St. Andrews, UK
| | - Rainer Pepperkok
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Correspondence to Yannick Schwab:
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6
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Mironov AA, Beznoussenko GV. Algorithm for Modern Electron Microscopic Examination of the Golgi Complex. Methods Mol Biol 2022; 2557:161-209. [PMID: 36512216 DOI: 10.1007/978-1-0716-2639-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Golgi complex (GC) is an essential organelle of the eukaryotic exocytic pathway. It has a very complexed structure and thus localization of its resident proteins is not trivial. Fast development of microscopic methods generates a huge difficulty for Golgi researchers to select the best protocol to use. Modern methods of light microscopy, such as super-resolution light microscopy (SRLM) and electron microscopy (EM), open new possibilities in analysis of various biological structures at organelle, cell, and organ levels. Nowadays, new generation of EM methods became available for the study of the GC; these include three-dimensional EM (3DEM), correlative light-EM (CLEM), immune EM, and new estimators within stereology that allow realization of maximal goal of any morphological study, namely, to achieve a three-dimensional model of the sample with optimal level of resolution and quantitative determination of its chemical composition. Methods of 3DEM have partially overlapping capabilities. This requires a careful comparison of these methods, identification of their strengths and weaknesses, and formulation of recommendations for their application to cell or tissue samples. Here, we present an overview of 3DEM methods for the study of the GC and some basics for how the images are formed and how the image quality can be improved.
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7
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Mejia I, Chen YC, Díaz B. Analysis of Golgi Morphology Using Immunofluorescence and CellProfiler Software. Methods Mol Biol 2022; 2557:765-784. [PMID: 36512250 DOI: 10.1007/978-1-0716-2639-9_46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The architecture of the Golgi apparatus in mammalian cells changes dynamically in response to internal and external cues and may be permanently altered in disease states. Here, we present a method to quantify changes in Golgi morphology using immunofluorescence and confocal microscopy followed by CellProfiler software analysis. This method will assist researchers in evaluating alterations in the Golgi complex morphology of cultured cells under a variety of different experimental conditions.
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Affiliation(s)
- Isabel Mejia
- Department of Internal Medicine, Division of Medical Hematology and Oncology, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yu-Chuan Chen
- Department of Internal Medicine, Division of Medical Hematology and Oncology, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Begoña Díaz
- Department of Internal Medicine, Division of Medical Hematology and Oncology, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA. .,David Geffen School of Medicine and Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, USA.
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8
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Ayala I, Colanzi A. Structural Organization and Function of the Golgi Ribbon During Cell Division. Front Cell Dev Biol 2022; 10:925228. [PMID: 35813197 PMCID: PMC9263219 DOI: 10.3389/fcell.2022.925228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/06/2022] [Indexed: 11/24/2022] Open
Abstract
The Golgi complex has a central role in the secretory traffic. In vertebrate cells it is generally organized in polarized stacks of cisternae that are laterally connected by membranous tubules, forming a structure known as Golgi ribbon. The steady state ribbon arrangement results from a dynamic equilibrium between formation and cleavage of the membrane tubules connecting the stacks. This balance is of great physiological relevance as the unlinking of the ribbon during G2 is required for mitotic entry. A block of this process induces a potent G2 arrest of the cell cycle, indicating that a mitotic “Golgi checkpoint” controls the correct pre-mitotic segregation of the Golgi ribbon. Then, after mitosis onset, the Golgi stacks undergo an extensive disassembly, which is necessary for proper spindle formation. Notably, several Golgi-associated proteins acquire new roles in spindle formation and mitotic progression during mitosis. Here we summarize the current knowledge about the basic principle of the Golgi architecture and its functional relationship with cell division to highlight crucial aspects that need to be addressed to help us understand the physiological significance of the ribbon and the pathological implications of alterations of this organization.
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9
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Janota CS, Pinto A, Pezzarossa A, Machado P, Costa J, Campinho P, Franco CA, Gomes ER. Shielding of actin by the endoplasmic reticulum impacts nuclear positioning. Nat Commun 2022; 13:2763. [PMID: 35589708 PMCID: PMC9120458 DOI: 10.1038/s41467-022-30388-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/28/2022] [Indexed: 11/09/2022] Open
Abstract
Nuclear position is central to cell polarization, and its disruption is associated with various pathologies. The nucleus is moved away from the leading edge of migrating cells through its connection to moving dorsal actin cables, and the absence of connections to immobile ventral stress fibers. It is unclear how these asymmetric nucleo-cytoskeleton connections are established. Here, using an in vitro wound assay, we find that remodeling of endoplasmic reticulum (ER) impacts nuclear positioning through the formation of a barrier that shields immobile ventral stress fibers. The remodeling of ER and perinuclear ER accumulation is mediated by the ER shaping protein Climp-63. Furthermore, ectopic recruitment of the ER to stress fibers restores nuclear positioning in the absence of Climp-63. Our findings suggest that the ER mediates asymmetric nucleo-cytoskeleton connections to position the nucleus.
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Affiliation(s)
- Cátia Silva Janota
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Andreia Pinto
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Royal Brompton Hospital and Harefield NHS Foundation Trust, London, UK
| | - Anna Pezzarossa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Champalimaud Foundation, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Pedro Machado
- Electron Microscopy Core Facility (EMCF), European Molecular Biology Laboratory, Heidelberg, Germany.,Centre for Ultrastructural Imaging, King's College London, London, UK
| | - Judite Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro Campinho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Champalimaud Foundation, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Cláudio A Franco
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Instituto de Histologia e Biologia do Desenvolvimento, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Edgar R Gomes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal. .,Instituto de Histologia e Biologia do Desenvolvimento, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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10
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Johkura K, Usuda N, Tanaka Y, Fukasawa M, Murata K, Noda T, Ohno N. OUP accepted manuscript. Microscopy (Oxf) 2022; 71:262-270. [PMID: 35535544 PMCID: PMC9535788 DOI: 10.1093/jmicro/dfac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/25/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Kohei Johkura
- Department of Histology and Embryology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Nobuteru Usuda
- *To whom correspondence should be addressed. E-mail: (N.U.); (N.O.)
| | - Yoshihiro Tanaka
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Motoaki Fukasawa
- Department of Biomedical Molecular Sciences (Anatomy II), Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Toru Noda
- Department of Occupational Therapy (Anatomy), Biwako Professional University of Rehabilitation, 967 Kitasakacho, Higashiomi, Shiga 527-0145, Japan
- Department of Cell Biology and Anatomy, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Nobuhiko Ohno
- *To whom correspondence should be addressed. E-mail: (N.U.); (N.O.)
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11
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Knudsen L, Brandenberger C, Ochs M. Stereology as the 3D tool to quantitate lung architecture. Histochem Cell Biol 2020; 155:163-181. [PMID: 33051774 PMCID: PMC7910236 DOI: 10.1007/s00418-020-01927-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2020] [Indexed: 01/12/2023]
Abstract
Stereology is the method of choice for the quantitative assessment of biological objects in microscopy. It takes into account the fact that, in traditional microscopy such as conventional light and transmission electron microscopy, although one has to rely on measurements on nearly two-dimensional sections from fixed and embedded tissue samples, the quantitative data obtained by these measurements should characterize the real three-dimensional properties of the biological objects and not just their “flatland” appearance on the sections. Thus, three-dimensionality is a built-in property of stereological sampling and measurement tools. Stereology is, therefore, perfectly suited to be combined with 3D imaging techniques which cover a wide range of complementary sample sizes and resolutions, e.g. micro-computed tomography, confocal microscopy and volume electron microscopy. Here, we review those stereological principles that are of particular relevance for 3D imaging and provide an overview of applications of 3D imaging-based stereology to the lung in health and disease. The symbiosis of stereology and 3D imaging thus provides the unique opportunity for unbiased and comprehensive quantitative characterization of the three-dimensional architecture of the lung from macro to nano scale.
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Affiliation(s)
- Lars Knudsen
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover, Germany
| | - Christina Brandenberger
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover, Germany
| | - Matthias Ochs
- Institute of Functional Anatomy, Charité-Universitätsmedizin Berlin, Philippstr. 11, 10115, Berlin, Germany. .,German Center for Lung Research (DZL), Berlin, Germany.
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12
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Jah N, Jobart-Malfait A, Ermoza K, Noteuil A, Chiocchia G, Breban M, André C. HLA-B27 Subtypes Predisposing to Ankylosing Spondylitis Accumulate in an Endoplasmic Reticulum-Derived Compartment Apart From the Peptide-Loading Complex. Arthritis Rheumatol 2020; 72:1534-1546. [PMID: 32270915 DOI: 10.1002/art.41281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 03/31/2020] [Indexed: 12/29/2022]
Abstract
OBJECTIVE It was previously shown that HLA-B27 subtypes predisposing to spondyloarthritis (SpA), i.e., B*27:02, B*27:05, and B*27:07, displayed an increased propensity to form intracellular oligomers and to accumulate at a high density in cytoplasmic vesicles, as compared to the non-SpA-associated HLA-B*07:02 and HLA-B*27:06. This study was undertaken to characterize the nature and content of HLA-B-containing vesicles and to further examine their relevance to SpA predisposition. METHODS Vesicles containing HLA-B proteins were detected in transfected HeLa cells and in cells from SpA patients or HLA-B27/human β2 -microglobulin (hβ2 m)-transgenic rats, by microscopy. The nature and content of HLA-B-containing vesicles were characterized in colocalization experiments with appropriate markers. RESULTS The SpA-associated HLA-B*27:04 subtype accumulated at higher levels (P < 10-5 ) in cytoplasmic vesicles compared to HLA-B*27:06, from which it differs only by 2 substitutions, reinforcing the correlation between vesicle formation and SpA predisposition. Colocalization studies showed that those vesicles contained misfolded HLA-B heavy chain along with β2 m and endoplasmic reticulum (ER) chaperones (calnexin, calreticulin, BiP, glucose-regulated protein 94-kd) and belonged to the ER but were distinct from the peptide-loading complex (PLC). Similar vesicles were observed in immune cells from HLA-B27+ SpA patients, in greater abundance than in healthy controls (P < 0.01), and in dendritic cells from HLA-B27/hβ2 m transgenic rats, correlating with SpA susceptibility. CONCLUSION Accumulation of misfolded HLA-B heavy chain along with β2 m and ER chaperones into ER-derived vesicles distinct from the PLC is a characteristic feature of HLA-B27 subtypes predisposing to SpA. This phenomenon could contribute to HLA-B27 pathogenicity, via a noncanonical mechanism.
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Affiliation(s)
- Nadège Jah
- Université Paris-Saclay, Universite' de Versailles St.-Quentin-en-Yvelines, INSERM (UMR 1173), Montigny-Le-Bretonneux, France, and Laboratoire d'Excellence INFLAMEX, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Aude Jobart-Malfait
- Université Paris-Saclay, Universite' de Versailles St.-Quentin-en-Yvelines, INSERM (UMR 1173), Montigny-Le-Bretonneux, France, and Laboratoire d'Excellence INFLAMEX, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Ketia Ermoza
- Université Paris-Saclay, Universite' de Versailles St.-Quentin-en-Yvelines, INSERM (UMR 1173), Montigny-Le-Bretonneux, France, and Laboratoire d'Excellence INFLAMEX, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Aurélie Noteuil
- Université Paris-Saclay, Universite' de Versailles St.-Quentin-en-Yvelines, INSERM (UMR 1173), Montigny-Le-Bretonneux, France, and Laboratoire d'Excellence INFLAMEX, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | | | - Maxime Breban
- Université Paris-Saclay, Universite' de Versailles St.-Quentin-en-Yvelines, INSERM (UMR 1173), Montigny-Le-Bretonneux, France, Laboratoire d'Excellence INFLAMEX, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, and Hôpital Ambroise Paré, AP-HP, Boulogne-Billancourt, France
| | - Claudine André
- Université Paris-Saclay, Universite' de Versailles St.-Quentin-en-Yvelines, INSERM (UMR 1173), Montigny-Le-Bretonneux, France, and Laboratoire d'Excellence INFLAMEX, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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Parton RG. Twenty years of traffic: A 2020 vision of cellular electron microscopy. Traffic 2019; 21:156-161. [DOI: 10.1111/tra.12684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 02/01/2023]
Affiliation(s)
- Robert G. Parton
- Institute for Molecular Bioscience and Centre for Microscopy and Microanalysis The University of Queensland Brisbane Queensland Australia
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Venditti R, Rega LR, Masone MC, Santoro M, Polishchuk E, Sarnataro D, Paladino S, D'Auria S, Varriale A, Olkkonen VM, Di Tullio G, Polishchuk R, De Matteis MA. Molecular determinants of ER-Golgi contacts identified through a new FRET-FLIM system. J Cell Biol 2019; 218:1055-1065. [PMID: 30659100 PMCID: PMC6400564 DOI: 10.1083/jcb.201812020] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 12/14/2018] [Accepted: 12/18/2018] [Indexed: 01/05/2023] Open
Abstract
ER-TGN contact sites (ERTGoCS) have been visualized by electron microscopy, but their location in the crowded perinuclear area has hampered their analysis via optical microscopy as well as their mechanistic study. To overcome these limits we developed a FRET-based approach and screened several candidates to search for molecular determinants of the ERTGoCS. These included the ER membrane proteins VAPA and VAPB and lipid transfer proteins possessing dual (ER and TGN) targeting motifs that have been hypothesized to contribute to the maintenance of ERTGoCS, such as the ceramide transfer protein CERT and several members of the oxysterol binding proteins. We found that VAP proteins, OSBP1, ORP9, and ORP10 are required, with OSBP1 playing a redundant role with ORP9, which does not involve its lipid transfer activity, and ORP10 being required due to its ability to transfer phosphatidylserine to the TGN. Our results indicate that both structural tethers and a proper lipid composition are needed for ERTGoCS integrity.
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Affiliation(s)
- Rossella Venditti
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy .,Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Medical School, Naples, Italy
| | - Laura Rita Rega
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | | | - Michele Santoro
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | | | - Daniela Sarnataro
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Medical School, Naples, Italy
| | - Simona Paladino
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Medical School, Naples, Italy
| | - Sabato D'Auria
- Institute of Food Science, Consiglio Nazionale delle Ricerche, Avellino, Italy
| | - Antonio Varriale
- Institute of Food Science, Consiglio Nazionale delle Ricerche, Avellino, Italy
| | - Vesa M Olkkonen
- Department of Anatomy, Faculty of Medicine, FI-00014 University of Helsinki, Helsinki, Finland.,Minerva Foundation Institute for Medical Research, Biomedicum 2U Helsinki, Helsinki, Finland
| | | | | | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy .,Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Medical School, Naples, Italy
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Napper RMA. Total Number Is Important: Using the Disector Method in Design-Based Stereology to Understand the Structure of the Rodent Brain. Front Neuroanat 2018; 12:16. [PMID: 29556178 PMCID: PMC5844935 DOI: 10.3389/fnana.2018.00016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 02/15/2018] [Indexed: 12/15/2022] Open
Abstract
The advantages of using design-based stereology in the collection of quantitative data, have been highlighted, in numerous publications, since the description of the disector method by Sterio (1984). This review article discusses the importance of total number derived with the disector method, as a key variable that must continue to be used to understand the rodent brain and that such data can be used to develop quantitative networks of the brain. The review article will highlight the huge impact total number has had on our understanding of the rodent brain and it will suggest that neuroscientists need to be aware of the increasing number of studies where density, not total number, is the quantitative measure used. It will emphasize that density can result in data that is misleading, most often in an unknown direction, and that we run the risk of this type of data being accepted into the collective neuroscience knowledge database. It will also suggest that design-based stereology using the disector method, can be used alongside recent developments in electron microscopy, such as serial block-face scanning electron microscopy (SEM), to obtain total number data very efficiently at the ultrastructural level. Throughout the article total number is discussed as a key parameter in understanding the micro-networks of the rodent brain as they can be represented as both anatomical and quantitative networks.
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Affiliation(s)
- Ruth M A Napper
- Brain Health Research Centre, Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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He X, Guo F, Liu B. Oolong tea and LR-White resin: a new method of plant sample preparation for transmission electron microscopy. J Microsc 2018; 270:244-251. [PMID: 29334400 DOI: 10.1111/jmi.12678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/22/2017] [Accepted: 12/17/2017] [Indexed: 11/27/2022]
Abstract
Simplifying sample processing, shortening the sample preparation time, and adjusting procedures to suitable for new health and safety regulations, these issues are the current challenges which electron microscopic examinations need to face. In order to resolve these problems, new plant tissue sample processing protocols for transmission electron microscopy should be developed. In the present study, we chose the LR-White resin-assisted processing protocol for the ultrastructural observation of different types of plant tissues. Moreover, we explored Oolong tea extract (OTE) as a substitute for UA in staining ultrathin sections of plant samples. The results revealed that there was no significant difference between the OTE double staining method and the traditional double staining method. Furthermore, in some organelles, such as mitochondria in root cells of tomatoes and chloroplast in leaf cells of watermelons, the OTE double staining method achieved little better results than the traditional double staining method. Therefore, OTE demonstrated good potentials in replacing UA as a counterstain on ultrathin sections. In addition, sample preparation time was significantly shortened and simplified using LR-White resin. This novel protocol reduced the time for preparing plant samples, and hazardous reagents in traditional method (acetone and UA) were also replaced by less toxic ones (ethanol and OTE).
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Affiliation(s)
- Xiaohua He
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi, China
| | - Fuzhen Guo
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi, China
| | - Bin Liu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China
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Taatjes DJ, Roth J. In focus in HCB. Histochem Cell Biol 2017; 147:651-652. [PMID: 28456845 DOI: 10.1007/s00418-017-1573-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2017] [Indexed: 10/19/2022]
Affiliation(s)
- Douglas J Taatjes
- Department of Pathology and Laboratory Medicine, The Robert Larner M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA.
| | - Jürgen Roth
- University of Zurich, 8091, Zurich, Switzerland
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