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Vue Z, Murphy A, Le H, Neikirk K, Garza-Lopez E, Marshall AG, Mungai M, Jenkins B, Vang L, Beasley HK, Ezedimma M, Manus S, Whiteside A, Forni MF, Harris C, Crabtree A, Albritton CF, Jamison S, Demirci M, Prasad P, Oliver A, Actkins KV, Shao J, Zaganjor E, Scudese E, Rodriguez B, Koh A, Rabago I, Moore JE, Nguyen D, Aftab M, Kirk B, Li Y, Wandira N, Ahmad T, Saleem M, Kadam A, Katti P, Koh HJ, Evans C, Koo YD, Wang E, Smith Q, Tomar D, Williams CR, Sweetwyne MT, Quintana AM, Phillips MA, Hubert D, Kirabo A, Dash C, Jadiya P, Kinder A, Ajijola OA, Miller-Fleming TW, McReynolds MR, Hinton A. MICOS Complex Loss Governs Age-Associated Murine Mitochondrial Architecture and Metabolism in the Liver, While Sam50 Dictates Diet Changes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599846. [PMID: 38979162 PMCID: PMC11230271 DOI: 10.1101/2024.06.20.599846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The liver, the largest internal organ and a metabolic hub, undergoes significant declines due to aging, affecting mitochondrial function and increasing the risk of systemic liver diseases. How the mitochondrial three-dimensional (3D) structure changes in the liver across aging, and the biological mechanisms regulating such changes confers remain unclear. In this study, we employed Serial Block Face-Scanning Electron Microscopy (SBF-SEM) to achieve high-resolution 3D reconstructions of murine liver mitochondria to observe diverse phenotypes and structural alterations that occur with age, marked by a reduction in size and complexity. We also show concomitant metabolomic and lipidomic changes in aged samples. Aged human samples reflected altered disease risk. To find potential regulators of this change, we examined the Mitochondrial Contact Site and Cristae Organizing System (MICOS) complex, which plays a crucial role in maintaining mitochondrial architecture. We observe that the MICOS complex is lost during aging, but not Sam50. Sam50 is a component of the sorting and assembly machinery (SAM) complex that acts in tandem with the MICOS complex to modulate cristae morphology. In murine models subjected to a high-fat diet, there is a marked depletion of the mitochondrial protein SAM50. This reduction in Sam50 expression may heighten the susceptibility to liver disease, as our human biobank studies corroborate that Sam50 plays a genetically regulated role in the predisposition to multiple liver diseases. We further show that changes in mitochondrial calcium dysregulation and oxidative stress accompany the disruption of the MICOS complex. Together, we establish that a decrease in mitochondrial complexity and dysregulated metabolism occur with murine liver aging. While these changes are partially be regulated by age-related loss of the MICOS complex, the confluence of a murine high-fat diet can also cause loss of Sam50, which contributes to liver diseases. In summary, our study reveals potential regulators that affect age-related changes in mitochondrial structure and metabolism, which can be targeted in future therapeutic techniques.
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Affiliation(s)
- Zer Vue
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Alexandria Murphy
- Department of Biochemistry and Molecular Biology, The Huck Institute of the Life Sciences, Pennsylvania State University, State College, PA 16801
| | - Han Le
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Kit Neikirk
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Edgar Garza-Lopez
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Andrea G. Marshall
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Margaret Mungai
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Brenita Jenkins
- Department of Biochemistry and Molecular Biology, The Huck Institute of the Life Sciences, Pennsylvania State University, State College, PA 16801
| | - Larry Vang
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Heather K. Beasley
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Mariaassumpta Ezedimma
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Sasha Manus
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Aaron Whiteside
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Maria Fernanda Forni
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520
| | - Chanel Harris
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
- Department of Biomedical Sciences, School of Graduate Studies, Meharry Medical College, Nashville, TN 37208-3501, USA
| | - Amber Crabtree
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Claude F. Albritton
- Department of Biomedical Sciences, School of Graduate Studies, Meharry Medical College, Nashville, TN 37208-3501, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sydney Jamison
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mert Demirci
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Praveena Prasad
- Department of Biochemistry and Molecular Biology, The Huck Institute of the Life Sciences, Pennsylvania State University, State College, PA 16801
| | - Ashton Oliver
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Ky’Era V. Actkins
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Jianqiang Shao
- Central Microscopy Research Facility, University of Iowa, Iowa City, IA, 52242, USA
| | - Elma Zaganjor
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Estevão Scudese
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Benjamin Rodriguez
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Alice Koh
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Izabella Rabago
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Johnathan E. Moore
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Desiree Nguyen
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Muhammad Aftab
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Benjamin Kirk
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Yahang Li
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Nelson Wandira
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Taseer Ahmad
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pharmacology, College of Pharmacy, University of Sargodha, Sargodha, Punjab,40100, Pakistan
| | - Mohammad Saleem
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ashlesha Kadam
- Department of Internal Medicine, Section of Cardiovascular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157 USA
| | - Prasanna Katti
- National Heart, Lung and Blood Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, AP, 517619, India
| | - Ho-Jin Koh
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Chantell Evans
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27708, USA
| | - Young Do Koo
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Fraternal Order of Eagles Diabetes Research Center, Iowa City, Iowa, USA1
| | - Eric Wang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, 92697, USA
| | - Quinton Smith
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, 92697, USA
| | - Dhanendra Tomar
- Department of Pharmacology, College of Pharmacy, University of Sargodha, Sargodha, Punjab,40100, Pakistan
| | - Clintoria R. Williams
- Department of Neuroscience, Cell Biology and Physiology, Wright State University, Dayton, OH 45435 USA
| | - Mariya T. Sweetwyne
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Anita M. Quintana
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, Texas, USA
| | - Mark A. Phillips
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
| | - David Hubert
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
| | - Annet Kirabo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Immunobiology, Nashville, TN, 37232, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, 37232, USA
- Vanderbilt Institute for Global Health, Nashville, TN, 37232, USA
| | - Chandravanu Dash
- Department of Microbiology, Immunology and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Pooja Jadiya
- Department of Internal Medicine, Section of Gerontology and Geriatric Medicine, Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest University School of Medicine, Winston-Salem, NC
| | - André Kinder
- Artur Sá Earp Neto University Center – UNIFASE-FMP, Petrópolis Medical School, Brazil
| | - Olujimi A. Ajijola
- UCLA Cardiac Arrhythmia Center, University of California, Los Angeles, CA, USA
| | - Tyne W. Miller-Fleming
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Melanie R. McReynolds
- Department of Biochemistry and Molecular Biology, The Huck Institute of the Life Sciences, Pennsylvania State University, State College, PA 16801
| | - Antentor Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
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2
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Dudka W, Salo VT, Mahamid J. Zooming into lipid droplet biology through the lens of electron microscopy. FEBS Lett 2024; 598:1127-1142. [PMID: 38726814 DOI: 10.1002/1873-3468.14899] [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: 01/26/2024] [Revised: 04/08/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Electron microscopy (EM), in its various flavors, has significantly contributed to our understanding of lipid droplets (LD) as central organelles in cellular metabolism. For example, EM has illuminated that LDs, in contrast to all other cellular organelles, are uniquely enclosed by a single phospholipid monolayer, revealed the architecture of LD contact sites with different organelles, and provided near-atomic resolution maps of key enzymes that regulate neutral lipid biosynthesis and LD biogenesis. In this review, we first provide a brief history of pivotal findings in LD biology unveiled through the lens of an electron microscope. We describe the main EM techniques used in the context of LD research and discuss their current capabilities and limitations, thereby providing a foundation for utilizing suitable EM methodology to address LD-related questions with sufficient level of structural preservation, detail, and resolution. Finally, we highlight examples where EM has recently been and is expected to be instrumental in expanding the frontiers of LD biology.
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Affiliation(s)
- Wioleta Dudka
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Veijo T Salo
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
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3
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Franzkoch R, Anand A, Breitsprecher L, Psathaki OE, Barisch C. Resolving exit strategies of mycobacteria in Dictyostelium discoideum by combining high-pressure freezing with 3D-correlative light and electron microscopy. Mol Microbiol 2024; 121:593-604. [PMID: 38063129 DOI: 10.1111/mmi.15205] [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: 05/15/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 03/12/2024]
Abstract
The infection course of Mycobacterium tuberculosis is highly dynamic and comprises sequential stages that require damaging and crossing of several membranes to enable the translocation of the bacteria into the cytosol or their escape from the host. Many important breakthroughs such as the restriction of mycobacteria by the autophagy pathway and the recruitment of sophisticated host repair machineries to the Mycobacterium-containing vacuole have been gained in the Dictyostelium discoideum/M. marinum system. Despite the availability of well-established light and advanced electron microscopy techniques in this system, a correlative approach integrating both methods with near-native ultrastructural preservation is currently lacking. This is most likely due to the low ability of D. discoideum to adhere to surfaces, which results in cell loss even after fixation. To address this problem, we improved the adhesion of cells and developed a straightforward and convenient workflow for 3D-correlative light and electron microscopy. This approach includes high-pressure freezing, which is an excellent technique for preserving membranes. Thus, our method allows to monitor the ultrastructural aspects of vacuole escape which is of central importance for the survival and dissemination of bacterial pathogens.
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Affiliation(s)
- Rico Franzkoch
- iBiOs-integrated Bioimaging Facility, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics, Osnabrück, Germany
- Division of Microbiology, Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Aby Anand
- Center of Cellular Nanoanalytics, Osnabrück, Germany
- Division of Molecular Infection Biology, Department of Biology, University of Osnabrück, Osnabrück, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Division of Host-Microbe Interactome, Research Center Borstel - Leibniz Lung Center (FZB), Borstel, Germany
- Department of Biology, University of Hamburg, Hamburg, Germany
| | - Leonhard Breitsprecher
- iBiOs-integrated Bioimaging Facility, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics, Osnabrück, Germany
- Division of Microbiology, Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Olympia E Psathaki
- iBiOs-integrated Bioimaging Facility, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics, Osnabrück, Germany
| | - Caroline Barisch
- Center of Cellular Nanoanalytics, Osnabrück, Germany
- Division of Molecular Infection Biology, Department of Biology, University of Osnabrück, Osnabrück, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Division of Host-Microbe Interactome, Research Center Borstel - Leibniz Lung Center (FZB), Borstel, Germany
- Department of Biology, University of Hamburg, Hamburg, Germany
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4
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Puchkov D, Müller PM, Lehmann M, Matthaeus C. Analyzing the cellular plasma membrane by fast and efficient correlative STED and platinum replica EM. Front Cell Dev Biol 2023; 11:1305680. [PMID: 38099299 PMCID: PMC10720448 DOI: 10.3389/fcell.2023.1305680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
The plasma membrane of mammalian cells links transmembrane receptors, various structural components, and membrane-binding proteins to subcellular processes, allowing inter- and intracellular communication. Therefore, membrane-binding proteins, together with structural components such as actin filaments, modulate the cell membrane in their flexibility, stiffness, and curvature. Investigating membrane components and curvature in cells remains challenging due to the diffraction limit in light microscopy. Preparation of 5-15-nm-thin plasma membrane sheets and subsequent inspection by metal replica transmission electron microscopy (TEM) reveal detailed information about the cellular membrane topology, including the structure and curvature. However, electron microscopy cannot identify proteins associated with specific plasma membrane domains. Here, we describe a novel adaptation of correlative super-resolution light microscopy and platinum replica TEM (CLEM-PREM), allowing the analysis of plasma membrane sheets with respect to their structural details, curvature, and associated protein composition. We suggest a number of shortcuts and troubleshooting solutions to contemporary PREM protocols. Thus, implementation of super-resolution stimulated emission depletion (STED) microscopy offers significant reduction in sample preparation time and reduced technical challenges for imaging and analysis. Additionally, highly technical challenges associated with replica preparation and transfer on a TEM grid can be overcome by scanning electron microscopy (SEM) imaging. The combination of STED microscopy and platinum replica SEM or TEM provides the highest spatial resolution of plasma membrane proteins and their underlying membrane and is, therefore, a suitable method to study cellular events like endocytosis, membrane trafficking, or membrane tension adaptations.
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Affiliation(s)
- Dmytro Puchkov
- Cellular Imaging Facility, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Paul Markus Müller
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Martin Lehmann
- Cellular Imaging Facility, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Claudia Matthaeus
- Cellular Physiology of Nutrition, Institute for Nutritional Science, University of Potsdam, Potsdam, Germany
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5
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Marshall AG, Neikirk K, Stephens DC, Vang L, Vue Z, Beasley HK, Crabtree A, Scudese E, Lopez EG, Shao B, Krystofiak E, Rutledge S, Davis J, Murray SA, Damo SM, Katti P, Hinton A. Serial Block Face-Scanning Electron Microscopy as a Burgeoning Technology. Adv Biol (Weinh) 2023; 7:e2300139. [PMID: 37246236 PMCID: PMC10950369 DOI: 10.1002/adbi.202300139] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/09/2023] [Indexed: 05/30/2023]
Abstract
Serial block face scanning electron microscopy (SBF-SEM), also referred to as serial block-face electron microscopy, is an advanced ultrastructural imaging technique that enables three-dimensional visualization that provides largerx- and y-axis ranges than other volumetric EM techniques. While SEM is first introduced in the 1930s, SBF-SEM is developed as a novel method to resolve the 3D architecture of neuronal networks across large volumes with nanometer resolution by Denk and Horstmann in 2004. Here, the authors provide an accessible overview of the advantages and challenges associated with SBF-SEM. Beyond this, the applications of SBF-SEM in biochemical domains as well as potential future clinical applications are briefly reviewed. Finally, the alternative forms of artificial intelligence-based segmentation which may contribute to devising a feasible workflow involving SBF-SEM, are also considered.
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Affiliation(s)
- Andrea G Marshall
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Kit Neikirk
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Dominique C Stephens
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Larry Vang
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Zer Vue
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Heather K Beasley
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Amber Crabtree
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Estevão Scudese
- Laboratory of Biosciences of Human Motricity (LABIMH) of the Federal University of State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
- Sport Sciences and Exercise Laboratory (LaCEE), Catholic University of Petrópolis (UCP), Catholic, 25685-100, Brazil
| | - Edgar Garza Lopez
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Bryanna Shao
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Evan Krystofiak
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Sharifa Rutledge
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Jaimaine Davis
- Department of Biochemistry, Cancer Biology, Neuroscience, Pharmacology, Meharry Medical College, Nashville, TN, 37232, USA
| | - Sandra A Murray
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Steven M Damo
- Department of Life and Physical Sciences, Fisk University, Nashville, TN, 37208, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Prasanna Katti
- National Heart, Lung and Blood Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Antentor Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
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6
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Mangione F, Titlow J, Maclachlan C, Gho M, Davis I, Collinson L, Tapon N. Co-option of epidermal cells enables touch sensing. Nat Cell Biol 2023; 25:540-549. [PMID: 36959505 PMCID: PMC10104782 DOI: 10.1038/s41556-023-01110-2] [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: 03/18/2022] [Accepted: 02/20/2023] [Indexed: 03/25/2023]
Abstract
The epidermis is equipped with specialized mechanosensory organs that enable the detection of tactile stimuli. Here, by examining the differentiation of the tactile bristles, mechanosensory organs decorating the Drosophila adult epidermis, we show that neighbouring epidermal cells are essential for touch perception. Each mechanosensory bristle signals to the surrounding epidermis to co-opt a single epidermal cell, which we named the F-Cell. Once specified, the F-Cell adopts a specialized morphology to ensheath each bristle. Functional assays reveal that adult mechanosensory bristles require association with the epidermal F-Cell for touch sensing. Our findings underscore the importance of resident epidermal cells in the assembly of functional touch-sensitive organs.
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Affiliation(s)
- Federica Mangione
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, London, UK.
| | - Joshua Titlow
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Catherine Maclachlan
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Michel Gho
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement, Institut de Biologie Paris Seine (LBD-IBPS), Paris, France
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Nicolas Tapon
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, London, UK.
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7
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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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8
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Zhao B, Luo Z, Zhang H, Zhang H. Imaging tools for plant nanobiotechnology. Front Genome Ed 2022; 4:1029944. [PMID: 36569338 PMCID: PMC9772283 DOI: 10.3389/fgeed.2022.1029944] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
The successful application of nanobiotechnology in biomedicine has greatly changed the traditional way of diagnosis and treating of disease, and is promising for revolutionizing the traditional plant nanobiotechnology. Over the past few years, nanobiotechnology has increasingly expanded into plant research area. Nanomaterials can be designed as vectors for targeted delivery and controlled release of fertilizers, pesticides, herbicides, nucleotides, proteins, etc. Interestingly, nanomaterials with unique physical and chemical properties can directly affect plant growth and development; improve plant resistance to disease and stress; design as sensors in plant biology; and even be used for plant genetic engineering. Similarly, there have been concerns about the potential biological toxicity of nanomaterials. Selecting appropriate characterization methods will help understand how nanomaterials interact with plants and promote advances in plant nanobiotechnology. However, there are relatively few reviews of tools for characterizing nanomaterials in plant nanobiotechnology. In this review, we present relevant imaging tools that have been used in plant nanobiotechnology to monitor nanomaterial migration, interaction with and internalization into plants at three-dimensional lengths. Including: 1) Migration of nanomaterial into plant organs 2) Penetration of nanomaterial into plant tissues (iii)Internalization of nanomaterials by plant cells and interactions with plant subcellular structures. We compare the advantages and disadvantages of current characterization tools and propose future optimal characterization methods for plant nanobiotechnology.
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Affiliation(s)
- Bin Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China,School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, China
| | - Zhongxu Luo
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China,Department of Chemistry, College of Chemistry and Materials Science, Jinan University, Guangzhou, China
| | - Honglu Zhang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, China,*Correspondence: Honglu Zhang, ; Huan Zhang,
| | - Huan Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Honglu Zhang, ; Huan Zhang,
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9
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Choi ML, Chappard A, Singh BP, Maclachlan C, Rodrigues M, Fedotova EI, Berezhnov AV, De S, Peddie CJ, Athauda D, Virdi GS, Zhang W, Evans JR, Wernick AI, Zanjani ZS, Angelova PR, Esteras N, Vinokurov AY, Morris K, Jeacock K, Tosatto L, Little D, Gissen P, Clarke DJ, Kunath T, Collinson L, Klenerman D, Abramov AY, Horrocks MH, Gandhi S. Pathological structural conversion of α-synuclein at the mitochondria induces neuronal toxicity. Nat Neurosci 2022; 25:1134-1148. [PMID: 36042314 PMCID: PMC9448679 DOI: 10.1038/s41593-022-01140-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/12/2022] [Indexed: 11/08/2022]
Abstract
Aggregation of alpha-synuclein (α-Syn) drives Parkinson's disease (PD), although the initial stages of self-assembly and structural conversion have not been directly observed inside neurons. In this study, we tracked the intracellular conformational states of α-Syn using a single-molecule Förster resonance energy transfer (smFRET) biosensor, and we show here that α-Syn converts from a monomeric state into two distinct oligomeric states in neurons in a concentration-dependent and sequence-specific manner. Three-dimensional FRET-correlative light and electron microscopy (FRET-CLEM) revealed that intracellular seeding events occur preferentially on membrane surfaces, especially at mitochondrial membranes. The mitochondrial lipid cardiolipin triggers rapid oligomerization of A53T α-Syn, and cardiolipin is sequestered within aggregating lipid-protein complexes. Mitochondrial aggregates impair complex I activity and increase mitochondrial reactive oxygen species (ROS) generation, which accelerates the oligomerization of A53T α-Syn and causes permeabilization of mitochondrial membranes and cell death. These processes were also observed in induced pluripotent stem cell (iPSC)-derived neurons harboring A53T mutations from patients with PD. Our study highlights a mechanism of de novo α-Syn oligomerization at mitochondrial membranes and subsequent neuronal toxicity.
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Affiliation(s)
- Minee L Choi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | | | - Bhanu P Singh
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
- School of Physics, University of Edinburgh, Edinburgh, UK
| | | | - Margarida Rodrigues
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Dementia Research institute at University of Cambridge, Cambridge, UK
| | - Evgeniya I Fedotova
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Russia
- Cell Physiology and Pathology Laboratory, Orel State University, Orel, Russia
| | - Alexey V Berezhnov
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Russia
- Cell Physiology and Pathology Laboratory, Orel State University, Orel, Russia
| | - Suman De
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Dementia Research institute at University of Cambridge, Cambridge, UK
| | | | - Dilan Athauda
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
| | - Gurvir S Virdi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Weijia Zhang
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
| | - James R Evans
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Anna I Wernick
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Zeinab Shadman Zanjani
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Plamena R Angelova
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Noemi Esteras
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Andrey Y Vinokurov
- Cell Physiology and Pathology Laboratory, Orel State University, Orel, Russia
| | - Katie Morris
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Kiani Jeacock
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Laura Tosatto
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Istituto di Biofisica, National Council of Research, Trento, Italy
| | - Daniel Little
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - Paul Gissen
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Tilo Kunath
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Dementia Research institute at University of Cambridge, Cambridge, UK
| | - Andrey Y Abramov
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.
- Cell Physiology and Pathology Laboratory, Orel State University, Orel, Russia.
| | - Mathew H Horrocks
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK.
| | - Sonia Gandhi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.
- The Francis Crick Institute, London, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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10
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Berkowitz BA, Podolsky RH, Childers KL, Burgoyne T, De Rossi G, Qian H, Roberts R, Katz R, Waseem R, Goodman C. Functional Changes Within the Rod Inner Segment Ellipsoid in Wildtype Mice: An Optical Coherence Tomography and Electron Microscopy Study. Invest Ophthalmol Vis Sci 2022; 63:8. [PMID: 35816042 PMCID: PMC9284466 DOI: 10.1167/iovs.63.8.8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Purpose To test the hypothesis that changing energy needs alter mitochondria distribution within the rod inner segment ellipsoid. Methods In mice with relatively smaller (C57BL/6J [B6J]) or greater (129S6/ev [S6]) retina mitochondria maximum reserve capacity, the profile shape of the rod inner segment ellipsoid zone (ISez) was measured with optical coherence tomography (OCT) under higher (dark) or lower (light) energy demand conditions. ISez profile shape was characterized using an unbiased ellipse descriptor (minor/major aspect ratio). Other bioenergy indexes evaluated include the external limiting membrane-retinal pigment epithelium (ELM-RPE) thickness and the magnitude of the signal intensity of a hyporeflective band located between the photoreceptor tips and apical RPE. The spatial distribution of rod ellipsoid mitochondria were also examined with electron microscopy. Results In B6J mice, darkness produced a greater ISez aspect ratio, thinner ELM-RPE, and a smaller hyporeflective band intensity than in light. In S6 mice, dark and light ISez aspect ratio values were not different and were greater than in light-adapted B6J mice; dark-adapted S6 mice showed smaller ELM-RPE thinning versus light, and negligible hyporeflective band intensity in the light. In B6J mice, mitochondria number in light increased in the distal inner segment ellipsoid and decreased proximally. In S6 mice, mitochondria number in the inner segment ellipsoid were not different between light and dark, and were greater than in B6J mice. Conclusions These data raise the possibility that rod mitochondria activity in mice can be noninvasively evaluated based on the ISez profile shape, a new OCT index that complements OCT energy biomarkers measured outside of the ISez region.
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Affiliation(s)
- Bruce A Berkowitz
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, Michigan, United States
| | - Robert H Podolsky
- Biostatistics and Study Methodology, Children's National Hospital, Silver Spring, Maryland, United States
| | - Karen Lins Childers
- Beaumont Research Institute, Beaumont Health, Royal Oak, Michigan, Unites States
| | - Tom Burgoyne
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Giulia De Rossi
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Haohua Qian
- Visual Function Core, National Eye Institute, National Institutes of Health, Bethesda, Maryland, Unites States
| | - Robin Roberts
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, Michigan, United States
| | - Ryan Katz
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, Michigan, United States
| | - Rida Waseem
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, Michigan, United States
| | - Cole Goodman
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, Michigan, United States
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11
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Peddie CJ, Genoud C, Kreshuk A, Meechan K, Micheva KD, Narayan K, Pape C, Parton RG, Schieber NL, Schwab Y, Titze B, Verkade P, Aubrey A, Collinson LM. Volume electron microscopy. NATURE REVIEWS. METHODS PRIMERS 2022; 2:51. [PMID: 37409324 PMCID: PMC7614724 DOI: 10.1038/s43586-022-00131-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 07/07/2023]
Abstract
Life exists in three dimensions, but until the turn of the century most electron microscopy methods provided only 2D image data. Recently, electron microscopy techniques capable of delving deep into the structure of cells and tissues have emerged, collectively called volume electron microscopy (vEM). Developments in vEM have been dubbed a quiet revolution as the field evolved from established transmission and scanning electron microscopy techniques, so early publications largely focused on the bioscience applications rather than the underlying technological breakthroughs. However, with an explosion in the uptake of vEM across the biosciences and fast-paced advances in volume, resolution, throughput and ease of use, it is timely to introduce the field to new audiences. In this Primer, we introduce the different vEM imaging modalities, the specialized sample processing and image analysis pipelines that accompany each modality and the types of information revealed in the data. We showcase key applications in the biosciences where vEM has helped make breakthrough discoveries and consider limitations and future directions. We aim to show new users how vEM can support discovery science in their own research fields and inspire broader uptake of the technology, finally allowing its full adoption into mainstream biological imaging.
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Affiliation(s)
- Christopher J. Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Christel Genoud
- Electron Microscopy Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Anna Kreshuk
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kimberly Meechan
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Present address: Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Kristina D. Micheva
- Department of Molecular and Cellular Physiology, Stanford University, Palo Alto, CA, USA
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Constantin Pape
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Robert G. Parton
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicole L. Schieber
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Yannick Schwab
- Cell Biology and Biophysics Unit/ Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Aubrey Aubrey
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Lucy M. Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
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12
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Bosch C, Ackels T, Pacureanu A, Zhang Y, Peddie CJ, Berning M, Rzepka N, Zdora MC, Whiteley I, Storm M, Bonnin A, Rau C, Margrie T, Collinson L, Schaefer AT. Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron microtomography and volume electron microscopy. Nat Commun 2022; 13:2923. [PMID: 35614048 PMCID: PMC9132960 DOI: 10.1038/s41467-022-30199-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
Understanding the function of biological tissues requires a coordinated study of physiology and structure, exploring volumes that contain complete functional units at a detail that resolves the relevant features. Here, we introduce an approach to address this challenge: Mouse brain tissue sections containing a region where function was recorded using in vivo 2-photon calcium imaging were stained, dehydrated, resin-embedded and imaged with synchrotron X-ray computed tomography with propagation-based phase contrast (SXRT). SXRT provided context at subcellular detail, and could be followed by targeted acquisition of multiple volumes using serial block-face electron microscopy (SBEM). In the olfactory bulb, combining SXRT and SBEM enabled disambiguation of in vivo-assigned regions of interest. In the hippocampus, we found that superficial pyramidal neurons in CA1a displayed a larger density of spine apparati than deeper ones. Altogether, this approach can enable a functional and structural investigation of subcellular features in the context of cells and tissues.
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Affiliation(s)
- Carles Bosch
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK.
| | - Tobias Ackels
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK
- Department of Neuroscience, Physiology and Pharmacology, University College, London, UK
| | - Alexandra Pacureanu
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK
- Department of Neuroscience, Physiology and Pharmacology, University College, London, UK
- ESRF, The European Synchrotron, Grenoble, France
| | - Yuxin Zhang
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK
- Department of Neuroscience, Physiology and Pharmacology, University College, London, UK
| | | | - Manuel Berning
- Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany
- Scalable minds GmbH, Potsdam, Germany
| | | | - Marie-Christine Zdora
- Department of Physics and Astronomy, University College London, London, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- School of Physics and Astronomy, University of Southampton, Highfield Campus, Southampton, UK
| | - Isabell Whiteley
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK
- Department of Neuroscience, Physiology and Pharmacology, University College, London, UK
| | - Malte Storm
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- Institute of Materials Physics, Helmholtz-Zentrum Hereon, Geesthacht, Germany
| | - Anne Bonnin
- Paul Scherrer Institut, Villigen, Switzerland
| | - Christoph Rau
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Troy Margrie
- Sainsbury Wellcome Centre, University College London, London, UK
| | - Lucy Collinson
- Electron Microscopy STP, The Francis Crick Institute, London, UK
| | - Andreas T Schaefer
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK.
- Department of Neuroscience, Physiology and Pharmacology, University College, London, UK.
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13
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Fermie J, de Jager L, Foster HE, Veenendaal T, de Heus C, van Dijk S, ten Brink C, Oorschot V, Yang L, Li W, Müller WH, Howes S, Carter AP, Förster F, Posthuma G, Gerritsen HC, Klumperman J, Liv N. Bimodal endocytic probe for three-dimensional correlative light and electron microscopy. CELL REPORTS METHODS 2022; 2:100220. [PMID: 35637912 PMCID: PMC9142762 DOI: 10.1016/j.crmeth.2022.100220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 02/04/2022] [Accepted: 04/26/2022] [Indexed: 12/03/2022]
Abstract
We present a bimodal endocytic tracer, fluorescent BSA-gold (fBSA-Au), as a fiducial marker for 2D and 3D correlative light and electron microscopy (CLEM) applications. fBSA-Au consists of colloidal gold (Au) particles stabilized with fluorescent BSA. The conjugate is efficiently endocytosed and distributed throughout the 3D endolysosomal network of cells and has an excellent visibility in both fluorescence microscopy (FM) and electron microscopy (EM). We demonstrate that fBSA-Au facilitates rapid registration in several 2D and 3D CLEM applications using Tokuyasu cryosections, resin-embedded material, and cryoelectron microscopy (cryo-EM). Endocytosed fBSA-Au benefits from a homogeneous 3D distribution throughout the endosomal system within the cell, does not obscure any cellular ultrastructure, and enables accurate (50-150 nm) correlation of fluorescence to EM data. The broad applicability and visibility in both modalities makes fBSA-Au an excellent endocytic fiducial marker for 2D and 3D (cryo)CLEM applications.
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Affiliation(s)
- Job Fermie
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands
| | - Leanne de Jager
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Helen E. Foster
- Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Cambridge, UK
| | - Tineke Veenendaal
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Cecilia de Heus
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Suzanne van Dijk
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Corlinda ten Brink
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Viola Oorschot
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Lin Yang
- Institute of Genetics & Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- Institute of Genetics & Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wally H. Müller
- Microbiology, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Stuart Howes
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Andrew P. Carter
- Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Cambridge, UK
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - George Posthuma
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Hans C. Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands
| | - Judith Klumperman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Nalan Liv
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
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14
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Lumkwana D, Peddie C, Kriel J, Michie LL, Heathcote N, Collinson L, Kinnear C, Loos B. Investigating the Role of Spermidine in a Model System of Alzheimer’s Disease Using Correlative Microscopy and Super-resolution Techniques. Front Cell Dev Biol 2022; 10:819571. [PMID: 35656544 PMCID: PMC9152225 DOI: 10.3389/fcell.2022.819571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/07/2022] [Indexed: 11/29/2022] Open
Abstract
Background: Spermidine has recently received major attention for its potential therapeutic benefits in the context of neurodegeneration, cancer, and aging. However, it is unclear whether concentration dependencies of spermidine exist, to differentially enhance autophagic flux. Moreover, the relationship between low or high autophagy activity relative to basal neuronal autophagy flux and subsequent protein clearance as well as cellular toxicity has remained largely unclear. Methods: Here, we used high-resolution imaging and biochemical techniques to investigate the effects of a low and of a high concentration of spermidine on autophagic flux, neuronal toxicity, and protein clearance in in vitro models of paraquat (PQ) induced neuronal toxicity and amyloid precursor protein (APP) overexpression, as well as in an in vivo model of PQ-induced rodent brain injury. Results: Our results reveal that spermidine induces autophagic flux in a concentration-dependent manner, however the detectable change in the autophagy response critically depends on the specificity and sensitivity of the method employed. By using correlative imaging techniques through Super-Resolution Structured Illumination Microscopy (SR-SIM) and Focused Ion Beam Scanning Electron Microscopy (FIB-SEM), we demonstrate that spermidine at a low concentration induces autophagosome formation capable of large volume clearance. In addition, we provide evidence of distinct, context-dependent protective roles of spermidine in models of Alzheimer’s disease. In an in vitro environment, a low concentration of spermidine protected against PQ-induced toxicity, while both low and high concentrations provided protection against cytotoxicity induced by APP overexpression. In the in vivo scenario, we demonstrate brain region-specific susceptibility to PQ-induced neuronal toxicity, with the hippocampus being highly susceptible compared to the cortex. Regardless of this, spermidine administered at both low and high dosages protected against paraquat-induced toxicity. Conclusions: Taken together, our results demonstrate that firstly, administration of spermidine may present a favourable therapeutic strategy for the treatment of Alzheimer’s disease and secondly, that concentration and dosage-dependent precision autophagy flux screening may be more critical for optimal autophagy and cell death control than previously thought.
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Affiliation(s)
- D. Lumkwana
- Microscopy and Imaging Translational Technology Platform, Cancer Research UK, University College London, London, United Kingdom
- *Correspondence: D. Lumkwana,
| | - C. Peddie
- Science Technology Platform, Electron Microscopy, Francis Crick Institute, London, United Kingdom
| | - J. Kriel
- Central Analytical Facilities, Electron Microscopy Unit, Stellenbosch University, Stellenbosch, South Africa
| | - L. L. Michie
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - N. Heathcote
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - L. Collinson
- Science Technology Platform, Electron Microscopy, Francis Crick Institute, London, United Kingdom
| | - C. Kinnear
- DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - B. Loos
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
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15
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Loginov SV, Fermie J, Fokkema J, Agronskaia AV, De Heus C, Blab GA, Klumperman J, Gerritsen HC, Liv N. Correlative Organelle Microscopy: Fluorescence Guided Volume Electron Microscopy of Intracellular Processes. Front Cell Dev Biol 2022; 10:829545. [PMID: 35478966 PMCID: PMC9035751 DOI: 10.3389/fcell.2022.829545] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/04/2022] [Indexed: 01/19/2023] Open
Abstract
Intracellular processes depend on a strict spatial and temporal organization of proteins and organelles. Therefore, directly linking molecular to nanoscale ultrastructural information is crucial in understanding cellular physiology. Volume or three-dimensional (3D) correlative light and electron microscopy (volume-CLEM) holds unique potential to explore cellular physiology at high-resolution ultrastructural detail across cell volumes. However, the application of volume-CLEM is hampered by limitations in throughput and 3D correlation efficiency. In order to address these limitations, we describe a novel pipeline for volume-CLEM that provides high-precision (<100 nm) registration between 3D fluorescence microscopy (FM) and 3D electron microscopy (EM) datasets with significantly increased throughput. Using multi-modal fiducial nanoparticles that remain fluorescent in epoxy resins and a 3D confocal fluorescence microscope integrated into a Focused Ion Beam Scanning Electron Microscope (FIB.SEM), our approach uses FM to target extremely small volumes of even single organelles for imaging in volume EM and obviates the need for post-correlation of big 3D datasets. We extend our targeted volume-CLEM approach to include live-cell imaging, adding information on the motility of intracellular membranes selected for volume-CLEM. We demonstrate the power of our approach by targeted imaging of rare and transient contact sites between the endoplasmic reticulum (ER) and lysosomes within hours rather than days. Our data suggest that extensive ER-lysosome and mitochondria-lysosome interactions restrict lysosome motility, highlighting the unique capabilities of our integrated CLEM pipeline for linking molecular dynamic data to high-resolution ultrastructural detail in 3D.
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Affiliation(s)
- Sergey V. Loginov
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Job Fermie
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Jantina Fokkema
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Alexandra V. Agronskaia
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Cilia De Heus
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Gerhard A. Blab
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Judith Klumperman
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Hans C. Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Nalan Liv
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- *Correspondence: Nalan Liv,
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16
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Godel-Jędrychowska K, Franke T, Kurczyńska E. Ultrastructural Analysis and Three-Dimensional Reconstruction of Plasmodesmata. Methods Mol Biol 2022; 2457:75-94. [PMID: 35349133 DOI: 10.1007/978-1-0716-2132-5_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Array tomography (AT) is a new high-throughput imaging method for high-resolution imaging of ultrastructure and for 3-D reconstruction of cells and organelles. Here, we describe the entire procedure for obtaining a spatial image of the distribution of plasmodesmata (PD). As example, the protocol is applied here to reconstruct the number and arrangement of PD between cells undergoing differentiation during Arabidopsis somatic embryogenesis.
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Affiliation(s)
- Kamila Godel-Jędrychowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland.
| | | | - Ewa Kurczyńska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
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17
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Schifferer M, Snaidero N, Djannatian M, Kerschensteiner M, Misgeld T. Niwaki Instead of Random Forests: Targeted Serial Sectioning Scanning Electron Microscopy With Reimaging Capabilities for Exploring Central Nervous System Cell Biology and Pathology. Front Neuroanat 2021; 15:732506. [PMID: 34720890 PMCID: PMC8548362 DOI: 10.3389/fnana.2021.732506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/24/2021] [Indexed: 11/13/2022] Open
Abstract
Ultrastructural analysis of discrete neurobiological structures by volume scanning electron microscopy (SEM) often constitutes a "needle-in-the-haystack" problem and therefore relies on sophisticated search strategies. The appropriate SEM approach for a given relocation task not only depends on the desired final image quality but also on the complexity and required accuracy of the screening process. Block-face SEM techniques like Focused Ion Beam or serial block-face SEM are "one-shot" imaging runs by nature and, thus, require precise relocation prior to acquisition. In contrast, "multi-shot" approaches conserve the sectioned tissue through the collection of serial sections onto solid support and allow reimaging. These tissue libraries generated by Array Tomography or Automated Tape Collecting Ultramicrotomy can be screened at low resolution to target high resolution SEM. This is particularly useful if a structure of interest is rare or has been predetermined by correlated light microscopy, which can assign molecular, dynamic and functional information to an ultrastructure. As such approaches require bridging mm to nm scales, they rely on tissue trimming at different stages of sample processing. Relocation is facilitated by endogenous or exogenous landmarks that are visible by several imaging modalities, combined with appropriate registration strategies that allow overlaying images of various sources. Here, we discuss the opportunities of using multi-shot serial sectioning SEM approaches, as well as suitable trimming and registration techniques, to slim down the high-resolution imaging volume to the actual structure of interest and hence facilitate ambitious targeted volume SEM projects.
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Affiliation(s)
- Martina Schifferer
- Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Nicolas Snaidero
- Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
- Hertie Institute for Clinical Brain Research, Tübingen, Germany
| | - Minou Djannatian
- Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
| | - Martin Kerschensteiner
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
- Faculty of Medicine, Biomedical Center (BMC), Ludwig-Maximilians-University Munich, Munich, Germany
| | - Thomas Misgeld
- Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
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18
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Skaar EP. Imaging Infection Across Scales of Size: From Whole Animals to Single Molecules. Annu Rev Microbiol 2021; 75:407-426. [PMID: 34343016 DOI: 10.1146/annurev-micro-041521-121457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Infectious diseases are a leading cause of global morbidity and mortality, and the threat of infectious diseases to human health is steadily increasing as new diseases emerge, existing diseases reemerge, and antimicrobial resistance expands. The application of imaging technology to the study of infection biology has the potential to uncover new factors that are critical to the outcome of host-pathogen interactions and to lead to innovations in diagnosis and treatment of infectious diseases. This article reviews current and future opportunities for the application of imaging to the study of infectious diseases, with a particular focus on the power of imaging objects across a broad range of sizes to expand the utility of these approaches. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Eric P Skaar
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA;
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19
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Gemin O, Serna P, Zamith J, Assendorp N, Fossati M, Rostaing P, Triller A, Charrier C. Unique properties of dually innervated dendritic spines in pyramidal neurons of the somatosensory cortex uncovered by 3D correlative light and electron microscopy. PLoS Biol 2021; 19:e3001375. [PMID: 34428203 PMCID: PMC8415616 DOI: 10.1371/journal.pbio.3001375] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 09/03/2021] [Accepted: 07/29/2021] [Indexed: 01/04/2023] Open
Abstract
Pyramidal neurons (PNs) are covered by thousands of dendritic spines receiving excitatory synaptic inputs. The ultrastructure of dendritic spines shapes signal compartmentalization, but ultrastructural diversity is rarely taken into account in computational models of synaptic integration. Here, we developed a 3D correlative light-electron microscopy (3D-CLEM) approach allowing the analysis of specific populations of synapses in genetically defined neuronal types in intact brain circuits. We used it to reconstruct segments of basal dendrites of layer 2/3 PNs of adult mouse somatosensory cortex and quantify spine ultrastructural diversity. We found that 10% of spines were dually innervated and 38% of inhibitory synapses localized to spines. Using our morphometric data to constrain a model of synaptic signal compartmentalization, we assessed the impact of spinous versus dendritic shaft inhibition. Our results indicate that spinous inhibition is locally more efficient than shaft inhibition and that it can decouple voltage and calcium signaling, potentially impacting synaptic plasticity.
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Affiliation(s)
- Olivier Gemin
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, Paris, France
| | - Pablo Serna
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, Paris, France
- Laboratoire de Physique de l’Ecole Normale Supérieure, ENS, PSL Research University, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | - Joseph Zamith
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, Paris, France
| | - Nora Assendorp
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, Paris, France
| | - Matteo Fossati
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, Paris, France
| | - Philippe Rostaing
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, Paris, France
| | - Antoine Triller
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, Paris, France
| | - Cécile Charrier
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, Paris, France
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20
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Reactive oxygen FIB spin milling enables correlative workflow for 3D super-resolution light microscopy and serial FIB/SEM of cultured cells. Sci Rep 2021; 11:13162. [PMID: 34162977 PMCID: PMC8222390 DOI: 10.1038/s41598-021-92608-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/08/2021] [Indexed: 12/28/2022] Open
Abstract
Correlative light and electron microscopy (CLEM) is a powerful tool for defining the ultrastructural context of molecularly-labeled biological specimens, particularly when superresolution fluorescence microscopy (SRM) is used for CLEM. Current CLEM, however, is limited by the stark differences in sample preparation requirements between the two modalities. For CLEM using SRM, the small region of interest (ROI) of either or both modalities also leads to low success rate and imaging throughput. To overcome these limitations, here we present a CLEM workflow based on a novel focused ion beam/scanning electron microscope (FIB/SEM) compatible with common SRM for imaging biological specimen with ultrahigh 3D resolution and improved imaging throughput. By using a reactive oxygen source in a plasma FIB (PFIB) and a rotating sample stage, the novel FIB/SEM was able to achieve several hundreds of micrometer large area 3D analysis of resin embedded cells through a process named oxygen serial spin mill (OSSM). Compared with current FIB mechanisms, OSSM offers gentle erosion, highly consistent slice thickness, reduced charging during SEM imaging, and improved SEM contrast without increasing the dose of post-staining and fixation. These characteristics of OSSM-SEM allowed us to pair it with interferometric photoactivated localization microscopy (iPALM), a recent SRM technique that affords 10–20 nm isotropic spatial resolution on hydrated samples, for 3D CLEM imaging. We demonstrate a CLEM workflow generalizable to using other SRM strategies using mitochondria in human osteosarcoma (U2OS) cells as a model system, where immunostained TOM20, a marker for the mitochondrial outer membrane, was used for iPALM. Owing to the large scan area of OSSM-SEM, it is now possible to select as many FOVs as needed for iPALM and conveniently re-locate them in EM, this improving the imaging throughput. The significantly reduced dose of post-fixation also helped to better preserve the sample ultrastructures as evidenced by the excellent 3D registration between OSSM-SEM and iPALM images and by the accurate localization of TOM20 (by iPALM) to the peripheries of mitochondria (by OSSM-SEM). These advantages make OSSM-SEM an ideal modality for CLEM applications. As OSSM-SEM is still in development, we also discuss some of the remaining issues and the implications to biological imaging with SEM alone or with CLEM.
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21
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Le Bideau M, Wurtz N, Baudoin JP, La Scola B. Innovative Approach to Fast Electron Microscopy Using the Example of a Culture of Virus-Infected Cells: An Application to SARS-CoV-2. Microorganisms 2021; 9:microorganisms9061194. [PMID: 34073053 PMCID: PMC8228702 DOI: 10.3390/microorganisms9061194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/23/2022] Open
Abstract
Despite the development of new diagnostic methods, co-culture, based on sample inoculation of cell monolayers coupled with electron microscopy (EM) observation, remains the gold standard in virology. Indeed, co-culture allows for the study of cell morphology (infected and not infected), the ultrastructure of the inoculated virus, and the different steps of the virus infectious cycle. Most EM methods for studying virus cycles are applied after infected cells are produced in large quantities and detached to obtain a pellet. Here, cell culture was performed in sterilized, collagen-coated single-break strip wells. After one day in culture, cells were infected with SARS-CoV-2. Wells of interest were fixed at different time points, from 2 to 36 h post-infection. Microwave-assisted resin embedding was accomplished directly in the wells in 4 h. Finally, ultra-thin sections were cut directly through the infected-cell monolayers. Our methodology requires, in total, less than four days for preparing and observing cells. Furthermore, by observing undetached infected cell monolayers, we were able to observe new ultrastructural findings, such as cell–cell interactions and baso-apical cellular organization related to the virus infectious cycle. Our innovative methodology thus not only saves time for preparation but also adds precision and new knowledge about viral infection, as shown here for SARS-CoV-2.
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Affiliation(s)
- Marion Le Bideau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.L.B.); (N.W.)
| | - Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.L.B.); (N.W.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Jean-Pierre Baudoin
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.L.B.); (N.W.)
- Correspondence: (J.-P.B.); (B.L.S.)
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.L.B.); (N.W.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Correspondence: (J.-P.B.); (B.L.S.)
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22
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Lubojemska A, Stefana MI, Sorge S, Bailey AP, Lampe L, Yoshimura A, Burrell A, Collinson L, Gould AP. Adipose triglyceride lipase protects renal cell endocytosis in a Drosophila dietary model of chronic kidney disease. PLoS Biol 2021; 19:e3001230. [PMID: 33945525 PMCID: PMC8121332 DOI: 10.1371/journal.pbio.3001230] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 05/14/2021] [Accepted: 04/13/2021] [Indexed: 12/13/2022] Open
Abstract
Obesity-related renal lipotoxicity and chronic kidney disease (CKD) are prevalent pathologies with complex aetiologies. One hallmark of renal lipotoxicity is the ectopic accumulation of lipid droplets in kidney podocytes and in proximal tubule cells. Renal lipid droplets are observed in human CKD patients and in high-fat diet (HFD) rodent models, but their precise role remains unclear. Here, we establish a HFD model in Drosophila that recapitulates renal lipid droplets and several other aspects of mammalian CKD. Cell type-specific genetic manipulations show that lipid can overflow from adipose tissue and is taken up by renal cells called nephrocytes. A HFD drives nephrocyte lipid uptake via the multiligand receptor Cubilin (Cubn), leading to the ectopic accumulation of lipid droplets. These nephrocyte lipid droplets correlate with endoplasmic reticulum (ER) and mitochondrial deficits, as well as with impaired macromolecular endocytosis, a key conserved function of renal cells. Nephrocyte knockdown of diglyceride acyltransferase 1 (DGAT1), overexpression of adipose triglyceride lipase (ATGL), and epistasis tests together reveal that fatty acid flux through the lipid droplet triglyceride compartment protects the ER, mitochondria, and endocytosis of renal cells. Strikingly, boosting nephrocyte expression of the lipid droplet resident enzyme ATGL is sufficient to rescue HFD-induced defects in renal endocytosis. Moreover, endocytic rescue requires a conserved mitochondrial regulator, peroxisome proliferator-activated receptor-gamma coactivator 1α (PGC1α). This study demonstrates that lipid droplet lipolysis counteracts the harmful effects of a HFD via a mitochondrial pathway that protects renal endocytosis. It also provides a genetic strategy for determining whether lipid droplets in different biological contexts function primarily to release beneficial or to sequester toxic lipids.
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Affiliation(s)
- Aleksandra Lubojemska
- Physiology and Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - M. Irina Stefana
- Physiology and Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Sebastian Sorge
- Physiology and Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrew P. Bailey
- Physiology and Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Lena Lampe
- Physiology and Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Azumi Yoshimura
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Alana Burrell
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Alex P. Gould
- Physiology and Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
- * E-mail:
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23
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Tanner H, Hodgson L, Mantell J, Verkade P. Fluorescent platinum nanoclusters as correlative light electron microscopy probes. Methods Cell Biol 2021; 162:39-68. [PMID: 33707021 DOI: 10.1016/bs.mcb.2020.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Correlative Imaging (CI) visualizes a single sample/region of interest with two or more imaging modalities. The technique seeks to elucidate information that may not be discernible by using either of the constituent techniques in isolation. Correlative Light Electron Microscopy (CLEM) can be employed to streamline workflows, i.e., using fluorescent signals in the light microscope (LM) to inform the user of regions which should be imaged with electron microscopy (EM). The efficacy of correlative techniques requires high spatial resolution of signals from both imaging modalities. Ideally, a single point should originate from both the fluorescence and electron density. However, many of the ubiquitously used probes have a significant distance between their fluorescence and electron dense portions. Furthermore, electron dense metal nanoparticles used for EM visualization readily quench any proximal adjacent fluorophores. Therefore, accurate registration of both signals becomes difficult. Here we describe fluorescent nanoclusters in the context of a CLEM probe as they are composed of several atoms of a noble metal, in this case platinum, providing electron density. In addition, their structure confers them with fluorescence via a mechanism analogous to quantum dots. The electron dense core gives rise to the fluorescence which enables highly accurate signal registration between epifluorescence and electron imaging modalities. We provide a protocol for the synthesis of the nanoclusters with some additional techniques for their characterization and finally show how they can be used in a CLEM set up.
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Affiliation(s)
- Hugh Tanner
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, United Kingdom
| | - Lorna Hodgson
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, United Kingdom
| | - Judith Mantell
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, United Kingdom
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, United Kingdom.
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24
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Park AJ, Wright MA, Roach EJ, Khursigara CM. Imaging host-pathogen interactions using epithelial and bacterial cell infection models. J Cell Sci 2021; 134:134/5/jcs250647. [PMID: 33622798 DOI: 10.1242/jcs.250647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The age-old saying, seeing is believing, could not be truer when we think about the value of imaging interactions between epithelial cells and bacterial pathogens. Imaging and culturing techniques have vastly improved over the years, and the breadth and depth of these methods is ever increasing. These technical advances have benefited researchers greatly; however, due to the large number of potential model systems and microscopy techniques to choose from, it can be overwhelming to select the most appropriate tools for your research question. This Review discusses a variety of available epithelial culturing methods and quality control experiments that can be performed, and outlines various options commonly used to fluorescently label bacterial and mammalian cell components. Both light- and electron-microscopy techniques are reviewed, with descriptions of both technical aspects and common applications. Several examples of imaging bacterial pathogens and their interactions with epithelial cells are discussed to provide researchers with an idea of the types of biological questions that can be successfully answered by using microscopy.
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Affiliation(s)
- Amber J Park
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Madison A Wright
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Elyse J Roach
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.,Molecular and Cellular Imaging Facility, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada .,Molecular and Cellular Imaging Facility, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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25
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Kabakov AY, Sengun E, Lu Y, Roder K, Bronk P, Baggett B, Turan NN, Moshal KS, Koren G. Three-Week-Old Rabbit Ventricular Cardiomyocytes as a Novel System to Study Cardiac Excitation and EC Coupling. Front Physiol 2021; 12:672360. [PMID: 34867432 PMCID: PMC8637404 DOI: 10.3389/fphys.2021.672360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/06/2021] [Indexed: 01/14/2023] Open
Abstract
Cardiac arrhythmias significantly contribute to cardiovascular morbidity and mortality. The rabbit heart serves as an accepted model system for studying cardiac cell excitation and arrhythmogenicity. Accordingly, primary cultures of adult rabbit ventricular cardiomyocytes serve as a preferable model to study molecular mechanisms of human cardiac excitation. However, the use of adult rabbit cardiomyocytes is often regarded as excessively costly. Therefore, we developed and characterized a novel low-cost rabbit cardiomyocyte model, namely, 3-week-old ventricular cardiomyocytes (3wRbCMs). Ventricular myocytes were isolated from whole ventricles of 3-week-old New Zealand White rabbits of both sexes by standard enzymatic techniques. Using wheat germ agglutinin, we found a clear T-tubule structure in acutely isolated 3wRbCMs. Cells were adenovirally infected (multiplicity of infection of 10) to express Green Fluorescent Protein (GFP) and cultured for 48 h. The cells showed action potential duration (APD90 = 253 ± 24 ms) and calcium transients similar to adult rabbit cardiomyocytes. Freshly isolated and 48-h-old-cultured cells expressed critical ion channel proteins: calcium voltage-gated channel subunit alpha1 C (Cavα1c), sodium voltage-gated channel alpha subunit 5 (Nav1.5), potassium voltage-gated channel subfamily D member 3 (Kv4.3), and subfamily A member 4 (Kv1.4), and also subfamily H member 2 (RERG. Kv11.1), KvLQT1 (K7.1) protein and inward-rectifier potassium channel (Kir2.1). The cells displayed an appropriate electrophysiological phenotype, including fast sodium current (I Na), transient outward potassium current (I to), L-type calcium channel peak current (I Ca,L), rapid and slow components of the delayed rectifier potassium current (I Kr and I Ks), and inward rectifier (I K1). Although expression of the channel proteins and some currents decreased during the 48 h of culturing, we conclude that 3wRbCMs are a new, low-cost alternative to the adult-rabbit-cardiomyocytes system, which allows the investigation of molecular mechanisms of cardiac excitation on morphological, biochemical, genetic, physiological, and biophysical levels.
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Affiliation(s)
- Anatoli Y Kabakov
- Department of Medicine, Division of Cardiology, Cardiovascular Research Center, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Elif Sengun
- Department of Medicine, Division of Cardiology, Cardiovascular Research Center, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, RI, United States.,Department of Pharmacology, Institute of Graduate Studies in Health Sciences, Istanbul University, Istanbul, Türkiye
| | - Yichun Lu
- Department of Medicine, Division of Cardiology, Cardiovascular Research Center, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Karim Roder
- Department of Medicine, Division of Cardiology, Cardiovascular Research Center, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Peter Bronk
- Department of Medicine, Division of Cardiology, Cardiovascular Research Center, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Brett Baggett
- Department of Medicine, Division of Cardiology, Cardiovascular Research Center, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Nilüfer N Turan
- Department of Medicine, Division of Cardiology, Cardiovascular Research Center, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Karni S Moshal
- Department of Medicine, Division of Cardiology, Cardiovascular Research Center, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Gideon Koren
- Department of Medicine, Division of Cardiology, Cardiovascular Research Center, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, RI, United States
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26
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Prabhakar N, Belevich I, Peurla M, Heiligenstein X, Chang HC, Sahlgren C, Jokitalo E, Rosenholm JM. Cell Volume (3D) Correlative Microscopy Facilitated by Intracellular Fluorescent Nanodiamonds as Multi-Modal Probes. NANOMATERIALS 2020; 11:nano11010014. [PMID: 33374705 PMCID: PMC7822478 DOI: 10.3390/nano11010014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 02/05/2023]
Abstract
Three-dimensional correlative light and electron microscopy (3D CLEM) is attaining popularity as a potential technique to explore the functional aspects of a cell together with high-resolution ultrastructural details across the cell volume. To perform such a 3D CLEM experiment, there is an imperative requirement for multi-modal probes that are both fluorescent and electron-dense. These multi-modal probes will serve as landmarks in matching up the large full cell volume datasets acquired by different imaging modalities. Fluorescent nanodiamonds (FNDs) are a unique nanosized, fluorescent, and electron-dense material from the nanocarbon family. We hereby propose a novel and straightforward method for executing 3D CLEM using FNDs as multi-modal landmarks. We demonstrate that FND is biocompatible and is easily identified both in living cell fluorescence imaging and in serial block-face scanning electron microscopy (SB-EM). We illustrate the method by registering multi-modal datasets.
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Affiliation(s)
- Neeraj Prabhakar
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- Correspondence:
| | - Ilya Belevich
- Electron Microscopy Unit, Helsinki Institute of Life Science—Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland; (I.B.); (E.J.)
| | - Markus Peurla
- Institute of Biomedicine, Faculty of Medicine, University of Turku, 20520 Turku, Finland;
- Cancer Research Laboratory FICAN West, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | | | - Huan-Cheng Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan;
| | - Cecilia Sahlgren
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
| | - Eija Jokitalo
- Electron Microscopy Unit, Helsinki Institute of Life Science—Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland; (I.B.); (E.J.)
| | - Jessica M. Rosenholm
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
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27
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Prabhakar N, Peurla M, Shenderova O, Rosenholm JM. Fluorescent and Electron-Dense Green Color Emitting Nanodiamonds for Single-Cell Correlative Microscopy. Molecules 2020; 25:E5897. [PMID: 33322105 PMCID: PMC7764487 DOI: 10.3390/molecules25245897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/07/2020] [Accepted: 12/12/2020] [Indexed: 02/07/2023] Open
Abstract
Correlative light and electron microscopy (CLEM) is revolutionizing how cell samples are studied. CLEM provides a combination of the molecular and ultrastructural information about a cell. For the execution of CLEM experiments, multimodal fiducial landmarks are applied to precisely overlay light and electron microscopy images. Currently applied fiducials such as quantum dots and organic dye-labeled nanoparticles can be irreversibly quenched by electron beam exposure during electron microscopy. Generally, the sample is therefore investigated with a light microscope first and later with an electron microscope. A versatile fiducial landmark should offer to switch back from electron microscopy to light microscopy while preserving its fluorescent properties. Here, we evaluated green fluorescent and electron dense nanodiamonds for the execution of CLEM experiments and precisely correlated light microscopy and electron microscopy images. We demonstrated that green color emitting fluorescent nanodiamonds withstand electron beam exposure, harsh chemical treatments, heavy metal straining, and, importantly, their fluorescent properties remained intact for light microscopy.
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Affiliation(s)
- Neeraj Prabhakar
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
| | - Markus Peurla
- Institute of Biomedicine, Faculty of Medicine, University of Turku, 20520 Turku, Finland;
- Cancer Research Laboratory FICAN West, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Olga Shenderova
- Adámas Nanotechnologies, Inc., 8100 Brownleigh Drive, Suite 120, Raleigh, NC 27617, USA;
| | - Jessica M. Rosenholm
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
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28
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Collins CR, Hackett F, Howell SA, Snijders AP, Russell MRG, Collinson LM, Blackman MJ. The malaria parasite sheddase SUB2 governs host red blood cell membrane sealing at invasion. eLife 2020; 9:e61121. [PMID: 33287958 PMCID: PMC7723409 DOI: 10.7554/elife.61121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/26/2020] [Indexed: 12/26/2022] Open
Abstract
Red blood cell (RBC) invasion by malaria merozoites involves formation of a parasitophorous vacuole into which the parasite moves. The vacuole membrane seals and pinches off behind the parasite through an unknown mechanism, enclosing the parasite within the RBC. During invasion, several parasite surface proteins are shed by a membrane-bound protease called SUB2. Here we show that genetic depletion of SUB2 abolishes shedding of a range of parasite proteins, identifying previously unrecognized SUB2 substrates. Interaction of SUB2-null merozoites with RBCs leads to either abortive invasion with rapid RBC lysis, or successful entry but developmental arrest. Selective failure to shed the most abundant SUB2 substrate, MSP1, reduces intracellular replication, whilst conditional ablation of the substrate AMA1 produces host RBC lysis. We conclude that SUB2 activity is critical for host RBC membrane sealing following parasite internalisation and for correct functioning of merozoite surface proteins.
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Affiliation(s)
- Christine R Collins
- Malaria Biochemistry Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Fiona Hackett
- Malaria Biochemistry Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Steven A Howell
- Protein Analysis and Proteomics Platform, The Francis Crick InstituteLondonUnited Kingdom
| | - Ambrosius P Snijders
- Protein Analysis and Proteomics Platform, The Francis Crick InstituteLondonUnited Kingdom
| | - Matthew RG Russell
- Electron Microscopy Science Technology Platform, The Francis Crick InstituteLondonUnited Kingdom
| | - Lucy M Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick InstituteLondonUnited Kingdom
| | - Michael J Blackman
- Malaria Biochemistry Laboratory, The Francis Crick InstituteLondonUnited Kingdom
- Faculty of Infectious Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
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29
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Bakkum T, Heemskerk MT, Bos E, Groenewold M, Oikonomeas-Koppasis N, Walburg KV, van Veen S, van der Lienden MJC, van Leeuwen T, Haks MC, Ottenhoff THM, Koster AJ, van Kasteren SI. Bioorthogonal Correlative Light-Electron Microscopy of Mycobacterium tuberculosis in Macrophages Reveals the Effect of Antituberculosis Drugs on Subcellular Bacterial Distribution. ACS CENTRAL SCIENCE 2020; 6:1997-2007. [PMID: 33274277 PMCID: PMC7706097 DOI: 10.1021/acscentsci.0c00539] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Indexed: 05/07/2023]
Abstract
Bioorthogonal correlative light-electron microscopy (B-CLEM) can give a detailed overview of multicomponent biological systems. It can provide information on the ultrastructural context of bioorthogonal handles and other fluorescent signals, as well as information about subcellular organization. We have here applied B-CLEM to the study of the intracellular pathogen Mycobacterium tuberculosis (Mtb) by generating a triply labeled Mtb through combined metabolic labeling of the cell wall and the proteome of a DsRed-expressing Mtb strain. Study of this pathogen in a B-CLEM setting was used to provide information about the intracellular distribution of the pathogen, as well as its in situ response to various clinical antibiotics, supported by flow cytometric analysis of the bacteria, after recovery from the host cell (ex cellula). The RNA polymerase-targeting drug rifampicin displayed the most prominent effect on subcellular distribution, suggesting the most direct effect on pathogenicity and/or viability, while the cell wall synthesis-targeting drugs isoniazid and ethambutol effectively rescued bacterial division-induced loss of metabolic labels. The three drugs combined did not give a more pronounced effect but rather an intermediate response, whereas gentamicin displayed a surprisingly strong additive effect on subcellular distribution.
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Affiliation(s)
- Thomas Bakkum
- Leiden
Institute of Chemistry and The Institute of Chemical Immunology, Leiden University, Einsteinweg 55, Leiden 2300 RA, The Netherlands
| | - Matthias T. Heemskerk
- Department
of Infectious Diseases, Leiden University
Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Erik Bos
- Department
of Cell and Chemical Biology, Leiden University
Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Mirjam Groenewold
- Leiden
Institute of Chemistry and The Institute of Chemical Immunology, Leiden University, Einsteinweg 55, Leiden 2300 RA, The Netherlands
| | - Nikolaos Oikonomeas-Koppasis
- Leiden
Institute of Chemistry and The Institute of Chemical Immunology, Leiden University, Einsteinweg 55, Leiden 2300 RA, The Netherlands
| | - Kimberley V. Walburg
- Department
of Infectious Diseases, Leiden University
Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Suzanne van Veen
- Department
of Infectious Diseases, Leiden University
Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Martijn J. C. van der Lienden
- Leiden
Institute of Chemistry and The Institute of Chemical Immunology, Leiden University, Einsteinweg 55, Leiden 2300 RA, The Netherlands
| | - Tyrza van Leeuwen
- Leiden
Institute of Chemistry and The Institute of Chemical Immunology, Leiden University, Einsteinweg 55, Leiden 2300 RA, The Netherlands
| | - Marielle C. Haks
- Department
of Infectious Diseases, Leiden University
Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Tom H. M. Ottenhoff
- Department
of Infectious Diseases, Leiden University
Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Abraham J. Koster
- Department
of Cell and Chemical Biology, Leiden University
Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Sander I. van Kasteren
- Leiden
Institute of Chemistry and The Institute of Chemical Immunology, Leiden University, Einsteinweg 55, Leiden 2300 RA, The Netherlands
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30
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Weiner A. Step-by-step guide to post-acquisition correlation of confocal and FIB/SEM volumes using Amira software. Methods Cell Biol 2020; 162:333-351. [PMID: 33707018 DOI: 10.1016/bs.mcb.2020.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In recent years new methodologies and workflow pipelines for acquiring correlated fluorescence microscopy and volume electron microscopy datasets have been extensively described and made accessible to users of different levels. Post-acquisition image processing, and particularly correlation of the optical and electron data in a single integrated three-dimensional framework can be key for extracting valuable information, especially when imaging large sample volumes such as whole cells or tissues. These tasks remain challenging and are often rate-limiting to most users. Here we provide a step-by-step guide to image processing and manual correlation using ImageJ and Amira software of a confocal microscopy stack and a focused ion beam/scanning electron microscopy (FIB/SEM) tomogram acquired using a correlative pipeline. These previously published datasets capture a highly transient invasion event by the bacterium Shigella flexneri infecting an epithelial cell grown in culture, and are made available here in their pre-processed form for readers who wish to gain hands-on experience in image processing and correlation using existing data. In this guide we describe a simple protocol for correlation based on internal sample features clearly visible by both fluorescence and electron microscopy, which is normally sufficient when correlating standard fluorescence microscopy stacks with FIB/SEM data. While the guide describes the treatment of specific datasets, it is applicable to a wide variety of samples and different microscopy approaches that require basic correlation and visualization of two or more datasets in a single integrated framework.
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Affiliation(s)
- Allon Weiner
- Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, Inserm, Sorbonne Université, Paris, France.
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31
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Kremer A, VAN Hamme E, Bonnardel J, Borghgraef P, GuÉrin CJ, Guilliams M, Lippens S. A workflow for 3D-CLEM investigating liver tissue. J Microsc 2020; 281:231-242. [PMID: 33034376 DOI: 10.1111/jmi.12967] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/22/2020] [Accepted: 10/07/2020] [Indexed: 12/31/2022]
Abstract
Correlative light and electron microscopy (CLEM) is a method used to investigate the exact same region in both light and electron microscopy (EM) in order to add ultrastructural information to a light microscopic (usually fluorescent) signal. Workflows combining optical or fluorescent data with electron microscopic images are complex, hence there is a need to communicate detailed protocols and share tips & tricks for successful application of these methods. With the development of volume-EM techniques such as serial blockface scanning electron microscopy (SBF-SEM) and Focussed Ion Beam-SEM, correlation in three dimensions has become more efficient. Volume electron microscopy allows automated acquisition of serial section imaging data that can be reconstructed in three dimensions (3D) to provide a detailed, geometrically accurate view of cellular ultrastructure. In addition, combining volume-EM with high-resolution light microscopy (LM) techniques decreases the resolution gap between LM and EM, making retracing of a region of interest and eventual overlays more straightforward. Here, we present a workflow for 3D CLEM on mouse liver, combining high-resolution confocal microscopy with SBF-SEM. In this workflow, we have made use of two types of landmarks: (1) near infrared laser branding marks to find back the region imaged in LM in the electron microscope and (2) landmarks present in the tissue but independent of the cell or structure of interest to make overlay images of LM and EM data. Using this approach, we were able to make accurate 3D-CLEM overlays of liver tissue and correlate the fluorescent signal to the ultrastructural detail provided by the electron microscope. This workflow can be adapted for other dense cellular tissues and thus act as a guide for other three-dimensional correlative studies. LAY DESCRIPTION: As cells and tissues exist in three dimensions, microscopy techniques have been developed to image samples, in 3D, at the highest possible detail. In light microscopy, fluorescent probes are used to identify specific proteins or structures either in live samples, (providing dynamic information), or in fixed slices of tissue. A disadvantage of fluorescence microscopy is that only the labeled proteins/structures are visible, while their cellular context remains hidden. Electron microscopy is able to image biological samples at high resolution and has the advantage that all structures in the tissue are visible at nanometer (10-9 m) resolution. Disadvantages of this technique are that it is more difficult to label a single structure and that the samples must be imaged under high vacuum, so biological samples need to be fixed and embedded in a plastic resin to stay as close to their natural state as possible inside the microscope. Correlative Light and Electron Microscopy aims to combine the advantages of both light and electron microscopy on the same sample. This results in datasets where fluorescent labels can be combined with the high-resolution contextual information provided by the electron microscope. In this study we present a workflow to guide a tissue sample from the light microscope to the electron microscope and image the ultra-structure of a specific cell type in the liver. In particular we focus on the incorporation of fiducial markers during the sample preparation to help navigate through the tissue in 3D in both microscopes. One sample is followed throughout the workflow to visualize the important steps in the process, showing the final result; a dataset combining fluorescent labels with ultra-structural detail.
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Affiliation(s)
- A Kremer
- VIB BioImaging Core, Technologiepark 71, Ghent, 9052, Belgium.,VIB Center for Inflammation Research, Technologiepark 71, Ghent, 9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
| | - E VAN Hamme
- VIB BioImaging Core, Technologiepark 71, Ghent, 9052, Belgium.,VIB Center for Inflammation Research, Technologiepark 71, Ghent, 9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
| | - J Bonnardel
- VIB BioImaging Core, Technologiepark 71, Ghent, 9052, Belgium.,VIB Center for Inflammation Research, Technologiepark 71, Ghent, 9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
| | - P Borghgraef
- VIB BioImaging Core, Technologiepark 71, Ghent, 9052, Belgium.,VIB Center for Inflammation Research, Technologiepark 71, Ghent, 9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
| | - C J GuÉrin
- VIB BioImaging Core, Technologiepark 71, Ghent, 9052, Belgium.,VIB Center for Inflammation Research, Technologiepark 71, Ghent, 9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
| | - M Guilliams
- VIB BioImaging Core, Technologiepark 71, Ghent, 9052, Belgium.,VIB Center for Inflammation Research, Technologiepark 71, Ghent, 9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
| | - S Lippens
- VIB BioImaging Core, Technologiepark 71, Ghent, 9052, Belgium.,VIB Center for Inflammation Research, Technologiepark 71, Ghent, 9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
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32
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McCallum S, Obata Y, Fourli E, Boeing S, Peddie CJ, Xu Q, Horswell S, Kelsh RN, Collinson L, Wilkinson D, Pin C, Pachnis V, Heanue TA. Enteric glia as a source of neural progenitors in adult zebrafish. eLife 2020; 9:e56086. [PMID: 32851974 PMCID: PMC7521928 DOI: 10.7554/elife.56086] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 08/26/2020] [Indexed: 12/23/2022] Open
Abstract
The presence and identity of neural progenitors in the enteric nervous system (ENS) of vertebrates is a matter of intense debate. Here, we demonstrate that the non-neuronal ENS cell compartment of teleosts shares molecular and morphological characteristics with mammalian enteric glia but cannot be identified by the expression of canonical glial markers. However, unlike their mammalian counterparts, which are generally quiescent and do not undergo neuronal differentiation during homeostasis, we show that a relatively high proportion of zebrafish enteric glia proliferate under physiological conditions giving rise to progeny that differentiate into enteric neurons. We also provide evidence that, similar to brain neural stem cells, the activation and neuronal differentiation of enteric glia are regulated by Notch signalling. Our experiments reveal remarkable similarities between enteric glia and brain neural stem cells in teleosts and open new possibilities for use of mammalian enteric glia as a potential source of neurons to restore the activity of intestinal neural circuits compromised by injury or disease.
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Affiliation(s)
- Sarah McCallum
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Yuuki Obata
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Evangelia Fourli
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Stefan Boeing
- Bionformatics & Biostatistics Science Technology Platform, The Francis Crick InstituteLondonUnited Kingdom
| | - Christopher J Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick InstituteLondonUnited Kingdom
| | - Qiling Xu
- Neural Development Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Stuart Horswell
- Bionformatics & Biostatistics Science Technology Platform, The Francis Crick InstituteLondonUnited Kingdom
| | - Robert N Kelsh
- Department of Biology and Biochemistry, University of BathBathUnited Kingdom
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick InstituteLondonUnited Kingdom
| | - David Wilkinson
- Neural Development Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Carmen Pin
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZenecaCambridgeUnited Kingdom
| | - Vassilis Pachnis
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Tiffany A Heanue
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick InstituteLondonUnited Kingdom
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33
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Keevend K, Coenen T, Herrmann IK. Correlative cathodoluminescence electron microscopy bioimaging: towards single protein labelling with ultrastructural context. NANOSCALE 2020; 12:15588-15603. [PMID: 32677648 DOI: 10.1039/d0nr02563a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The understanding of living systems and their building blocks relies heavily on the assessment of structure-function relationships at the nanoscale. Ever since the development of the first optical microscope, the reliance of scientists across disciplines on microscopy has increased. The development of the first electron microscope and with it the access to information at the nanoscale has prompted numerous disruptive discoveries. While fluorescence imaging allows identification of specific entities based on the labelling with fluorophores, the unlabelled constituents of the samples remain invisible. In electron microscopy on the other hand, structures can be comprehensively visualized based on their distinct electron density and geometry. Although electron microscopy is a powerful tool, it does not implicitly provide information on the location and activity of specific organic molecules. While correlative light and electron microscopy techniques have attempted to unify the two modalities, the resolution mismatch between the two data sets poses major challenges. Recent developments in optical super resolution microscopy enable high resolution correlative light and electron microscopy, however, with considerable constraints due to sample preparation requirements. Labelling of specific structures directly for electron microscopy using small gold nanoparticles (i.e. immunogold) has been used extensively. However, identification of specific entities solely based on electron contrast, and the differentiation from endogenous dense granules, remains challenging. Recently, the use of correlative cathodoluminescence electron microscopy (CCLEM) imaging based on luminescent inorganic nanocrystals has been proposed. While nanometric resolution can be reached for both the electron and the optical signal, high energy electron beams are potentially damaging to the sample. In this review, we discuss the opportunities of (volumetric) multi-color single protein labelling based on correlative cathodoluminescence electron microscopy, and its prospective impact on biomedical research in general. We elaborate on the potential challenges of correlative cathodoluminescence electron microscopy-based bioimaging and benchmark CCLEM against alternative high-resolution correlative imaging techniques.
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Affiliation(s)
- Kerda Keevend
- Laboratory for Particles Biology Interactions, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, CH-9014, St Gallen, Switzerland.
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34
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Lerner TR, Queval CJ, Lai RP, Russell MR, Fearns A, Greenwood DJ, Collinson L, Wilkinson RJ, Gutierrez MG. Mycobacterium tuberculosis cords within lymphatic endothelial cells to evade host immunity. JCI Insight 2020; 5:136937. [PMID: 32369443 PMCID: PMC7259532 DOI: 10.1172/jci.insight.136937] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/15/2020] [Indexed: 01/18/2023] Open
Abstract
The ability of Mycobacterium tuberculosis to form serpentine cords is intrinsically related to its virulence, but specifically how M. tuberculosis cording contributes to pathogenesis remains obscure. Here, we show that several M. tuberculosis clinical isolates form intracellular cords in primary human lymphatic endothelial cells (hLECs) in vitro and in the lymph nodes of patients with tuberculosis. We identified via RNA-Seq a transcriptional program that activated, in infected-hLECs, cell survival and cytosolic surveillance of pathogens pathways. Consistent with this, cytosolic access was required for intracellular M. tuberculosis cording. Mycobacteria lacking ESX-1 type VII secretion system or phthiocerol dimycocerosates expression, which failed to access the cytosol, were indeed unable to form cords within hLECs. Finally, we show that M. tuberculosis cording is a size-dependent mechanism used by the pathogen to avoid its recognition by cytosolic sensors and evade either resting or IFN-γ-induced hLEC immunity. These results explain the long-standing association between M. tuberculosis cording and virulence and how virulent mycobacteria use intracellular cording as strategy to successfully adapt and persist in the lymphatic tracts.
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Affiliation(s)
| | | | | | - Matthew R.G. Russell
- Electron Microscopy Scientific Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Antony Fearns
- Host-pathogen interactions in tuberculosis laboratory
| | | | - Lucy Collinson
- Electron Microscopy Scientific Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Robert J. Wilkinson
- Tuberculosis laboratory, and,Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, Cape Town, Republic of South Africa.,Department of Medicine, Imperial College London, London, United Kingdom
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35
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Godel-Jedrychowska K, Kulinska-Lukaszek K, Horstman A, Soriano M, Li M, Malota K, Boutilier K, Kurczynska EU. Symplasmic isolation marks cell fate changes during somatic embryogenesis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2612-2628. [PMID: 31974549 PMCID: PMC7210756 DOI: 10.1093/jxb/eraa041] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/22/2020] [Indexed: 05/05/2023]
Abstract
Cell-to-cell signalling is a major mechanism controlling plant morphogenesis. Transport of signalling molecules through plasmodesmata is one way in which plants promote or restrict intercellular signalling over short distances. Plasmodesmata are membrane-lined pores between cells that regulate the intercellular flow of signalling molecules through changes in their size, creating symplasmic fields of connected cells. Here we examine the role of plasmodesmata and symplasmic communication in the establishment of plant cell totipotency, using somatic embryo induction from Arabidopsis explants as a model system. Cell-to-cell communication was evaluated using fluorescent tracers, supplemented with histological and ultrastructural analysis, and correlated with expression of a WOX2 embryo reporter. We showed that embryogenic cells are isolated symplasmically from non-embryogenic cells regardless of the explant type (immature zygotic embryos or seedlings) and inducer system (2,4-dichlorophenoxyacetic acid or the BABY BOOM (BBM) transcription factor), but that the symplasmic domains in different explants differ with respect to the maximum size of molecule capable of moving through the plasmodesmata. Callose deposition in plasmodesmata preceded WOX2 expression in future sites of somatic embryo development, but later was greatly reduced in WOX2-expressing domains. Callose deposition was also associated with a decrease DR5 auxin response in embryogenic tissue. Treatment of explants with the callose biosynthesis inhibitor 2-deoxy-D-glucose supressed somatic embryo formation in all three systems studied, and also blocked the observed decrease in DR5 expression. Together these data suggest that callose deposition at plasmodesmata is required for symplasmic isolation and establishment of cell totipotency in Arabidopsis.
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Affiliation(s)
- Kamila Godel-Jedrychowska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Katarzyna Kulinska-Lukaszek
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Anneke Horstman
- Bioscience, Wageningen University and Research, AA Wageningen, Netherlands
- Laboratory of Molecular Biology, Wageningen University and Research, AA Wageningen, Netherlands
| | - Mercedes Soriano
- Bioscience, Wageningen University and Research, AA Wageningen, Netherlands
| | - Mengfan Li
- Bioscience, Wageningen University and Research, AA Wageningen, Netherlands
- Laboratory of Molecular Biology, Wageningen University and Research, AA Wageningen, Netherlands
| | - Karol Malota
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in KatowiceKatowice, Poland
| | - Kim Boutilier
- Bioscience, Wageningen University and Research, AA Wageningen, Netherlands
| | - Ewa U Kurczynska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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36
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ER-to-Golgi Transport: A Sizeable Problem. Trends Cell Biol 2019; 29:940-953. [DOI: 10.1016/j.tcb.2019.08.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 11/16/2022]
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37
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Pape C, Matskevych A, Wolny A, Hennies J, Mizzon G, Louveaux M, Musser J, Maizel A, Arendt D, Kreshuk A. Leveraging Domain Knowledge to Improve Microscopy Image Segmentation With Lifted Multicuts. FRONTIERS IN COMPUTER SCIENCE 2019. [DOI: 10.3389/fcomp.2019.00006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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38
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Hunt A, Russell MRG, Wagener J, Kent R, Carmeille R, Peddie CJ, Collinson L, Heaslip A, Ward GE, Treeck M. Differential requirements for cyclase-associated protein (CAP) in actin-dependent processes of Toxoplasma gondii. eLife 2019; 8:e50598. [PMID: 31577230 PMCID: PMC6785269 DOI: 10.7554/elife.50598] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/26/2019] [Indexed: 12/26/2022] Open
Abstract
Toxoplasma gondii contains a limited subset of actin binding proteins. Here we show that the putative actin regulator cyclase-associated protein (CAP) is present in two different isoforms and its deletion leads to significant defects in some but not all actin dependent processes. We observe defects in cell-cell communication, daughter cell orientation and the juxtanuclear accumulation of actin, but only modest defects in synchronicity of division and no defect in the replication of the apicoplast. 3D electron microscopy reveals that loss of CAP results in a defect in formation of a normal central residual body, but parasites remain connected within the vacuole. This dissociates synchronicity of division and parasite rosetting and reveals that establishment and maintenance of the residual body may be more complex than previously thought. These results highlight the different spatial requirements for F-actin regulation in Toxoplasma which appear to be achieved by partially overlapping functions of actin regulators.
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Affiliation(s)
- Alex Hunt
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | | | - Jeanette Wagener
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Robyn Kent
- Department of Microbiology and Molecular GeneticsUniversity of Vermont Larner College of MedicineBurlingtonUnited States
| | - Romain Carmeille
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsUnited States
| | - Christopher J Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick InstituteLondonUnited Kingdom
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick InstituteLondonUnited Kingdom
| | - Aoife Heaslip
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsUnited States
| | - Gary E Ward
- Department of Microbiology and Molecular GeneticsUniversity of Vermont Larner College of MedicineBurlingtonUnited States
| | - Moritz Treeck
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick InstituteLondonUnited Kingdom
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39
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Ulloa G, Hamati F, Dick A, Fitzgerald J, Mantell J, Verkade P, Collinson L, Arkill K, Larijani B, Poccia D. Lipid species affect morphology of endoplasmic reticulum: a sea urchin oocyte model of reversible manipulation. J Lipid Res 2019; 60:1880-1891. [PMID: 31548365 PMCID: PMC6824487 DOI: 10.1194/jlr.ra119000210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/11/2019] [Indexed: 12/22/2022] Open
Abstract
The ER is a large multifunctional organelle of eukaryotic cells. Malfunction of the ER in various disease states, such as atherosclerosis, diabetes, cancer, Alzheimer’s and Parkinson’s and amyotrophic lateral sclerosis, often correlates with alterations in its morphology. The ER exhibits regionally variable membrane morphology that includes, at the extremes, large relatively flat surfaces and interconnected tubular structures highly curved in cross-section. ER morphology is controlled by shaping proteins that associate with membrane lipids. To investigate the role of these lipids, we developed a sea urchin oocyte model, a relatively quiescent cell in which the ER consists mostly of tubules. We altered levels of endogenous diacylglycerol (DAG), phosphatidylethanolamine (PtdEth), and phosphatidylcholine by microinjection of enzymes or lipid delivery by liposomes and evaluated shape changes with 2D and 3D confocal imaging and 3D electron microscopy. Decreases and increases in the levels of lipids such as DAG or PtdEth characterized by negative spontaneous curvature correlated with conversion to sheet structures or tubules, respectively. The effects of endogenous alterations of DAG were reversible upon exogenous delivery of lipids of negative spontaneous curvature. These data suggest that proteins require threshold amounts of such lipids and that localized deficiencies of the lipids could contribute to alterations of ER morphology. The oocyte modeling system should be beneficial to studies directed at understanding requirements of lipid species in interactions leading to alterations of organelle shaping.
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Affiliation(s)
| | - Fadi Hamati
- Department of Biology, Amherst College, Amherst, MA
| | | | | | - Judith Mantell
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | | | - Kenton Arkill
- School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham Medical School, Nottingham, United Kingdom
| | - Banafshe Larijani
- Centre for Therapeutic Innovation, Cell Biophysics Laboratory, Department of Pharmacy and Pharmacology and Department of Physics, University of Bath, Claverton Down, Bath, United Kingdom, and Cell Biophysics Laboratory, Ikerbasque, Basque Foundation for Science, Research Centre for Experimental Marine Biology and Biotechnology (PiE) and Biophysics Institute (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain
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40
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Taraska JW. A primer on resolving the nanoscale structure of the plasma membrane with light and electron microscopy. J Gen Physiol 2019; 151:974-985. [PMID: 31253697 PMCID: PMC6683668 DOI: 10.1085/jgp.201812227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Taraska reviews the imaging methods that are being used to understand the structure of the plasma membrane at the molecular level. The plasma membrane separates a cell from its external environment. All materials and signals that enter or leave the cell must cross this hydrophobic barrier. Understanding the architecture and dynamics of the plasma membrane has been a central focus of general cellular physiology. Both light and electron microscopy have been fundamental in this endeavor and have been used to reveal the dense, complex, and dynamic nanoscale landscape of the plasma membrane. Here, I review classic and recent developments in the methods used to image and study the structure of the plasma membrane, particularly light, electron, and correlative microscopies. I will discuss their history and use for mapping the plasma membrane and focus on how these tools have provided a structural framework for understanding the membrane at the scale of molecules. Finally, I will describe how these studies provide a roadmap for determining the nanoscale architecture of other organelles and entire cells in order to bridge the gap between cellular form and function.
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Affiliation(s)
- Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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41
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Greenwood DJ, Dos Santos MS, Huang S, Russell MRG, Collinson LM, MacRae JI, West A, Jiang H, Gutierrez MG. Subcellular antibiotic visualization reveals a dynamic drug reservoir in infected macrophages. Science 2019; 364:1279-1282. [PMID: 31249058 DOI: 10.1126/science.aat9689] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 02/20/2019] [Accepted: 05/13/2019] [Indexed: 12/29/2022]
Abstract
Tuberculosis, caused by the intracellular pathogen Mycobacterium tuberculosis, remains the world's deadliest infectious disease. Sterilizing chemotherapy requires at least 6 months of multidrug therapy. Difficulty visualizing the subcellular localization of antibiotics in infected host cells means that it is unclear whether antibiotics penetrate all mycobacteria-containing compartments in the cell. Here, we combined correlated light, electron, and ion microscopy to image the distribution of bedaquiline in infected human macrophages at submicrometer resolution. Bedaquiline accumulated primarily in host cell lipid droplets, but heterogeneously in mycobacteria within a variety of intracellular compartments. Furthermore, lipid droplets did not sequester antibiotic but constituted a transferable reservoir that enhanced antibacterial efficacy. Thus, strong lipid binding facilitated drug trafficking by host organelles to an intracellular target during antimicrobial treatment.
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Affiliation(s)
| | | | - Song Huang
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth, Australia
| | | | | | | | | | - Haibo Jiang
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth, Australia. .,School of Molecular Sciences, University of Western Australia, Perth, Australia
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42
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Melia CE, Peddie CJ, de Jong AWM, Snijder EJ, Collinson LM, Koster AJ, van der Schaar HM, van Kuppeveld FJM, Bárcena M. Origins of Enterovirus Replication Organelles Established by Whole-Cell Electron Microscopy. mBio 2019; 10:e00951-19. [PMID: 31186324 PMCID: PMC6561026 DOI: 10.1128/mbio.00951-19] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/06/2019] [Indexed: 11/24/2022] Open
Abstract
Enterovirus genome replication occurs at virus-induced structures derived from cellular membranes and lipids. However, the origin of these replication organelles (ROs) remains uncertain. Ultrastructural evidence of the membrane donor is lacking, suggesting that the sites of its transition into ROs are rare or fleeting. To overcome this challenge, we combined live-cell imaging and serial block-face scanning electron microscopy of whole cells to capture emerging enterovirus ROs. The first foci of fluorescently labeled viral protein correlated with ROs connected to the endoplasmic reticulum (ER) and preceded the appearance of ROs stemming from the trans-Golgi network. Whole-cell data sets further revealed striking contact regions between ROs and lipid droplets that may represent a route for lipid shuttling to facilitate RO proliferation and genome replication. Our data provide direct evidence that enteroviruses use ER and then Golgi membranes to initiate RO formation, demonstrating the remarkable flexibility with which enteroviruses usurp cellular organelles.IMPORTANCE Enteroviruses are causative agents of a range of human diseases. The replication of these viruses within cells relies on specialized membranous structures termed replication organelles (ROs) that form during infection but whose origin remains elusive. To capture the emergence of enterovirus ROs, we use correlative light and serial block-face scanning electron microscopy, a powerful method to pinpoint rare events in their whole-cell ultrastructural context. RO biogenesis was found to occur first at ER and then at Golgi membranes. Extensive contacts were found between early ROs and lipid droplets (LDs), which likely serve to provide LD-derived lipids required for replication. Together, these data establish the dual origin of enterovirus ROs and the chronology of their biogenesis at different supporting cellular membranes.
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Affiliation(s)
- Charlotte E Melia
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Anja W M de Jong
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Lucy M Collinson
- Electron Microscopy STP, The Francis Crick Institute, London, United Kingdom
| | - Abraham J Koster
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hilde M van der Schaar
- Virology Division, Faculty of Veterinary Medicine, Department of Infectious Diseases & Immunology, Utrecht University, Utrecht, The Netherlands
| | - Frank J M van Kuppeveld
- Virology Division, Faculty of Veterinary Medicine, Department of Infectious Diseases & Immunology, Utrecht University, Utrecht, The Netherlands
| | - Montserrat Bárcena
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
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43
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Weiner A, Enninga J. The Pathogen–Host Interface in Three Dimensions: Correlative FIB/SEM Applications. Trends Microbiol 2019; 27:426-439. [DOI: 10.1016/j.tim.2018.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/17/2022]
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44
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Lee Y, Hamann JC, Pellegrino M, Durgan J, Domart MC, Collinson LM, Haynes CM, Florey O, Overholtzer M. Entosis Controls a Developmental Cell Clearance in C. elegans. Cell Rep 2019; 26:3212-3220.e4. [PMID: 30893595 PMCID: PMC6475604 DOI: 10.1016/j.celrep.2019.02.073] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 02/07/2019] [Accepted: 02/19/2019] [Indexed: 12/14/2022] Open
Abstract
Metazoan cell death mechanisms are diverse and include numerous non-apoptotic programs. One program called entosis involves the invasion of live cells into their neighbors and is known to occur in cancers. Here, we identify a developmental function for entosis: to clear the male-specific linker cell in C. elegans. The linker cell leads migration to shape the gonad and is removed to facilitate fusion of the gonad to the cloaca. We find that the linker cell is cleared in a manner involving cell-cell adhesions and cell-autonomous control of uptake through linker cell actin. Linker cell entosis generates a lobe structure that is deposited at the site of gonad-to-cloaca fusion and is removed during mating. Inhibition of lobe scission inhibits linker cell death, demonstrating that the linker cell invades its host while alive. Our findings demonstrate a developmental function for entosis: to eliminate a migrating cell and facilitate gonad-to-cloaca fusion, which is required for fertility.
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Affiliation(s)
- Yongchan Lee
- Cell Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Jens C Hamann
- Cell Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mark Pellegrino
- Department of Biology, University of Texas Arlington, 500 UTA Blvd, Arlington, TX 76019, USA
| | - Joanne Durgan
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Marie-Charlotte Domart
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Lucy M Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Cole M Haynes
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Oliver Florey
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Michael Overholtzer
- Cell Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; BCMB Allied Program, Weill Cornell Medical College, New York, NY 10065, USA.
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45
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Boey A, Rybakin V, Kalicharan D, Vints K, Gounko NV. Gold-substituted Silver-intensified Peroxidase Immunolabeling for FIB-SEM Imaging. J Histochem Cytochem 2019; 67:351-360. [PMID: 30624131 DOI: 10.1369/0022155418824335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Modern electron microscopy offers a wide variety of tools to investigate the ultrastructural organization of cells and tissues and to accurately pinpoint intracellular localizations of macromolecules of interest. New volumetric electron microscopy techniques and new instrumentation provide unique opportunities for high-throughput analysis of comparatively large volumes of tissue and their complete reconstitution in three-dimensional (3D) electron microscopy. However, due to a variety of technical issues such as the limited penetration of label into the tissue, low antigen preservation, substantial electron density of secondary detection reagents, and many others, the adaptation of immuno-detection techniques for use with such 3D imaging methods as focused ion beam-scanning electron microscopy (FIB-SEM) has been challenging. Here, we describe a sample preparation method for 3D FIB-SEM, which results in an optimal preservation and staining of ultrastructural details at a resolution necessary for tracing immunolabeled neuronal structures and detailed reconstruction of synapses. This technique is applicable to neuronal and non-neuronal cells, tissues, and a wide variety of antigens.
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Affiliation(s)
- Adrian Boey
- Institute of Molecular and Cell Biology-Institute of Medical Biology Joint Electron Microscopy Suite, Agency for Science, Technology and Research, Singapore, Singapore
| | - Vasily Rybakin
- Laboratory of Immunobiology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Dharamdajal Kalicharan
- Institute of Molecular and Cell Biology-Institute of Medical Biology Joint Electron Microscopy Suite, Agency for Science, Technology and Research, Singapore, Singapore
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium.,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Natalia V Gounko
- Institute of Molecular and Cell Biology-Institute of Medical Biology Joint Electron Microscopy Suite, Agency for Science, Technology and Research, Singapore, Singapore.,VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium.,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
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46
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Ando T, Bhamidimarri SP, Brending N, Colin-York H, Collinson L, De Jonge N, de Pablo PJ, Debroye E, Eggeling C, Franck C, Fritzsche M, Gerritsen H, Giepmans BNG, Grunewald K, Hofkens J, Hoogenboom JP, Janssen KPF, Kaufman R, Klumpermann J, Kurniawan N, Kusch J, Liv N, Parekh V, Peckys DB, Rehfeldt F, Reutens DC, Roeffaers MBJ, Salditt T, Schaap IAT, Schwarz US, Verkade P, Vogel MW, Wagner R, Winterhalter M, Yuan H, Zifarelli G. The 2018 correlative microscopy techniques roadmap. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:443001. [PMID: 30799880 PMCID: PMC6372154 DOI: 10.1088/1361-6463/aad055] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/14/2018] [Accepted: 07/01/2018] [Indexed: 05/19/2023]
Abstract
Developments in microscopy have been instrumental to progress in the life sciences, and many new techniques have been introduced and led to new discoveries throughout the last century. A wide and diverse range of methodologies is now available, including electron microscopy, atomic force microscopy, magnetic resonance imaging, small-angle x-ray scattering and multiple super-resolution fluorescence techniques, and each of these methods provides valuable read-outs to meet the demands set by the samples under study. Yet, the investigation of cell development requires a multi-parametric approach to address both the structure and spatio-temporal organization of organelles, and also the transduction of chemical signals and forces involved in cell-cell interactions. Although the microscopy technologies for observing each of these characteristics are well developed, none of them can offer read-out of all characteristics simultaneously, which limits the information content of a measurement. For example, while electron microscopy is able to disclose the structural layout of cells and the macromolecular arrangement of proteins, it cannot directly follow dynamics in living cells. The latter can be achieved with fluorescence microscopy which, however, requires labelling and lacks spatial resolution. A remedy is to combine and correlate different readouts from the same specimen, which opens new avenues to understand structure-function relations in biomedical research. At the same time, such correlative approaches pose new challenges concerning sample preparation, instrument stability, region of interest retrieval, and data analysis. Because the field of correlative microscopy is relatively young, the capabilities of the various approaches have yet to be fully explored, and uncertainties remain when considering the best choice of strategy and workflow for the correlative experiment. With this in mind, the Journal of Physics D: Applied Physics presents a special roadmap on the correlative microscopy techniques, giving a comprehensive overview from various leading scientists in this field, via a collection of multiple short viewpoints.
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Affiliation(s)
- Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | | | | | - H Colin-York
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
| | | | - Niels De Jonge
- INM-Leibniz Institute for New Materials, 66123 Saarbrücken, Germany
- Saarland University, 66123 Saarbrücken, Germany
| | - P J de Pablo
- Dpto. Física de la Materia Condensada Universidad Autónoma de Madrid 28049, Madrid, Spain
- Instituto de Física de la Materia Condensada IFIMAC, Universidad Autónoma de Madrid 28049, Madrid, Spain
| | - Elke Debroye
- KU Leuven, Department of Chemistry, B-3001 Heverlee, Belgium
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
- Institute of Applied Optics, Friedrich-Schiller University, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
| | - Christian Franck
- Department of Mechanical Engineering, University of Wisconsin-Madison, 1513 University Ave, Madison, WI 53706, United States of America
| | - Marco Fritzsche
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Hans Gerritsen
- Debye Institute, Utrecht University, Utrecht, Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Kay Grunewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Centre of Structural Systems Biology Hamburg and University of Hamburg, Hamburg, Germany
- Heinrich-Pette-Institute, Leibniz Institute of Virology, Hamburg, Germany
| | - Johan Hofkens
- KU Leuven, Department of Chemistry, B-3001 Heverlee, Belgium
| | | | | | - Rainer Kaufman
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Centre of Structural Systems Biology Hamburg and University of Hamburg, Hamburg, Germany
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Judith Klumpermann
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584CX Utrecht, Netherlands
| | - Nyoman Kurniawan
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584CX Utrecht, Netherlands
| | - Viha Parekh
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Diana B Peckys
- Faculty of Medicine, Saarland University, 66421 Homburg, Germany
| | - Florian Rehfeldt
- University of Göttingen, Third Institute of Physics-Biophysics, 37077 Göttingen, Germany
| | - David C Reutens
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Tim Salditt
- University of Göttingen, Institute for X-Ray Physics, 37077 Göttingen, Germany
| | - Iwan A T Schaap
- SmarAct GmbH, Schütte-Lanz-Str. 9, D-26135 Oldenburg, Germany
| | - Ulrich S Schwarz
- Institute for Theoretical Physics and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Michael W Vogel
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Richard Wagner
- Department of Life Sciences & Chemistry, Jacobs University, Bremen, Germany
| | | | - Haifeng Yuan
- KU Leuven, Department of Chemistry, B-3001 Heverlee, Belgium
| | - Giovanni Zifarelli
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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47
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Ounkomol C, Seshamani S, Maleckar MM, Collman F, Johnson GR. Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy. Nat Methods 2018; 15:917-920. [PMID: 30224672 PMCID: PMC6212323 DOI: 10.1038/s41592-018-0111-2] [Citation(s) in RCA: 242] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/23/2018] [Accepted: 07/23/2018] [Indexed: 02/07/2023]
Abstract
Understanding cells as integrated systems is central to modern biology. Although fluorescence microscopy can resolve subcellular structure in living cells, it is expensive, is slow, and can damage cells. We present a label-free method for predicting three-dimensional fluorescence directly from transmitted-light images and demonstrate that it can be used to generate multi-structure, integrated images. The method can also predict immunofluorescence (IF) from electron micrograph (EM) inputs, extending the potential applications.
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48
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Luckner M, Wanner G. From Light Microscopy to Analytical Scanning Electron Microscopy (SEM) and Focused Ion Beam (FIB)/SEM in Biology: Fixed Coordinates, Flat Embedding, Absolute References. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2018; 24:526-544. [PMID: 30246679 PMCID: PMC6378657 DOI: 10.1017/s1431927618015015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/05/2018] [Accepted: 07/16/2018] [Indexed: 05/07/2023]
Abstract
Correlative light and electron microscopy (CLEM) has been in use for several years, however it has remained a costly method with difficult sample preparation. Here, we report a series of technical improvements developed for precise and cost-effective correlative light and scanning electron microscopy (SEM) and focused ion beam (FIB)/SEM microscopy of single cells, as well as large tissue sections. Customized coordinate systems for both slides and coverslips were established for thin and ultra-thin embedding of a wide range of biological specimens. Immobilization of biological samples was examined with a variety of adhesives. For histological sections, a filter system for flat embedding was developed. We validated ultra-thin embedding on laser marked slides for efficient, high-resolution CLEM. Target cells can be re-located within minutes in SEM without protracted searching and correlative investigations were reduced to a minimum of preparation steps, while still reaching highest resolution. The FIB/SEM milling procedure is facilitated and significantly accelerated as: (i) milling a ramp becomes needless, (ii) significant re-deposition of milled material does not occur; and (iii) charging effects are markedly reduced. By optimizing all technical parameters FIB/SEM stacks with 2 nm iso-voxels were achieved over thousands of sections, in a wide range of biological samples.
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Affiliation(s)
- Manja Luckner
- Department Biology I, Ultrastructural Research, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Gerhard Wanner
- Department Biology I, Ultrastructural Research, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
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49
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Lysova I, Spiegelhalter C, Réal E, Zgheib S, Anton H, Mély Y. ReAsH/tetracystein-based correlative light-electron microscopy for HIV-1 imaging during the early stages of infection. Methods Appl Fluoresc 2018; 6:045001. [PMID: 29938685 DOI: 10.1088/2050-6120/aacec1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Visualization of viruses in the host cell during the course of infection by correlative light-electron microscopy (CLEM) requires a specific labelling of the viral structures in order to recognize the nanometric viral cores in the intracellular environment. For Human immunodeficiency virus type 1 (HIV-1), the labelling approaches developed for fluorescence microscopy are generally not suited for transmission electron microscopy (TEM), so that imaging of HIV-1 particles in infected cells by CLEM is not straightforward. Herein, we adapt the labeling approach with a tetracystein tag (TC) and a biarsenical resorufin-based label (ReAsH) for monitoring the HIV-1 particles during the early stages of HIV-1 infection by CLEM. In this approach, the ReAsH fluorophore triggers the photo-conversion of 3,3-diaminobenzidine tetrahydrochloride (DAB), generating a precipitate sensitive to osmium tetroxide staining that can be visualized by transmission electron microscopy. The TC tag is fused to the nucleocapsid protein NCp7, a nucleic acid chaperone that binds to the viral genome. HeLa cells, infected by ReAsH-labeled pseudoviruses containg NCp7-TC proteins exhibit strong fluorescent cytoplasmic spots that overlap with dark precipitates in the TEM sections. The DAB precipitates corresponding to single viral cores are observed all over the cytoplasm, and notably near microtubules and nuclear pores. This work describes for the first time a specific contrast given by HIV-1 viral proteins in TEM images and opens new perspectives for the use of CLEM to monitor the intracellular traffic of viral complexes.
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Affiliation(s)
- Iryna Lysova
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Strasbourg University, Faculty of Pharmacy, 74 route du Rhin, Illkirch, France
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50
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Durgan J, Florey O. Cancer cell cannibalism: Multiple triggers emerge for entosis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2018; 1865:831-841. [PMID: 29548938 DOI: 10.1016/j.bbamcr.2018.03.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/02/2018] [Accepted: 03/06/2018] [Indexed: 12/22/2022]
Abstract
Entosis is a form of epithelial cell engulfment and cannibalism prevalent in human cancer. Until recently, the only known trigger for entosis was loss of attachment to the extracellular matrix, as often occurs in the tumour microenvironment. However, two new studies now reveal that entosis can also occur among adherent epithelial cells, induced by mitosis or glucose starvation. Together, these findings point to the intriguing notion that certain hallmark properties of cancer cells, including anchorage independence, aberrant proliferation and metabolic stress, can converge on the induction of cell cannibalism, a phenomenon so frequently observed in tumours. In this review, we explore the molecular, cellular and biophysical mechanisms underlying entosis and discuss the impact of cell cannibalism on tumour biology.
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Affiliation(s)
- J Durgan
- Babraham Institute, Cambridge, UK.
| | - O Florey
- Babraham Institute, Cambridge, UK
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