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Wacker IU, Veith L, Spomer W, Hofmann A, Thaler M, Hillmer S, Gengenbach U, Schröder RR. Multimodal Hierarchical Imaging of Serial Sections for Finding Specific Cellular Targets within Large Volumes. J Vis Exp 2018:57059. [PMID: 29630046 PMCID: PMC5933231 DOI: 10.3791/57059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Targeting specific cells at ultrastructural resolution within a mixed cell population or a tissue can be achieved by hierarchical imaging using a combination of light and electron microscopy. Samples embedded in resin are sectioned into arrays consisting of ribbons of hundreds of ultrathin sections and deposited on pieces of silicon wafer or conductively coated coverslips. Arrays are imaged at low resolution using a digital consumer like smartphone camera or light microscope (LM) for a rapid large area overview, or a wide field fluorescence microscope (fluorescence light microscopy (FLM)) after labeling with fluorophores. After post-staining with heavy metals, arrays are imaged in a scanning electron microscope (SEM). Selection of targets is possible from 3D reconstructions generated by FLM or from 3D reconstructions made from the SEM image stacks at intermediate resolution if no fluorescent markers are available. For ultrastructural analysis, selected targets are finally recorded in the SEM at high-resolution (a few nanometer image pixels). A ribbon-handling tool that can be retrofitted to any ultramicrotome is demonstrated. It helps with array production and substrate removal from the sectioning knife boat. A software platform that allows automated imaging of arrays in the SEM is discussed. Compared to other methods generating large volume EM data, such as serial block-face SEM (SBF-SEM) or focused ion beam SEM (FIB-SEM), this approach has two major advantages: (1) The resin-embedded sample is conserved, albeit in a sliced-up version. It can be stained in different ways and imaged with different resolutions. (2) As the sections can be post-stained, it is not necessary to use samples strongly block-stained with heavy metals to introduce contrast for SEM imaging or render the tissue blocks conductive. This makes the method applicable to a wide variety of materials and biological questions. Particularly prefixed materials e.g., from biopsy banks and pathology labs, can directly be embedded and reconstructed in 3D.
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Affiliation(s)
- Irene U Wacker
- Cryo Electron Microscopy, Centre for Advanced Materials, Universität Heidelberg; Heidelberg Karlsruhe Research Partnership (HEiKA);
| | - Lisa Veith
- Cryo Electron Microscopy, BioQuant, Universitätsklinikum Heidelberg
| | - Waldemar Spomer
- Heidelberg Karlsruhe Research Partnership (HEiKA); Institute for Automation and Applied Computer Science, Karlsruhe Institute of Technology (KIT)
| | - Andreas Hofmann
- Heidelberg Karlsruhe Research Partnership (HEiKA); Institute for Automation and Applied Computer Science, Karlsruhe Institute of Technology (KIT)
| | | | - Stefan Hillmer
- Electron Microscopy Core Facility, Universität Heidelberg
| | - Ulrich Gengenbach
- Heidelberg Karlsruhe Research Partnership (HEiKA); Institute for Automation and Applied Computer Science, Karlsruhe Institute of Technology (KIT)
| | - Rasmus R Schröder
- Cryo Electron Microscopy, Centre for Advanced Materials, Universität Heidelberg; Heidelberg Karlsruhe Research Partnership (HEiKA); Cryo Electron Microscopy, BioQuant, Universitätsklinikum Heidelberg
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López CS, Bouchet-Marquis C, Arthur CP, Riesterer JL, Heiss G, Thibault G, Pullan L, Kwon S, Gray JW. A fully integrated, three-dimensional fluorescence to electron microscopy correlative workflow. Methods Cell Biol 2017; 140:149-164. [PMID: 28528631 DOI: 10.1016/bs.mcb.2017.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
While fluorescence microscopy provides tools for highly specific labeling and sensitive detection, its resolution limit and lack of general contrast has hindered studies of cellular structure and protein localization. Recent advances in correlative light and electron microscopy (CLEM), including the fully integrated CLEM workflow instrument, the FEI CorrSight with MAPS, have allowed for a more reliable, reproducible, and quicker approach to correlate three-dimensional time-lapse confocal fluorescence data, with three-dimensional focused ion beam-scanning electron microscopy data. Here we demonstrate the entire integrated CLEM workflow using fluorescently tagged MCF7 breast cancer cells.
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Affiliation(s)
- Claudia S López
- Oregon Health and Sciences University, Portland, OR, United States
| | | | - Christopher P Arthur
- Thermo Fisher Scientific, Hillsboro, OR, United States; Genentech, San Francisco, CA, United States
| | | | - Gregor Heiss
- Thermo Fisher Scientific, Hillsboro, OR, United States
| | | | - Lee Pullan
- Thermo Fisher Scientific, Hillsboro, OR, United States
| | - Sunjong Kwon
- Oregon Health and Sciences University, Portland, OR, United States
| | - Joe W Gray
- Oregon Health and Sciences University, Portland, OR, United States
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Illuminating the Sites of Enterovirus Replication in Living Cells by Using a Split-GFP-Tagged Viral Protein. mSphere 2016; 1:mSphere00104-16. [PMID: 27390781 PMCID: PMC4935779 DOI: 10.1128/msphere.00104-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/02/2016] [Indexed: 12/13/2022] Open
Abstract
Enteroviruses induce the formation of membranous structures (replication organelles [ROs]) with a unique protein and lipid composition specialized for genome replication. Electron microscopy has revealed the morphology of enterovirus ROs, and immunofluorescence studies have been conducted to investigate their origin and formation. Yet, immunofluorescence analysis of fixed cells results in a rather static view of RO formation, and the results may be compromised by immunolabeling artifacts. While live-cell imaging of ROs would be preferred, enteroviruses encoding a membrane-anchored viral protein fused to a large fluorescent reporter have thus far not been described. Here, we tackled this constraint by introducing a small tag from a split-GFP system into an RO-resident enterovirus protein. This new tool bridges a methodological gap by circumventing the need for immunolabeling fixed cells and allows the study of the dynamics and formation of enterovirus ROs in living cells. Like all other positive-strand RNA viruses, enteroviruses generate new organelles (replication organelles [ROs]) with a unique protein and lipid composition on which they multiply their viral genome. Suitable tools for live-cell imaging of enterovirus ROs are currently unavailable, as recombinant enteroviruses that carry genes that encode RO-anchored viral proteins tagged with fluorescent reporters have not been reported thus far. To overcome this limitation, we used a split green fluorescent protein (split-GFP) system, comprising a large fragment [strands 1 to 10; GFP(S1-10)] and a small fragment [strand 11; GFP(S11)] of only 16 residues. The GFP(S11) (GFP with S11 fragment) fragment was inserted into the 3A protein of the enterovirus coxsackievirus B3 (CVB3), while the large fragment was supplied by transient or stable expression in cells. The introduction of GFP(S11) did not affect the known functions of 3A when expressed in isolation. Using correlative light electron microscopy (CLEM), we showed that GFP fluorescence was detected at ROs, whose morphologies are essentially identical to those previously observed for wild-type CVB3, indicating that GFP(S11)-tagged 3A proteins assemble with GFP(S1-10) to form GFP for illumination of bona fide ROs. It is well established that enterovirus infection leads to Golgi disintegration. Through live-cell imaging of infected cells expressing an mCherry-tagged Golgi marker, we monitored RO development and revealed the dynamics of Golgi disassembly in real time. Having demonstrated the suitability of this virus for imaging ROs, we constructed a CVB3 encoding GFP(S1-10) and GFP(S11)-tagged 3A to bypass the need to express GFP(S1-10) prior to infection. These tools will have multiple applications in future studies on the origin, location, and function of enterovirus ROs. IMPORTANCE Enteroviruses induce the formation of membranous structures (replication organelles [ROs]) with a unique protein and lipid composition specialized for genome replication. Electron microscopy has revealed the morphology of enterovirus ROs, and immunofluorescence studies have been conducted to investigate their origin and formation. Yet, immunofluorescence analysis of fixed cells results in a rather static view of RO formation, and the results may be compromised by immunolabeling artifacts. While live-cell imaging of ROs would be preferred, enteroviruses encoding a membrane-anchored viral protein fused to a large fluorescent reporter have thus far not been described. Here, we tackled this constraint by introducing a small tag from a split-GFP system into an RO-resident enterovirus protein. This new tool bridges a methodological gap by circumventing the need for immunolabeling fixed cells and allows the study of the dynamics and formation of enterovirus ROs in living cells.
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4
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Schorb M, Gaechter L, Avinoam O, Sieckmann F, Clarke M, Bebeacua C, Bykov YS, Sonnen AFP, Lihl R, Briggs JAG. New hardware and workflows for semi-automated correlative cryo-fluorescence and cryo-electron microscopy/tomography. J Struct Biol 2016; 197:83-93. [PMID: 27368127 PMCID: PMC5287355 DOI: 10.1016/j.jsb.2016.06.020] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/17/2016] [Accepted: 06/27/2016] [Indexed: 12/17/2022]
Abstract
Correlative light and electron microscopy allows features of interest defined by fluorescence signals to be located in an electron micrograph of the same sample. Rare dynamic events or specific objects can be identified, targeted and imaged by electron microscopy or tomography. To combine it with structural studies using cryo-electron microscopy or tomography, fluorescence microscopy must be performed while maintaining the specimen vitrified at liquid-nitrogen temperatures and in a dry environment during imaging and transfer. Here we present instrumentation, software and an experimental workflow that improves the ease of use, throughput and performance of correlated cryo-fluorescence and cryo-electron microscopy. The new cryo-stage incorporates a specially modified high-numerical aperture objective lens and provides a stable and clean imaging environment. It is combined with a transfer shuttle for contamination-free loading of the specimen. Optimized microscope control software allows automated acquisition of the entire specimen area by cryo-fluorescence microscopy. The software also facilitates direct transfer of the fluorescence image and associated coordinates to the cryo-electron microscope for subsequent fluorescence-guided automated imaging. Here we describe these technological developments and present a detailed workflow, which we applied for automated cryo-electron microscopy and tomography of various specimens.
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Affiliation(s)
- Martin Schorb
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Electron Microscopy Core Facility, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Leander Gaechter
- Leica Microsystems (Schweiz) AG, Max Schmidheiny-Strasse 201, 9435 Heerbrugg, Switzerland
| | - Ori Avinoam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Frank Sieckmann
- Leica Microsystems GmbH, Am Friedensplatz 3, 68165 Mannheim, Germany
| | - Mairi Clarke
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Cecilia Bebeacua
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Yury S Bykov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Andreas F-P Sonnen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, EMBL/Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Reinhard Lihl
- Leica Mikrosysteme GmbH, Hernalser Hauptstraße 219, 1170 Vienna, Austria
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, EMBL/Universitätsklinikum Heidelberg, Heidelberg, Germany.
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Boykins LG, Jones JCR, Estraño CE, Schwartzbach SD, Skalli O. Pre-embedding Double-Label Immunoelectron Microscopy of Chemically Fixed Tissue Culture Cells. Methods Mol Biol 2016; 1474:217-32. [PMID: 27515083 PMCID: PMC5734918 DOI: 10.1007/978-1-4939-6352-2_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Localization of specific proteins within cells at the nanometer level of resolution is central to understanding how these proteins function in cell processes such as motility and intracellular trafficking. Such localization can be achieved by combining transmission electron microscopy (TEM) with immunogold labeling. Here we describe a pre-embedding, indirect gold immunolabeling approach to localize two different proteins of interest with secondary antibodies labeled with gold particles of different sizes in cells grown on cover slips. In this protocol, the cells are immunolabeled prior to being embedded in an epoxy resin for ultrathin sectioning. The protocol also includes strategies for optimizing the balance between ultrastructure and antigen preservation, steps to minimize nonspecific antibody binding, and steps to optimize antibody penetration.
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Affiliation(s)
- Lou G Boykins
- Department of Biological Sciences, The University of Memphis, 103 Life Sciences Bldg, Memphis, TN, 38152, USA
| | - Jonathan C R Jones
- School of Molecular Biosciences, Washington State University, BLS 202F, 1770 NE Stadium Way, Pullman, WA, 99164, USA
| | - Carlos E Estraño
- Department of Biological Sciences, The University of Memphis, 103 Life Sciences Bldg, Memphis, TN, 38152, USA
| | - Steven D Schwartzbach
- Department of Biological Sciences, The University of Memphis, 103 Life Sciences Bldg, Memphis, TN, 38152, USA
| | - Omar Skalli
- Department of Biological Sciences, The University of Memphis, 103 Life Sciences Bldg, Memphis, TN, 38152, USA.
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Self-labelling enzymes as universal tags for fluorescence microscopy, super-resolution microscopy and electron microscopy. Sci Rep 2015; 5:17740. [PMID: 26643905 PMCID: PMC4672345 DOI: 10.1038/srep17740] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/04/2015] [Indexed: 11/17/2022] Open
Abstract
Research in cell biology demands advanced microscopy techniques such as confocal fluorescence microscopy (FM), super-resolution microscopy (SRM) and transmission electron microscopy (TEM). Correlative light and electron microscopy (CLEM) is an approach to combine data on the dynamics of proteins or protein complexes in living cells with the ultrastructural details in the low nanometre scale. To correlate both data sets, markers functional in FM, SRM and TEM are required. Genetically encoded markers such as fluorescent proteins or self-labelling enzyme tags allow observations in living cells. Various genetically encoded tags are available for FM and SRM, but only few tags are suitable for CLEM. Here, we describe the red fluorescent dye tetramethylrhodamine (TMR) as a multimodal marker for CLEM. TMR is used as fluorochrome coupled to ligands of genetically encoded self-labelling enzyme tags HaloTag, SNAP-tag and CLIP-tag in FM and SRM. We demonstrate that TMR can additionally photooxidize diaminobenzidine (DAB) to an osmiophilic polymer visible on TEM sections, thus being a marker suitable for FM, SRM and TEM. We evaluated various organelle markers with enzymatic tags in mammalian cells labelled with TMR-coupled ligands and demonstrate the use as efficient and versatile DAB photooxidizer for CLEM approaches.
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Goudarzi M, Mildner K, Babatz F, Riedel D, Klämbt C, Zeuschner D, Raz E. Correlative Light and Electron Microscopy of Rare Cell Populations in Zebrafish Embryos Using Laser Marks. Zebrafish 2015; 12:470-3. [PMID: 26448280 PMCID: PMC4677546 DOI: 10.1089/zeb.2015.1148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
- Mohammad Goudarzi
- 1 Institute of Cell Biology, ZMBE, University of Münster , Münster, Germany
| | - Karina Mildner
- 2 Electron Microscopy Unit, Max Planck Institute for Molecular Biomedicine , Münster, Germany
| | - Felix Babatz
- 3 Institute for Neurobiology, University of Münster , Münster, Germany
| | - Dietmar Riedel
- 4 Electron Microscopy Group, Max-Planck-Institute for Biophysical Chemistry , Göttingen, Germany
| | - Christian Klämbt
- 3 Institute for Neurobiology, University of Münster , Münster, Germany
| | - Dagmar Zeuschner
- 2 Electron Microscopy Unit, Max Planck Institute for Molecular Biomedicine , Münster, Germany
| | - Erez Raz
- 1 Institute of Cell Biology, ZMBE, University of Münster , Münster, Germany
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Takizawa T, Powell RD, Hainfeld JF, Robinson JM. FluoroNanogold: an important probe for correlative microscopy. J Chem Biol 2015; 8:129-42. [PMID: 26884817 PMCID: PMC4744603 DOI: 10.1007/s12154-015-0145-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 07/24/2015] [Indexed: 10/23/2022] Open
Abstract
Correlative microscopy is a powerful imaging approach that refers to observing the same exact structures within a specimen by two or more imaging modalities. In biological samples, this typically means examining the same sub-cellular feature with different imaging methods. Correlative microscopy is not restricted to the domains of fluorescence microscopy and electron microscopy; however, currently, most correlative microscopy studies combine these two methods, and in this review, we will focus on the use of fluorescence and electron microscopy. Successful correlative fluorescence and electron microscopy requires probes, or reporter systems, from which useful information can be obtained with each of the imaging modalities employed. The bi-functional immunolabeling reagent, FluoroNanogold, is one such probe that provides robust signals in both fluorescence and electron microscopy. It consists of a gold cluster compound that is visualized by electron microscopy and a covalently attached fluorophore that is visualized by fluorescence microscopy. FluoroNanogold has been an extremely useful labeling reagent in correlative microscopy studies. In this report, we present an overview of research using this unique probe.
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Affiliation(s)
| | - Richard D. Powell
- />Nanoprobes, Incorporated, 95 Horseblock Road, Unit 1, Yaphank, NY 11980-9710 USA
| | - James F. Hainfeld
- />Nanoprobes, Incorporated, 95 Horseblock Road, Unit 1, Yaphank, NY 11980-9710 USA
| | - John M. Robinson
- />Department of Physiology and Cell Biology, Ohio State University, Columbus, OH 43210 USA
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