1
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Ropert B, Gallrein C, Schumacher B. DNA repair deficiencies and neurodegeneration. DNA Repair (Amst) 2024; 138:103679. [PMID: 38640601 DOI: 10.1016/j.dnarep.2024.103679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 04/21/2024]
Abstract
Neurodegenerative diseases are the second most prevalent cause of death in industrialized countries. Alzheimer's Disease is the most widespread and also most acknowledged form of dementia today. Together with Parkinson's Disease they account for over 90 % cases of neurodegenerative disorders caused by proteopathies. Far less known are the neurodegenerative pathologies in DNA repair deficiency syndromes. Such diseases like Cockayne - or Werner Syndrome are described as progeroid syndromes - diseases that cause the premature ageing of the affected persons, and there are clear implications of such diseases in neurologic dysfunction and degeneration. In this review, we aim to draw the attention on commonalities between proteopathy-associated neurodegeneration and neurodegeneration caused by DNA repair defects and discuss how mitochondria are implicated in the development of both disorder classes. Furthermore, we highlight how nematodes are a valuable and indispensable model organism to study conserved neurodegenerative processes in a fast-forward manner.
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Affiliation(s)
- Baptiste Ropert
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Str. 26, Cologne 50931, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, Cologne 50931, Germany
| | - Christian Gallrein
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Str. 26, Cologne 50931, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, Cologne 50931, Germany; Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, Jena 07745, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Str. 26, Cologne 50931, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, Cologne 50931, Germany.
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2
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Chen J, Stephan T, Gaedke F, Liu T, Li Y, Schauss A, Chen P, Wulff V, Jakobs S, Jüngst C, Chen Z. An aldehyde-crosslinking mitochondrial probe for STED imaging in fixed cells. Proc Natl Acad Sci U S A 2024; 121:e2317703121. [PMID: 38687792 PMCID: PMC11087744 DOI: 10.1073/pnas.2317703121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/22/2024] [Indexed: 05/02/2024] Open
Abstract
Fluorescence labeling of chemically fixed specimens, especially immunolabeling, plays a vital role in super-resolution imaging as it offers a convenient way to visualize cellular structures like mitochondria or the distribution of biomolecules with high detail. Despite the development of various distinct probes that enable super-resolved stimulated emission depletion (STED) imaging of mitochondria in live cells, most of these membrane-potential-dependent fluorophores cannot be retained well in mitochondria after chemical fixation. This lack of suitable mitochondrial probes has limited STED imaging of mitochondria to live cell samples. In this study, we introduce a mitochondria-specific probe, PK Mito Orange FX (PKMO FX), which features a fixation-driven cross-linking motif and accumulates in the mitochondrial inner membrane. It exhibits high fluorescence retention after chemical fixation and efficient depletion at 775 nm, enabling nanoscopic imaging both before and after aldehyde fixation. We demonstrate the compatibility of this probe with conventional immunolabeling and other strategies commonly used for fluorescence labeling of fixed samples. Moreover, we show that PKMO FX facilitates correlative super-resolution light and electron microscopy, enabling the correlation of multicolor fluorescence images and transmission EM images via the characteristic mitochondrial pattern. Our probe further expands the mitochondrial toolkit for multimodal microscopy at nanometer resolutions.
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Affiliation(s)
- Jingting Chen
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing100871, China
| | - Till Stephan
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen37077, Germany
- Clinic of Neurology, University Medical Center Göttingen, Göttingen37075, Germany
| | - Felix Gaedke
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Tianyan Liu
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Yiyan Li
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Astrid Schauss
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Peng Chen
- Peking University-Nanjing Institute of Translational Medicine, Nanjing211800, China
- Genvivo Biotech (PuHaiJingShan), Nanjing211800, China
| | - Veronika Wulff
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen37077, Germany
- Clinic of Neurology, University Medical Center Göttingen, Göttingen37075, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology Translational, Neuroinflammation and Automated Microscopy, Göttingen37075, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells”, University of Göttingen, Göttingen37099, Germany
| | - Christian Jüngst
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Zhixing Chen
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
- Peking University-Nanjing Institute of Translational Medicine, Nanjing211800, China
- Genvivo Biotech (PuHaiJingShan), Nanjing211800, China
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3
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Franek M, Koptašíková L, Mikšátko J, Liebl D, Macíčková E, Pospíšil J, Esner M, Dvořáčková M, Fajkus J. In-section Click-iT detection and super-resolution CLEM analysis of nucleolar ultrastructure and replication in plants. Nat Commun 2024; 15:2445. [PMID: 38503728 PMCID: PMC10950858 DOI: 10.1038/s41467-024-46324-6] [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: 06/23/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
Correlative light and electron microscopy (CLEM) is an important tool for the localisation of target molecule(s) and their spatial correlation with the ultrastructural map of subcellular features at the nanometre scale. Adoption of these advanced imaging methods has been limited in plant biology, due to challenges with plant tissue permeability, fluorescence labelling efficiency, indexing of features of interest throughout the complex 3D volume and their re-localization on micrographs of ultrathin cross-sections. Here, we demonstrate an imaging approach based on tissue processing and embedding into methacrylate resin followed by imaging of sections by both, single-molecule localization microscopy and transmission electron microscopy using consecutive CLEM and same-section CLEM correlative workflow. Importantly, we demonstrate that the use of a particular type of embedding resin is not only compatible with single-molecule localization microscopy but shows improvements in the fluorophore blinking behavior relative to the whole-mount approaches. Here, we use a commercially available Click-iT ethynyl-deoxyuridine cell proliferation kit to visualize the DNA replication sites of wild-type Arabidopsis thaliana seedlings, as well as fasciata1 and nucleolin1 plants and apply our in-section CLEM imaging workflow for the analysis of S-phase progression and nucleolar organization in mutant plants with aberrant nucleolar phenotypes.
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Affiliation(s)
- Michal Franek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic.
| | - Lenka Koptašíková
- Charles University, Faculty of Science, Biology Section, Imaging Methods Core Facility at BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
- University of Exeter, Faculty of Health and Life Sciences, Bioimaging Centre, Geoffrey Pope Building, Stocker Road, EX4 4QD, Exeter, UK
| | - Jíří Mikšátko
- Charles University, Faculty of Science, Biology Section, Imaging Methods Core Facility at BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - David Liebl
- Charles University, Faculty of Science, Biology Section, Imaging Methods Core Facility at BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Eliška Macíčková
- Charles University, Faculty of Science, Biology Section, Imaging Methods Core Facility at BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Jakub Pospíšil
- Cellular Imaging Core Facility CELLIM, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology Masaryk University (CEITEC MU), Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Milan Esner
- Cellular Imaging Core Facility CELLIM, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology Masaryk University (CEITEC MU), Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic.
| | - Jíří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-61137, Brno, Czech Republic
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4
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Vojnovic I, Caspari OD, Hoşkan MA, Endesfelder U. Combining single-molecule and expansion microscopy in fission yeast to visualize protein structures at the nanostructural level. Open Biol 2024; 14:230414. [PMID: 38320620 PMCID: PMC10846934 DOI: 10.1098/rsob.230414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/04/2023] [Indexed: 02/08/2024] Open
Abstract
In this work, we have developed an expansion microscopy (ExM) protocol that combines ExM with photoactivated localization microscopy (ExPALM) for yeast cell imaging, and report a robust protocol for single-molecule and expansion microscopy of fission yeast, abbreviated as SExY. Our optimized SExY protocol retains about 50% of the fluorescent protein signal, doubling the amount obtained compared to the original protein retention ExM (proExM) protocol. It allows for a fivefold, highly isotropic expansion of fission yeast cells, which we carefully controlled while optimizing protein yield. We demonstrate the SExY method on several exemplary molecular targets and explicitly introduce low-abundant protein targets (e.g. nuclear proteins such as cbp1 and mis16, and the centromere-specific histone protein cnp1). The SExY protocol optimizations increasing protein yield could be beneficial for many studies, when targeting low abundance proteins, or for studies that rely on genetic labelling for various reasons (e.g. for proteins that cannot be easily targeted by extrinsic staining or in case artefacts introduced by unspecific staining interfere with data quality).
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Affiliation(s)
- Ilijana Vojnovic
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Oliver D. Caspari
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Microbiology, Institute Pasteur, Paris, France
| | - Mehmet Ali Hoşkan
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ulrike Endesfelder
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
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5
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Gandhi L, Venkataramana M. Protocol for simultaneous detection of dual subcellular localized dengue virus protease by co-transfection. STAR Protoc 2023; 4:102697. [PMID: 37952159 PMCID: PMC10682249 DOI: 10.1016/j.xpro.2023.102697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/22/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
It is difficult to track virus-coded proteins simultaneously if they localize to multiple subcellular organelles. Here, we present a protocol for the simultaneous detection of dual subcellular localized dengue virus protease by co-transfection. We describe steps for cell seeding, co-transfection with mitochondria targeted red fluorescent protein, cell fixation, permeabilization, and staining of transfected cells with Hoechst stain. Further, we describe how to generate fluorescent intensity profiles using the NIS-Elements software. We then detail procedures for subcellular fractionation followed by western blotting. For complete details on the use and execution of this protocol, please refer to Gandhi et al.1.
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Affiliation(s)
- Lekha Gandhi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India
| | - Musturi Venkataramana
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India.
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6
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Xu X, Qiu K, Tian Z, Aryal C, Rowan F, Chen R, Sun Y, Diao J. Probing the dynamic crosstalk of lysosomes and mitochondria with structured illumination microscopy. Trends Analyt Chem 2023; 169:117370. [PMID: 37928815 PMCID: PMC10621629 DOI: 10.1016/j.trac.2023.117370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Structured illumination microscopy (SIM) is a super-resolution technology for imaging living cells and has been used for studying the dynamics of lysosomes and mitochondria. Recently, new probes and analyzing methods have been developed for SIM imaging, enabling the quantitative analysis of these subcellular structures and their interactions. This review provides an overview of the working principle and advances of SIM, as well as the organelle-targeting principles and types of fluorescence probes, including small molecules, metal complexes, nanoparticles, and fluorescent proteins. Additionally, quantitative methods based on organelle morphology and distribution are outlined. Finally, the review provides an outlook on the current challenges and future directions for improving the combination of SIM imaging and image analysis to further advance the study of organelles. We hope that this review will be useful for researchers working in the field of organelle research and help to facilitate the development of SIM imaging and analysis techniques.
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Affiliation(s)
- Xiuqiong Xu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Kangqiang Qiu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Zhiqi Tian
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Chinta Aryal
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Fiona Rowan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Rui Chen
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Yujie Sun
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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7
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Andrian T, Muela Y, Delgado L, Albertazzi L, Pujals S. A super-resolution and transmission electron microscopy correlative approach to study intracellular trafficking of nanoparticles. NANOSCALE 2023; 15:14615-14627. [PMID: 37614108 DOI: 10.1039/d3nr02838k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Nanoparticles (NPs) are used to encapsulate therapeutic cargos and deliver them specifically to the target site. The intracellular trafficking of NPs dictates the NP-cargo distribution within different cellular compartments, and thus governs their efficacy and safety. Knowledge in this field is crucial to understand their biological fate and improve their rational design. However, there is a lack of methods that allow precise localization and quantification of individual NPs within distinct cellular compartments simultaneously. Here, we address this issue by proposing a correlative light and electron microscopy (CLEM) method combining direct stochastic optical reconstruction microscopy (dSTORM) and transmission electron microscopy (TEM). We aim at combining the advantages of both techniques to precisely address NP localization in the context of the cell ultrastructure. Individual fluorescently-labelled poly(lactide-co-glycolide)-poly(ethylene glycol) (PLGA-PEG) NPs were directly visualized by dSTORM and assigned to cellular compartments by TEM. We first tracked NPs along the endo-lysosomal pathway at different time points, then demonstrated the effect of chloroquine on their intracellular distribution (i.e. endosomal escape). The proposed protocol can be applied to fluorescently labelled NPs and/or cargo, including those not detectable by TEM alone. Our studies are of great relevance to obtain important information on NP trafficking, and crucial for the design of more complex nanomaterials aimed at cytoplasmic/nucleic drug delivery.
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Affiliation(s)
- Teodora Andrian
- Institute for Bioengineering of Catalonia (IBEC), Carrer Baldiri Reixac 15-21, 08024 Barcelona, Spain.
| | - Yolanda Muela
- Electron Cryomicroscopy Unit, Centres Científics i Tecnològics de la Universitat de Barcelona (CCiTUB), Carrer Baldiri i Reixac 10-12, 08028 Barcelona, Spain
| | - Lidia Delgado
- Electron Cryomicroscopy Unit, Centres Científics i Tecnològics de la Universitat de Barcelona (CCiTUB), Carrer Baldiri i Reixac 10-12, 08028 Barcelona, Spain
| | - Lorenzo Albertazzi
- Institute for Bioengineering of Catalonia (IBEC), Carrer Baldiri Reixac 15-21, 08024 Barcelona, Spain.
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Silvia Pujals
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Carrer Jordi Girona 18-26, 08034 Barcelona, Spain.
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8
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Chang HF, Schirra C, Pattu V, Krause E, Becherer U. Lytic granule exocytosis at immune synapses: lessons from neuronal synapses. Front Immunol 2023; 14:1177670. [PMID: 37275872 PMCID: PMC10233144 DOI: 10.3389/fimmu.2023.1177670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/09/2023] [Indexed: 06/07/2023] Open
Abstract
Regulated exocytosis is a central mechanism of cellular communication. It is not only the basis for neurotransmission and hormone release, but also plays an important role in the immune system for the release of cytokines and cytotoxic molecules. In cytotoxic T lymphocytes (CTLs), the formation of the immunological synapse is required for the delivery of the cytotoxic substances such as granzymes and perforin, which are stored in lytic granules and released via exocytosis. The molecular mechanisms of their fusion with the plasma membrane are only partially understood. In this review, we discuss the molecular players involved in the regulated exocytosis of CTL, highlighting the parallels and differences to neuronal synaptic transmission. Additionally, we examine the strengths and weaknesses of both systems to study exocytosis.
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9
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Heiligenstein X, Lucas MS. One for All, All for One: A Close Look at In-Resin Fluorescence Protocols for CLEM. Front Cell Dev Biol 2022; 10:866472. [PMID: 35846358 PMCID: PMC9280628 DOI: 10.3389/fcell.2022.866472] [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: 01/31/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Sample preparation is the novel bottleneck for high throughput correlative light and electron microscopy (CLEM). Protocols suitable for both imaging methods must therefore balance the requirements of each technique. For fluorescence light microscopy, a structure of interest can be targeted using: 1) staining, which is often structure or tissue specific rather than protein specific, 2) dye-coupled proteins or antibodies, or 3) genetically encoded fluorescent proteins. Each of these three methods has its own advantages. For ultrastructural investigation by electron microscopy (EM) resin embedding remains a significant sample preparation approach, as it stabilizes the sample such that it withstands the vacuum conditions of the EM, and enables long-term storage. Traditionally, samples are treated with heavy metal salts prior to resin embedding, in order to increase imaging contrast for EM. This is particularly important for volume EM (vEM) techniques. Yet, commonly used contrasting agents (e.g., osmium tetroxide, uranyl acetate) tend to impair fluorescence. The discovery that fluorescence can be preserved in resin-embedded specimens after mild heavy metal staining was a game changer for CLEM. These so-called in-resin fluorescence protocols present a significant leap forward for CLEM approaches towards high precision localization of a fluorescent signal in (volume) EM data. Integrated microscopy approaches, combining LM and EM detection into a single instrument certainly require such an “all in one” sample preparation. Preserving, or adding, dedicated fluorescence prior to resin embedding requires a compromise, which often comes at the expense of EM imaging contrast and membrane visibility. Especially vEM can be strongly hampered by a lack of heavy metal contrasting. This review critically reflects upon the fundamental aspects of resin embedding with regard to 1) specimen fixation and the physics and chemistry underlying the preservation of protein structure with respect to fluorescence and antigenicity, 2) optimization of EM contrast for transmission or scanning EM, and 3) the choice of embedding resin. On this basis, various existing workflows employing in-resin fluorescence are described, highlighting their common features, discussing advantages and disadvantages of the respective approach, and finally concluding with promising future developments for in-resin CLEM.
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Affiliation(s)
| | - Miriam S. Lucas
- Scientific Center for Light and Electron Microscopy (ScopeM), ETH Zurich, Zurich, Switzerland
- *Correspondence: Miriam S. Lucas,
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10
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Nienhaus K, Nienhaus GU. Genetically encodable fluorescent protein markers in advanced optical imaging. Methods Appl Fluoresc 2022; 10. [PMID: 35767981 DOI: 10.1088/2050-6120/ac7d3f] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/29/2022] [Indexed: 11/12/2022]
Abstract
Optical fluorescence microscopy plays a pivotal role in the exploration of biological structure and dynamics, especially on live specimens. Progress in the field relies, on the one hand, on technical advances in imaging and data processing and, on the other hand, on progress in fluorescent marker technologies. Among these, genetically encodable fluorescent proteins (FPs) are invaluable tools, as they allow facile labeling of live cells, tissues or organisms, as these produce the FP markers all by themselves after introduction of a suitable gene. Here we cover FP markers from the GFP family of proteins as well as tetrapyrrole-binding proteins, which further complement the FP toolbox in important ways. A broad range of FP variants have been endowed, by using protein engineering, with photophysical properties that are essential for specific fluorescence microscopy techniques, notably those offering nanoscale image resolution. We briefly introduce various advanced imaging methods and show how they utilize the distinct properties of the FP markers in exciting imaging applications, with the aim to guide researchers toward the design of powerful imaging experiments that are optimally suited to address their biological questions.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
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11
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van den Dries K, Fransen J, Cambi A. Fluorescence CLEM in biology: historic developments and current super-resolution applications. FEBS Lett 2022; 596:2486-2496. [PMID: 35674424 DOI: 10.1002/1873-3468.14421] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/12/2022]
Abstract
Correlative light and electron microscopy (CLEM) is a powerful imaging approach that allows the direct correlation of information obtained on a light and an electron microscope. There is a growing interest in the application of CLEM in biology, mainly attributable to technical advances in field of fluorescence microscopy in the past two decades. In this review, we summarize the important developments in CLEM for biological applications, focusing on the combination of fluorescence microscopy and electron microscopy. We first provide a brief overview of the early days of fluorescence CLEM usage starting with the initial rise in the late 1970s and the subsequent optimization of CLEM workflows during the following two decades. Next, we describe how the engineering of fluorescent proteins and the development of super-resolution fluorescence microscopy have significantly renewed the interest in CLEM resulting in the present application of fluorescence CLEM in many different areas of cellular and molecular biology. Lastly, we present the promises and challenges for the future of fluorescence CLEM discussing novel workflows, probe development and quantification possibilities.
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Affiliation(s)
- Koen van den Dries
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Jack Fransen
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands.,Microscopic Imaging Center, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Alessandra Cambi
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
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12
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Mazal H, Wieser FF, Sandoghdar V. Deciphering a hexameric protein complex with Angstrom optical resolution. eLife 2022; 11:76308. [PMID: 35616526 PMCID: PMC9142145 DOI: 10.7554/elife.76308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/12/2022] [Indexed: 12/24/2022] Open
Abstract
Cryogenic optical localization in three dimensions (COLD) was recently shown to resolve up to four binding sites on a single protein. However, because COLD relies on intensity fluctuations that result from the blinking behavior of fluorophores, it is limited to cases where individual emitters show different brightness. This significantly lowers the measurement yield. To extend the number of resolved sites as well as the measurement yield, we employ partial labeling and combine it with polarization encoding in order to identify single fluorophores during their stochastic blinking. We then use a particle classification scheme to identify and resolve heterogenous subsets and combine them to reconstruct the three-dimensional arrangement of large molecular complexes. We showcase this method (polarCOLD) by resolving the trimer arrangement of proliferating cell nuclear antigen (PCNA) and six different sites of the hexamer protein Caseinolytic Peptidase B (ClpB) of Thermus thermophilus in its quaternary structure, both with Angstrom resolution. The combination of polarCOLD and single-particle cryogenic electron microscopy (cryoEM) promises to provide crucial insight into intrinsic heterogeneities of biomolecular structures. Furthermore, our approach is fully compatible with fluorescent protein labeling and can, thus, be used in a wide range of studies in cell and membrane biology.
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Affiliation(s)
- Hisham Mazal
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Franz-Ferdinand Wieser
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.,Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.,Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
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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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Lork AA, Vo KLL, Phan NTN. Chemical Imaging and Analysis of Single Nerve Cells by Secondary Ion Mass Spectrometry Imaging and Cellular Electrochemistry. Front Synaptic Neurosci 2022; 14:854957. [PMID: 35651734 PMCID: PMC9149580 DOI: 10.3389/fnsyn.2022.854957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
A nerve cell is a unit of neuronal communication in the nervous system and is a heterogeneous molecular structure, which is highly mediated to accommodate cellular functions. Understanding the complex regulatory mechanisms of neural communication at the single cell level requires analytical techniques with high sensitivity, specificity, and spatial resolution. Challenging technologies for chemical imaging and analysis of nerve cells will be described in this review. Secondary ion mass spectrometry (SIMS) allows for non-targeted and targeted molecular imaging of nerve cells and synapses at subcellular resolution. Cellular electrochemistry is well-suited for quantifying the amount of reactive chemicals released from living nerve cells. These techniques will also be discussed regarding multimodal imaging approaches that have recently been shown to be advantageous for the understanding of structural and functional relationships in the nervous system. This review aims to provide an insight into the strengths, limitations, and potentials of these technologies for synaptic and neuronal analyses.
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15
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Parallel gold enhancement of quantum dots 565/655 for double-labelling correlative light and electron microscopy on human autopsied samples. Sci Rep 2022; 12:6113. [PMID: 35413968 PMCID: PMC9005520 DOI: 10.1038/s41598-022-09849-8] [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: 10/22/2021] [Accepted: 03/23/2022] [Indexed: 11/24/2022] Open
Abstract
Cadmium selenide quantum dots (QDs) are fluorescent and electron-dense nanoparticles. When used as reporter of immunolabeling, this dual visibility is essential for direct comparison of its fluorescent signals on light microscopy (LM) and their ultrastructrual counterparts on electron microscopy (EM) as correlative light and electron microscopy (CLEM). To facilitate EM recognition, QDs on EM grid were gold enhanced, which increased their size and electron density. On histological sections as well, gold-enhanced QDs, used as a reporter of immunolabeling, were easily recognized on EM. Because target structures are visible on bright field microscopy, gold enhancement facilitated trimming the target structures into final EM sections. Furthermore, gold enhancement of rod-shaped QD655 on EM grid was accentuated on their tips while spherical QD565 was gold-enhanced as sphere in contrast. This EM distinction was evident on histological sections where QD565 (green fluorescence) and QD655 (red fluorescence) were used as a reporter pair for double immunolabeling. Double-labeled immuno-fluorescent images, initially captured before EM processing, are now compared with their respective immuno EM counterparts. Specific labeling of each epitope was corroborated by mutual comparison between LM and EM. Although fluoronanogold may be a candidate reporter partner with QDs for gold-enhanced, double-labeling CLEM, its limited penetration into fixed tissue hampers universal use for thick histological sections. Gold-enhancement of QD immunolabeling, now expanded to double-labeling CLEM for human brain samples, will pave the way to translate molecular events into ultrastructural morphopathogenesis in situ.
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16
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Improved Fluorescent Proteins for Dual-Colour Post-Embedding CLEM. Cells 2022; 11:cells11071077. [PMID: 35406640 PMCID: PMC8997867 DOI: 10.3390/cells11071077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 02/04/2023] Open
Abstract
Post-embedding correlative light and electron microscopy (CLEM) has the advantage of high-precision registration and enables light and electron microscopy imaging of the same slice. However, its broad application has been hampered by the limited available fluorescent proteins (FPs) and a low signal-to-background ratio (SBR). Here, we developed a green photoswitchable FP, mEosEM-E with substantially high on/off contrast in EM samples embedded in Epon resin, which maximally preserves cellular structures but quenches the fluorescence of FPs. Taking advantage of the photoswitching property of mEosEM-E, the autofluorescence background from the resin was significantly reduced by a subtraction-based CLEM (sCLEM) method. Meanwhile, we identified a red fluorescent protein (RFP) mScarlet-H that exhibited higher brightness and SBR in resin than previously reported RFPs. With mEosEM-E and mScarlet-H, dual-colour post-Epon-embedding CLEM images with high SBR and no cross-talk signal were successfully performed to reveal the organization of nucleolar proteins. Moreover, a dissection of the influences of different EM sample preparation steps on the fluorescence preservation for several RFPs provides useful guidance for further probe development.
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17
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Jeong D, Kim D. Recent Developments in Correlative Super-Resolution Fluorescence Microscopy and Electron Microscopy. Mol Cells 2022; 45:41-50. [PMID: 35114646 PMCID: PMC8819494 DOI: 10.14348/molcells.2021.5011] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/31/2021] [Accepted: 12/31/2021] [Indexed: 11/27/2022] Open
Abstract
The recently developed correlative super-resolution fluorescence microscopy (SRM) and electron microscopy (EM) is a hybrid technique that simultaneously obtains the spatial locations of specific molecules with SRM and the context of the cellular ultrastructure by EM. Although the combination of SRM and EM remains challenging owing to the incompatibility of samples prepared for these techniques, the increasing research attention on these methods has led to drastic improvements in their performances and resulted in wide applications. Here, we review the development of correlative SRM and EM (sCLEM) with a focus on the correlation of EM with different SRM techniques. We discuss the limitations of the integration of these two microscopy techniques and how these challenges can be addressed to improve the quality of correlative images. Finally, we address possible future improvements and advances in the continued development and wide application of sCLEM approaches.
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Affiliation(s)
- Dokyung Jeong
- Department of Chemistry, Hanyang University, Seoul 04763, Korea
| | - Doory Kim
- Department of Chemistry, Hanyang University, Seoul 04763, Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Korea
- Institute of Nano Science and Technology, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
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18
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Lane R, Wolters AHG, Giepmans BNG, Hoogenboom JP. Integrated Array Tomography for 3D Correlative Light and Electron Microscopy. Front Mol Biosci 2022; 8:822232. [PMID: 35127826 PMCID: PMC8809480 DOI: 10.3389/fmolb.2021.822232] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/15/2021] [Indexed: 12/22/2022] Open
Abstract
Volume electron microscopy (EM) of biological systems has grown exponentially in recent years due to innovative large-scale imaging approaches. As a standalone imaging method, however, large-scale EM typically has two major limitations: slow rates of acquisition and the difficulty to provide targeted biological information. We developed a 3D image acquisition and reconstruction pipeline that overcomes both of these limitations by using a widefield fluorescence microscope integrated inside of a scanning electron microscope. The workflow consists of acquiring large field of view fluorescence microscopy (FM) images, which guide to regions of interest for successive EM (integrated correlative light and electron microscopy). High precision EM-FM overlay is achieved using cathodoluminescent markers. We conduct a proof-of-concept of our integrated workflow on immunolabelled serial sections of tissues. Acquisitions are limited to regions containing biological targets, expediting total acquisition times and reducing the burden of excess data by tens or hundreds of GBs.
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Affiliation(s)
- Ryan Lane
- Imaging Physics, Delft University of Technology, Delft, Netherlands
- *Correspondence: Ryan Lane,
| | - Anouk H. G. Wolters
- Department of Biomedical Sciences of Cells and Systems, University Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ben N. G. Giepmans
- Department of Biomedical Sciences of Cells and Systems, University Groningen, University Medical Center Groningen, Groningen, Netherlands
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19
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Baatsen P, Gabarre S, Vints K, Wouters R, Vandael D, Goodchild R, Munck S, Gounko NV. Preservation of Fluorescence Signal and Imaging Optimization for Integrated Light and Electron Microscopy. Front Cell Dev Biol 2022; 9:737621. [PMID: 34977003 PMCID: PMC8715528 DOI: 10.3389/fcell.2021.737621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Life science research often needs to define where molecules are located within the complex environment of a cell or tissue. Genetically encoded fluorescent proteins and or fluorescence affinity-labeling are the go-to methods. Although recent fluorescent microscopy methods can provide localization of fluorescent molecules with relatively high resolution, an ultrastructural context is missing. This is solved by imaging a region of interest with correlative light and electron microscopy (CLEM). We have adopted a protocol that preserves both genetically-encoded and antibody-derived fluorescent signals in resin-embedded cell and tissue samples and provides high-resolution electron microscopy imaging of the same thin section. This method is particularly suitable for dedicated CLEM instruments that combine fluorescence and electron microscopy optics. In addition, we optimized scanning EM imaging parameters for samples of varying thicknesses. These protocols will enable rapid acquisition of CLEM information from samples and can be adapted for three-dimensional EM.
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Affiliation(s)
- Pieter Baatsen
- VIB-KU Leuven Center for Brain and Disease Research, Electron Microscopy Platform and VIB-Bioimaging Core, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Sergio Gabarre
- VIB-KU Leuven Center for Brain and Disease Research, Electron Microscopy Platform and VIB-Bioimaging Core, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium.,VIB-KU Leuven Center for Brain and Disease Research, Light Microscopy Expertise Unit and VIB Bioimaging Core, Leuven, Belgium
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain and Disease Research, Electron Microscopy Platform and VIB-Bioimaging Core, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Rosanne Wouters
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium.,VIB-KU Leuven Center for Brain and Disease Research, Laboratory for Membrane Trafficking, Leuven, Belgium
| | - Dorien Vandael
- VIB-KU Leuven Center for Brain and Disease Research, Electron Microscopy Platform and VIB-Bioimaging Core, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Rose Goodchild
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium.,VIB-KU Leuven Center for Brain and Disease Research, Laboratory for Dystonia Research, Leuven, Belgium
| | - Sebastian Munck
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium.,VIB-KU Leuven Center for Brain and Disease Research, Light Microscopy Expertise Unit and VIB Bioimaging Core, Leuven, Belgium
| | - Natalia V Gounko
- VIB-KU Leuven Center for Brain and Disease Research, Electron Microscopy Platform and VIB-Bioimaging Core, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
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20
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Tian B, Xu X, Xue Y, Ji W, Xu T. Cryogenic superresolution correlative light and electron microscopy on the frontier of subcellular imaging. Biophys Rev 2021; 13:1163-1171. [DOI: 10.1007/s12551-021-00851-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/03/2021] [Indexed: 12/22/2022] Open
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21
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Parlanti P, Cappello V. Microscopes, tools, probes, and protocols: A guide in the route of correlative microscopy for biomedical investigation. Micron 2021; 152:103182. [PMID: 34801960 DOI: 10.1016/j.micron.2021.103182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/12/2021] [Accepted: 11/14/2021] [Indexed: 12/11/2022]
Abstract
In the last decades, the advancements of microscopes technology, together with the development of new imaging approaches, are trying to address some biological questions that have been unresolved in the past: the need to combine in the same analysis temporal, functional and morphological information on the biological sample has become pressing. For this reason, the use of correlative microscopy, in which two or more imaging techniques are combined in the same analysis, is getting increasingly widespread. In fact, correlative microscopy can overcome limitations of a single imaging method, giving access to a larger amount of information from the same specimen. However, correlative microscopy can be challenging, and appropriate protocols for sample preparation and imaging methods must be selected. Here we review the state of the art of correlating electron microscopy with different imaging methods, focusing on sample preparation, tools, and labeling methods, with the aim to provide a comprehensive guide for those scientists who are approaching the field of correlative methods.
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Affiliation(s)
- Paola Parlanti
- Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography, Viale Rinaldo Piaggio 34, I-56025, Pontedera (PI), Italy.
| | - Valentina Cappello
- Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography, Viale Rinaldo Piaggio 34, I-56025, Pontedera (PI), Italy.
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22
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Abstract
Fluorescence imaging techniques play a pivotal role in our understanding of the nervous system. The emergence of various super-resolution microscopy methods and specialized fluorescent probes enables direct insight into neuronal structure and protein arrangements in cellular subcompartments with so far unmatched resolution. Super-resolving visualization techniques in neurons unveil a novel understanding of cytoskeletal composition, distribution, motility, and signaling of membrane proteins, subsynaptic structure and function, and neuron-glia interaction. Well-defined molecular targets in autoimmune and neurodegenerative disease models provide excellent starting points for in-depth investigation of disease pathophysiology using novel and innovative imaging methodology. Application of super-resolution microscopy in human brain samples and for testing clinical biomarkers is still in its infancy but opens new opportunities for translational research in neurology and neuroscience. In this review, we describe how super-resolving microscopy has improved our understanding of neuronal and brain function and dysfunction in the last two decades.
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Affiliation(s)
- Christian Werner
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Christian Geis
- Section Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
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23
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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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24
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Turek M, Banasiak K, Piechota M, Shanmugam N, Macias M, Śliwińska MA, Niklewicz M, Kowalski K, Nowak N, Chacinska A, Pokrzywa W. Muscle-derived exophers promote reproductive fitness. EMBO Rep 2021; 22:e52071. [PMID: 34288362 PMCID: PMC8339713 DOI: 10.15252/embr.202052071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 05/08/2021] [Accepted: 05/21/2021] [Indexed: 01/18/2023] Open
Abstract
Organismal functionality and reproduction depend on metabolic rewiring and balanced energy resources. However, the crosstalk between organismal homeostasis and fecundity and the associated paracrine signaling mechanisms are still poorly understood. Using Caenorhabditis elegans, we discovered that large extracellular vesicles (known as exophers) previously found to remove damaged subcellular elements in neurons and cardiomyocytes are released by body wall muscles (BWM) to support embryonic growth. Exopher formation (exopheresis) by BWM is sex-specific and a non-cell autonomous process regulated by developing embryos in the uterus. Embryo-derived factors induce the production of exophers that transport yolk proteins produced in the BWM and ultimately deliver them to newly formed oocytes. Consequently, offspring of mothers with a high number of muscle-derived exophers grew faster. We propose that the primary role of muscular exopheresis is to stimulate reproductive capacity, thereby influencing the adaptation of worm populations to the current environmental conditions.
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Affiliation(s)
- Michał Turek
- ReMedy International Research Agenda Unit, University of Warsaw, Warsaw, Poland.,Laboratory of Mitochondrial Biogenesis, Centre of New Technologies, University of Warsaw, Warsaw, Poland.,Laboratory of Animal Molecular Physiology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Banasiak
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Małgorzata Piechota
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Nilesh Shanmugam
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Matylda Macias
- Core Facility, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Małgorzata Alicja Śliwińska
- Laboratory of Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology Polish Academy of Sciences, Warsaw, Poland
| | - Marta Niklewicz
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Konrad Kowalski
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Natalia Nowak
- Laboratory of Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Chacinska
- ReMedy International Research Agenda Unit, University of Warsaw, Warsaw, Poland.,Laboratory of Mitochondrial Biogenesis, Centre of New Technologies, University of Warsaw, Warsaw, Poland.,IMol Polish Academy of Sciences, Warsaw, Poland
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology, Warsaw, Poland
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25
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Sladowska M, Turek M, Kim MJ, Drabikowski K, Mussulini BHM, Mohanraj K, Serwa RA, Topf U, Chacinska A. Proteasome activity contributes to pro-survival response upon mild mitochondrial stress in Caenorhabditis elegans. PLoS Biol 2021; 19:e3001302. [PMID: 34252079 PMCID: PMC8274918 DOI: 10.1371/journal.pbio.3001302] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/27/2021] [Indexed: 12/15/2022] Open
Abstract
Defects in mitochondrial function activate compensatory responses in the cell. Mitochondrial stress that is caused by unfolded proteins inside the organelle induces a transcriptional response (termed the "mitochondrial unfolded protein response" [UPRmt]) that is mediated by activating transcription factor associated with stress 1 (ATFS-1). The UPRmt increases mitochondrial protein quality control. Mitochondrial dysfunction frequently causes defects in the import of proteins, resulting in the accumulation of mitochondrial proteins outside the organelle. In yeast, cells respond to mistargeted mitochondrial proteins by increasing activity of the proteasome in the cytosol (termed the "unfolded protein response activated by mistargeting of proteins" [UPRam]). The presence and relevance of this response in higher eukaryotes is unclear. Here, we demonstrate that defects in mitochondrial protein import in Caenorhabditis elegans lead to proteasome activation and life span extension. Both proteasome activation and life span prolongation partially depend on ATFS-1, despite its lack of influence on proteasomal gene transcription. Importantly, life span prolongation depends on the fully assembled proteasome. Our data provide a link between mitochondrial dysfunction and proteasomal activity and demonstrate its direct relevance to mechanisms that promote longevity.
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Affiliation(s)
- Maria Sladowska
- ReMedy International Research Agenda Unit, University of Warsaw, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michał Turek
- ReMedy International Research Agenda Unit, University of Warsaw, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Min-Ji Kim
- ReMedy International Research Agenda Unit, University of Warsaw, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Krzysztof Drabikowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Karthik Mohanraj
- ReMedy International Research Agenda Unit, University of Warsaw, Warsaw, Poland
| | - Remigiusz A. Serwa
- ReMedy International Research Agenda Unit, University of Warsaw, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Ulrike Topf
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Chacinska
- ReMedy International Research Agenda Unit, University of Warsaw, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- IMol Polish Academy of Sciences, Warsaw, Poland
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26
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Andrian T, Delcanale P, Pujals S, Albertazzi L. Correlating Super-Resolution Microscopy and Transmission Electron Microscopy Reveals Multiparametric Heterogeneity in Nanoparticles. NANO LETTERS 2021; 21:5360-5368. [PMID: 34125548 PMCID: PMC8227466 DOI: 10.1021/acs.nanolett.1c01666] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/03/2021] [Indexed: 05/22/2023]
Abstract
The functionalization of nanoparticles with functional moieties is a key strategy to achieve cell targeting in nanomedicine. The interplay between size and ligand number is crucial for the formulation performance and needs to be properly characterized to understand nanoparticle structure-activity relations. However, there is a lack of methods able to measure both size and ligand number at the same time and at the single particle level. Here, we address this issue by introducing a correlative light and electron microscopy (CLEM) method combining super-resolution microscopy (SRM) and transmission electron microscopy (TEM) imaging. We apply our super-resCLEM method to characterize the relationship between size and ligand number and density in PLGA-PEG nanoparticles. We highlight how heterogeneity found in size can impact ligand distribution and how a significant part of the nanoparticle population goes completely undetected in the single-technique analysis. Super-resCLEM holds great promise for the multiparametric analysis of other parameters and nanomaterials.
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Affiliation(s)
- Teodora Andrian
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 15-21, 08028 Barcelona, Spain
| | - Pietro Delcanale
- Dipartimento
di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parco area delle Scienze 7/A, 43124 Parma, Italy
| | - Silvia Pujals
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 15-21, 08028 Barcelona, Spain
- Department
of Electronics and Biomedical Engineering, Faculty of Physics, Universitat de Barcelona, Avenido Diagonal 647, 08028, Barcelona, Spain
| | - Lorenzo Albertazzi
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 15-21, 08028 Barcelona, Spain
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
- ;
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27
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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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28
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Calovi S, Soria FN, Tønnesen J. Super-resolution STED microscopy in live brain tissue. Neurobiol Dis 2021; 156:105420. [PMID: 34102277 DOI: 10.1016/j.nbd.2021.105420] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/25/2022] Open
Abstract
STED microscopy is one of several fluorescence microscopy techniques that permit imaging at higher spatial resolution than what the diffraction-limit of light dictates. STED imaging is unique among these super-resolution modalities in being a beam-scanning microscopy technique based on confocal or 2-photon imaging, which provides the advantage of superior optical sectioning in thick samples. Compared to the other super-resolution techniques that are based on widefield microscopy, this makes STED particularly suited for imaging inside live brain tissue, such as in slices or in vivo. Notably, the 50 nm resolution provided by STED microscopy enables analysis of neural morphologies that conventional confocal and 2-photon microscopy approaches cannot resolve, including all-important synaptic structures. Over the course of the last 20 years, STED microscopy has undergone extensive developments towards ever more versatile use, and has facilitated remarkable neurophysiological discoveries. The technique is still not widely adopted for live tissue imaging, even though one of its particular strengths is exactly in resolving the nanoscale dynamics of synaptic structures in brain tissue, as well as in addressing the complex morphologies of glial cells, and revealing the intricate structure of the brain extracellular space. Not least, live tissue STED microscopy has so far hardly been applied in settings of pathophysiology, though also here it shows great promise for providing new insights. This review outlines the technical advantages of STED microscopy for imaging in live brain tissue, and highlights key neurobiological findings brought about by the technique.
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Affiliation(s)
- Stefano Calovi
- Laboratory of Molecular Pharmacology, Institute of Experimental Medicine, Budapest, Hungary; János Szentágothai Doctoral School, Semmelweis University, Budapest, Hungary; Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Federico N Soria
- Achucarro Basque Center for Neuroscience, Leioa, Spain; Department of Neuroscience, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jan Tønnesen
- Achucarro Basque Center for Neuroscience, Leioa, Spain; Department of Neuroscience, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain.
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29
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Lange F, Agüi-Gonzalez P, Riedel D, Phan NTN, Jakobs S, Rizzoli SO. Correlative fluorescence microscopy, transmission electron microscopy and secondary ion mass spectrometry (CLEM-SIMS) for cellular imaging. PLoS One 2021; 16:e0240768. [PMID: 33970908 PMCID: PMC8109779 DOI: 10.1371/journal.pone.0240768] [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: 09/29/2020] [Accepted: 04/13/2021] [Indexed: 11/24/2022] Open
Abstract
Electron microscopy (EM) has been employed for decades to analyze cell structure. To also analyze the positions and functions of specific proteins, one typically relies on immuno-EM or on a correlation with fluorescence microscopy, in the form of correlated light and electron microscopy (CLEM). Nevertheless, neither of these procedures is able to also address the isotopic composition of cells. To solve this, a correlation with secondary ion mass spectrometry (SIMS) would be necessary. SIMS has been correlated in the past to EM or to fluorescence microscopy in biological samples, but not to CLEM. We achieved this here, using a protocol based on transmission EM, conventional epifluorescence microscopy and nanoSIMS. The protocol is easily applied, and enables the use of all three technologies at high performance parameters. We suggest that CLEM-SIMS will provide substantial information that is currently beyond the scope of conventional correlative approaches.
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Affiliation(s)
- Felix Lange
- Research Group Mitochondrial Structure and Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Clinic for Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Paola Agüi-Gonzalez
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Dietmar Riedel
- Laboratory of Electron Microscopy, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Nhu T. N. Phan
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Stefan Jakobs
- Research Group Mitochondrial Structure and Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Clinic for Neurology, University Medical Center Göttingen, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
- * E-mail: (SJ); (SOR)
| | - Silvio O. Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
- * E-mail: (SJ); (SOR)
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30
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Ohta K, Hirashima S, Miyazono Y, Togo A, Nakamura KI. Correlation of organelle dynamics between light microscopic live imaging and electron microscopic 3D architecture using FIB-SEM. Microscopy (Oxf) 2021; 70:161-170. [PMID: 33216938 PMCID: PMC7989057 DOI: 10.1093/jmicro/dfaa071] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/02/2020] [Accepted: 11/18/2020] [Indexed: 12/17/2022] Open
Abstract
Correlative light and electron microscopy (CLEM) methods combined with live imaging can be applied to understand the dynamics of organelles. Although recent advances in cell biology and light microscopy have helped in visualizing the details of organelle activities, observing their ultrastructure or organization of surrounding microenvironments is a challenging task. Therefore, CLEM, which allows us to observe the same area as an optical microscope with an electron microscope, has become a key technique in cell biology. Unfortunately, most CLEM methods have technical drawbacks, and many researchers face difficulties in applying CLEM methods. Here, we propose a live three-dimensional CLEM method, combined with a three-dimensional reconstruction technique using focused ion beam scanning electron microscopy tomography, as a solution to such technical barriers. We review our method, the associated technical limitations and the options considered to perform live CLEM.
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Affiliation(s)
- Keisuke Ohta
- Advanced Imaging Research Center, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka 830-0011, Japan.,Department of Anatomy, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka 830-0011, Japan
| | - Shingo Hirashima
- Department of Anatomy, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka 830-0011, Japan
| | - Yoshihiro Miyazono
- Department of Anatomy, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka 830-0011, Japan
| | - Akinobu Togo
- Advanced Imaging Research Center, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka 830-0011, Japan
| | - Kei-Ichiro Nakamura
- Department of Anatomy, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka 830-0011, Japan
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31
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Zhang X, Man Y, Zhuang X, Shen J, Zhang Y, Cui Y, Yu M, Xing J, Wang G, Lian N, Hu Z, Ma L, Shen W, Yang S, Xu H, Bian J, Jing Y, Li X, Li R, Mao T, Jiao Y, Sodmergen, Ren H, Lin J. Plant multiscale networks: charting plant connectivity by multi-level analysis and imaging techniques. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1392-1422. [PMID: 33974222 DOI: 10.1007/s11427-020-1910-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/04/2021] [Indexed: 12/21/2022]
Abstract
In multicellular and even single-celled organisms, individual components are interconnected at multiscale levels to produce enormously complex biological networks that help these systems maintain homeostasis for development and environmental adaptation. Systems biology studies initially adopted network analysis to explore how relationships between individual components give rise to complex biological processes. Network analysis has been applied to dissect the complex connectivity of mammalian brains across different scales in time and space in The Human Brain Project. In plant science, network analysis has similarly been applied to study the connectivity of plant components at the molecular, subcellular, cellular, organic, and organism levels. Analysis of these multiscale networks contributes to our understanding of how genotype determines phenotype. In this review, we summarized the theoretical framework of plant multiscale networks and introduced studies investigating plant networks by various experimental and computational modalities. We next discussed the currently available analytic methodologies and multi-level imaging techniques used to map multiscale networks in plants. Finally, we highlighted some of the technical challenges and key questions remaining to be addressed in this emerging field.
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Affiliation(s)
- Xi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yi Man
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaohong Zhuang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yi Zhang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing, 100875, China
| | - Yaning Cui
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Meng Yu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jingjing Xing
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 457004, China
| | - Guangchao Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Na Lian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Zijian Hu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Lingyu Ma
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Weiwei Shen
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Shunyao Yang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Huimin Xu
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jiahui Bian
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yanping Jing
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaojuan Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Ruili Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Tonglin Mao
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, 100101, China
| | - Sodmergen
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Haiyun Ren
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing, 100875, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China. .,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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32
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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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33
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Heiligenstein X, de Beer M, Heiligenstein J, Eyraud F, Manet L, Schmitt F, Lamers E, Lindenau J, Kea-Te Lindert M, Salamero J, Raposo G, Sommerdijk N, Belle M, Akiva A. HPM live μ for a full CLEM workflow. Methods Cell Biol 2021; 162:115-149. [PMID: 33707009 DOI: 10.1016/bs.mcb.2020.10.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
With the development of advanced imaging methods that took place in the last decade, the spatial correlation of microscopic and spectroscopic information-known as multimodal imaging or correlative microscopy (CM)-has become a broadly applied technique to explore biological and biomedical materials at different length scales. Among the many different combinations of techniques, Correlative Light and Electron Microscopy (CLEM) has become the flagship of this revolution. Where light (mainly fluorescence) microscopy can be used directly for the live imaging of cells and tissues, for almost all applications, electron microscopy (EM) requires fixation of the biological materials. Although sample preparation for EM is traditionally done by chemical fixation and embedding in a resin, rapid cryogenic fixation (vitrification) has become a popular way to avoid the formation of artifacts related to the chemical fixation/embedding procedures. During vitrification, the water in the sample transforms into an amorphous ice, keeping the ultrastructure of the biological sample as close as possible to the native state. One immediate benefit of this cryo-arrest is the preservation of protein fluorescence, allowing multi-step multi-modal imaging techniques for CLEM. To minimize the delay separating live imaging from cryo-arrest, we developed a high-pressure freezing (HPF) system directly coupled to a light microscope. We address the optimization of sample preservation and the time needed to capture a biological event, going from live imaging to cryo-arrest using HPF. To further explore the potential of cryo-fixation related to the forthcoming transition from imaging 2D (cell monolayers) to imaging 3D samples (tissue) and the associated importance of homogeneous deep vitrification, the HPF core technology has been revisited to allow easy modification of the environmental parameters during vitrification. Lastly, we will discuss the potential of our HPM within CLEM protocols especially for correlating live imaging using the Zeiss LSM900 with electron microscopy.
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Affiliation(s)
| | - Marit de Beer
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Cell Biology, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Biochemistry, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | | | | | | | | | - Mariska Kea-Te Lindert
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Cell Biology, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jean Salamero
- SERPICO Inria Team/UMR 144 CNRS & National Biology and Health Infrastructure "France Bioimaging", Institut Curie, Paris, France
| | - Graça Raposo
- Institut Curie, PSL Research University, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France; Institut Curie, PSL Research University, CNRS, UMR144, Structure and Membrane Compartments, Paris, France
| | - Nico Sommerdijk
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Biochemistry, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Anat Akiva
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Cell Biology, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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34
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Wang X, Xiong H, Liu Y, Yang T, Li A, Huang F, Yin F, Su L, Liu L, Li N, Li L, Cheng S, Liu X, Lv X, Liu X, Chu J, Xu T, Xu F, Gong H, Luo Q, Yuan J, Zeng S. Chemical sectioning fluorescence tomography: high-throughput, high-contrast, multicolor, whole-brain imaging at subcellular resolution. Cell Rep 2021; 34:108709. [PMID: 33535048 DOI: 10.1016/j.celrep.2021.108709] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/18/2020] [Accepted: 01/08/2021] [Indexed: 01/23/2023] Open
Abstract
A thorough neuroanatomical study of the brain architecture is crucial for understanding its cellular compositions, connections, and working mechanisms. However, the fine- and multiscale features of neuron structures make it challenging for microscopic imaging, as it requires high contrast and high throughput simultaneously. Here, we propose chemical sectioning fluorescence tomography (CSFT) to solve this problem. By chemically switching OFF/ON the fluorescent state of the labeled proteins (FPs), we light only the top layer as thin as submicron for imaging without background interference. Combined with the wide-field fluorescence micro-optical sectioning tomography (fMOST) system, we have shown multicolor CSFT imaging. We also demonstrate mouse whole-brain imaging at the subcellular resolution, as well as the power for quantitative acquisition of synaptic-connection-related pyramidal dendritic spines and axon boutons on the brain-wide scale at the complete single-neuron level. We believe that the CSFT method would greatly facilitate our understanding of the brain-wide neuron networks.
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Affiliation(s)
- Xiaojun Wang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Hanqing Xiong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yurong Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Tao Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Fei Huang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Fangfang Yin
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Lei Su
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ling Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ning Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Longhui Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shenghua Cheng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaoxiang Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaohua Lv
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiuli Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jun Chu
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tonghui Xu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Fuqiang Xu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, CAS Centre for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jing Yuan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
| | - Shaoqun Zeng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
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35
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Vos Y, Lane RI, Peddie CJ, Wolters AHG, Hoogenboom JP. Retarding Field Integrated Fluorescence and Electron Microscope. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2021; 27:109-120. [PMID: 33349285 DOI: 10.1017/s1431927620024745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The authors present the application of a retarding field between the electron objective lens and sample in an integrated fluorescence and electron microscope. The retarding field enhances signal collection and signal strength in the electron microscope. This is beneficial for samples prepared for integrated fluorescence and electron microscopy as the amount of staining material added to enhance electron microscopy signal is typically lower compared to conventional samples in order to preserve fluorescence. We demonstrate signal enhancement through the applied retarding field for both 80-nm post-embedding immunolabeled sections and 100-nm in-resin preserved fluorescence sections. Moreover, we show that tuning the electron landing energy particularly improves imaging conditions for ultra-thin (50 nm) sections, where optimization of both retarding field and interaction volume contribute to the signal improvement. Finally, we show that our integrated retarding field setup allows landing energies down to a few electron volts with 0.3 eV dispersion, which opens new prospects for assessing electron beam induced damage by in situ quantification of the observed bleaching of the fluorescence following irradiation.
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Affiliation(s)
- Yoram Vos
- Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, Delft2628CJ, The Netherlands
| | - Ryan I Lane
- Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, Delft2628CJ, The Netherlands
| | - Chris J Peddie
- Electron Microscopy STP, The Francis Crick Institute, 1 Midland Road, LondonNW1 1AT, UK
| | - Anouk H G Wolters
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, A. Deusinglaan 1, Groningen9713 AV, The Netherlands
| | - Jacob P Hoogenboom
- Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, Delft2628CJ, The Netherlands
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36
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Kanemaru T, Kondo T, Nakamura KI, Morimoto H, Nishi K, Isobe SI. A Simple Preparation Method for CLEM Using Pre-Embedding Immunohistochemistry with a Novel Fluorescent Probe and Stable Embedding Resin. Microscopy (Oxf) 2021; 70:368-374. [PMID: 33501988 DOI: 10.1093/jmicro/dfab005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 01/22/2021] [Indexed: 11/13/2022] Open
Abstract
Correlative light and electron microscopy (CLEM) is an excellent approach for examining the cellular localization of biomolecules. Here, we developed a simple method for CLEM by combining pre-embedding immunohistochemistry with a novel fluorescent probe, namely Fluolid NS Orange, and an embedding resin called 'Durcupan™'. Specimens were embedded in Durcupan™ or LR White after immunolabeling and post-fixation using glutaraldehyde and osmium tetroxide. Next, ultrathin sections were prepared on a finder grid with navigation markers. The section of the specimen embedded in Durcupan™ was found to be more stable against electron beam irradiation than specimens embedded in LR White. A fluorescence light microscopy (FLM) image and a transmission electron microscopy (TEM) image, at wide-field, and low magnification, were independently obtained with the same ultrathin section. Using the three corners between finder grid bars as landmarks, FLM images were superimposed with wide-field, low magnification TEM images to identify the region of interest (ROI), which was subsequently enlarged to ascertain cellular structures localized beneath fluorescent signals. However, the enlarged TEM images appeared blurred and fluorescence signals had a hazy appearance. To resolve this, the enlarged TEM images were replaced by high-resolution TEM images focused directly on the ROI, thereby facilitating the collection of high-resolution CLEM images. The simple sample processing method for CLEM using osmium-resistant Fluolid NS Orange and electron beam damage-resistant Durcupan™ allowed the determination of the precise localization of fluorescence signals at subcellular levels.
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Affiliation(s)
- Takaaki Kanemaru
- Department of Morphology Core Unit, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka-city, Fukuoka, 812-8582, Japan
| | - Teruyoshi Kondo
- Department of Animal Pharmaceutical Sciences, School of Pharmaceutical Sciences, Kyushu University of Health and Welfare, 1714-1 Yoshinomachi, Nobeoka-city, Miyazaki, 882-8508, Japan
| | - Kei-Ichiro Nakamura
- Division of Microscopic and Developmental Anatomy, Department of Anatomy, Kurume University School of Medicine, 67 Asahi-machi, Kurume-city, Fukuoka, 830-0011, Japan
| | - Hiroyuki Morimoto
- Second Department of Anatomy, Faculty of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu-city, Fukuoka, 807-8555, Japan
| | - Kentaro Nishi
- Department of Life Science, Faculty of Life Science, Kyushu Sangyo University, 2-3-1 Matsukadai, Higashi-ku, Fukuoka-city, Fukuoka, 813-8503, Japan
| | - Shin-Ichiro Isobe
- Department of Life Science, Faculty of Life Science, Kyushu Sangyo University, 2-3-1 Matsukadai, Higashi-ku, Fukuoka-city, Fukuoka, 813-8503, Japan
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37
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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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38
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Moro L. The Mitochondrial Proteome of Tumor Cells: A SnapShot on Methodological Approaches and New Biomarkers. BIOLOGY 2020; 9:biology9120479. [PMID: 33353059 PMCID: PMC7766083 DOI: 10.3390/biology9120479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/12/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022]
Abstract
Simple Summary Mitochondria are central hubs of cellular signaling, energy metabolism, and redox balance. The plasticity of these cellular organelles is an essential requisite for the cells to cope with different stimuli and stress conditions. Cancer cells are characterized by changes in energy metabolism, mitochondrial signaling, and dynamics. These changes are driven by alterations in the mitochondrial proteome. For this reason, in the last years a focus of basic and cancer research has been the implementation and optimization of technologies to investigate changes in the mitochondrial proteome during cancer initiation and progression. This review presents an overview of the most used technologies to investigate the mitochondrial proteome and recent evidence on changes in the expression levels and delocalization of certain proteins in and out the mitochondria for shaping the functional properties of tumor cells. Abstract Mitochondria are highly dynamic and regulated organelles implicated in a variety of important functions in the cell, including energy production, fatty acid metabolism, iron homeostasis, programmed cell death, and cell signaling. Changes in mitochondrial metabolism, signaling and dynamics are hallmarks of cancer. Understanding whether these modifications are associated with alterations of the mitochondrial proteome is particularly relevant from a translational point of view because it may contribute to better understanding the molecular bases of cancer development and progression and may provide new potential prognostic and diagnostic biomarkers as well as novel molecular targets for anti-cancer treatment. Making an inventory of the mitochondrial proteins has been particularly challenging given that there is no unique consensus targeting sequence that directs protein import into mitochondria, some proteins are present at very low levels, while other proteins are expressed only in some cell types, in a particular developmental stage or under specific stress conditions. This review aims at providing the state-of-the-art on methodologies used to characterize the mitochondrial proteome in tumors and highlighting the biological relevance of changes in expression and delocalization of proteins in and out the mitochondria in cancer biology.
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Affiliation(s)
- Loredana Moro
- Institute of Biomembranes, Bioenergetic and Molecular Biotechnologies, National Research Council, Via Amendola 122/O, 70125 Bari, Italy
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39
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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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40
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Domart F, Cloetens P, Roudeau S, Carmona A, Verdier E, Choquet D, Ortega R. Correlating STED and synchrotron XRF nano-imaging unveils cosegregation of metals and cytoskeleton proteins in dendrites. eLife 2020; 9:62334. [PMID: 33289481 PMCID: PMC7787660 DOI: 10.7554/elife.62334] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/07/2020] [Indexed: 12/20/2022] Open
Abstract
Zinc and copper are involved in neuronal differentiation and synaptic plasticity but the molecular mechanisms behind these processes are still elusive due in part to the difficulty of imaging trace metals together with proteins at the synaptic level. We correlate stimulated-emission-depletion microscopy of proteins and synchrotron X-ray fluorescence imaging of trace metals, both performed with 40 nm spatial resolution, on primary rat hippocampal neurons. We reveal the co-localization at the nanoscale of zinc and tubulin in dendrites with a molecular ratio of about one zinc atom per tubulin-αβ dimer. We observe the co-segregation of copper and F-actin within the nano-architecture of dendritic protrusions. In addition, zinc chelation causes a decrease in the expression of cytoskeleton proteins in dendrites and spines. Overall, these results indicate new functions for zinc and copper in the modulation of the cytoskeleton morphology in dendrites, a mechanism associated to neuronal plasticity and memory formation.
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Affiliation(s)
- Florelle Domart
- Chemical Imaging and Speciation, CENBG, Univ. Bordeaux, Gradignan, France.,CNRS, IN2P3, CENBG, UMR 5797, Gradignan, France.,Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France
| | | | - Stéphane Roudeau
- Chemical Imaging and Speciation, CENBG, Univ. Bordeaux, Gradignan, France.,CNRS, IN2P3, CENBG, UMR 5797, Gradignan, France
| | - Asuncion Carmona
- Chemical Imaging and Speciation, CENBG, Univ. Bordeaux, Gradignan, France.,CNRS, IN2P3, CENBG, UMR 5797, Gradignan, France
| | - Emeline Verdier
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France
| | - Daniel Choquet
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France.,Univ. Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS, Bordeaux, France
| | - Richard Ortega
- Chemical Imaging and Speciation, CENBG, Univ. Bordeaux, Gradignan, France.,CNRS, IN2P3, CENBG, UMR 5797, Gradignan, France
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41
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Photonic-chip assisted correlative light and electron microscopy. Commun Biol 2020; 3:739. [PMID: 33288833 PMCID: PMC7721707 DOI: 10.1038/s42003-020-01473-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 11/10/2020] [Indexed: 11/23/2022] Open
Abstract
Correlative light and electron microscopy (CLEM) unifies the versatility of light microscopy (LM) with the high resolution of electron microscopy (EM), allowing one to zoom into the complex organization of cells. Here, we introduce photonic chip assisted CLEM, enabling multi-modal total internal reflection fluorescence (TIRF) microscopy over large field of view and high precision localization of the target area of interest within EM. The photonic chips are used as a substrate to hold, to illuminate and to provide landmarking of the sample through specially designed grid-like numbering systems. Using this approach, we demonstrate its applicability for tracking the area of interest, imaging the three-dimensional (3D) structural organization of nano-sized morphological features on liver sinusoidal endothelial cells such as fenestrations (trans-cytoplasmic nanopores), and correlating specific endo-lysosomal compartments with its cargo protein upon endocytosis. Tinguely et al. develop a photonic chip-based correlative light-electron microscopy system to generate co-registered multi-modal total internal reflection fluorescence microscopy (TIRF) and electron microscopy (EM) images of biological samples at nanometer scale.
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42
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Luo T, Deng L, Li A, Zhou C, Shao S, Sun Q, Gong H, Yang X, Li X. Scalable Resin Embedding Method for Large-Volume Brain Tissues with High Fluorescence Preservation Capacity. iScience 2020; 23:101717. [PMID: 33196032 PMCID: PMC7645060 DOI: 10.1016/j.isci.2020.101717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/06/2020] [Accepted: 10/16/2020] [Indexed: 01/15/2023] Open
Abstract
Resin embedding is widely used to dissect the fine structure of bio-tissue with electron and optical microscopy. However, it is difficult to embed large-volume tissues with resin. Here, we modified the formula of LR-White resin to prevent the sample cracking during polymerization process and applied this method to the intact brains of mouse, ferret, and macaque. Meanwhile, we increased the fluorescence preservation rate for green fluorescent protein (GFP) from 73 ± 4.0% to 126 ± 3.0% and tdTomato from 60 ± 3.3% to 117 ± 2.8%. Combined with the whole-brain imaging system, we acquired the cytoarchitectonic information and the circuit information such as individual axon and boutons which were labeled with multiple fluorescent proteins. This method shows great potential in the study of continuous fine microstructure information in large-volume tissues from different species, which can facilitate the neuroscience research and help the understanding of the structure-function relationship in complex bio-tissues. Modified LR-White resin embedding was proposed to embed large-volume tissues Retarder α-methyl-styrene was added to prevent cracking during polymerization Resin formula was modified to preserve multiple fluorescent proteins Microstructure information was acquired from the brains of different species
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Affiliation(s)
- Ting Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Lei Deng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,HUST-Suzhou Institute for Brainsmatics, Suzhou 215125, China
| | - Can Zhou
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shuai Shao
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Qingtao Sun
- HUST-Suzhou Institute for Brainsmatics, Suzhou 215125, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,HUST-Suzhou Institute for Brainsmatics, Suzhou 215125, China
| | - Xiaoquan Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,HUST-Suzhou Institute for Brainsmatics, Suzhou 215125, China
| | - Xiangning Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,HUST-Suzhou Institute for Brainsmatics, Suzhou 215125, China
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Andrian T, Bakkum T, van Elsland DM, Bos E, Koster AJ, Albertazzi L, van Kasteren SI, Pujals S. Super-resolution correlative light-electron microscopy using a click-chemistry approach for studying intracellular trafficking. Methods Cell Biol 2020; 162:303-331. [PMID: 33707017 DOI: 10.1016/bs.mcb.2020.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Correlative light and electron microscopy (CLEM) entails a group of multimodal imaging techniques that are combined to pinpoint to the location of fluorescently labeled molecules in the context of their ultrastructural cellular environment. Here we describe a detailed workflow for STORM-CLEM, in which STochastic Optical Reconstruction Microscopy (STORM), an optical super-resolution technique, is correlated with transmission electron microscopy (TEM). This protocol has the advantage that both imaging modalities have resolution at the nanoscale, bringing higher synergies on the information obtained. The sample is prepared according to the Tokuyasu method followed by click-chemistry labeling and STORM imaging. Then, after heavy metal staining, electron microscopy imaging is performed followed by correlation of the two images. The case study presented here is on intracellular pathogens, but the protocol is versatile and could potentially be applied to many types of samples.
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Affiliation(s)
- Teodora Andrian
- Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Thomas Bakkum
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Leiden, The Netherlands
| | - Daphne M van Elsland
- Department of Cell and Chemical Biology, The Institute for Chemical Immunology, Leiden University Medical Center LUMC, Leiden, The Netherlands
| | - Erik Bos
- Department of Cell and Chemical Biology, Section Electron Microscopy, Leiden University Medical Center LUMC, Leiden, The Netherlands
| | - Abraham J Koster
- Department of Cell and Chemical Biology, Section Electron Microscopy, Leiden University Medical Center LUMC, Leiden, The Netherlands
| | - Lorenzo Albertazzi
- Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, Barcelona, Spain; Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Sander I van Kasteren
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Leiden, The Netherlands.
| | - Sílvia Pujals
- Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, Barcelona, Spain; Department of Electronics and Biomedical Engineering, Faculty of Physics, Universitat de Barcelona, Barcelona, Spain.
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Naya M, Sato C. Pyrene Excimer-Based Fluorescent Labeling of Cysteines Brought into Close Proximity by Protein Dynamics: ASEM-Induced Thiol-Ene Click Reaction for High Spatial Resolution CLEM. Int J Mol Sci 2020; 21:E7550. [PMID: 33066147 PMCID: PMC7589919 DOI: 10.3390/ijms21207550] [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: 09/04/2020] [Revised: 10/02/2020] [Accepted: 10/08/2020] [Indexed: 12/16/2022] Open
Abstract
Fluorescence microscopy (FM) has revealed vital molecular mechanisms of life. Mainly, molecules labeled by fluorescent probes are imaged. However, the diversity of labeling probes and their functions remain limited. We synthesized a pyrene-based fluorescent probe targeting SH groups, which are important for protein folding and oxidative stress sensing in cells. The labeling achieved employs thiol-ene click reactions between the probes and SH groups and is triggered by irradiation by UV light or an electron beam. When two tagged pyrene groups were close enough to be excited as a dimer (excimer), they showed red-shifted fluorescence; theoretically, the proximity of two SH residues within ~30 Å can thus be monitored. Moreover, correlative light/electron microscopy (CLEM) was achieved using our atmospheric scanning electron microscope (ASEM); radicals formed in liquid by the electron beam caused the thiol-ene click reactions, and excimer fluorescence of the labeled proteins in cells and tissues was visualized by FM. Since the fluorescent labeling is induced by a narrow electron beam, high spatial resolution labeling is expected. The method can be widely applied to biological fields, for example, to study protein dynamics with or without cysteine mutagenesis, and to beam-induced micro-fabrication and the precise post-modification of materials.
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Affiliation(s)
- Masami Naya
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan;
| | - Chikara Sato
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan;
- Master’s and Doctoral Programs in Neuroscience, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba 305-8574, Japan
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Keevend K, Krummenacher R, Kungas E, Gerken LRH, Gogos A, Stiefel M, Herrmann IK. Correlative Cathodoluminescence Electron Microscopy: Immunolabeling Using Rare-Earth Element Doped Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2004615. [PMID: 33090693 DOI: 10.1002/smll.202004615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/10/2020] [Indexed: 06/11/2023]
Abstract
The understanding of living systems and their building blocks relies on the assessment of structure-function relationships at the nanoscale. Although electron microscopy (EM) gives access to ultrastructural imaging with nanometric resolution, the unambiguous localization of specific molecules is challenging. An EM approach capable of localizing biomolecules with respect to the cellular ultrastructure will offer a direct route to the molecular blueprints of biological systems. In an approach departing from conventional correlative imaging, an electron beam may be used as excitation source to generate optical emission with nanometric resolution, that is, cathodoluminescence (CL). Once suitable luminescent labels become available, CL may be harnessed to enable identification of biomolecule labels based on spectral signatures rather than electron density and size. This work presents CL-enabled immunolabeling based on rare-earth element doped nanoparticle-labels allowing specific molecules to be visualized at nanoscale resolution in the context of the cellular ultrastructure. Folic acid decorated nanoparticles exhibiting single particle CL emission are employed to specifically label receptors and identify characteristic receptor clustering on the surface of cancer cells. This demonstration of CL immunotargeting gives access to protein localization in the context of the cellular ultrastructure and paves the way for immunolabeling of multiple proteins in EM.
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Affiliation(s)
- Kerda Keevend
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, CH-9014, Switzerland
- Nanoparticle Systems Engineering Laboratory, Institute of Process Engineering, Department of Mechanical and Process Engineering, ETH Zürich, Sonneggstrasse 3, Zürich, CH-8092, Switzerland
| | - Roman Krummenacher
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, CH-9014, Switzerland
| | - Egle Kungas
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, CH-9014, Switzerland
| | - Lukas R H Gerken
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, CH-9014, Switzerland
- Nanoparticle Systems Engineering Laboratory, Institute of Process Engineering, Department of Mechanical and Process Engineering, ETH Zürich, Sonneggstrasse 3, Zürich, CH-8092, Switzerland
| | - Alexander Gogos
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, CH-9014, Switzerland
| | - Michael Stiefel
- Laboratory for Transport at Nanoscale Interfaces, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Überlandstrasse 129, Dübendorf, CH-8600, Switzerland
| | - Inge K Herrmann
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, CH-9014, Switzerland
- Nanoparticle Systems Engineering Laboratory, Institute of Process Engineering, Department of Mechanical and Process Engineering, ETH Zürich, Sonneggstrasse 3, Zürich, CH-8092, Switzerland
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46
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Ning X, Wu T, Xiong Q, Zhang F, He PG. Identification of Cell Status via Simultaneous Multitarget Imaging Using Programmable Scanning Electrochemical Microscopy. Anal Chem 2020; 92:12111-12115. [PMID: 32799521 DOI: 10.1021/acs.analchem.0c02457] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A programmable multitarget-response electrochemical imaging technique was presented using scanning electrochemical microscopy (SECM) combined with a self-designed waveform. The potential waveform applied to the tip decreased the charging current caused by the potential switch, enhancing the signal-to-noise ratio. This programmable SECM (P-SECM) method was used to scan a metal strip for verifying its feasibility in feedback mode. Since it could achieve simultaneous multitarget imaging during one single imaging process, PC12 cells status was imaged and identified through three different molecules (FcMeOH, Ru(NH3)63+, and oxygen). The FcMeOH image eliminated the error from cell height, and the Ru(NH3)63+ image verified the change of membrane permeability. Moreover, the oxygen image demonstrated the bioactivity of the cell via its intensity of respiration. Combining information from these three molecules, the cell status could be determined accurately and also the error caused by time consumption with multiple scans in traditional SECM was eliminated.
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Affiliation(s)
- Xin Ning
- School of Chemistry and Molecular Engineering, East China Normal University, No. 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tao Wu
- School of Chemistry and Molecular Engineering, East China Normal University, No. 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Qiang Xiong
- School of Chemistry and Molecular Engineering, East China Normal University, No. 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Fan Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, No. 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Pin-Gang He
- School of Chemistry and Molecular Engineering, East China Normal University, No. 500 Dongchuan Road, Shanghai 200241, P. R. China
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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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Phillips MA, Harkiolaki M, Susano Pinto DM, Parton RM, Palanca A, Garcia-Moreno M, Kounatidis I, Sedat JW, Stuart DI, Castello A, Booth MJ, Davis I, Dobbie IM. CryoSIM: super-resolution 3D structured illumination cryogenic fluorescence microscopy for correlated ultrastructural imaging. OPTICA 2020; 7:802-812. [PMID: 34277893 PMCID: PMC8262592 DOI: 10.1364/optica.393203] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/27/2020] [Accepted: 06/05/2020] [Indexed: 05/19/2023]
Abstract
Rapid cryopreservation of biological specimens is the gold standard for visualizing cellular structures in their true structural context. However, current commercial cryo-fluorescence microscopes are limited to low resolutions. To fill this gap, we have developed cryoSIM, a microscope for 3D super-resolution fluorescence cryo-imaging for correlation with cryo-electron microscopy or cryo-soft X-ray tomography. We provide the full instructions for replicating the instrument mostly from off-the-shelf components and accessible, user-friendly, open-source Python control software. Therefore, cryoSIM democratizes the ability to detect molecules using super-resolution fluorescence imaging of cryopreserved specimens for correlation with their cellular ultrastructure.
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Affiliation(s)
- Michael A. Phillips
- Micron Advanced Bio-imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
- STRUBI, Division of Structural Biology, Wellcome Centre for Human Genetics, Old Road Campus, Roosevelt Drive, Oxford OX3 7BN,
UK
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE,
UK
| | - Maria Harkiolaki
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE,
UK
| | - David Miguel Susano Pinto
- Micron Advanced Bio-imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
| | - Richard M. Parton
- Micron Advanced Bio-imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
| | - Ana Palanca
- Department of Anatomy and Cell Biology, Faculty of Medicine, Universidad de Cantabria, CP39011 Santander,
Spain
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
| | - Manuel Garcia-Moreno
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
| | - Ilias Kounatidis
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE,
UK
| | - John W. Sedat
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143,
USA
| | - David I. Stuart
- STRUBI, Division of Structural Biology, Wellcome Centre for Human Genetics, Old Road Campus, Roosevelt Drive, Oxford OX3 7BN,
UK
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE,
UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
| | - Martin J. Booth
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ,
UK
| | - Ilan Davis
- Micron Advanced Bio-imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
- e-mail:
| | - Ian M. Dobbie
- Micron Advanced Bio-imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
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Ganeva I, Kukulski W. Membrane Architecture in the Spotlight of Correlative Microscopy. Trends Cell Biol 2020; 30:577-587. [DOI: 10.1016/j.tcb.2020.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 12/19/2022]
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50
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Qiu K, Du Y, Liu J, Guan JL, Chao H, Diao J. Super-resolution observation of lysosomal dynamics with fluorescent gold nanoparticles. Theranostics 2020; 10:6072-6081. [PMID: 32483439 PMCID: PMC7254985 DOI: 10.7150/thno.42134] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/30/2020] [Indexed: 02/05/2023] Open
Abstract
Because lysosomes play critical roles in multiple cellular functions and are associated with many diseases, studying them at the subcellular level could elucidate their functionality and support the discovery of therapeutic drugs for treating those diseases. The commonly used dyes for super-resolution imaging of lysosomes are the commercial molecular LysoTrackers. But the tolerance to changes in the lysosomal microenvironment and to lysosomal membrane permeabilization (LMP) and the photostability of the LysoTrackers are worrisome. The purpose of our study was to evaluate the feasibility of performing a fluorescent gold nanoprobe for super-resolution observation of lysosomal dynamics in living cells and compare it to the commercial LysoTrackers. Methods: The nanoprobe Cy5@Au NP contained three parts: a bio-inert gold core, a biocompatible polyethylene glycol spacer, and a fluorophore cyanine 5. Structured illumination microscopy (SIM) was employed to capture the fluorescence of Cy5@Au NPs in cells. The tolerance assays to changes in the lysosomal microenvironment and to LMP, the photobleaching assay, and the long-term lysosomes labelling assay of Cy5@Au NPs were compared with commercial LysoTrackers. The super-resolution observation of lysosomal dynamics with Cy5@Au NPs was performed. Results: Cy5@Au NPs can light up lysosomes specifically under SIM. Compared with commercial lysosomal molecular probes, Cy5@Au NPs exhibited stronger tolerance in lysosomes during various treatments, and changes in the lysosomal microenvironment and LMP did not cause Cy5@Au NPs to lose track of their targets. Cy5@Au NPs demonstrated an excellent anti-photobleaching ability, and a long-term labelling assay revealed that they could label lysosomes more than 3 d. Biological events of lysosomes such as the kiss-and-run process, fusion, fission, and mitophagy were recorded with the fluorescent Cy5@Au NPs under SIM. Conclusions: The nanoprobe Cy5@Au NP was successfully used as a lysosomal probe for the super-resolution observation in living cells and found to overcome the limitations of commercial LysoTrackers. Our results thus confirm that nanoparticles can be useful tools for subcellular super-resolution imaging and highlight new avenues for using nanoparticles in biology.
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