1
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Vijayakrishnan S. In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview. Subcell Biochem 2023; 106:3-36. [PMID: 38159222 DOI: 10.1007/978-3-031-40086-5_1] [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] [Indexed: 01/03/2024]
Abstract
Cryo-electron tomography (cryo-ET) has emerged as a powerful tool in structural biology to study viruses and is undergoing a resolution revolution. Enveloped viruses comprise several RNA and DNA pleomorphic viruses that are pathogens of clinical importance to humans and animals. Considerable efforts in cryogenic correlative light and electron microscopy (cryo-CLEM), cryogenic focused ion beam milling (cryo-FIB), and integrative structural techniques are helping to identify virus structures within cells leading to a rise of in situ discoveries shedding light on how viruses interact with their hosts during different stages of infection. This chapter reviews recent advances in the application of cryo-ET in imaging enveloped viruses and the structural and mechanistic insights revealed studying the viral infection cycle within their eukaryotic cellular hosts, with particular attention to viral entry, replication, assembly, and egress during infection.
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Affiliation(s)
- Swetha Vijayakrishnan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, Glasgow, Scotland, UK.
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2
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Abstract
The three-dimensional organization of biomolecules important for the functioning of all living systems can be determined by cryo-electron tomography imaging under native biological contexts. Cryo-electron tomography is continually expanding and evolving, and the development of new methods that use the latest technology for sample thinning is enabling the visualization of ever larger and more complex biological systems, allowing imaging across scales. Quantitative cryo-electron tomography possesses the capability of visualizing the impact of molecular and environmental perturbations in subcellular structure and function to understand fundamental biological processes. This review provides an overview of current hardware and software developments that allow quantitative cryo-electron tomography studies and their limitations and how overcoming them may allow us to unleash the full power of cryo-electron tomography.
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Affiliation(s)
- Paula P Navarro
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
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3
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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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4
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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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5
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Gabarre S, Vernaillen F, Baatsen P, Vints K, Cawthorne C, Boeynaems S, Michiels E, Vandael D, Gounko NV, Munck S. A workflow for streamlined acquisition and correlation of serial regions of interest in array tomography. BMC Biol 2021; 19:152. [PMID: 34330271 PMCID: PMC8323292 DOI: 10.1186/s12915-021-01072-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 06/14/2021] [Indexed: 11/20/2022] Open
Abstract
Background Array tomography (AT) is a high-resolution imaging method to resolve fine details at the organelle level and has the advantage that it can provide 3D volumes to show the tissue context. AT can be carried out in a correlative way, combing light and electron microscopy (LM, EM) techniques. However, the correlation between modalities can be a challenge and delineating specific regions of interest in consecutive sections can be time-consuming. Integrated light and electron microscopes (iLEMs) offer the possibility to provide well-correlated images and may pose an ideal solution for correlative AT. Here, we report a workflow to automate navigation between regions of interest. Results We use a targeted approach that allows imaging specific tissue features, like organelles, cell processes, and nuclei at different scales to enable fast, directly correlated in situ AT using an integrated light and electron microscope (iLEM-AT). Our workflow is based on the detection of section boundaries on an initial transmitted light acquisition that serves as a reference space to compensate for changes in shape between sections, and we apply a stepwise refinement of localizations as the magnification increases from LM to EM. With minimal user interaction, this enables autonomous and speedy acquisition of regions containing cells and cellular organelles of interest correlated across different magnifications for LM and EM modalities, providing a more efficient way to obtain 3D images. We provide a proof of concept of our approach and the developed software tools using both Golgi neuronal impregnation staining and fluorescently labeled protein condensates in cells. Conclusions Our method facilitates tracing and reconstructing cellular structures over multiple sections, is targeted at high resolution ILEMs, and can be integrated into existing devices, both commercial and custom-built systems. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01072-7.
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Affiliation(s)
- Sergio Gabarre
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,VIB-KU Leuven Center for Brain & Disease Research, Light Microscopy Expertise Unit & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Frank Vernaillen
- VIB BioInformatics Core, Technologiepark 75, 9052, Ghent, Belgium
| | - Pieter Baatsen
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | | | - Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Emiel Michiels
- VIB Center for Brain and Disease Research, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium
| | - Dorien Vandael
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Natalia V Gounko
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium. .,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.
| | - Sebastian Munck
- KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium. .,VIB-KU Leuven Center for Brain & Disease Research, Light Microscopy Expertise Unit & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.
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6
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Ikegami H, Akiba K, Minoda H. Evaluation of electron radiation damage to green fluorescent protein. Ultramicroscopy 2021; 225:113272. [PMID: 33932732 DOI: 10.1016/j.ultramic.2021.113272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/25/2021] [Accepted: 04/02/2021] [Indexed: 12/01/2022]
Abstract
Green fluorescent protein (GFP) emits light when irradiated by not only light but also electrons. This electron-induced light emission called cathodoluminescence (CL) can be used to realize a high-resolution light emission microscopy based on the irradiation of a very narrow electron beam. To implement CL mapping in life sciences the investigation of the damage resistance of GFP to electron irradiation needs to be clarified. In this study, we investigated the electron radiation damage to GFP by analyzing the change in the CL intensity during electron beam irradiation. Since some of the CL spectra changed in shape during electron irradiation, the change in the intensity between 585 and 605 nm were measured. The characteristic doses at different electron current densities and electron energies were investigated. The characteristic dose of EGFP is much larger than that of coronene, which is one of the stable organic molecules against the electron beam irradiation.
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Affiliation(s)
- H Ikegami
- Department of Applied Physics, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo 184-8588, Japan
| | - K Akiba
- Department of Applied Physics, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo 184-8588, Japan
| | - H Minoda
- Department of Applied Physics, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo 184-8588, Japan.
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7
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Yang JE, Larson MR, Sibert BS, Shrum S, Wright ER. CorRelator: Interactive software for real-time high precision cryo-correlative light and electron microscopy. J Struct Biol 2021; 213:107709. [PMID: 33610654 PMCID: PMC8601405 DOI: 10.1016/j.jsb.2021.107709] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/06/2021] [Accepted: 02/11/2021] [Indexed: 12/31/2022]
Abstract
Cryo-correlative light and electron microscopy (CLEM) is a technique that uses the spatiotemporal cues from fluorescence light microscopy (FLM) to investigate the high-resolution ultrastructure of biological samples by cryo-electron microscopy (cryo-EM). Cryo-CLEM provides advantages for identifying and distinguishing fluorescently labeled proteins, macromolecular complexes, and organelles from the cellular environment. Challenges remain on how correlation workflows and software tools are implemented on different microscope platforms to support automated cryo-EM data acquisition. Here, we present CorRelator: an open-source desktop application that bridges between cryo-FLM and real-time cryo-EM/ET automated data collection. CorRelator implements a pixel-coordinate-to-stage-position transformation for flexible, high accuracy on-the-fly and post-acquisition correlation. CorRelator can be integrated into cryo-CLEM workflows and easily adapted to standard fluorescence and transmission electron microscope (TEM) system configurations. CorRelator was benchmarked under live-cell and cryogenic conditions using several FLM and TEM instruments, demonstrating that CorRelator reliably supports real-time, automated correlative cryo-EM/ET acquisition, through a combination of software-aided and interactive alignment. CorRelator is a cross-platform software package featuring an intuitive Graphical User Interface (GUI) that guides the user through the correlation process. CorRelator source code is available at: https://github.com/wright-cemrc-projects/corr.
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Affiliation(s)
- Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States
| | - Matthew R Larson
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States
| | - Bryan S Sibert
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States
| | - Samantha Shrum
- Biophysics Graduate Program, University of Wisconsin, Madison, WI 53706, United States
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Biophysics Graduate Program, University of Wisconsin, Madison, WI 53706, United States; Morgridge Institute for Research, Madison, WI, 53715, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States.
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8
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KUBA JAKUB, MITCHELS JOHN, HOVORKA MILOŠ, ERDMANN PHILIPP, BERKA LUKÁŠ, KIRMSE ROBERT, KÖNIG JULIA, DE BOCK JAN, GOETZE BERNHARD, RIGORT ALEXANDER. Advanced cryo‐tomography workflow developments – correlative microscopy, milling automation and cryo‐lift‐out. J Microsc 2020; 281:112-124. [DOI: 10.1111/jmi.12939] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/22/2020] [Accepted: 06/16/2020] [Indexed: 01/13/2023]
Affiliation(s)
- JAKUB KUBA
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | - JOHN MITCHELS
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | - MILOŠ HOVORKA
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | - PHILIPP ERDMANN
- Department of Molecular Structural Biology Max Planck Institute of Biochemistry Martinsried Germany
| | - LUKÁŠ BERKA
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | | | | | - JAN DE BOCK
- Leica Microsystems CMS GmbH Mannheim Germany
| | - BERNHARD GOETZE
- Thermo Fisher Scientific FEI Deutschland GmbH Planegg Germany
| | - ALEXANDER RIGORT
- Department of Molecular Structural Biology Max Planck Institute of Biochemistry Martinsried Germany
- Thermo Fisher Scientific FEI Deutschland GmbH Planegg Germany
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9
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Mohammadian S, Agronskaia AV, Blab GA, van Donselaar EG, de Heus C, Liv N, Klumperman J, Gerritsen HC. Integrated super resolution fluorescence microscopy and transmission electron microscopy. Ultramicroscopy 2020; 215:113007. [PMID: 32470633 DOI: 10.1016/j.ultramic.2020.113007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/14/2020] [Accepted: 04/19/2020] [Indexed: 10/24/2022]
Abstract
In correlative light and electron microscopy (CLEM), the capabilities of fluorescence microscopy (FM) and electron microscopy (EM) are united. FM combines a large field of view with high sensitivity for detecting fluorescence, which makes it an excellent tool for identifying regions of interest. EM has a much smaller field of view but offers superb resolution that allows studying cellular ultrastructure. In CLEM, the potentials of both techniques are combined but a limiting factor is the large difference in resolution between the two imaging modalities. Adding super resolution FM to CLEM reduces the resolution gap between FM and EM; it offers the possibility of identifying multiple targets within the diffraction limit and can increase correlation accuracy. CLEM is usually carried out in two separate setups, which requires transfer of the sample. This may result in distortion and damage of the specimen, which can complicate finding back regions of interest. By integrating the two imaging modalities, such problems can be avoided. Here, an integrated super resolution correlative microscopy approach is presented based on a wide-field super resolution FM integrated in a Transmission Electron Microscope (TEM). Switching imaging modalities is accomplished by rotation of the TEM sample holder. First imaging experiments are presented on sections of Lowicryl embedded Human Umbilical Vein Endothelial Cells labeled for Caveolin both with Protein A-Gold, and Alexa Fluor®647. TEM and FM images were overlaid using fiducial markers visible in both imaging modalities with an overlay accuracy of 28 ± 11 nm. This is close to the optical resolution of ~50 nm.
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Affiliation(s)
- Sajjad Mohammadian
- Molecular Biophysics, Department of Physics, Faculty of Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands
| | - Alexandra V Agronskaia
- Molecular Biophysics, Department of Physics, Faculty of Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands
| | - Gerhard A Blab
- Molecular Biophysics, Department of Physics, Faculty of Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands
| | - Elly G van Donselaar
- Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Cecilia de Heus
- Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Nalan Liv
- Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Judith Klumperman
- Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Hans C Gerritsen
- Molecular Biophysics, Department of Physics, Faculty of Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands.
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10
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Gorelick S, Buckley G, Gervinskas G, Johnson TK, Handley A, Caggiano MP, Whisstock JC, Pocock R, de Marco A. PIE-scope, integrated cryo-correlative light and FIB/SEM microscopy. eLife 2019; 8:e45919. [PMID: 31259689 PMCID: PMC6609333 DOI: 10.7554/elife.45919] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/26/2019] [Indexed: 11/14/2022] Open
Abstract
Cryo-electron tomography (cryo-ET) is emerging as a revolutionary method for resolving the structure of macromolecular complexes in situ. However, sample preparation for in situ Cryo-ET is labour-intensive and can require both cryo-lamella preparation through cryo-focused ion beam (FIB) milling and correlative light microscopy to ensure that the event of interest is present in the lamella. Here, we present an integrated cryo-FIB and light microscope setup called the Photon Ion Electron microscope (PIE-scope) that enables direct and rapid isolation of cellular regions containing protein complexes of interest. Specifically, we demonstrate the versatility of PIE-scope by preparing targeted cryo-lamellae from subcellular compartments of neurons from transgenic Caenorhabditis elegans and Drosophila melanogaster expressing fluorescent proteins. We designed PIE-scope to enable retrofitting of existing microscopes, which will increase the throughput and accuracy on projects requiring correlative microscopy to target protein complexes. This new approach will make cryo-correlative workflow safer and more accessible.
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Affiliation(s)
- Sergey Gorelick
- ARC Centre of Excellence in Advanced Molecular ImagingMonash UniversityClaytonAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
| | - Genevieve Buckley
- ARC Centre of Excellence in Advanced Molecular ImagingMonash UniversityClaytonAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
| | | | | | - Ava Handley
- Department of Anatomy and Developmental Biology, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
| | - Monica Pia Caggiano
- ARC Centre of Excellence in Advanced Molecular ImagingMonash UniversityClaytonAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
| | - James C Whisstock
- ARC Centre of Excellence in Advanced Molecular ImagingMonash UniversityClaytonAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
- University of WarwickCoventryUnited Kingdom
- EMBL AustraliaClaytonAustralia
| | - Roger Pocock
- Department of Anatomy and Developmental Biology, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
| | - Alex de Marco
- ARC Centre of Excellence in Advanced Molecular ImagingMonash UniversityClaytonAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
- University of WarwickCoventryUnited Kingdom
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11
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Saarinen J, Gütter F, Lindman M, Agopov M, Fraser-Miller SJ, Scherließ R, Jokitalo E, Santos HA, Peltonen L, Isomäki A, Strachan CJ. Cell-Nanoparticle Interactions at (Sub)-Nanometer Resolution Analyzed by Electron Microscopy and Correlative Coherent Anti-Stokes Raman Scattering. Biotechnol J 2018; 14:e1800413. [PMID: 30350922 DOI: 10.1002/biot.201800413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/25/2018] [Indexed: 01/15/2023]
Abstract
A wide variety of nanoparticles are playing an increasingly important role in drug delivery. Label-free imaging techniques are especially desirable to follow the cellular uptake and intracellular fate of nanoparticles. The combined correlative use of different techniques, each with unique advantages, facilitates more detailed investigation about such interactions. The synergistic use of correlative coherent anti-Stokes Raman scattering and electron microscopy (C-CARS-EM) imaging offers label-free, chemically-specific, and (sub)-nanometer spatial resolution for studying nanoparticle uptake into cells as demonstrated in the current study. Coherent anti-Stokes Raman scattering (CARS) microscopy offers chemically-specific (sub)micron spatial resolution imaging without fluorescent labels while transmission electron microscopy (TEM) offers (sub)-nanometer scale spatial resolution and thus visualization of precise nanoparticle localization at the sub-cellular level. This proof-of-concept imaging platform with unlabeled drug nanocrystals and macrophage cells revealed good colocalization between the CARS signal and electron dense nanocrystals in TEM images. The correlative TEM images revealed subcellular localization of nanocrystals inside membrane bound vesicles, showing multivesicular body (MVB)-like morphology typical for late endosomes (LEs), endolysosomes, and phagolysosomes. C-CARS-EM imaging has much potential to study the interactions between a wide range of nanoparticles and cells with high precision and confidence.
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Affiliation(s)
- Jukka Saarinen
- Drug Research Program, Division of Pharmaceutical Chemistry and , University of Helsinki, Viikinkaari 5 E (PO Box 56), 00014 Helsinki, Finland
| | - Friederike Gütter
- Pharmaceutical Institute Department of Pharmaceutics and Biopharmaceutics, Faculty of Mathematics and Natural Sciences, Kiel University, Grasweg 9a, 24118 Kiel, Germany
| | - Mervi Lindman
- Institute of Biotechnology, Electron Microscopy Unit, University of Helsinki, Viikinkaari 9 (PO Box 56), 00014 Helsinki, Finland
| | - Mikael Agopov
- Drug Research Program, Division of Pharmaceutical Chemistry and , University of Helsinki, Viikinkaari 5 E (PO Box 56), 00014 Helsinki, Finland
| | - Sara J Fraser-Miller
- Drug Research Program, Division of Pharmaceutical Chemistry and , University of Helsinki, Viikinkaari 5 E (PO Box 56), 00014 Helsinki, Finland.,Dodd-Walls Centre, Department of Chemistry, University of Otago, PO Box 56, 9056 Dunedin, New Zealand
| | - Regina Scherließ
- Pharmaceutical Institute Department of Pharmaceutics and Biopharmaceutics, Faculty of Mathematics and Natural Sciences, Kiel University, Grasweg 9a, 24118 Kiel, Germany
| | - Eija Jokitalo
- Institute of Biotechnology, Electron Microscopy Unit, University of Helsinki, Viikinkaari 9 (PO Box 56), 00014 Helsinki, Finland
| | - Hélder A Santos
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Viikinkaari 5 E (PO Box 56), 00014 Helsinki, Finland
| | - Leena Peltonen
- Drug Research Program, Division of Pharmaceutical Chemistry and , University of Helsinki, Viikinkaari 5 E (PO Box 56), 00014 Helsinki, Finland
| | - Antti Isomäki
- Biomedicum Imaging Unit, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8 (PO Box 63), 00014 Helsinki, Finland
| | - Clare J Strachan
- Drug Research Program, Division of Pharmaceutical Chemistry and , University of Helsinki, Viikinkaari 5 E (PO Box 56), 00014 Helsinki, Finland
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12
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Ando T, Bhamidimarri SP, Brending N, Colin-York H, Collinson L, De Jonge N, de Pablo PJ, Debroye E, Eggeling C, Franck C, Fritzsche M, Gerritsen H, Giepmans BNG, Grunewald K, Hofkens J, Hoogenboom JP, Janssen KPF, Kaufman R, Klumpermann J, Kurniawan N, Kusch J, Liv N, Parekh V, Peckys DB, Rehfeldt F, Reutens DC, Roeffaers MBJ, Salditt T, Schaap IAT, Schwarz US, Verkade P, Vogel MW, Wagner R, Winterhalter M, Yuan H, Zifarelli G. The 2018 correlative microscopy techniques roadmap. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:443001. [PMID: 30799880 PMCID: PMC6372154 DOI: 10.1088/1361-6463/aad055] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/14/2018] [Accepted: 07/01/2018] [Indexed: 05/19/2023]
Abstract
Developments in microscopy have been instrumental to progress in the life sciences, and many new techniques have been introduced and led to new discoveries throughout the last century. A wide and diverse range of methodologies is now available, including electron microscopy, atomic force microscopy, magnetic resonance imaging, small-angle x-ray scattering and multiple super-resolution fluorescence techniques, and each of these methods provides valuable read-outs to meet the demands set by the samples under study. Yet, the investigation of cell development requires a multi-parametric approach to address both the structure and spatio-temporal organization of organelles, and also the transduction of chemical signals and forces involved in cell-cell interactions. Although the microscopy technologies for observing each of these characteristics are well developed, none of them can offer read-out of all characteristics simultaneously, which limits the information content of a measurement. For example, while electron microscopy is able to disclose the structural layout of cells and the macromolecular arrangement of proteins, it cannot directly follow dynamics in living cells. The latter can be achieved with fluorescence microscopy which, however, requires labelling and lacks spatial resolution. A remedy is to combine and correlate different readouts from the same specimen, which opens new avenues to understand structure-function relations in biomedical research. At the same time, such correlative approaches pose new challenges concerning sample preparation, instrument stability, region of interest retrieval, and data analysis. Because the field of correlative microscopy is relatively young, the capabilities of the various approaches have yet to be fully explored, and uncertainties remain when considering the best choice of strategy and workflow for the correlative experiment. With this in mind, the Journal of Physics D: Applied Physics presents a special roadmap on the correlative microscopy techniques, giving a comprehensive overview from various leading scientists in this field, via a collection of multiple short viewpoints.
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Affiliation(s)
- Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | | | | | - H Colin-York
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
| | | | - Niels De Jonge
- INM-Leibniz Institute for New Materials, 66123 Saarbrücken, Germany
- Saarland University, 66123 Saarbrücken, Germany
| | - P J de Pablo
- Dpto. Física de la Materia Condensada Universidad Autónoma de Madrid 28049, Madrid, Spain
- Instituto de Física de la Materia Condensada IFIMAC, Universidad Autónoma de Madrid 28049, Madrid, Spain
| | - Elke Debroye
- KU Leuven, Department of Chemistry, B-3001 Heverlee, Belgium
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
- Institute of Applied Optics, Friedrich-Schiller University, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
| | - Christian Franck
- Department of Mechanical Engineering, University of Wisconsin-Madison, 1513 University Ave, Madison, WI 53706, United States of America
| | - Marco Fritzsche
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Hans Gerritsen
- Debye Institute, Utrecht University, Utrecht, Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Kay Grunewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Centre of Structural Systems Biology Hamburg and University of Hamburg, Hamburg, Germany
- Heinrich-Pette-Institute, Leibniz Institute of Virology, Hamburg, Germany
| | - Johan Hofkens
- KU Leuven, Department of Chemistry, B-3001 Heverlee, Belgium
| | | | | | - Rainer Kaufman
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Centre of Structural Systems Biology Hamburg and University of Hamburg, Hamburg, Germany
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Judith Klumpermann
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584CX Utrecht, Netherlands
| | - Nyoman Kurniawan
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584CX Utrecht, Netherlands
| | - Viha Parekh
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Diana B Peckys
- Faculty of Medicine, Saarland University, 66421 Homburg, Germany
| | - Florian Rehfeldt
- University of Göttingen, Third Institute of Physics-Biophysics, 37077 Göttingen, Germany
| | - David C Reutens
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Tim Salditt
- University of Göttingen, Institute for X-Ray Physics, 37077 Göttingen, Germany
| | - Iwan A T Schaap
- SmarAct GmbH, Schütte-Lanz-Str. 9, D-26135 Oldenburg, Germany
| | - Ulrich S Schwarz
- Institute for Theoretical Physics and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Michael W Vogel
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Richard Wagner
- Department of Life Sciences & Chemistry, Jacobs University, Bremen, Germany
| | | | - Haifeng Yuan
- KU Leuven, Department of Chemistry, B-3001 Heverlee, Belgium
| | - Giovanni Zifarelli
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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Möbius W, Posthuma G. Sugar and ice: Immunoelectron microscopy using cryosections according to the Tokuyasu method. Tissue Cell 2018; 57:90-102. [PMID: 30201442 DOI: 10.1016/j.tice.2018.08.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/26/2018] [Accepted: 08/22/2018] [Indexed: 11/29/2022]
Abstract
Since the pioneering work of Kiyoteru Tokuyasu in the 70ths the use of thawed cryosections prepared according to the "Tokuyasu-method" for immunoelectron microscopy did not lose popularity. We owe this method a whole subcellular world described by discrete gold particles pointing at cargo, receptors and organelle markers on delicate images of the inner life of a cell. Here we explain the procedure of sample preparation, sectioning and immunolabeling in view of recent developments and the reasoning behind protocols including some historical perspective. Cryosections are prepared from chemically fixed and sucrose infiltrated samples and labeled with affinity probes and electron dense markers. These sections are ideal substrates for immunolabeling, since antigens are not exposed to organic solvent dehydration or masked by resin. Instead, the structures remain fully hydrated throughout the labeling procedure. Furthermore, target molecules inside dense intercellular structural elements, cells and organelles are accessible to antibodies from the section surface. For the validation of antibody specificity several approaches are recommended including knock-out tissue and reagent controls. Correlative light and electron microscopy strategies involving correlative probes are possible as well as correlation of live imaging with the underlying ultrastructure. By applying stereology, gold labeling can be quantified and evaluated for specificity.
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Affiliation(s)
- Wiebke Möbius
- Electron Microscopy Core Unit, Department of Neurogenetics, Max Planck Institute of Experimental Medicine, 37075, Göttingen, Germany; Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany.
| | - George Posthuma
- Department of Cell Biology, Cell Microscopy Core, University Medical Center Utrecht, Utrecht University, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands.
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The application of CorrSight™ in correlative light and electron microscopy of vitrified biological specimens. BIOPHYSICS REPORTS 2018. [DOI: 10.1007/s41048-018-0059-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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15
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Engberts KB, Seinen C, Geerts WJC, Heijnen HFG. Electron Tomography and Correlative Approaches in Platelet Studies. Methods Mol Biol 2018; 1812:55-79. [PMID: 30171572 DOI: 10.1007/978-1-4939-8585-2_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Blood platelets play a central role in the arrest of bleeding and the development of thrombosis. Unraveling the complex processes of platelet biogenesis from megakaryocytes, platelet adhesion, aggregation, and secretory responses are important topics in the field of hemostasis and thrombosis. Analysis of the ultrastructural changes that occur during these processes is essential for understanding the rapid membrane dynamics and has contributed substantially to our present knowledge of platelet formation and functioning. Recent developments in real-time imaging, correlative light and electron microscopy imaging (CLEM), and 3D (cryo) electron microscopy and tomography offer exciting opportunities to improve studies of the platelet adhesive responses and secretion at the ultrastructural level in a close to native environment. In this chapter we discuss and illustrate cryo preparation techniques (high-pressure freezing, vitrification), correlative LM and EM workflows, and 3D cryo-electron tomography that we apply in our current research projects.
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Affiliation(s)
- Kasia B Engberts
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Cor Seinen
- Laboratory of Clinical Chemistry and Hematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Willie J C Geerts
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Harry F G Heijnen
- Laboratory of Clinical Chemistry and Hematology, University Medical Center Utrecht, Utrecht, The Netherlands. .,Department of Cell Biology, Cell Microscopy Core, University Medical Center Utrecht, Utrecht, The Netherlands.
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17
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Anderson KL, Page C, Swift MF, Hanein D, Volkmann N. Marker-free method for accurate alignment between correlated light, cryo-light, and electron cryo-microscopy data using sample support features. J Struct Biol 2018; 201:46-51. [PMID: 29113849 PMCID: PMC5748349 DOI: 10.1016/j.jsb.2017.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 12/30/2022]
Abstract
Combining fluorescence microscopy with electron cryo-tomography allows, in principle, spatial localization of tagged macromolecular assemblies and structural features within the cellular environment. To allow precise localization and scale integration between the two disparate imaging modalities, accurate alignment procedures are needed. Here, we describe a marker-free method for aligning images from light or cryo-light fluorescence microscopy and from electron cryo-microscopy that takes advantage of sample support features, namely the holes in the carbon film. We find that the accuracy of this method, as judged by prediction errors of the hole center coordinates, is better than 100 nm.
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Affiliation(s)
- Karen L Anderson
- Sanford-Burnham-Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, CA, USA
| | - Christopher Page
- Sanford-Burnham-Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, CA, USA
| | - Mark F Swift
- Sanford-Burnham-Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, CA, USA
| | - Dorit Hanein
- Sanford-Burnham-Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, CA, USA
| | - Niels Volkmann
- Sanford-Burnham-Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, CA, USA.
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18
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Hackley PC, Valentine BJ, Voortman LM, VAN Oosten Slingeland DSB, Hatcherian J. Utilization of integrated correlative light and electron microscopy (iCLEM) for imaging sedimentary organic matter. J Microsc 2017; 267:371-383. [PMID: 28665484 DOI: 10.1111/jmi.12576] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/17/2017] [Accepted: 04/12/2017] [Indexed: 01/13/2023]
Abstract
We report here a new microscopic technique for imaging and identifying sedimentary organic matter in geologic materials that combines inverted fluorescence microscopy with scanning electron microscopy and allows for sequential imaging of the same region of interest without transferring the sample between instruments. This integrated correlative light and electron microscopy technique is demonstrated with observations from an immature lacustrine oil shale from the Eocene Green River Mahogany Zone and mid-oil window paralic shale from the Upper Cretaceous Tuscaloosa Group. This technique has the potential to allow for identification and characterization of organic matter in shale hydrocarbon reservoirs that is not possible using either light or electron microscopy alone, and may be applied to understanding the organic matter type and thermal regime in which organic nanoporosity forms, thereby reducing uncertainty in the estimation of undiscovered hydrocarbon resources.
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Affiliation(s)
- Paul C Hackley
- U.S. Geological Survey, MS 956 National Center, Reston, Virginia, U.S.A
| | - Brett J Valentine
- U.S. Geological Survey, MS 956 National Center, Reston, Virginia, U.S.A
| | | | | | - Javin Hatcherian
- U.S. Geological Survey, MS 956 National Center, Reston, Virginia, U.S.A
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19
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Relocation is the key to successful correlative fluorescence and scanning electron microscopy. Methods Cell Biol 2017; 140:215-244. [PMID: 28528635 DOI: 10.1016/bs.mcb.2017.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this chapter the authors report on an automated hardware and software solution enabling swift correlative sample array mapping of fluorescently stained molecules within cells and tissues across length scales. Samples are first observed utilizing wide-field optical and fluorescence microscopy, followed by scanning electron microscopy, using calibration points on a dedicated sample-relocation holder. We investigated HeLa cells in vitro, fluorescently labeled for monosialoganglioside one (GM-1), across both imaging platforms within tens of minutes of initial sample preparation. This resulted in a high-throughput and high spatially resolved correlative fluorescence and electron microscopy analysis and allowed us to collect complementary nanoscopic information on the molecular and structural composition of two differently distinct HeLa cell populations expressing different levels of GM-1. Furthermore, using the small zebrafish animal model Danio rerio, we showed the versatility and relocation accuracy of the sample-relocation holder to locate fluo-tagged macromolecular complexes within large volumes using long ribbons of serial tissue sections. The subsequent electron microscopy imaging of the tissue arrays of interest enabled the generation of correlated information on the fine distribution of albumin within hepatic and kidney tissue. Our approach underpins the merits that an automated sample-relocation holder solution brings in support of results-driven research, where relevant biological questions can be answered, and high-throughput data can be generated in a rigorous statistical manner.
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Hampton CM, Strauss JD, Ke Z, Dillard RS, Hammonds JE, Alonas E, Desai TM, Marin M, Storms RE, Leon F, Melikyan GB, Santangelo PJ, Spearman PW, Wright ER. Correlated fluorescence microscopy and cryo-electron tomography of virus-infected or transfected mammalian cells. Nat Protoc 2016; 12:150-167. [PMID: 27977021 DOI: 10.1038/nprot.2016.168] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Correlative light and electron microscopy (CLEM) combines spatiotemporal information from fluorescence light microscopy (fLM) with high-resolution structural data from cryo-electron tomography (cryo-ET). These technologies provide opportunities to bridge knowledge gaps between cell and structural biology. Here we describe our protocol for correlated cryo-fLM, cryo-electron microscopy (cryo-EM), and cryo-ET (i.e., cryo-CLEM) of virus-infected or transfected mammalian cells. Mammalian-derived cells are cultured on EM substrates, using optimized conditions that ensure that the cells are spread thinly across the substrate and are not physically disrupted. The cells are then screened by fLM and vitrified before acquisition of cryo-fLM and cryo-ET images, which is followed by data processing. A complete session from grid preparation through data collection and processing takes 5-15 d for an individual experienced in cryo-EM.
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Affiliation(s)
- Cheri M Hampton
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Joshua D Strauss
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Zunlong Ke
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rebecca S Dillard
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Jason E Hammonds
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Eric Alonas
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
| | - Tanay M Desai
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Mariana Marin
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Rachel E Storms
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Fredrick Leon
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Gregory B Melikyan
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Philip J Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
| | - Paul W Spearman
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Elizabeth R Wright
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia, USA.,Robert P. Apkarian Integrated Electron Microscopy Core, Emory University, Atlanta, Georgia, USA
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Zachman MJ, Asenath-Smith E, Estroff LA, Kourkoutis LF. Site-Specific Preparation of Intact Solid-Liquid Interfaces by Label-Free In Situ Localization and Cryo-Focused Ion Beam Lift-Out. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2016; 22:1338-1349. [PMID: 27869059 DOI: 10.1017/s1431927616011892] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Scanning transmission electron microscopy (STEM) allows atomic scale characterization of solid-solid interfaces, but has seen limited applications to solid-liquid interfaces due to the volatility of liquids in the microscope vacuum. Although cryo-electron microscopy is routinely used to characterize hydrated samples stabilized by rapid freezing, sample thinning is required to access the internal interfaces of thicker specimens. Here, we adapt cryo-focused ion beam (FIB) "lift-out," a technique recently developed for biological specimens, to prepare intact internal solid-liquid interfaces for high-resolution structural and chemical analysis by cryo-STEM. To guide the milling process we introduce a label-free in situ method of localizing subsurface structures in suitable materials by energy dispersive X-ray spectroscopy (EDX). Monte Carlo simulations are performed to evaluate the depth-probing capability of the technique, and show good qualitative agreement with experiment. We also detail procedures to produce homogeneously thin lamellae, which enable nanoscale structural, elemental, and chemical analysis of intact solid-liquid interfaces by analytical cryo-STEM. This work demonstrates the potential of cryo-FIB lift-out and cryo-STEM for understanding physical and chemical processes at solid-liquid interfaces.
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Affiliation(s)
- Michael J Zachman
- 1School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
| | - Emily Asenath-Smith
- 3Department of Materials Science and Engineering,Cornell University,Ithaca,NY 14853,USA
| | - Lara A Estroff
- 2Kavli Institute at Cornell for Nanoscale Science,Cornell University,Ithaca,NY 14853,USA
| | - Lena F Kourkoutis
- 1School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
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22
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Killingsworth MC, Bobryshev YV. Correlative Light- and Electron Microscopy Using Quantum Dot Nanoparticles. J Vis Exp 2016. [PMID: 27584907 DOI: 10.3791/54307] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
A method is described whereby quantum dot (QD) nanoparticles can be used for correlative immunocytochemical studies of human pathology tissue using widefield fluorescence light microscopy and transmission electron microscopy (TEM). To demonstrate the protocol we have immunolabeled ultrathin epoxy sections of human somatostatinoma tumor using a primary antibody to somatostatin, followed by a biotinylated secondary antibody and visualization with streptavidin conjugated 585 nm cadmium-selenium (CdSe) quantum dots (QDs). The sections are mounted on a TEM specimen grid then placed on a glass slide for observation by widefield fluorescence light microscopy. Light microscopy reveals 585 nm QD labeling as bright orange fluorescence forming a granular pattern within the tumor cell cytoplasm. At low to mid-range magnification by light microscopy the labeling pattern can be easily recognized and the level of non-specific or background labeling assessed. This is a critical step for subsequent interpretation of the immunolabeling pattern by TEM and evaluation of the morphological context. The same section is then blotted dry and viewed by TEM. QD probes are seen to be attached to amorphous material contained in individual secretory granules. Images are acquired from the same region of interest (ROI) seen by light microscopy for correlative analysis. Corresponding images from each modality may then be blended to overlay fluorescence data on TEM ultrastructure of the corresponding region.
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Affiliation(s)
- Murray C Killingsworth
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales Australia; School of Medicine, Western Sydney University; Correlative Microscopy Group, Ingham Institute for Applied Medical Research; Electron Microscopy Laboratory, Department of Anatomical Pathology, Sydney South West Pathology Service, New South Wales Health Pathology;
| | - Yuri V Bobryshev
- Correlative Microscopy Group, Ingham Institute for Applied Medical Research; Electron Microscopy Laboratory, Department of Anatomical Pathology, Sydney South West Pathology Service, New South Wales Health Pathology; School of Medical Sciences, Faculty of Medicine, University of New South Wales Australia
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Kobayashi S, Iwamoto M, Haraguchi T. Live correlative light-electron microscopy to observe molecular dynamics in high resolution. Microscopy (Oxf) 2016; 65:296-308. [DOI: 10.1093/jmicro/dfw024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/01/2016] [Indexed: 12/19/2022] Open
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Loussert Fonta C, Humbel BM. Correlative microscopy. Arch Biochem Biophys 2015; 581:98-110. [DOI: 10.1016/j.abb.2015.05.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/26/2015] [Accepted: 05/29/2015] [Indexed: 11/15/2022]
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25
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de Boer P, Hoogenboom JP, Giepmans BNG. Correlated light and electron microscopy: ultrastructure lights up! Nat Methods 2015; 12:503-13. [PMID: 26020503 DOI: 10.1038/nmeth.3400] [Citation(s) in RCA: 300] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 04/15/2015] [Indexed: 12/15/2022]
Abstract
Microscopy has gone hand in hand with the study of living systems since van Leeuwenhoek observed living microorganisms and cells in 1674 using his light microscope. A spectrum of dyes and probes now enable the localization of molecules of interest within living cells by fluorescence microscopy. With electron microscopy (EM), cellular ultrastructure has been revealed. Bridging these two modalities, correlated light microscopy and EM (CLEM) opens new avenues. Studies of protein dynamics with fluorescent proteins (FPs), which leave the investigator 'in the dark' concerning cellular context, can be followed by EM examination. Rare events can be preselected at the light microscopy level before EM analysis. Ongoing development-including of dedicated probes, integrated microscopes, large-scale and three-dimensional EM and super-resolution fluorescence microscopy-now paves the way for broad CLEM implementation in biology.
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Affiliation(s)
- Pascal de Boer
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jacob P Hoogenboom
- Faculty of Applied Sciences, Delft University of Technology, Delft, the Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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26
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Bruckner JJ, Zhan H, O'Connor-Giles KM. Advances in imaging ultrastructure yield new insights into presynaptic biology. Front Cell Neurosci 2015; 9:196. [PMID: 26052269 PMCID: PMC4440913 DOI: 10.3389/fncel.2015.00196] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/05/2015] [Indexed: 11/13/2022] Open
Abstract
Synapses are the fundamental functional units of neural circuits, and their dysregulation has been implicated in diverse neurological disorders. At presynaptic terminals, neurotransmitter-filled synaptic vesicles are released in response to calcium influx through voltage-gated calcium channels activated by the arrival of an action potential. Decades of electrophysiological, biochemical, and genetic studies have contributed to a growing understanding of presynaptic biology. Imaging studies are yielding new insights into how synapses are organized to carry out their critical functions. The development of techniques for rapid immobilization and preservation of neuronal tissues for electron microscopy (EM) has led to a new renaissance in ultrastructural imaging that is rapidly advancing our understanding of synapse structure and function.
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Affiliation(s)
- Joseph J Bruckner
- Cell and Molecular Biology Training Program, University of Wisconsin-Madison Madison, WI, USA
| | - Hong Zhan
- Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison Madison, WI, USA
| | - Kate M O'Connor-Giles
- Cell and Molecular Biology Training Program, University of Wisconsin-Madison Madison, WI, USA ; Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison Madison, WI, USA ; Laboratory of Genetics, University of Wisconsin-Madison Madison, WI, USA
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27
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Aslanidi KB. Spectral measurements of the functional heterogeneity of cells and their organelles. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915010030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Saibil HR, Grünewald K, Stuart DI. A national facility for biological cryo-electron microscopy. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:127-35. [PMID: 25615867 PMCID: PMC4304693 DOI: 10.1107/s1399004714025280] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 11/18/2014] [Indexed: 11/16/2022]
Abstract
Three-dimensional electron microscopy is an enormously powerful tool for structural biologists. It is now able to provide an understanding of the molecular machinery of cells, disease processes and the actions of pathogenic organisms from atomic detail through to the cellular context. However, cutting-edge research in this field requires very substantial resources for equipment, infrastructure and expertise. Here, a brief overview is provided of the plans for a UK national three-dimensional electron-microscopy facility for integrated structural biology to enable internationally leading research on the machinery of life. State-of-the-art equipment operated with expert support will be provided, optimized for both atomic-level single-particle analysis of purified macromolecules and complexes and for tomography of cell sections. The access to and organization of the facility will be modelled on the highly successful macromolecular crystallography (MX) synchrotron beamlines, and will be embedded at the Diamond Light Source, facilitating the development of user-friendly workflows providing near-real-time experimental feedback.
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Affiliation(s)
- Helen R. Saibil
- Crystallography, Institute for Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
| | - Kay Grünewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
| | - David I. Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
- Diamond Light Source, Didcot OX11 0DE, England
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Timmermans FJ, Otto C. Contributed review: Review of integrated correlative light and electron microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:011501. [PMID: 25638065 DOI: 10.1063/1.4905434] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
New developments in the field of microscopy enable to acquire increasing amounts of information from large sample areas and at an increased resolution. Depending on the nature of the technique, the information may reveal morphological, structural, chemical, and still other sample characteristics. In research fields, such as cell biology and materials science, there is an increasing demand to correlate these individual levels of information and in this way to obtain a better understanding of sample preparation and specific sample properties. To address this need, integrated systems were developed that combine nanometer resolution electron microscopes with optical microscopes, which produce chemically or label specific information through spectroscopy. The complementary information from electron microscopy and light microscopy presents an opportunity to investigate a broad range of sample properties in a correlated fashion. An important part of correlating the differences in information lies in bridging the different resolution and image contrast features. The trend to analyse samples using multiple correlated microscopes has resulted in a new research field. Current research is focused, for instance, on (a) the investigation of samples with nanometer scale distribution of inorganic and organic materials, (b) live cell analysis combined with electron microscopy, and (c) in situ spectroscopic and electron microscopy analysis of catalytic materials, but more areas will benefit from integrated correlative microscopy.
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Affiliation(s)
- F J Timmermans
- Medical Cell Biophysics Group, MIRA Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - C Otto
- Medical Cell Biophysics Group, MIRA Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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Tatsumi S, Uchihara T, Aiba I, Iwasaki Y, Mimuro M, Takahashi R, Yoshida M. Ultrastructural differences in pretangles between Alzheimer disease and corticobasal degeneration revealed by comparative light and electron microscopy. Acta Neuropathol Commun 2014; 2:161. [PMID: 25497147 PMCID: PMC4269873 DOI: 10.1186/s40478-014-0161-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 11/05/2014] [Indexed: 11/11/2022] Open
Abstract
Pretangles are defined under the light microscope as diffuse and granular tau immunoreactivity in neurons in tissue from patients with Alzheimer disease (AD) or corticobasal degeneration (CBD) and are considered to be a premature stage before neurofibrillary tangle formation. However, the ultrastructure of pretangles remains to be described. To clarify the similarities and differences between pretangles from patients with AD and CBD (AD-pretangles and CBD-pretangles, respectively), we examined cortical pretangles in tissue from patients with each of diseases. For direct light and electron microscopic (LM/EM) correlation of the pretangles, we used quantum dot nanocrystals (QDs) with dual fluorescent and electron-dense properties. We first identified tau-labeled pretangles on fluorescence LM and subsequently examined the same neurons on EM. Energy dispersive X-ray spectrometry (EDX) color mapping identified selenium (Se) and cadmium (Cd) as elementary components of QDs and highlighted each QD particle clearly against gray-scale EM images. With these methods, we were successful for the first time in demonstrating accurately that LM-defined pretangles are tau-positive straight filaments sparsely distributed throughout neuronal cytoplasm and neurites in both AD and CBD at the EM level. Notably, AD-pretangles showed a strong tendency to form fibrillary tangles even at an early stage, whereas pretangles or Pick-like inclusions in tissue from patients with CBD did not even at an advanced stage. In conclusion, AD-pretangles and CBD-pretangles showed essential differences at the EM level.
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Kolotuev I. Positional correlative anatomy of invertebrate model organisms increases efficiency of TEM data production. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2014; 20:1392-1403. [PMID: 25180638 DOI: 10.1017/s1431927614012999] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Transmission electron microscopy (TEM) is an important tool for studies in cell biology, and is essential to address research questions from bacteria to animals. Recent technological innovations have advanced the entire field of TEM, yet classical techniques still prevail for most present-day studies. Indeed, the majority of cell and developmental biology studies that use TEM do not require cutting-edge methodologies, but rather fast and efficient data generation. Although access to state-of-the-art equipment is frequently problematic, standard TEM microscopes are typically available, even in modest research facilities. However, a major unmet need in standard TEM is the ability to quickly prepare and orient a sample to identify a region of interest. Here, I provide a detailed step-by-step method for a positional correlative anatomy approach to flat-embedded samples. These modifications make the TEM preparation and analytic procedures faster and more straightforward, supporting a higher sampling rate. To illustrate the modified procedures, I provide numerous examples addressing research questions in Caenorhabditis elegans and Drosophila. This method can be equally applied to address questions of cell and developmental biology in other small multicellular model organisms.
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Affiliation(s)
- Irina Kolotuev
- 1Fédération de Recherche BIOSIT,Université de Rennes 1,Plateforme microscopie électronique MRic,Campus santé,2 avenue du Professeur Léon-Bernard,35043 Rennes,France
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Abstract
Correlative fluorescence and electron microscopy (CFEM) is a multimodal technique that combines dynamic and localization information from fluorescence methods with ultrastructural data from electron microscopy, to give new information about how cellular components change relative to the spatiotemporal dynamics within their environment. In this review, we will discuss some of the basic techniques and tools of the trade for utilizing this attractive research method, which is becoming a very powerful tool for biology labs. The information obtained from correlative methods has proven to be invaluable in creating consensus between the two types of microscopy, extending the capability of each, and cutting the time and expense associated with using each method separately for comparative analysis. The realization of the advantages of these methods in cell biology has led to rapid improvement in the protocols and has ushered in a new generation of instruments to reach the next level of correlation--integration.
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Affiliation(s)
- Randall T Schirra
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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Fukuda Y, Schrod N, Schaffer M, Feng LR, Baumeister W, Lucic V. Coordinate transformation based cryo-correlative methods for electron tomography and focused ion beam milling. Ultramicroscopy 2014; 143:15-23. [DOI: 10.1016/j.ultramic.2013.11.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 10/25/2022]
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Peddie CJ, Blight K, Wilson E, Melia C, Marrison J, Carzaniga R, Domart MC, O'Toole P, Larijani B, Collinson LM. Correlative and integrated light and electron microscopy of in-resin GFP fluorescence, used to localise diacylglycerol in mammalian cells. Ultramicroscopy 2014; 143:3-14. [PMID: 24637200 PMCID: PMC4045205 DOI: 10.1016/j.ultramic.2014.02.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 02/10/2014] [Accepted: 02/12/2014] [Indexed: 12/11/2022]
Abstract
Fluorescence microscopy of GFP-tagged proteins is a fundamental tool in cell biology, but without seeing the structure of the surrounding cellular space, functional information can be lost. Here we present a protocol that preserves GFP and mCherry fluorescence in mammalian cells embedded in resin with electron contrast to reveal cellular ultrastructure. Ultrathin in-resin fluorescence (IRF) sections were imaged simultaneously for fluorescence and electron signals in an integrated light and scanning electron microscope. We show, for the first time, that GFP is stable and active in resin sections in vacuo. We applied our protocol to study the subcellular localisation of diacylglycerol (DAG), a modulator of membrane morphology and membrane dynamics in nuclear envelope assembly. We show that DAG is localised to the nuclear envelope, nucleoplasmic reticulum and curved tips of the Golgi apparatus. With these developments, we demonstrate that integrated imaging is maturing into a powerful tool for accurate molecular localisation to structure.
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Affiliation(s)
- Christopher J Peddie
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
| | - Ken Blight
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
| | - Emma Wilson
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
| | - Charlotte Melia
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK; Cell Biophysics Laboratory, London Research Institute, Cancer Research UK, London WC2A 3LY, UK; Department of Molecular Cell Biology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Jo Marrison
- Department of Biology, The University of York, Heslington, York, UK
| | - Raffaella Carzaniga
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
| | - Marie-Charlotte Domart
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK; Cell Biophysics Laboratory, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
| | - Peter O'Toole
- Department of Biology, The University of York, Heslington, York, UK
| | - Banafshe Larijani
- Cell Biophysics Laboratory, London Research Institute, Cancer Research UK, London WC2A 3LY, UK; Cell Biophysics Laboratory, Unidad de Biofísica (CSIC-UPV/EHU),Sarriena s/n, 48940 Leioa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Lucy M Collinson
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
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MAVIS: An integrated system for live microscopy and vitrification. Ultramicroscopy 2014; 143:67-76. [DOI: 10.1016/j.ultramic.2013.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/04/2013] [Accepted: 10/08/2013] [Indexed: 11/24/2022]
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Roudeau S, Carmona A, Perrin L, Ortega R. Correlative organelle fluorescence microscopy and synchrotron X-ray chemical element imaging in single cells. Anal Bioanal Chem 2014; 406:6979-91. [PMID: 25023971 DOI: 10.1007/s00216-014-8004-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/18/2014] [Accepted: 06/26/2014] [Indexed: 02/05/2023]
Abstract
X-ray chemical element imaging has the potential to enable fundamental breakthroughs in the understanding of biological systems because chemical element interactions with organelles can be studied at the sub-cellular level. What is the distribution of trace metals in cells? Do some elements accumulate within sub-cellular organelles? What are the chemical species of the elements in these organelles? These are some of the fundamental questions that can be addressed by use of X-ray chemical element imaging with synchrotron radiation beams. For precise location of the distribution of the elements, identification of cellular organelles is required; this can be achieved, after appropriate labelling, by use of fluorescence microscopy. As will be discussed, this approach imposes some limitations on sample preparation. For example, standard immunolabelling procedures strongly modify the distribution of the elements in cells as a result of the chemical fixation and permeabilization steps. Organelle location can, however, be performed, by use of a variety of specific fluorescent dyes or fluorescent proteins, on living cells before cryogenic fixation, enabling preservation of element distribution. This article reviews the methods used for fluorescent organelle labelling and X-ray chemical element imaging and speciation of single cells. Selected cases from our work and from other research groups are presented to illustrate the potential of the combination of the two techniques.
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Affiliation(s)
- Stéphane Roudeau
- University of Bordeaux, CNRS, CENBG, UMR 5797, 33170, Gradignan, France
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38
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Bos E, Hussaarts L, van Weering JRT, Ellisman MH, de Wit H, Koster AJ. Vitrification of Tokuyasu-style immuno-labelled sections for correlative cryo light microscopy and cryo electron tomography. J Struct Biol 2014; 186:273-82. [PMID: 24704216 DOI: 10.1016/j.jsb.2014.03.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 03/24/2014] [Accepted: 03/25/2014] [Indexed: 10/25/2022]
Abstract
We present an approach for the preparation of immuno-labelled ultrathin sections from cells or tissue that are compatible with both fluorescence and transmission electron microscopy. Our approach is inspired by a method of Sabanay et al. (1991) that is based on the Tokuyasu technique for immunogold labelling of sections from aldehyde-fixed samples. The difference of this method with the original Tokuyasu technique is that the immuno-labelled sections are stabilized in a thin layer of vitreous water by plunge-freezing prior to electron microscopical observation. The vitrification step allows for phase contrast-based imaging at cryogenic conditions. We show that this immuno-labelling method is well-suited for imaging cellular ultrastructure in three dimensions (tomography) at cryogenic conditions, and that fluorescence associated with the sections is retained. This method is a valuable tool for Correlative Light and Electron Microscopy (CLEM), and we refer to this method in combination with CLEM as VOS (vitrification of sections). We provide examples for the application of VOS using dendritic cells and neurons, and show specifically that this method enables the researcher to navigate to lysosomes and synapses.
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Affiliation(s)
- Erik Bos
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Leonie Hussaarts
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan R T van Weering
- Department of Functional Genomics and Clinical Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University and VU Medical Center, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research (NCMIR), Department of Neurosciences, University of California San Diego, 9500 Gilman Drive MC0608, La Jolla, CA 92093-0608, United States
| | - Heidi de Wit
- Department of Functional Genomics and Clinical Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University and VU Medical Center, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Abraham J Koster
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.
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Abstract
Electron cryo tomography (cryoET) is an ideal technique to study virus-host interactions at molecular resolution. Imaging of biological specimens in a frozen-hydrated state assures a close to native environment. Various virus-host cell interactions have been analysed in this way, with the herpesvirus 'life' cycle being the most comprehensively studied. The data obtained were further integrated with fluorescence and soft X-ray cryo microscopy data applied on experimental systems covering a wide range of biological complexity. This hybrid approach combines dynamic with static imaging and spans a resolution range from micrometres to angstroms. Along selected aspects of the herpesvirus replication cycle, we describe dedicated combinations of approaches and how subsequent data integration enables insights towards a functional understanding of the underlying processes.
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40
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Koning RI, Celler K, Willemse J, Bos E, van Wezel GP, Koster AJ. Correlative cryo-fluorescence light microscopy and cryo-electron tomography of Streptomyces. Methods Cell Biol 2014; 124:217-39. [PMID: 25287843 DOI: 10.1016/b978-0-12-801075-4.00010-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Light microscopy and electron microscopy are complementary techniques that in a correlative approach enable identification and targeting of fluorescently labeled structures in situ for three-dimensional imaging at nanometer resolution. Correlative imaging allows electron microscopic images to be positioned in a broader temporal and spatial context. We employed cryo-correlative light and electron microscopy (cryo-CLEM), combining cryo-fluorescence light microscopy and cryo-electron tomography, on vitrified Streptomyces bacteria to study cell division. Streptomycetes are mycelial bacteria that grow as long hyphae and reproduce via sporulation. On solid media, Streptomyces subsequently form distinct aerial mycelia where cell division leads to the formation of unigenomic spores which separate and disperse to form new colonies. In liquid media, only vegetative hyphae are present divided by noncell separating crosswalls. Their multicellular life style makes them exciting model systems for the study of bacterial development and cell division. Complex intracellular structures have been visualized with transmission electron microscopy. Here, we describe the methods for cryo-CLEM that we applied for studying Streptomyces. These methods include cell growth, fluorescent labeling, cryo-fixation by vitrification, cryo-light microscopy using a Linkam cryo-stage, image overlay and relocation, cryo-electron tomography using a Titan Krios, and tomographic reconstruction. Additionally, methods for segmentation, volume rendering, and visualization of the correlative data are described.
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Affiliation(s)
- Roman I Koning
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Center, Leiden, The Netherlands
| | - Katherine Celler
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, Leiden, The Netherlands
| | - Joost Willemse
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, Leiden, The Netherlands
| | - Erik Bos
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Center, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, Leiden, The Netherlands
| | - Abraham J Koster
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Center, Leiden, The Netherlands
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41
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Peddie CJ, Liv N, Hoogenboom JP, Collinson LM. Integrated Light and Scanning Electron Microscopy of GFP-Expressing Cells. Methods Cell Biol 2014; 124:363-89. [DOI: 10.1016/b978-0-12-801075-4.00017-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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42
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Correlative Light Microscopy and Electron Tomography to Study Von Willebrand Factor Exocytosis from Vascular Endothelial Cells. Methods Cell Biol 2014; 124:71-92. [DOI: 10.1016/b978-0-12-801075-4.00004-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Lučič V, Rigort A, Baumeister W. Cryo-electron tomography: the challenge of doing structural biology in situ. ACTA ACUST UNITED AC 2013; 202:407-19. [PMID: 23918936 PMCID: PMC3734081 DOI: 10.1083/jcb.201304193] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Electron microscopy played a key role in establishing cell biology as a discipline, by producing fundamental insights into cellular organization and ultrastructure. Many seminal discoveries were made possible by the development of new sample preparation methods and imaging modalities. Recent technical advances include sample vitrification that faithfully preserves molecular structures, three-dimensional imaging by electron tomography, and improved image-processing methods. These new techniques have enabled the extraction of high fidelity structural information and are beginning to reveal the macromolecular organization of unperturbed cellular environments.
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Affiliation(s)
- Vladan Lučič
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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45
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Schorb M, Briggs JAG. Correlated cryo-fluorescence and cryo-electron microscopy with high spatial precision and improved sensitivity. Ultramicroscopy 2013; 143:24-32. [PMID: 24275379 DOI: 10.1016/j.ultramic.2013.10.015] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/29/2013] [Accepted: 10/31/2013] [Indexed: 01/24/2023]
Abstract
Performing fluorescence microscopy and electron microscopy on the same sample allows fluorescent signals to be used to identify and locate features of interest for subsequent imaging by electron microscopy. To carry out such correlative microscopy on vitrified samples appropriate for structural cryo-electron microscopy it is necessary to perform fluorescence microscopy at liquid-nitrogen temperatures. Here we describe an adaptation of a cryo-light microscopy stage to permit use of high-numerical aperture objectives. This allows high-sensitivity and high-resolution fluorescence microscopy of vitrified samples. We describe and apply a correlative cryo-fluorescence and cryo-electron microscopy workflow together with a fiducial bead-based image correlation procedure. This procedure allows us to locate fluorescent bacteriophages in cryo-electron microscopy images with an accuracy on the order of 50 nm, based on their fluorescent signal. It will allow the user to precisely and unambiguously identify and locate objects and events for subsequent high-resolution structural study, based on fluorescent signals.
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Affiliation(s)
- Martin Schorb
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.
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46
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Hybrid fluorescence and electron cryo-microscopy for simultaneous electron and photon imaging. J Struct Biol 2013; 185:107-15. [PMID: 24211820 DOI: 10.1016/j.jsb.2013.10.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 10/28/2013] [Accepted: 10/31/2013] [Indexed: 02/02/2023]
Abstract
Integration of fluorescence light and transmission electron microscopy into the same device would represent an important advance in correlative microscopy, which traditionally involves two separate microscopes for imaging. To achieve such integration, the primary technical challenge that must be solved regards how to arrange two objective lenses used for light and electron microscopy in such a manner that they can properly focus on a single specimen. To address this issue, both lateral displacement of the specimen between two lenses and specimen rotation have been proposed. Such movement of the specimen allows sequential collection of two kinds of microscopic images of a single target, but prevents simultaneous imaging. This shortcoming has been made up by using a simple optical device, a reflection mirror. Here, we present an approach toward the versatile integration of fluorescence and electron microscopy for simultaneous imaging. The potential of simultaneous hybrid microscopy was demonstrated by fluorescence and electron sequential imaging of a fluorescent protein expressed in cells and cathodoluminescence imaging of fluorescent beads.
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47
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Schellenberger P, Kaufmann R, Siebert CA, Hagen C, Wodrich H, Grünewald K. High-precision correlative fluorescence and electron cryo microscopy using two independent alignment markers. Ultramicroscopy 2013; 143:41-51. [PMID: 24262358 PMCID: PMC4045203 DOI: 10.1016/j.ultramic.2013.10.011] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 10/08/2013] [Accepted: 10/10/2013] [Indexed: 11/29/2022]
Abstract
Correlative light and electron microscopy (CLEM) is an emerging technique which combines functional information provided by fluorescence microscopy (FM) with the high-resolution structural information of electron microscopy (EM). So far, correlative cryo microscopy of frozen-hydrated samples has not reached better than micrometre range accuracy. Here, a method is presented that enables the correlation between fluorescently tagged proteins and electron cryo tomography (cryoET) data with nanometre range precision. Specifically, thin areas of vitrified whole cells are examined by correlative fluorescence cryo microscopy (cryoFM) and cryoET. Novel aspects of the presented cryoCLEM workflow not only include the implementation of two independent electron dense fluorescent markers to improve the precision of the alignment, but also the ability of obtaining an estimate of the correlation accuracy for each individual object of interest. The correlative workflow from plunge-freezing to cryoET is detailed step-by-step for the example of locating fluorescence-labelled adenovirus particles trafficking inside a cell. Vitrified mammalian cell were imaged by fluorescence and electron cryo microscopy. TetraSpeck fluorescence markers were added to correct shifts between cryo fluorescence channels. FluoSpheres fiducials were used as reference points to assign new coordinates to cryoEM images. Adenovirus particles were localised with an average correlation precision of 63 nm.
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Affiliation(s)
- Pascale Schellenberger
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Rainer Kaufmann
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - C Alistair Siebert
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christoph Hagen
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Harald Wodrich
- Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, University of Bordeaux SEGALEN, 146 rue Leo Seignat, 33076 Bordeaux, France
| | - Kay Grünewald
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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48
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Correlative cryo-electron tomography and optical microscopy of cells. Curr Opin Struct Biol 2013; 23:763-70. [PMID: 23962486 DOI: 10.1016/j.sbi.2013.07.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/02/2013] [Accepted: 07/28/2013] [Indexed: 12/11/2022]
Abstract
The biological processes occurring in a cell are complex and dynamic, and to achieve a comprehensive understanding of the molecular mechanisms underlying these processes, both temporal and spatial information is required. While cryo-electron tomography (cryoET) provides three-dimensional (3D) still pictures of near-native state cells and organelles at molecular resolution, fluorescence light microscopy (fLM) offers movies of dynamic cellular processes in living cells. Combining and integrating these two commonly used imaging modalities (termed correlative microscopy) provides a powerful means to not only expand the imaging scale and resolution but also to complement the dynamic information available from optical microscopy with the molecular-level, 3D ultrastructure detail provided by cryoET. As such, a correlative approach performed on a given specimen can provide high resolution snapshots of dynamic cellular events. In this article, I review recent advances in correlative light microscopy and cryoET and discuss major findings made available by applying this method.
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