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Shih CP, Tang WC, Chen P, Chen BC. Applications of Lightsheet Fluorescence Microscopy by High Numerical Aperture Detection Lens. J Phys Chem B 2024; 128:8273-8289. [PMID: 39177503 PMCID: PMC11382282 DOI: 10.1021/acs.jpcb.4c01721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
This Review explores the evolution, improvements, and recent applications of Light Sheet Fluorescence Microscopy (LSFM) in biological research using a high numerical aperture detection objective (lens) for imaging subcellular structures. The Review begins with an overview of the development of LSFM, tracing its evolution from its inception to its current state and emphasizing key milestones and technological advancements over the years. Subsequently, we will discuss various improvements of LSFM techniques, covering advancements in hardware such as illumination strategies, optical designs, and sample preparation methods that have enhanced imaging capabilities and resolution. The advancements in data acquisition and processing are also included, which provides a brief overview of the recent development of artificial intelligence. Fluorescence probes that were commonly used in LSFM will be highlighted, together with some insights regarding the selection of potential probe candidates for future LSFM development. Furthermore, we also discuss recent advances in the application of LSFM with a focus on high numerical aperture detection objectives for various biological studies. For sample preparation techniques, there are discussions regarding fluorescence probe selection, tissue clearing protocols, and some insights into expansion microscopy. Integrated setups such as adaptive optics, single objective modification, and microfluidics will also be some of the key discussion points in this Review. We hope that this comprehensive Review will provide a holistic perspective on the historical development, technical enhancements, and cutting-edge applications of LSFM, showcasing its pivotal role and future potential in advancing biological research.
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Affiliation(s)
- Chun-Pei Shih
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 106319, Taiwan
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan University, Taipei 11529, Taiwan
| | - Wei-Chun Tang
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Peilin Chen
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
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2
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Hümpfer N, Thielhorn R, Ewers H. Expanding boundaries - a cell biologist's guide to expansion microscopy. J Cell Sci 2024; 137:jcs260765. [PMID: 38629499 PMCID: PMC11058692 DOI: 10.1242/jcs.260765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
Expansion microscopy (ExM) is a revolutionary novel approach to increase resolution in light microscopy. In contrast to super-resolution microscopy methods that rely on sophisticated technological advances, including novel instrumentation, ExM instead is entirely based on sample preparation. In ExM, labeled target molecules in fixed cells are anchored in a hydrogel, which is then physically enlarged by osmotic swelling. The isotropic swelling of the hydrogel pulls the labels apart from one another, and their relative organization can thus be resolved using conventional microscopes even if it was below the diffraction limit of light beforehand. As ExM can additionally benefit from the technical resolution enhancements achieved by super-resolution microscopy, it can reach into the nanometer range of resolution with an astoundingly low degree of error induced by distortion during the physical expansion process. Because the underlying chemistry is well understood and the technique is based on a relatively simple procedure, ExM is easily reproducible in non-expert laboratories and has quickly been adopted to address an ever-expanding spectrum of problems across the life sciences. In this Review, we provide an overview of this rapidly expanding new field, summarize the most important insights gained so far and attempt to offer an outlook on future developments.
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Affiliation(s)
- Nadja Hümpfer
- Department of Biology, Chemistry and Pharmacy, Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Ria Thielhorn
- Department of Biology, Chemistry and Pharmacy, Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Helge Ewers
- Department of Biology, Chemistry and Pharmacy, Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
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3
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Pesce L, Ricci P, Sportelli G, Belcari N, Sancataldo G. Expansion and Light-Sheet Microscopy for Nanoscale 3D Imaging. SMALL METHODS 2024:e2301715. [PMID: 38461540 DOI: 10.1002/smtd.202301715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/10/2024] [Indexed: 03/12/2024]
Abstract
Expansion Microscopy (ExM) and Light-Sheet Fluorescence Microscopy (LSFM) are forefront imaging techniques that enable high-resolution visualization of biological specimens. ExM enhances nanoscale investigation using conventional fluorescence microscopes, while LSFM offers rapid, minimally invasive imaging over large volumes. This review explores the joint advancements of ExM and LSFM, focusing on the excellent performance of the integrated modality obtained from the combination of the two, which is refer to as ExLSFM. In doing so, the chemical processes required for ExM, the tailored optical setup of LSFM for examining expanded samples, and the adjustments in sample preparation for accurate data collection are emphasized. It is delve into various specimen types studied using this integrated method and assess its potential for future applications. The goal of this literature review is to enrich the comprehension of ExM and LSFM, encouraging their wider use and ongoing development, looking forward to the upcoming challenges, and anticipating innovations in these imaging techniques.
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Affiliation(s)
- Luca Pesce
- Department of Physics - Enrico Fermi, University of Pisa, Largo Pontecorvo, 3, Pisa, 56127, Italy
| | - Pietro Ricci
- Department of Applied Physics, University of Barcelona, C/Martí i Franquès, 1, Barcelona, 08028, Spain
| | - Giancarlo Sportelli
- Department of Physics - Enrico Fermi, University of Pisa, Largo Pontecorvo, 3, Pisa, 56127, Italy
| | - Nicola Belcari
- Department of Physics - Enrico Fermi, University of Pisa, Largo Pontecorvo, 3, Pisa, 56127, Italy
| | - Giuseppe Sancataldo
- Department of Physics - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, Palermo, 90128, Italy
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4
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Haak A, Lesslich HM, Dietzel ID. Visualization of the membrane surface and cytoskeleton of oligodendrocyte progenitor cell growth cones using a combination of scanning ion conductance and four times expansion microscopy. Biol Chem 2024; 405:31-41. [PMID: 37950644 DOI: 10.1515/hsz-2023-0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/17/2023] [Indexed: 11/13/2023]
Abstract
Growth cones of oligodendrocyte progenitor cells (OPCs) are challenging to investigate with conventional light microscopy due to their small size. Especially substructures such as filopodia, lamellipodia and their underlying cytoskeleton are difficult to resolve with diffraction limited microscopy. Light microscopy techniques, which surpass the diffraction limit such as stimulated emission depletion microscopy, often require expensive setups and specially trained personnel rendering them inaccessible to smaller research groups. Lately, the invention of expansion microscopy (ExM) has enabled super-resolution imaging with any light microscope without the need for additional equipment. Apart from the necessary resolution, investigating OPC growth cones comes with another challenge: Imaging the topography of membranes, especially label- and contact-free, is only possible with very few microscopy techniques one of them being scanning ion conductance microscopy (SICM). We here present a new imaging workflow combining SICM and ExM, which enables the visualization of OPC growth cone nanostructures. We correlated SICM recordings and ExM images of OPC growth cones captured with a conventional widefield microscope. This enabled the visualization of the growth cones' membrane topography as well as their underlying actin and tubulin cytoskeleton.
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Affiliation(s)
- Annika Haak
- Nanoscopy, RUBION, Ruhr-Universität Bochum, Universitätsstraße 150, D-44801 Bochum, Germany
| | - Heiko M Lesslich
- Nanoscopy, RUBION, Ruhr-Universität Bochum, Universitätsstraße 150, D-44801 Bochum, Germany
| | - Irmgard D Dietzel
- Department of Biochemistry II, Electrobiochemistry of Neural Cells, Ruhr-Universität Bochum, D-44801 Bochum, Germany
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5
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Chansoria P, Rütsche D, Wang A, Liu H, D'Angella D, Rizzo R, Hasenauer A, Weber P, Qiu W, Ibrahim NBM, Korshunova N, Qin X, Zenobi‐Wong M. Synergizing Algorithmic Design, Photoclick Chemistry and Multi-Material Volumetric Printing for Accelerating Complex Shape Engineering. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300912. [PMID: 37400372 PMCID: PMC10502818 DOI: 10.1002/advs.202300912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/12/2023] [Indexed: 07/05/2023]
Abstract
The field of biomedical design and manufacturing has been rapidly evolving, with implants and grafts featuring complex 3D design constraints and materials distributions. By combining a new coding-based design and modeling approach with high-throughput volumetric printing, a new approach is demonstrated to transform the way complex shapes are designed and fabricated for biomedical applications. Here, an algorithmic voxel-based approach is used that can rapidly generate a large design library of porous structures, auxetic meshes and cylinders, or perfusable constructs. By deploying finite cell modeling within the algorithmic design framework, large arrays of selected auxetic designs can be computationally modeled. Finally, the design schemes are used in conjunction with new approaches for multi-material volumetric printing based on thiol-ene photoclick chemistry to rapidly fabricate complex heterogeneous shapes. Collectively, the new design, modeling and fabrication techniques can be used toward a wide spectrum of products such as actuators, biomedical implants and grafts, or tissue and disease models.
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Affiliation(s)
- Parth Chansoria
- Department of Health Sciences and TechnologyETH Zürich UniversityZürich8092Switzerland
| | - Dominic Rütsche
- Department of Health Sciences and TechnologyETH Zürich UniversityZürich8092Switzerland
- Department of SurgeryUniversity Children's HospitalBasel4056Switzerland
| | - Anny Wang
- Department of Health Sciences and TechnologyETH Zürich UniversityZürich8092Switzerland
- Hyperganic Group GmbH80799MunichGermany
| | - Hao Liu
- Department of Health Sciences and TechnologyETH Zürich UniversityZürich8092Switzerland
| | | | - Riccardo Rizzo
- Department of Health Sciences and TechnologyETH Zürich UniversityZürich8092Switzerland
| | - Amelia Hasenauer
- Department of Health Sciences and TechnologyETH Zürich UniversityZürich8092Switzerland
| | - Patrick Weber
- Department of Health Sciences and TechnologyETH Zürich UniversityZürich8092Switzerland
| | - Wanwan Qiu
- Department of Health Sciences and TechnologyETH Zürich UniversityZürich8092Switzerland
| | | | | | - Xiao‐Hua Qin
- Department of Health Sciences and TechnologyETH Zürich UniversityZürich8092Switzerland
| | - Marcy Zenobi‐Wong
- Department of Health Sciences and TechnologyETH Zürich UniversityZürich8092Switzerland
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6
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Wen G, Leen V, Rohand T, Sauer M, Hofkens J. Current Progress in Expansion Microscopy: Chemical Strategies and Applications. Chem Rev 2023; 123:3299-3323. [PMID: 36881995 DOI: 10.1021/acs.chemrev.2c00711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Expansion microscopy (ExM) is a newly developed super-resolution technique, allowing visualization of biological targets at nanoscale resolution on conventional fluorescence microscopes. Since its introduction in 2015, many efforts have been dedicated to broaden its application range or increase the resolution that can be achieved. As a consequence, recent years have witnessed remarkable advances in ExM. This review summarizes recent progress in ExM, with the focus on the chemical aspects of the method, from chemistries for biomolecule grafting to polymer synthesis and the impact on biological analysis. The combination of ExM with other microscopy techniques, in search of additional resolution improvement, is also discussed. In addition, we compare pre- and postexpansion labeling strategies and discuss the impact of fixation methods on ultrastructure preservation. We conclude this review with a perspective on existing challenges and future directions. We believe that this review will provide a comprehensive understanding of ExM and facilitate its usage and further development.
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Affiliation(s)
- Gang Wen
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium
| | - Volker Leen
- Chrometra Scientific, Kortenaken 3470, Belgium
| | - Taoufik Rohand
- Laboratory of Analytical and Molecular Chemistry, Faculty Polydisciplinaire of Safi, University Cadi Ayyad Marrakech, BP 4162, 46000 Safi, Morocco
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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7
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Gan Y, Ma Y, Gong W, Liu W, Wang Z, Hao X, Han Y, Kuang C, Liu X. Enhanced axial resolution of lattice light sheet microscopy by fluorescence differential detection. OPTICS EXPRESS 2022; 30:27381-27394. [PMID: 36236910 DOI: 10.1364/oe.462516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/01/2022] [Indexed: 06/16/2023]
Abstract
Lattice light-sheet microscopy (LLSM) is promising in long-term biological volumetric imaging due to its high spatiotemporal resolution and low phototoxicity. However, three-dimensional (3D) isotropic spatial resolution remains an unmet goal in LLSM because of its poorer axial resolution. Combing LLSM with fluorescence differential detection, namely LLSDM, has been proposed to improve the axial resolution of LLSM in simulation. It demonstrates the possibility of further enhancing the axial resolution in 3D volumetric imaging with LLSM by specifically discarding the off-focus photons captured using a complementary optical lattice (OL) profile generated with additional 0-π phase modulation at the objective pupil plane. The direct generation of the complementary lattice profile using the binary phase modulator conjugated to the sample plane for amplitude modulation, as used in LLSM, is also permittable. Nevertheless, the previously proposed configuration fails to provide a symmetric complementary lattice pattern along the axial axis, thus leading to the imbalanced off-focus photon suppression in the reconstructed images after subtraction [Opt. Lett.45, 2854 (2020)10.1364/OL.393378]. Here, we modified the LLSDM theory which can produce an ideal complementary lattice pattern with central zero intensity and symmetrically distributed sidelobes. We also analyzed the impact of numerical aperture matching between the original and complementary lattice patterns and presented the consistency between the simulated and experimental results. As demonstrated by imaging the distribution of fluorescent beads and microtubules in fixed U2OS cells, as well as the dynamics of filopodia in live U2OS cells, LLSDM provides about 1.5 times improvement in axial resolution, and higher imaging contrast compared with traditional LLSM.
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8
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Haynes EM, Ulland TK, Eliceiri KW. A Model of Discovery: The Role of Imaging Established and Emerging Non-mammalian Models in Neuroscience. Front Mol Neurosci 2022; 15:867010. [PMID: 35493325 PMCID: PMC9046975 DOI: 10.3389/fnmol.2022.867010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/18/2022] [Indexed: 11/24/2022] Open
Abstract
Rodents have been the dominant animal models in neurobiology and neurological disease research over the past 60 years. The prevalent use of rats and mice in neuroscience research has been driven by several key attributes including their organ physiology being more similar to humans, the availability of a broad variety of behavioral tests and genetic tools, and widely accessible reagents. However, despite the many advances in understanding neurobiology that have been achieved using rodent models, there remain key limitations in the questions that can be addressed in these and other mammalian models. In particular, in vivo imaging in mammals at the cell-resolution level remains technically difficult and demands large investments in time and cost. The simpler nervous systems of many non-mammalian models allow for precise mapping of circuits and even the whole brain with impressive subcellular resolution. The types of non-mammalian neuroscience models available spans vertebrates and non-vertebrates, so that an appropriate model for most cell biological questions in neurodegenerative disease likely exists. A push to diversify the models used in neuroscience research could help address current gaps in knowledge, complement existing rodent-based bodies of work, and bring new insight into our understanding of human disease. Moreover, there are inherent aspects of many non-mammalian models such as lifespan and tissue transparency that can make them specifically advantageous for neuroscience studies. Crispr/Cas9 gene editing and decreased cost of genome sequencing combined with advances in optical microscopy enhances the utility of new animal models to address specific questions. This review seeks to synthesize current knowledge of established and emerging non-mammalian model organisms with advances in cellular-resolution in vivo imaging techniques to suggest new approaches to understand neurodegeneration and neurobiological processes. We will summarize current tools and in vivo imaging approaches at the single cell scale that could help lead to increased consideration of non-mammalian models in neuroscience research.
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Affiliation(s)
- Elizabeth M. Haynes
- Morgridge Institute for Research, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
| | - Tyler K. Ulland
- Department of Pathology, University of Wisconsin-Madison, Madison, WI, United States
| | - Kevin W. Eliceiri
- Morgridge Institute for Research, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
- Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, United States
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9
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Jalalvand E, Alvelid J, Coceano G, Edwards S, Robertson B, Grillner S, Testa I. ExSTED microscopy reveals contrasting functions of dopamine and somatostatin CSF-c neurons along the lamprey central canal. eLife 2022; 11:73114. [PMID: 35103591 PMCID: PMC8809891 DOI: 10.7554/elife.73114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/19/2022] [Indexed: 01/04/2023] Open
Abstract
Cerebrospinal fluid-contacting (CSF-c) neurons line the central canal of the spinal cord and a subtype of CSF-c neurons expressing somatostatin, forms a homeostatic pH regulating system. Despite their importance, their intricate spatial organization is poorly understood. The function of another subtype of CSF-c neurons expressing dopamine is also investigated. Imaging methods with a high spatial resolution (5-10 nm) are used to resolve the synaptic and ciliary compartments of each individual cell in the spinal cord of the lamprey to elucidate their signalling pathways and to dissect the cellular organization. Here, light-sheet and expansion microscopy resolved the persistent ventral and lateral organization of dopamine- and somatostatin-expressing CSF-c neuronal subtypes. The density of somatostatin-containing dense-core vesicles, resolved by stimulated emission depletion microscopy, was shown to be markedly reduced upon each exposure to either alkaline or acidic pH and being part of a homeostatic response inhibiting movements. Their cilia symmetry was unravelled by stimulated emission depletion microscopy in expanded tissues as sensory with 9 + 0 microtubule duplets. The dopaminergic CSF-c neurons on the other hand have a motile cilium with the characteristic 9 + 2 duplets and are insensitive to pH changes. This novel experimental workflow elucidates the functional role of CSF-c neuron subtypes in situ paving the way for further spatial and functional cell-type classification.
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Affiliation(s)
- Elham Jalalvand
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jonatan Alvelid
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Giovanna Coceano
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Steven Edwards
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Brita Robertson
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Sten Grillner
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
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10
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Scardigli M, Pesce L, Brady N, Mazzamuto G, Gavryusev V, Silvestri L, Hof PR, Destrieux C, Costantini I, Pavone FS. Comparison of Different Tissue Clearing Methods for Three-Dimensional Reconstruction of Human Brain Cellular Anatomy Using Advanced Imaging Techniques. Front Neuroanat 2021; 15:752234. [PMID: 34867215 PMCID: PMC8632656 DOI: 10.3389/fnana.2021.752234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/13/2021] [Indexed: 01/29/2023] Open
Abstract
The combination of tissue clearing techniques with advanced optical microscopy facilitates the achievement of three-dimensional (3D) reconstruction of macroscopic specimens at high resolution. Whole mouse organs or even bodies have been analyzed, while the reconstruction of the human nervous system remains a challenge. Although several tissue protocols have been proposed, the high autofluorescence and variable post-mortem conditions of human specimens negatively affect the quality of the images in terms of achievable transparency and staining contrast. Moreover, homogeneous staining of high-density epitopes, such as neuronal nuclear antigen (NeuN), creates an additional challenge. Here, we evaluated different tissue transformation approaches to find the best solution to uniformly clear and label all neurons in the human cerebral cortex using anti-NeuN antibodies in combination with confocal and light-sheet fluorescence microscopy (LSFM). Finally, we performed mesoscopic high-resolution 3D reconstruction of the successfully clarified and stained samples with LSFM.
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Affiliation(s)
- Marina Scardigli
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Luca Pesce
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Niamh Brady
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
| | - Giacomo Mazzamuto
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
| | - Vladislav Gavryusev
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
| | - Patrick R. Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Irene Costantini
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
- Department of Biology, University of Florence, Florence, Italy
| | - Francesco S. Pavone
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
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11
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Chen R, Cheng X, Zhang Y, Yang X, Wang Y, Liu X, Zeng S. Expansion tomography for large volume tissue imaging with nanoscale resolution. BIOMEDICAL OPTICS EXPRESS 2021; 12:5614-5628. [PMID: 34692204 PMCID: PMC8515992 DOI: 10.1364/boe.431696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 05/10/2023]
Abstract
Expansion microscopy enables conventional diffraction limit microscopy to achieve super-resolution imaging. However, the enlarged tissue lacks an objective lens with sufficient working distance that can image tissues with whole-brain-scale coverage. Here, we present expansion tomography (ExT) to solve this problem. We have established a modified super-absorbent hydrogel (ExT gel) that possesses high mechanical strength and enables serial sectioning. ExT gel enables tissue and cell imaging and is compatible with various fluorescent labeling strategies. Combining with the high-throughput light-sheet tomography (HLTP) system, we have shown the capability of large volume imaging with nanoscale resolution of mouse brain intact neuronal circuits. The ExT method would allow image samples to support super-resolution imaging of intact tissues with virtually unlimited axial extensions.
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Affiliation(s)
- Ruixi Chen
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaofeng Cheng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yongsheng Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiong Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yu Wang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiuli Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shaoqun Zeng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics Huazhong University of Science and Technology, Wuhan 430074, China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan 430074, China
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12
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Campbell LA, Pannoni KE, Savory NA, Lal D, Farris S. Protein-retention expansion microscopy for visualizing subcellular organelles in fixed brain tissue. J Neurosci Methods 2021; 361:109285. [PMID: 34242703 PMCID: PMC8370715 DOI: 10.1016/j.jneumeth.2021.109285] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 11/21/2022]
Abstract
BACKGROUND Protein expansion microscopy (proExM) is a powerful technique that crosslinks proteins to a swellable hydrogel to physically expand and optically clear biological samples. The resulting increased resolution (~70 nm) and physical separation of labeled proteins make it an attractive tool for studying the localization of subcellular organelles in densely packed tissues, such as the brain. However, the digestion and expansion process greatly reduce fluorescence signals making it necessary to optimize ExM conditions per sample for specific end goals. NEW METHOD Here we compare the staining and digestion conditions of existing proExM workflows to identify the optimal protocol for visualizing subcellular organelles (mitochondria and the Golgi apparatus) within reporter-labeled neurons in fixed mouse brain tissue. RESULTS We found that immunostaining before proExM and using a proteinase K based digestion for 8 h consistently resulted in robust fluorescence retention for immunolabeled subcellular organelles and genetically-encoded reporters. COMPARISON WITH EXISTING METHODS With these methods, we more accurately quantified mitochondria size and number and better visualized Golgi ultrastructure in individual CA2 neurons in the mouse hippocampus. CONCLUSIONS This organelle optimized proExM protocol will be broadly useful for investigators interested in visualizing the spatial distribution of immunolabeled subcellular organelles in various reporter mouse lines, reducing effort, time and resources on the optimization process.
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Affiliation(s)
- Logan A Campbell
- Fralin Biomedical Research Institute, Center for Neurobiology Research, Virginia Tech Carilion, Roanoke, VA, USA
| | - Katy E Pannoni
- Fralin Biomedical Research Institute, Center for Neurobiology Research, Virginia Tech Carilion, Roanoke, VA, USA
| | - Niesha A Savory
- Fralin Biomedical Research Institute, Center for Neurobiology Research, Virginia Tech Carilion, Roanoke, VA, USA; School of Neuroscience, Virginia Tech, Blacksburg, VA, USA
| | - Dinesh Lal
- Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | - Shannon Farris
- Fralin Biomedical Research Institute, Center for Neurobiology Research, Virginia Tech Carilion, Roanoke, VA, USA; Virginia Tech Carilion School of Medicine, Roanoke, VA, USA; Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA.
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13
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Liu J, Fang X, Liu Z, Li R, Yang Y, Sun Y, Zhao Z, Wu C. Expansion Microscopy with Multifunctional Polymer Dots. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007854. [PMID: 33988880 DOI: 10.1002/adma.202007854] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Expansion microscopy (ExM) provides nanoscale resolution on conventional microscopes via physically enlarging specimens with swellable polyelectrolyte gels. However, challenges involving fluorophore degradation and dilution during sample expansion have yet to be overcome. Herein, sequential cellular targeting, gel anchoring, and high-fidelity fluorescence reported using multifunctional polymer dots (Pdots) designed for ExM applications are demonstrated. The impressive brightness of the Pdots facilitates multicolor ExM, thereby enabling visualization of a variety of subcellular structures and neuron synapses. The average fluorescence intensities of Pdots in ExM range from ≈3 to 6 times higher than those achieved using commercially available Alexa dyes. Moreover, the fluorescence brightness and optical fluctuation are significantly improved by a surfactant-containing expansion buffer, which enables further resolution enhancement via super-resolution optical fluctuation imaging (SOFI). The combination of ExM and SOFI allows subcellular structures of ≈30 nm to be resolved by conventional microscopes. These results highlight the immense potential of multifunctional Pdots for ExM-enhanced super-resolution imaging.
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Affiliation(s)
- Jie Liu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Xiaofeng Fang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Zhihe Liu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Rongqin Li
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yicheng Yang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Changfeng Wu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
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14
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Yao L, Zhang L, Fei Y, Chen L, Mi L, Ma J. Application of SNAP-Tag in Expansion Super-Resolution Microscopy Using DNA Oligostrands. Front Chem 2021; 9:640519. [PMID: 33996746 PMCID: PMC8119759 DOI: 10.3389/fchem.2021.640519] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Expansion super-resolution technology is a new technology developed in recent years. It anchors the dye on the hydrogel and the dye expands with the expansion of the hydrogel so that a super-resolution map can be obtained under an ordinary microscope. However, by labeling the target protein with a first antibody and secondary antibody, the distance between the fluorescent group and the actual target protein is greatly increased. Although fluorescent proteins can also be used for expansion super-resolution to reduce this effect, the fluorescent protein is often destroyed during sample preparation. To solve this problem, we developed a novel label system for expansion microscopy, based on a DNA oligostrand linked with a fluorescent dye, acrylamide group (linker), and benzoylguanine (BG, a small substrate molecule for SNAP-tag). This protocol greatly reduced the error between the position of fluorescent group and the actual target protein, and also reduced loss of the fluorescent group during sample preparation.
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Affiliation(s)
- Longfang Yao
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Li Zhang
- Shanghai Engineering Research Center of Industrial Microorganisms, The Multiscale Research Institute of Complex Systems, School of Life Sciences, Fudan University, Shanghai, China
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Liwen Chen
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Lan Mi
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Jiong Ma
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Industrial Microorganisms, The Multiscale Research Institute of Complex Systems, School of Life Sciences, Fudan University, Shanghai, China.,Insititute of Biomedical Engineering and Technology, Academy for Engineering and Technology, Fudan University, Shanghai, China
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15
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Light-Sheet Fluorescence Microscopy for Multiscale Biological Imaging. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00026-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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16
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Kubalová I, Schmidt Černohorská M, Huranová M, Weisshart K, Houben A, Schubert V. Prospects and limitations of expansion microscopy in chromatin ultrastructure determination. Chromosome Res 2020; 28:355-368. [PMID: 32939606 PMCID: PMC7691311 DOI: 10.1007/s10577-020-09637-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/28/2020] [Accepted: 08/05/2020] [Indexed: 02/04/2023]
Abstract
Expansion microscopy (ExM) is a method to magnify physically a specimen with preserved ultrastructure. It has the potential to explore structural features beyond the diffraction limit of light. The procedure has been successfully used for different animal species, from isolated macromolecular complexes through cells to tissue slices. Expansion of plant-derived samples is still at the beginning, and little is known, whether the chromatin ultrastructure becomes altered by physical expansion. In this study, we expanded isolated barley nuclei and compared whether ExM can provide a structural view of chromatin comparable with super-resolution microscopy. Different fixation and denaturation/digestion conditions were tested to maintain the chromatin ultrastructure. We achieved up to ~4.2-times physically expanded nuclei corresponding to a maximal resolution of ~50-60 nm when imaged by wild-field (WF) microscopy. By applying structured illumination microscopy (SIM, super-resolution) doubling the WF resolution, the chromatin structures were observed at a resolution of ~25-35 nm. WF microscopy showed a preserved nucleus shape and nucleoli. Moreover, we were able to detect chromatin domains, invisible in unexpanded nuclei. However, by applying SIM, we observed that the preservation of the chromatin ultrastructure after the expansion was not complete and that the majority of the tested conditions failed to keep the ultrastructure. Nevertheless, using expanded nuclei, we localized successfully centromere repeats by fluorescence in situ hybridization (FISH) and the centromere-specific histone H3 variant CENH3 by indirect immunolabelling. However, although these repeats and proteins were localized at the correct position within the nuclei (indicating a Rabl orientation), their ultrastructural arrangement was impaired.
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Affiliation(s)
- Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Markéta Schmidt Černohorská
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics,, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Martina Huranová
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics,, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | | | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany.
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17
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Düring DN, Dittrich F, Rocha MD, Tachibana RO, Mori C, Okanoya K, Boehringer R, Ehret B, Grewe BF, Gerber S, Ma S, Rauch M, Paterna JC, Kasper R, Gahr M, Hahnloser RHR. Fast Retrograde Access to Projection Neuron Circuits Underlying Vocal Learning in Songbirds. Cell Rep 2020; 33:108364. [PMID: 33176132 PMCID: PMC8236207 DOI: 10.1016/j.celrep.2020.108364] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/29/2020] [Accepted: 10/19/2020] [Indexed: 02/06/2023] Open
Abstract
Understanding the structure and function of neural circuits underlying speech and language is a vital step toward better treatments for diseases of these systems. Songbirds, among the few animal orders that share with humans the ability to learn vocalizations from a conspecific, have provided many insights into the neural mechanisms of vocal development. However, research into vocal learning circuits has been hindered by a lack of tools for rapid genetic targeting of specific neuron populations to meet the quick pace of developmental learning. Here, we present a viral tool that enables fast and efficient retrograde access to projection neuron populations. In zebra finches, Bengalese finches, canaries, and mice, we demonstrate fast retrograde labeling of cortical or dopaminergic neurons. We further demonstrate the suitability of our construct for detailed morphological analysis, for in vivo imaging of calcium activity, and for multi-color brainbow labeling. Düring et al. describe a fast and efficient viral vector to dissect structure and function of neural circuits underlying learned vocalizations in songbirds. The AAV variant provides retrograde access to projection neuron circuits, including dopaminergic pathways in songbirds and additionally in mice, and allows for retrograde calcium imaging and multispectral brainbow labeling.
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Affiliation(s)
- Daniel N Düring
- Institute of Neuroinformatics, University of Zurich/ETH Zurich, Zurich, Switzerland; Neuroscience Center Zurich, Zurich, Switzerland; Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany.
| | - Falk Dittrich
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Mariana D Rocha
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | | | - Chihiro Mori
- Department of Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazuo Okanoya
- Department of Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Roman Boehringer
- Institute of Neuroinformatics, University of Zurich/ETH Zurich, Zurich, Switzerland; Neuroscience Center Zurich, Zurich, Switzerland
| | - Benjamin Ehret
- Institute of Neuroinformatics, University of Zurich/ETH Zurich, Zurich, Switzerland; Neuroscience Center Zurich, Zurich, Switzerland
| | - Benjamin F Grewe
- Institute of Neuroinformatics, University of Zurich/ETH Zurich, Zurich, Switzerland; Neuroscience Center Zurich, Zurich, Switzerland
| | - Stefan Gerber
- Institute of Neuroinformatics, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Shouwen Ma
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Melanie Rauch
- Viral Vector Facility, Neuroscience Center Zurich, Zurich, Switzerland
| | | | - Robert Kasper
- Imaging Facility at the Max Planck Institute of Neurobiology, Munich, Germany
| | - Manfred Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Richard H R Hahnloser
- Institute of Neuroinformatics, University of Zurich/ETH Zurich, Zurich, Switzerland; Neuroscience Center Zurich, Zurich, Switzerland
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18
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Mascheroni L, Scherer KM, Manton JD, Ward E, Dibben O, Kaminski CF. Combining sample expansion and light sheet microscopy for the volumetric imaging of virus-infected cells with super-resolution. BIOMEDICAL OPTICS EXPRESS 2020; 11:5032-5044. [PMID: 33014598 PMCID: PMC7510880 DOI: 10.1364/boe.399404] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/17/2020] [Accepted: 07/17/2020] [Indexed: 05/25/2023]
Abstract
Expansion microscopy is a sample preparation technique that enables the optical imaging of biological specimens at super-resolution owing to their physical magnification, which is achieved through water-absorbing polymers. The technique uses readily available chemicals and does not require sophisticated equipment, thus offering super-resolution to laboratories that are not microscopy-specialised. Here we present a protocol combining sample expansion with light sheet microscopy to generate high-contrast, high-resolution 3D reconstructions of whole virus-infected cells. The results are superior to those achievable with comparable imaging modalities and reveal details of the infection cycle that are not discernible before expansion. An image resolution of approximately 95 nm could be achieved in samples labelled in 3 colours. We resolve that the viral nucleoprotein is accumulated at the membrane of vesicular structures within the cell cytoplasm and how these vesicles are positioned relative to cellular structures. We provide detailed guidance and a video protocol for the optimal application of the method and demonstrate its potential to study virus-host cell interactions.
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Affiliation(s)
- Luca Mascheroni
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- These authors contributed equally
| | - Katharina M Scherer
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- These authors contributed equally
| | | | - Edward Ward
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Oliver Dibben
- Flu-MSAT, Biopharmaceutical Development, R&D, AstraZeneca, Liverpool, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
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19
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Enhanced expansion microscopy to measure nanoscale structural and biochemical remodeling in single cells. Methods Cell Biol 2020; 161:147-180. [PMID: 33478687 DOI: 10.1016/bs.mcb.2020.04.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Resolution is a key feature in microscopy which allows the visualization of the fine structure of cells. Much of the life processes within these cells depend on the three-dimensional (3D) complexity of these structures. Optical super-resolution microscopies are currently the preferred choice of molecular and cell biologists who seek to visualize the organization of specific protein species at the nanometer scale. Traditional super-resolution microscopy techniques have often been limited by sample thickness, axial resolution, specialist optical instrumentation and computationally-demanding software for assembling the images. In this chapter we detail the protocol, "enhanced expansion microscopy" (EExM), which combines X10 expansion microscopy with Airyscan confocal microscopy. EExM enables 15nm lateral (and 35nm axial) resolution, and is a relatively cheap, accessible option allowing single protein resolution for the non-specialist optical microscopists. We illustrate how EExM has been utilized for mapping the 3D topology of intracellular protein arrays at sample depths which are not always compatible with some of the traditional super-resolution techniques. We demonstrate that antibody markers can recognize and map post-translational modifications of individual proteins in addition to their 3D positions. Finally, we discuss the current uncertainties and validations in EExM which include the isotropy in gel expansion and assessment of the expansion factor (of resolution improvement).
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20
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Rocha MD, Düring DN, Bethge P, Voigt FF, Hildebrand S, Helmchen F, Pfeifer A, Hahnloser RHR, Gahr M. Tissue Clearing and Light Sheet Microscopy: Imaging the Unsectioned Adult Zebra Finch Brain at Cellular Resolution. Front Neuroanat 2019; 13:13. [PMID: 30837847 PMCID: PMC6382697 DOI: 10.3389/fnana.2019.00013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/28/2019] [Indexed: 12/28/2022] Open
Abstract
The inherent complexity of brain tissue, with brain cells intertwining locally and projecting to distant regions, has made three-dimensional visualization of intact brains a highly desirable but challenging task in neuroscience. The natural opaqueness of tissue has traditionally limited researchers to techniques short of single cell resolution such as computer tomography or magnetic resonance imaging. By contrast, techniques with single-cell resolution required mechanical slicing into thin sections, which entails tissue distortions that severely hinder accurate reconstruction of large volumes. Recent developments in tissue clearing and light sheet microscopy have made it possible to investigate large volumes at micrometer resolution. The value of tissue clearing has been shown in a variety of tissue types and animal models. However, its potential for examining the songbird brain remains unexplored. Songbirds are an established model system for the study of vocal learning and sensorimotor control. They share with humans the capacity to adapt vocalizations based on auditory input. Song learning and production are controlled in songbirds by the song system, which forms a network of interconnected discrete brain nuclei. Here, we use the CUBIC and iDISCO+ protocols for clearing adult songbird brain tissue. Combined with light sheet imaging, we show the potential of tissue clearing for the investigation of connectivity between song nuclei, as well as for neuroanatomy and brain vasculature studies.
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Affiliation(s)
- Mariana Diales Rocha
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Daniel Normen Düring
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany.,Institute of Neuroinformatics, University of Zurich/ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich (ZNZ), Zurich, Switzerland
| | - Philipp Bethge
- Neuroscience Center Zurich (ZNZ), Zurich, Switzerland.,Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - Fabian F Voigt
- Neuroscience Center Zurich (ZNZ), Zurich, Switzerland.,Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - Staffan Hildebrand
- Institute of Pharmacology and Toxicology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Fritjof Helmchen
- Neuroscience Center Zurich (ZNZ), Zurich, Switzerland.,Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - Alexander Pfeifer
- Institute of Pharmacology and Toxicology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Richard Hans Robert Hahnloser
- Institute of Neuroinformatics, University of Zurich/ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich (ZNZ), Zurich, Switzerland
| | - Manfred Gahr
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
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