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Liu J, Tan YY, Zheng W, Wang Y, Ju LA, Su QP. Nanoscale insights into hematology: super-resolved imaging on blood cell structure, function, and pathology. J Nanobiotechnology 2024; 22:363. [PMID: 38910248 PMCID: PMC11194919 DOI: 10.1186/s12951-024-02605-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/30/2024] [Indexed: 06/25/2024] Open
Abstract
Fluorescence nanoscopy, also known as super-resolution microscopy, has transcended the conventional resolution barriers and enabled visualization of biological samples at nanometric resolutions. A series of super-resolution techniques have been developed and applied to investigate the molecular distribution, organization, and interactions in blood cells, as well as the underlying mechanisms of blood-cell-associated diseases. In this review, we provide an overview of various fluorescence nanoscopy technologies, outlining their current development stage and the challenges they are facing in terms of functionality and practicality. We specifically explore how these innovations have propelled forward the analysis of thrombocytes (platelets), erythrocytes (red blood cells) and leukocytes (white blood cells), shedding light on the nanoscale arrangement of subcellular components and molecular interactions. We spotlight novel biomarkers uncovered by fluorescence nanoscopy for disease diagnosis, such as thrombocytopathies, malignancies, and infectious diseases. Furthermore, we discuss the technological hurdles and chart out prospective avenues for future research directions. This review aims to underscore the significant contributions of fluorescence nanoscopy to the field of blood cell analysis and disease diagnosis, poised to revolutionize our approach to exploring, understanding, and managing disease at the molecular level.
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Affiliation(s)
- Jinghan Liu
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Yuping Yolanda Tan
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, 2006, Australia
- Heart Research Institute, Newtown, NSW, 2042, Australia
| | - Wen Zheng
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Yao Wang
- School of Biomedical Engineering, The University of Sydney, Darlington, NSW, 2008, Australia
| | - Lining Arnold Ju
- School of Biomedical Engineering, The University of Sydney, Darlington, NSW, 2008, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, 2006, Australia
- Heart Research Institute, Newtown, NSW, 2042, Australia
| | - Qian Peter Su
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia.
- Heart Research Institute, Newtown, NSW, 2042, Australia.
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2
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Castagnini D, Palma K, Jara-Wilde J, Navarro N, González MJ, Toledo J, Canales-Huerta N, Scavone P, Härtel S. Proteus mirabilis biofilm expansion microscopy yields over 4-fold magnification for super-resolution of biofilm structure and subcellular DNA organization. J Microbiol Methods 2024; 220:106927. [PMID: 38561125 DOI: 10.1016/j.mimet.2024.106927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Bacterial biofilms form when bacteria attach to surfaces and generate an extracellular matrix that embeds and stabilizes a growing community. Detailed visualization and quantitative analysis of biofilm architecture by optical microscopy are limited by the law of diffraction. Expansion Microscopy (ExM) is a novel Super-Resolution technique where specimens are physically enlarged by a factor of ∼4, prior to observation by conventional fluorescence microscopy. ExM requires homogenization of rigid constituents of biological components by enzymatic digestion. We developed an ExM approach capable of expanding 48-h old Proteus mirabilis biofilms 4.3-fold (termed PmbExM), close to the theoretic maximum expansion factor without gross shape distortions. Our protocol, based on lytic and glycoside-hydrolase enzymatic treatments, degrades rigid components in bacteria and extracellular matrix. Our results prove PmbExM to be a versatile and easy-to-use Super-Resolution approach for enabling studies of P. mirabilis biofilm architecture, assembly, and even intracellular features, such as DNA organization.
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Affiliation(s)
- Dante Castagnini
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Independencia, Santiago, Chile
| | - Karina Palma
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Independencia, Santiago, Chile; Centro de Informática Médica y Telemedicina CIMT, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Jorge Jara-Wilde
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Independencia, Santiago, Chile; Centro de Informática Médica y Telemedicina CIMT, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Nicolás Navarro
- Advanced Center for Chronic Diseases ACCDiS, Santiago, Chile.; Laboratorio de Biofilms Microbianos, Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - María José González
- Laboratorio de Biofilms Microbianos, Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Jorge Toledo
- Red de Equipamiento Científico Avanzado REDECA, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Nicole Canales-Huerta
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Independencia, Santiago, Chile
| | - Paola Scavone
- Laboratorio de Biofilms Microbianos, Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Steffen Härtel
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Independencia, Santiago, Chile; Centro de Informática Médica y Telemedicina CIMT, Faculty of Medicine, University of Chile, Santiago, Chile; National Center for Health Information Systems CENS, Santiago, Chile.; Red de Equipamiento Científico Avanzado REDECA, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Centro de Modelamiento Matemático, Universidad de Chile, Beauchef 851, Casilla 170-3, Santiago, Chile.
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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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Bandeira PT, Ortiz SFDN, Benchimol M, de Souza W. Expansion Microscopy of trichomonads. Exp Parasitol 2023; 255:108629. [PMID: 37802179 DOI: 10.1016/j.exppara.2023.108629] [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: 07/14/2023] [Revised: 09/24/2023] [Accepted: 10/03/2023] [Indexed: 10/08/2023]
Abstract
Light microscopy has significantly advanced in recent decades, especially concerning the increased resolution obtained in fluorescence images. Here we present the Expansion Microscopy (ExM) technique in two parasites, Trichomonas vaginalis and Tritrichomonas foetus, which significantly improved the localization of distinct proteins closely associated with cytoskeleton by immunofluorescence microscopy. The ExM techniques have been used in various cell types, tissues and other protist parasites. It requires the embedment of the samples in a swellable gel that is highly hydrophilic. As a result, cells are expanded 4.5 times in an isotropic manner, offering a spatial resolution of ∼70 nm. We used this new methodology not only to observe the structural organization of protozoa in more detail but also to increase the resolution by immunofluorescence microscopy of two major proteins such as tubulin, found in structures formed by microtubules, and costain 1, the only protein identified until now in the T. foetus's costa, a unique rod-shaped like structure. The individualized microtubules of the axostyle were seen for the first time in fluorescence microscopy and several other details are presented after this technique.
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Affiliation(s)
- Paula Terra Bandeira
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Centro de Pesquisa em Medicina de Precisão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens e Centro Nacional de Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Sharmila Fiama das Neves Ortiz
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Centro de Pesquisa em Medicina de Precisão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Marlene Benchimol
- BIOTRANS-CAXIAS, Universidade do Grande Rio. UNIGRANRIO, Rio de Janeiro, 96200-000, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens e Centro Nacional de Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil.
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Centro de Pesquisa em Medicina de Precisão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens e Centro Nacional de Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
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5
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Atchou K, Berger BM, Heussler V, Ochsenreiter T. Pre-gelation staining expansion microscopy for visualisation of the Plasmodium liver stage. J Cell Sci 2023; 136:jcs261377. [PMID: 37942994 PMCID: PMC10729816 DOI: 10.1242/jcs.261377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/01/2023] [Indexed: 11/10/2023] Open
Abstract
Fluorescence and light microscopy are important tools in the history of natural science. However, the resolution of microscopes is limited by the diffraction of light. One possible method to circumvent this physical restriction is the recently developed expansion microscopy (ExM). However, the original ultrastructure ExM (U-ExM) protocol is very time-consuming, and some epitopes are lost during the process. In this study, we developed a shortened pre-gelation staining ExM (PS-ExM) protocol and tested it to investigate the Plasmodium liver stage. The protocol presented in this study allows expanding of pre-stained samples, which results in shorter incubation times, better preservation of some epitopes and the advantage that non-expanded controls can be performed alongside using the same staining protocol. The protocol applicability was accessed throughout the Plasmodium liver stage, showing isotropic five-fold expansion. Furthermore, we used PS-ExM to visualise parasite mitochondria as well as the association of lysosomes to the parasitophorous vacuole membrane (PVM) as an example of visualising host-pathogen interaction. We are convinced that this new tool will be helpful for a deeper understanding of the biology of the Plasmodium liver stage.
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Affiliation(s)
- Kodzo Atchou
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Bianca Manuela Berger
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Volker Heussler
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
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Greenstreet L, Afanassiev A, Kijima Y, Heitz M, Ishiguro S, King S, Yachie N, Schiebinger G. DNA-GPS: A theoretical framework for optics-free spatial genomics and synthesis of current methods. Cell Syst 2023; 14:844-859.e4. [PMID: 37751737 DOI: 10.1016/j.cels.2023.08.005] [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: 04/27/2022] [Revised: 04/19/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023]
Abstract
While single-cell sequencing technologies provide unprecedented insights into genomic profiles at the cellular level, they lose the spatial context of cells. Over the past decade, diverse spatial transcriptomics and multi-omics technologies have been developed to analyze molecular profiles of tissues. In this article, we categorize current spatial genomics technologies into three classes: optical imaging, positional indexing, and mathematical cartography. We discuss trade-offs in resolution and scale, identify limitations, and highlight synergies between existing single-cell and spatial genomics methods. Further, we propose DNA-GPS (global positioning system), a theoretical framework for large-scale optics-free spatial genomics that combines ideas from mathematical cartography and positional indexing. DNA-GPS has the potential to achieve scalable spatial genomics for multiple measurement modalities, and by eliminating the need for optical measurement, it has the potential to position cells in three-dimensions (3D).
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Affiliation(s)
- Laura Greenstreet
- Department of Mathematics, The University of British Columbia, Vancouver, BC, Canada
| | - Anton Afanassiev
- Department of Mathematics, The University of British Columbia, Vancouver, BC, Canada
| | - Yusuke Kijima
- School of Biomedical Engineering, The University of British Columbia, Vancouver, BC, Canada; Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| | - Matthieu Heitz
- Department of Mathematics, The University of British Columbia, Vancouver, BC, Canada
| | - Soh Ishiguro
- School of Biomedical Engineering, The University of British Columbia, Vancouver, BC, Canada
| | - Samuel King
- School of Biomedical Engineering, The University of British Columbia, Vancouver, BC, Canada
| | - Nozomu Yachie
- School of Biomedical Engineering, The University of British Columbia, Vancouver, BC, Canada; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan; Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka, Japan; Graduate School of Media and Governance, Keio University, Fujisawa, Japan.
| | - Geoffrey Schiebinger
- Department of Mathematics, The University of British Columbia, Vancouver, BC, Canada; School of Biomedical Engineering, The University of British Columbia, Vancouver, BC, Canada.
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7
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Kraft N, Muenz TS, Reinhard S, Werner C, Sauer M, Groh C, Rössler W. Expansion microscopy in honeybee brains for high-resolution neuroanatomical analyses in social insects. Cell Tissue Res 2023; 393:489-506. [PMID: 37421435 PMCID: PMC10484815 DOI: 10.1007/s00441-023-03803-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023]
Abstract
The diffraction limit of light microscopy poses a problem that is frequently faced in structural analyses of social insect brains. With the introduction of expansion microscopy (ExM), a tool became available to overcome this limitation by isotropic physical expansion of preserved specimens. Our analyses focus on synaptic microcircuits (microglomeruli, MG) in the mushroom body (MB) of social insects, high-order brain centers for sensory integration, learning, and memory. MG undergo significant structural reorganizations with age, sensory experience, and during long-term memory formation. However, the changes in subcellular architecture involved in this plasticity have only partially been accessed yet. Using the western honeybee Apis mellifera as an experimental model, we established ExM for the first time in a social insect species and applied it to investigate plasticity in synaptic microcircuits within MG of the MB calyces. Using combinations of antibody staining and neuronal tracing, we demonstrate that this technique enables quantitative and qualitative analyses of structural neuronal plasticity at high resolution in a social insect brain.
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Affiliation(s)
- Nadine Kraft
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany.
| | - Thomas S Muenz
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Sebastian Reinhard
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Christian Werner
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Claudia Groh
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Wolfgang Rössler
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
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8
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Ghosh S, Sapkota BS, Rao RS, Patil S, Rajkumar C, Lakshminarayan S. Expansion microscopy: A revolution in diagnostic pathology. J Microsc 2023; 290:3-9. [PMID: 36641735 DOI: 10.1111/jmi.13170] [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: 11/20/2022] [Revised: 12/21/2022] [Accepted: 01/09/2023] [Indexed: 01/16/2023]
Abstract
Expansion microscopy (ExM) is a recent discovery in diagnostic pathology and microbiology that promotes a physical magnification of the tissue specimen instead of optical magnification. It not only improves the resolution of the specimen but also enhances the diagnostic precision, and permits nanoscale imaging of the specimen. Optical microscopy is routinely used in histopathology and microbiology for ages. Due to its simplicity, compatibility with different types of specimens, and ease of operation it is accepted by pathologists. ExM and its variants have been widely tested in different types of tissue specimens and microbiological specimens and yielded brilliant results.
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Affiliation(s)
- Snehashish Ghosh
- Department of Oral Pathology, College of Medical Sciences, Bharatpur, Nepal
| | | | - Roopa S Rao
- Faculty of Dental Sciences, Department of Oral Pathology, Ramaiah University of Applied Sciences, Bangalore, India
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, Utah
- Centre of Molecular Medicine and Diagnostics (COMManD), Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Chandini Rajkumar
- Department of Oral Pathology and Microbiology, Sathyabama Dental College and Hospital, Chennai, India
| | - Surendra Lakshminarayan
- Department of Oral Pathology and Microbiology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, India
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Affiliation(s)
- Sven Truckenbrodt
- Convergent Research, E11 Bio. 1600 Harbor Bay Parkway, Alameda, California94502, United States
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10
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Almogbil HH, Montecinos-Franjola F, Daszynski C, Conlon WJ, Hachey JS, Corazza G, Rodriguez EA, Zderic V. Therapeutic Ultrasound for Topical Corneal Delivery of Macromolecules. Transl Vis Sci Technol 2022; 11:23. [PMID: 35998058 PMCID: PMC9424970 DOI: 10.1167/tvst.11.8.23] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/23/2022] [Indexed: 11/24/2022] Open
Abstract
Purpose The objective of this study was to utilize therapeutic ultrasound in enhancing delivery of topical macromolecules into the cornea. Methods Rabbit corneas were dissected and placed in a diffusion cell with a small ultra-red fluorescent protein (smURFP; molecular weight of 32,000 Da) as a macromolecule solution. The corneas were treated with continuous ultrasound application at frequencies of 400 or 600 kHz and intensities of 0.8 to 1.0 W/cm2 for 5 minutes, or sham-treated. Fluorescence imaging of the cornea sections was used to observe the delivery of macromolecules into individual epithelial cells. Spectrophotometric analysis at smURFP maximal absorbance of 640 nm was done to determine the presence of macromolecules in the receiver compartment. Safety of ultrasound application was studied through histology analysis. Results Ultrasound-treated corneas showed smURFP delivery into epithelial cells by fluorescence in the cytoplasm, whereas sham-treated corneas lacked any appreciable fluorescence in the individual cells. The sham group showed 0% of subcellular penetration, whereas the 400 kHz ultrasound-treated group and 600 kHz ultrasound-treated group showed 31% and 57% of subcellular penetration, respectively. Spectrophotometry measurements indicated negligible presence of smURFP macromolecules in the receiver compartment solution in both the sham and ultrasound treatment groups, and these macromolecules did not cross the entire depth of the cornea. Histological studies showed no significant corneal damage due to ultrasound application. Conclusions Therapeutic ultrasound application was shown to increase the delivery of smURFP macromolecules into the cornea. Translational Relevance Our study offers a clinical potential for a minimally invasive macromolecular treatment of corneal diseases.
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Affiliation(s)
- Hanaa H. Almogbil
- Department of Biomedical Engineering, The George Washington University, Washington, DC, USA
| | | | - Camille Daszynski
- Department of Biomedical Engineering, The George Washington University, Washington, DC, USA
| | - William J. Conlon
- Department of Chemistry, The George Washington University, Washington, DC, USA
| | - Justin S. Hachey
- Department of Chemistry, The George Washington University, Washington, DC, USA
| | - Giavanna Corazza
- Department of Biomedical Engineering, The George Washington University, Washington, DC, USA
| | - Erik A. Rodriguez
- Department of Chemistry, The George Washington University, Washington, DC, USA
| | - Vesna Zderic
- Department of Biomedical Engineering, The George Washington University, Washington, DC, USA
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11
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Wang W, Chan YH, Kwon S, Tandukar J, Gao R. Nanoscale fluorescence imaging of biological ultrastructure via molecular anchoring and physical expansion. NANO CONVERGENCE 2022; 9:30. [PMID: 35810234 PMCID: PMC9271151 DOI: 10.1186/s40580-022-00318-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/26/2022] [Indexed: 05/25/2023]
Abstract
Nanoscale imaging of biological samples can provide rich morphological and mechanistic information about biological functions and dysfunctions at the subcellular and molecular level. Expansion microscopy (ExM) is a recently developed nanoscale fluorescence imaging method that takes advantage of physical enlargement of biological samples. In ExM, preserved cells and tissues are embedded in a swellable hydrogel, to which the molecules and fluorescent tags in the samples are anchored. When the hydrogel swells several-fold, the effective resolution of the sample images can be improved accordingly via physical separation of the retained molecules and fluorescent tags. In this review, we focus on the early conception and development of ExM from a biochemical and materials perspective. We first examine the general workflow as well as the numerous variations of ExM developed to retain and visualize a broad range of biomolecules, such as proteins, nucleic acids, and membranous structures. We then describe a number of inherent challenges facing ExM, including those associated with expansion isotropy and labeling density, as well as the ongoing effort to address these limitations. Finally, we discuss the prospect and possibility of pushing the resolution and accuracy of ExM to the single-molecule scale and beyond.
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Affiliation(s)
- Wei Wang
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Yat Ho Chan
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - SoYoung Kwon
- Department of Biomedical and Health Information Sciences, College of Applied Health Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Jamuna Tandukar
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Ruixuan Gao
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA.
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA.
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12
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Faulkner EL, Pike JA, Densham RM, Garlick E, Thomas SG, Neely RK, Morris JR. Imaging nanoscale nuclear structures with expansion microscopy. J Cell Sci 2022; 135:276027. [PMID: 35748225 PMCID: PMC9450888 DOI: 10.1242/jcs.259009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/21/2022] [Indexed: 11/20/2022] Open
Abstract
Commonly applied super-resolution light microscopies have provided insight into subcellular processes at the nanoscale. However, imaging depth, speed, throughput and cost remain significant challenges, limiting the numbers of three-dimensional (3D) nanoscale processes that can be investigated and the number of laboratories able to undertake such analysis. Expansion microscopy (ExM) solves many of these limitations, but its application to imaging nuclear processes has been constrained by concerns of unequal nuclear expansion. Here, we demonstrate the conditions for isotropic expansion of the nucleus at a resolution equal to or better than 120–130 nm (pre-expansion). Using the DNA damage response proteins BRCA1, 53BP1 (also known as TP53BP1) and RAD51 as exemplars, we quantitatively describe the 3D nanoscale organisation of over 50,000 DNA damage response structures. We demonstrate the ability to assess chromatin-regulated events and show the simultaneous assessment of four elements. This study thus demonstrates how ExM can contribute to the investigation of nanoscale nuclear processes. Summary: Expansion microscopy provides quantitative insight into the impact of chromatin modifiers on spatiotemporal organisation of the DNA repair proteins BRCA1, 53BP1 and RAD51 at a resolution of 65–70 nm.
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Affiliation(s)
- Emma L Faulkner
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Jeremy A Pike
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,COMPARE, University of Birmingham and University of Nottingham, Midlands, UK
| | - Ruth M Densham
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, B15 2TT, UK
| | - Evelyn Garlick
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,COMPARE, University of Birmingham and University of Nottingham, Midlands, UK
| | - Steven G Thomas
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,COMPARE, University of Birmingham and University of Nottingham, Midlands, UK
| | - Robert K Neely
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, B15 2TT, UK
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13
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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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14
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Endo M, Maruoka H, Okabe S. Advanced Technologies for Local Neural Circuits in the Cerebral Cortex. Front Neuroanat 2021; 15:757499. [PMID: 34803616 PMCID: PMC8595196 DOI: 10.3389/fnana.2021.757499] [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: 08/12/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
The neural network in the brain can be viewed as an integrated system assembled from a large number of local neural circuits specialized for particular brain functions. Activities of neurons in local neural circuits are thought to be organized both spatially and temporally under the rules optimized for their roles in information processing. It is well perceived that different areas of the mammalian neocortex have specific cognitive functions and distinct computational properties. However, the organizational principles of the local neural circuits in different cortical regions have not yet been clarified. Therefore, new research principles and related neuro-technologies that enable efficient and precise recording of large-scale neuronal activities and synaptic connections are necessary. Innovative technologies for structural analysis, including tissue clearing and expansion microscopy, have enabled super resolution imaging of the neural circuits containing thousands of neurons at a single synapse resolution. The imaging resolution and volume achieved by new technologies are beyond the limits of conventional light or electron microscopic methods. Progress in genome editing and related technologies has made it possible to label and manipulate specific cell types and discriminate activities of multiple cell types. These technologies will provide a breakthrough for multiscale analysis of the structure and function of local neural circuits. This review summarizes the basic concepts and practical applications of the emerging technologies and new insight into local neural circuits obtained by these technologies.
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Affiliation(s)
| | | | - Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
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15
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Schwarz MK, Kubitscheck U. Expansion light sheet fluorescence microscopy of extended biological samples: Applications and perspectives. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 168:33-36. [PMID: 34626664 DOI: 10.1016/j.pbiomolbio.2021.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/25/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Martin K Schwarz
- Institute Experimental Epileptology and Cognition Research (EECR), University of Bonn Medical School, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
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16
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Trinks N, Reinhard S, Drobny M, Heilig L, Löffler J, Sauer M, Terpitz U. Subdiffraction-resolution fluorescence imaging of immunological synapse formation between NK cells and A. fumigatus by expansion microscopy. Commun Biol 2021; 4:1151. [PMID: 34608260 PMCID: PMC8490467 DOI: 10.1038/s42003-021-02669-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Expansion microscopy (ExM) enables super-resolution fluorescence imaging on standard microscopes by physical expansion of the sample. However, the investigation of interactions between different organisms such as mammalian and fungal cells by ExM remains challenging because different cell types require different expansion protocols to ensure identical, ideally isotropic expansion of both partners. Here, we introduce an ExM method that enables super-resolved visualization of the interaction between NK cells and Aspergillus fumigatus hyphae. 4-fold expansion in combination with confocal fluorescence imaging allows us to resolve details of cytoskeleton rearrangement as well as NK cells' lytic granules triggered by contact with an RFP-expressing A. fumigatus strain. In particular, subdiffraction-resolution images show polarized degranulation upon contact formation and the presence of LAMP1 surrounding perforin at the NK cell-surface post degranulation. Our data demonstrate that optimized ExM protocols enable the investigation of immunological synapse formation between two different species with so far unmatched spatial resolution.
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Affiliation(s)
- Nora Trinks
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, Germany
| | - Sebastian Reinhard
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, Germany
| | - Matthias Drobny
- Department of Internal Medicine II, WÜ4i, University Hospital Würzburg, Würzburg, Germany
| | - Linda Heilig
- Department of Internal Medicine II, WÜ4i, University Hospital Würzburg, Würzburg, Germany
| | - Jürgen Löffler
- Department of Internal Medicine II, WÜ4i, University Hospital Würzburg, Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, Germany
| | - Ulrich Terpitz
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, Germany.
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17
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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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18
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Valli J, Sanderson J. Super-Resolution Fluorescence Microscopy Methods for Assessing Mouse Biology. Curr Protoc 2021; 1:e224. [PMID: 34436832 DOI: 10.1002/cpz1.224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Super-resolution (diffraction unlimited) microscopy was developed 15 years ago; the developers were awarded the Nobel Prize in Chemistry in recognition of their work in 2014. Super-resolution microscopy is increasingly being applied to diverse scientific fields, from single molecules to cell organelles, viruses, bacteria, plants, and animals, especially the mammalian model organism Mus musculus. In this review, we explain how super-resolution microscopy, along with fluorescence microscopy from which it grew, has aided the renaissance of the light microscope. We cover experiment planning and specimen preparation and explain structured illumination microscopy, super-resolution radial fluctuations, stimulated emission depletion microscopy, single-molecule localization microscopy, and super-resolution imaging by pixel reassignment. The final section of this review discusses the strengths and weaknesses of each super-resolution technique and how to choose the best approach for your research. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Jessica Valli
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
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19
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Gallagher BR, Zhao Y. Expansion microscopy: A powerful nanoscale imaging tool for neuroscientists. Neurobiol Dis 2021; 154:105362. [PMID: 33813047 PMCID: PMC8600979 DOI: 10.1016/j.nbd.2021.105362] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 01/13/2023] Open
Abstract
One of the biggest unsolved questions in neuroscience is how molecules and neuronal circuitry create behaviors, and how their misregulation or dysfunction results in neurological disease. Light microscopy is a vital tool for the study of neural molecules and circuits. However, the fundamental optical diffraction limit precludes the use of conventional light microscopy for sufficient characterization of critical signaling compartments and nanoscopic organizations of synapse-associated molecules. We have witnessed rapid development of super-resolution microscopy methods that circumvent the resolution limit by controlling the number of emitting molecules in specific imaging volumes and allow highly resolved imaging in the 10-100 nm range. Most recently, Expansion Microscopy (ExM) emerged as an alternative solution to overcome the diffraction limit by physically magnifying biological specimens, including nervous systems. Here, we discuss how ExM works in general and currently available ExM methods. We then review ExM imaging in a wide range of nervous systems, including Caenorhabditis elegans, Drosophila, zebrafish, mouse, and human, and their applications to synaptic imaging, neuronal tracing, and the study of neurological disease. Finally, we provide our prospects for expansion microscopy as a powerful nanoscale imaging tool in the neurosciences.
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Affiliation(s)
- Brendan R Gallagher
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yongxin Zhao
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
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20
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Kang S, Park S, Song H, Choi D, Park HE, Ahn BH, Kim SY, Lee Y. Expansion Microscopy with a Thermally Adjustable Expansion Factor Using Thermoresponsive Biospecimen-Hydrogel Hybrids. ACS APPLIED MATERIALS & INTERFACES 2021; 13:28962-28974. [PMID: 34107679 DOI: 10.1021/acsami.1c07592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Expansion microscopy (ExM) is a technique in which swellable hydrogel-embedded biological samples are physically expanded to effectively increase imaging resolution. Here, we develop thermoresponsive reversible ExM (T-RevExM), in which the expansion factor can be thermally adjusted in a reversible manner. In this method, samples are embedded in thermoresponsive hydrogels and partially digested to allow for reversible swelling of the sample-gel hybrid in a temperature-dependent manner. We first synthesized hydrogels exhibiting lower critical solution temperature (LCST)- and upper critical solution temperature (UCST)-phase transition properties with N-alkyl acrylamide or sulfobetaine monomers, respectively. We then formed covalent hybrids between the LCST or UCST hydrogel and biomolecules across the cultured cells and tissues. The resulting hybrid could be reversibly swelled or deswelled in a temperature-dependent manner, with LCST- and UCST-based hybrids negatively and positively responding to the increase in temperature (termed thermonegative RevExM and thermopositive RevExM, respectively). We further showed reliable imaging of both unexpanded and expanded cells and tissues and demonstrated minimal distortions from the original sample using conventional confocal microscopy. Thus, T-RevExM enables easy adjustment of the size of biological samples and therefore the effective magnification and resolution of the sample, simply by changing the sample temperature.
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Affiliation(s)
- Sunah Kang
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sohyun Park
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hojoon Song
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Dongkil Choi
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Han-Eol Park
- Institute of Molecular Biology and Genetics, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Benjamin H Ahn
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sung-Yon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Yan Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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21
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Gao R, Yu CCJ, Gao L, Piatkevich KD, Neve RL, Munro JB, Upadhyayula S, Boyden ES. A highly homogeneous polymer composed of tetrahedron-like monomers for high-isotropy expansion microscopy. NATURE NANOTECHNOLOGY 2021; 16:698-707. [PMID: 33782587 PMCID: PMC8197733 DOI: 10.1038/s41565-021-00875-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/11/2021] [Indexed: 05/08/2023]
Abstract
Expansion microscopy (ExM) physically magnifies biological specimens to enable nanoscale-resolution imaging using conventional microscopes. Current ExM methods permeate specimens with free-radical-chain-growth-polymerized polyacrylate hydrogels, whose network structure limits the local isotropy of expansion as well as the preservation of morphology and shape at the nanoscale. Here we report that ExM is possible using hydrogels that have a more homogeneous network structure, assembled via non-radical terminal linking of tetrahedral monomers. As with earlier forms of ExM, such 'tetra-gel'-embedded specimens can be iteratively expanded for greater physical magnification. Iterative tetra-gel expansion of herpes simplex virus type 1 (HSV-1) virions by ~10× in linear dimension results in a median spatial error of 9.2 nm for localizing the viral envelope layer, rather than 14.3 nm from earlier versions of ExM. Moreover, tetra-gel-based expansion better preserves the virion spherical shape. Thus, tetra-gels may support ExM with reduced spatial errors and improved local isotropy, pointing the way towards single-biomolecule accuracy ExM.
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Affiliation(s)
- Ruixuan Gao
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
- Media Arts and Sciences, MIT, Cambridge, MA, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Chih-Chieh Jay Yu
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
- Media Arts and Sciences, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Linyi Gao
- Media Arts and Sciences, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Broad Institute, MIT, Cambridge, MA, USA
| | - Kiryl D Piatkevich
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
- Media Arts and Sciences, MIT, Cambridge, MA, USA
| | - Rachael L Neve
- Department of Neurology, Massachusetts General Hospital, Cambridge, MA, USA
| | - James B Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Srigokul Upadhyayula
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Advanced Bioimaging Center, University of California at Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Edward S Boyden
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA.
- Media Arts and Sciences, MIT, Cambridge, MA, USA.
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
- MIT Center for Neurobiological Engineering, MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
- Koch Institute, MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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22
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Kolesová H, Olejníčková V, Kvasilová A, Gregorovičová M, Sedmera D. Tissue clearing and imaging methods for cardiovascular development. iScience 2021; 24:102387. [PMID: 33981974 PMCID: PMC8086021 DOI: 10.1016/j.isci.2021.102387] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tissue imaging in 3D using visible light is limited and various clearing techniques were developed to increase imaging depth, but none provides universal solution for all tissues at all developmental stages. In this review, we focus on different tissue clearing methods for 3D imaging of heart and vasculature, based on chemical composition (solvent-based, simple immersion, hyperhydration, and hydrogel embedding techniques). We discuss in detail compatibility of various tissue clearing techniques with visualization methods: fluorescence preservation, immunohistochemistry, nuclear staining, and fluorescent dyes vascular perfusion. We also discuss myocardium visualization using autofluorescence, tissue shrinking, and expansion. Then we overview imaging methods used to study cardiovascular system and live imaging. We discuss heart and vessels segmentation methods and image analysis. The review covers the whole process of cardiovascular system 3D imaging, starting from tissue clearing and its compatibility with various visualization methods to the types of imaging methods and resulting image analysis.
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Affiliation(s)
- Hana Kolesová
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
| | - Veronika Olejníčková
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
| | - Alena Kvasilová
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martina Gregorovičová
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
| | - David Sedmera
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
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23
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Kunz TC, Rühling M, Moldovan A, Paprotka K, Kozjak-Pavlovic V, Rudel T, Fraunholz M. The Expandables: Cracking the Staphylococcal Cell Wall for Expansion Microscopy. Front Cell Infect Microbiol 2021; 11:644750. [PMID: 33796486 PMCID: PMC8008081 DOI: 10.3389/fcimb.2021.644750] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/08/2021] [Indexed: 12/03/2022] Open
Abstract
Expansion Microscopy (ExM) is a novel tool improving the resolution of fluorescence microscopy by linking the sample into a hydrogel that gets physically expanded in water. Previously, we have used ExM to visualize the intracellular Gram-negative pathogens Chlamydia trachomatis, Simkania negevensis, and Neisseria gonorrhoeae. Gram-positive bacteria have a rigid and thick cell wall that impedes classic expansion strategies. Here we developed an approach, which included a series of enzymatic treatments resulting in isotropic 4× expansion of the Gram-positive pathogen Staphylococcus aureus. We further demonstrate the suitability of the technique for imaging of planktonic bacteria as well as endocytosed, intracellular bacteria at a spatial resolution of approximately 60 nm with conventional confocal laser scanning microscopy.
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Affiliation(s)
- Tobias C Kunz
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Marcel Rühling
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Adriana Moldovan
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Kerstin Paprotka
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Vera Kozjak-Pavlovic
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Thomas Rudel
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Martin Fraunholz
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
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24
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Wunderlich LCS, Ströhl F, Ströhl S, Vanderpoorten O, Mascheroni L, Kaminski CF. Superresolving the kidney-a practical comparison of fluorescence nanoscopy of the glomerular filtration barrier. Anal Bioanal Chem 2021; 413:1203-1214. [PMID: 33277998 PMCID: PMC7813708 DOI: 10.1007/s00216-020-03084-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/31/2020] [Accepted: 11/19/2020] [Indexed: 01/19/2023]
Abstract
Immunofluorescence microscopy is routinely used in the diagnosis of and research on renal impairments. However, this highly specific technique is restricted in its maximum resolution to about 250 nm in the lateral and 700 nm in the axial directions and thus not sufficient to investigate the fine subcellular structure of the kidney's glomerular filtration barrier. In contrast, electron microscopy offers high resolution, but this comes at the cost of poor preservation of immunogenic epitopes and antibody penetration alongside a low throughput. Many of these drawbacks were overcome with the advent of super-resolution microscopy methods. So far, four different super-resolution approaches have been used to study the kidney: single-molecule localization microscopy (SMLM), stimulated emission depletion (STED) microscopy, structured illumination microscopy (SIM), and expansion microscopy (ExM), however, using different preservation methods and widely varying labelling strategies. In this work, all four methods were applied and critically compared on kidney slices obtained from samples treated with the most commonly used preservation technique: fixation by formalin and embedding in paraffin (FFPE). Strengths and weaknesses, as well as the practicalities of each method, are discussed to enable users of super-resolution microscopy in renal research make an informed decision on the best choice of technique. The methods discussed enable the efficient investigation of biopsies stored in kidney banks around the world. Graphical abstract.
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Affiliation(s)
- Lucia C S Wunderlich
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Florian Ströhl
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
- Department of Physics and Technology, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Stefan Ströhl
- Department of Nephrology, University Hospital Regensburg, 93053, Regensburg, Germany
| | - Oliver Vanderpoorten
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
- Department of Physics and Technology, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Luca Mascheroni
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK.
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25
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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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26
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Bianchini P, Pesce L, Diaspro A. Expansion microscopy at the nanoscale: The nuclear pore complex as a fiducial landmark. Methods Cell Biol 2020; 161:275-295. [PMID: 33478693 DOI: 10.1016/bs.mcb.2020.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Expansion microscopy (ExM) is a magnification method that allows achieving super-resolved images using a conventional light microscope. In ExM, biomolecules, fluorescent proteins, and dyes are functionalized with specific handles to link a dense polyelectrolyte hydrogel, which can achieve an isotropic expansion of 4.5-fold in water. The use of ExM coupled with STED nanoscopy allows examining macromolecular machinery in life science, like the nuclear pore complex (NPC). In particular, in this chapter, we show a general protocol for labeling one of its subunit, i.e. the Nup153. Such method shows the nanoscale isotropy of the expansion process and enables precise measurement of the expansion factor. Finally, we used ExM for the visualization of a peculiar nuclear invagination in normal and aged cells.
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Affiliation(s)
- Paolo Bianchini
- Nanoscopy and NIC@IIT, CHT, Istituto Italiano di Tecnologia, Genova, Italy.
| | - Luca Pesce
- Nanoscopy and NIC@IIT, CHT, Istituto Italiano di Tecnologia, Genova, Italy
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, CHT, Istituto Italiano di Tecnologia, Genova, Italy; DIFILAB, Dipartimento di Fisica, Universita` degli Studi di Genova, Genova, Italy
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27
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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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28
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Abstract
The recently developed expansion microscopy method (ExM) allows for the resolution of structures below the diffraction limit of light not by sophisticated instrumentation, but rather by physically expanding the molecular structure of cells. This happens by crosslinking the protein in the sample to a hydrogel that is polymerized in situ and subsequently expanded, tearing the proteins apart in a nearly isotropic manner. In the resulting, larger facsimile of the original sample, the fluorescence-labeled molecules of interest can be optically separated by conventional fluorescence microscopy since the intermolecular distances are enlarged by a factor ranging from ~4 to 20 depending on the chemistry used for the hydrogel. The achieved improvement in resolution thus corresponds to the expansion factor. Further increase in resolution beyond this value may be achieved by combining ExM with established super-resolution microscopy methods. Indeed, this is possible using structured illumination microscopy (SIM) (Halpern et al., 2017; Wang et al., 2018), single molecule localization microscopy (SMLM) (Zwettler et al., 2020) and stimulated emission depletion (STED), as we and others have shown recently (Gambarotto et al., 2019; Gao et al., 2018; Kim, Kim, Lee, & Shim, 2019; Unnersjö-Jess et al., 2016). Here, we provide a protocol, for our method, called ExSTED, which enabled us to achieve an increase in resolution of up to 30-fold compared to conventional microscopy, well beyond what is possible with conventional STED microscopy. Our protocol includes a strategy to achieve very high intensity fluorescence labeling, which is essential for optimal signal retention during the expansion process for ExSTED.
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Affiliation(s)
- Mengfei Gao
- Max Planck Institut für molekulare Zellbiologie und Genetik, Dresden, Germany; Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Ria Thielhorn
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Jakob Rentsch
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Alf Honigmann
- Max Planck Institut für molekulare Zellbiologie und Genetik, Dresden, Germany
| | - Helge Ewers
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany.
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29
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Brenna C, Khan AUM, Picascia T, Sun Q, Heuveline V, Gretz N. New technical approaches for
3D
morphological imaging and quantification of measurements. Anat Rec (Hoboken) 2020; 303:2702-2715. [DOI: 10.1002/ar.24463] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 03/31/2020] [Accepted: 04/10/2020] [Indexed: 01/31/2023]
Affiliation(s)
- Cinzia Brenna
- Medical Research Center, Medical Faculty MannheimUniversity of Heidelberg Mannheim Germany
| | - Arif ul Maula Khan
- Medical Research Center, Medical Faculty MannheimUniversity of Heidelberg Mannheim Germany
| | - Tiziana Picascia
- Medical Research Center, Medical Faculty MannheimUniversity of Heidelberg Mannheim Germany
| | - Quanchao Sun
- Medical Research Center, Medical Faculty MannheimUniversity of Heidelberg Mannheim Germany
- Department of Thoracic Surgery, Union HospitalTongji Medical College, Huazhong University of Science and Technology Wuhan China
| | - Vincent Heuveline
- University Computing CenterUniversity of Heidelberg Heidelberg Germany
| | - Norbert Gretz
- Medical Research Center, Medical Faculty MannheimUniversity of Heidelberg Mannheim Germany
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30
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Abstract
The mitotic spindle is a dynamic and complex cellular structure made of microtubules and associated proteins. Although the general localization of most proteins has been identified, the arrangement of the microtubules in the mitotic spindle and precise localization of various proteins are still under intensive research. However, techniques used previously to decipher such puzzles are resolution limited or require complex microscopy systems. On the other hand, expansion microscopy is a novel super-resolution microscopy technique that uses physical expansion of fixed specimens to allow features closer than the diffraction limit of light (~250nm) to become resolvable in the expanded specimen on a conventional confocal microscope. This chapter focuses on expansion microscopy of the mitotic spindle, specifically using tubulin labeling to visualize all microtubule subpopulations within the spindle. Furthermore, we discuss a protocol for expansion of GFP-tagged proteins, such as protein regulator of cytokinesis 1 (PRC1). We also discuss various approaches for image analysis pointing out main advantages of expansion microscopy when compared to previously used techniques. This approach is currently used in our laboratory to study the architecture of the microtubules in the mitotic spindle after perturbations of various proteins important for the structural and dynamical properties of the mitotic spindle.
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31
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Abstract
Expansion microscopy is a recently developed super-resolution imaging technique, which provides an alternative to optics-based methods such as deterministic approaches (e.g. STED) or stochastic approaches (e.g. PALM/STORM). The idea behind expansion microscopy is to embed the biological sample in a swellable gel, and then to expand it isotropically, thereby increasing the distance between the fluorophores. This approach breaks the diffraction barrier by simply separating the emission point-spread-functions of the fluorophores. The resolution attainable in expansion microscopy is thus directly dependent on the separation that can be achieved, i.e. on the expansion factor. The original implementation of the technique achieved an expansion factor of fourfold, for a resolution of 70-80nm. The subsequently developed X10 method achieves an expansion factor of 10-fold, for a resolution of 25-30nm. This technique can be implemented with minimal technical requirements on any standard fluorescence microscope, and is more easily applied for multi-color imaging than either deterministic or stochastic super-resolution approaches. This renders X10 expansion microscopy a highly promising tool for new biological discoveries, as discussed here, and as demonstrated by several recent applications.
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Affiliation(s)
- Sven Truckenbrodt
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria.
| | - Silvio O Rizzoli
- Institute for Neuro- and Sensory Physiology, Göttingen, Germany; Center for Biostructural Imaging of Neurodegeneration, Göttingen, Germany
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32
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Faulkner EL, Thomas SG, Neely RK. An introduction to the methodology of expansion microscopy. Int J Biochem Cell Biol 2020; 124:105764. [PMID: 32407880 DOI: 10.1016/j.biocel.2020.105764] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/30/2020] [Accepted: 05/03/2020] [Indexed: 01/21/2023]
Abstract
Expansion microscopy is a novel, fluorescence imaging technique, which allows three-dimensional nanoscale imaging of specimens on a conventional fluorescence microscope. This is achieved through an innovative sample treatment, which culminates in approximately 4.5-fold expansion of specimens in each dimension. This allows 70 nm lateral and 200 nm axial resolution. To further develop application of the technique, there has been considerable focus on improving the methodology by i) extending the efficacy of labelling, ii) enabling multi-colour labelling of different biomolecules simultaneously, iii) further improving resolving power through alterations to sample preparation and iv) by combination of expansion microscopy with other well-established super resolution techniques. This review will highlight some of these recent advances and suggest ways that the technique could be developed further in the future.
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Affiliation(s)
- Emma L Faulkner
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Steven G Thomas
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Birmingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Robert K Neely
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK; School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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33
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Götz R, Panzer S, Trinks N, Eilts J, Wagener J, Turrà D, Di Pietro A, Sauer M, Terpitz U. Expansion Microscopy for Cell Biology Analysis in Fungi. Front Microbiol 2020; 11:574. [PMID: 32318047 PMCID: PMC7147297 DOI: 10.3389/fmicb.2020.00574] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/16/2020] [Indexed: 12/11/2022] Open
Abstract
Super-resolution microscopy has evolved as a powerful method for subdiffraction-resolution fluorescence imaging of cells and cellular organelles, but requires sophisticated and expensive installations. Expansion microscopy (ExM), which is based on the physical expansion of the cellular structure of interest, provides a cheap alternative to bypass the diffraction limit and enable super-resolution imaging on a conventional fluorescence microscope. While ExM has shown impressive results for the magnified visualization of proteins and RNAs in cells and tissues, it has not yet been applied in fungi, mainly due to their complex cell wall. Here we developed a method that enables reliable isotropic expansion of ascomycetes and basidiomycetes upon treatment with cell wall degrading enzymes. Confocal laser scanning microscopy (CLSM) and structured illumination microscopy (SIM) images of 4.5-fold expanded sporidia of Ustilago maydis expressing fluorescent fungal rhodopsins and hyphae of Fusarium oxysporum or Aspergillus fumigatus expressing either histone H1-mCherry together with Lifeact-sGFP or mRFP targeted to mitochondria, revealed details of subcellular structures with an estimated spatial resolution of around 30 nm. ExM is thus well suited for cell biology studies in fungi on conventional fluorescence microscopes.
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Affiliation(s)
- Ralph Götz
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius-Maximilian-University, Würzburg, Germany
| | - Sabine Panzer
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius-Maximilian-University, Würzburg, Germany
| | - Nora Trinks
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius-Maximilian-University, Würzburg, Germany
| | - Janna Eilts
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius-Maximilian-University, Würzburg, Germany
| | - Johannes Wagener
- Institut für Hygiene und Mikrobiologie, Julius-Maximilian-University, Würzburg, Germany
| | - David Turrà
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | | | - Markus Sauer
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius-Maximilian-University, Würzburg, Germany
| | - Ulrich Terpitz
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius-Maximilian-University, Würzburg, Germany
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34
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Bucur O, Fu F, Calderon M, Mylvaganam GH, Ly NL, Day J, Watkin S, Walker BD, Boyden ES, Zhao Y. Nanoscale imaging of clinical specimens using conventional and rapid-expansion pathology. Nat Protoc 2020; 15:1649-1672. [PMID: 32238952 DOI: 10.1038/s41596-020-0300-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 01/16/2020] [Indexed: 11/09/2022]
Abstract
In pathology, microscopy is an important tool for the analysis of human tissues, both for the scientific study of disease states and for diagnosis. However, the microscopes commonly used in pathology are limited in resolution by diffraction. Recently, we discovered that it was possible, through a chemical process, to isotropically expand preserved cells and tissues by 4-5× in linear dimension. We call this process expansion microscopy (ExM). ExM enables nanoscale resolution imaging on conventional microscopes. Here we describe protocols for the simple and effective physical expansion of a variety of human tissues and clinical specimens, including paraffin-embedded, fresh frozen and chemically stained human tissues. These protocols require only inexpensive, commercially available reagents and hardware commonly found in a routine pathology laboratory. Our protocols are written for researchers and pathologists experienced in conventional fluorescence microscopy. The conventional protocol, expansion pathology, can be completed in ~1 d with immunostained tissue sections and 2 d with unstained specimens. We also include a new, fast variant, rapid expansion pathology, that can be performed on <5-µm-thick tissue sections, taking <4 h with immunostained tissue sections and <8 h with unstained specimens.
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Affiliation(s)
- Octavian Bucur
- Department of Pathology and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Ludwig Center at Harvard Medical School, Boston, MA, USA.,Institute of Biochemistry of the Romanian Academy, Bucharest, Romania.,QPathology, Boston, MA, USA
| | - Feifei Fu
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Mike Calderon
- Center for Biologic Imaging, Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Geetha H Mylvaganam
- Ragon Institute of MGH, MIT and Harvard and Harvard University Center for AIDS Research, Cambridge, MA, USA.,Massachussetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ngoc L Ly
- Ragon Institute of MGH, MIT and Harvard and Harvard University Center for AIDS Research, Cambridge, MA, USA.,Massachussetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jimmy Day
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Simon Watkin
- Center for Biologic Imaging, Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard and Harvard University Center for AIDS Research, Cambridge, MA, USA.,Massachussetts General Hospital, Harvard Medical School, Boston, MA, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Edward S Boyden
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Center for Neurobiological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Yongxin Zhao
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA. .,Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.
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35
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Park H, Choi D, Park JS, Sim C, Park S, Kang S, Yim H, Lee M, Kim J, Pac J, Rhee K, Lee J, Lee Y, Lee Y, Kim S. Scalable and Isotropic Expansion of Tissues with Simply Tunable Expansion Ratio. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1901673. [PMID: 31763149 PMCID: PMC6864509 DOI: 10.1002/advs.201901673] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/17/2019] [Indexed: 05/06/2023]
Abstract
Tissue expansion techniques physically expand swellable gel-embedded biological specimens to overcome the resolution limit of light microscopy. As the benefits of expansion come at the expense of signal concentration, imaging volume and time, and mechanical integrity of the sample, the optimal expansion ratio may widely differ depending on the experiment. However, existing expansion methods offer only fixed expansion ratios that cannot be easily adjusted to balance the gain and loss associated with expansion. Here, a hydrogel conversion-based expansion method is presented, that enables easy adjustment of the expansion ratio for individual needs, simply by changing the duration of a heating step. This method, termed ZOOM, isotropically expands samples up to eightfold in a single expansion process. ZOOM preserves biomolecules for post-processing labelings and supports multi-round expansion for the imaging of a single sample at multiple zoom factors. ZOOM can be flexibly and scalably applied to nanoscale imaging of diverse samples, ranging from cultured cells to thick tissues, as well as bacteria, exoskeletal Caenorhabditis elegans, and human brain samples.
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Affiliation(s)
- Han‐Eol Park
- Institute of Molecular Biology and GeneticsSeoul National UniversitySeoul08826South Korea
- Department of Biological SciencesSeoul National UniversitySeoul08826South Korea
| | - Dongkil Choi
- Department of ChemistrySeoul National UniversitySeoul08826South Korea
| | - Ji Su Park
- Institute of Molecular Biology and GeneticsSeoul National UniversitySeoul08826South Korea
| | - Changgon Sim
- Institute of Molecular Biology and GeneticsSeoul National UniversitySeoul08826South Korea
- Department of ChemistrySeoul National UniversitySeoul08826South Korea
| | - Sohyun Park
- Department of ChemistrySeoul National UniversitySeoul08826South Korea
| | - Sunah Kang
- Department of ChemistrySeoul National UniversitySeoul08826South Korea
| | - Hyunsoo Yim
- Institute of Molecular Biology and GeneticsSeoul National UniversitySeoul08826South Korea
- Department of Biological SciencesSeoul National UniversitySeoul08826South Korea
| | - Myungsun Lee
- Institute of Molecular Biology and GeneticsSeoul National UniversitySeoul08826South Korea
- Department of ChemistrySeoul National UniversitySeoul08826South Korea
| | - Jaeyoun Kim
- Department of Biological SciencesSeoul National UniversitySeoul08826South Korea
| | - Jinyoung Pac
- Department of ChemistrySeoul National UniversitySeoul08826South Korea
| | - Kunsoo Rhee
- Department of Biological SciencesSeoul National UniversitySeoul08826South Korea
| | - Junho Lee
- Institute of Molecular Biology and GeneticsSeoul National UniversitySeoul08826South Korea
- Department of Biological SciencesSeoul National UniversitySeoul08826South Korea
| | - Yunjong Lee
- Division of PharmacologyDepartment of Molecular Cell BiologySamsung Biomedical Research InstituteSungkyunkwan University School of MedicineSuwon16419South Korea
| | - Yan Lee
- Department of ChemistrySeoul National UniversitySeoul08826South Korea
| | - Sung‐Yon Kim
- Institute of Molecular Biology and GeneticsSeoul National UniversitySeoul08826South Korea
- Department of ChemistrySeoul National UniversitySeoul08826South Korea
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36
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CHEN K, ZHANG YC, ZHAO GF. Expansion Microscopy Imaging Technique and Its Application. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(19)61156-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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37
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Abstract
Expansion microscopy is a relatively new approach to super-resolution imaging that uses expandable hydrogels to isotropically increase the physical distance between fluorophores in biological samples such as cell cultures or tissue slices. The classic gel recipe results in an expansion factor of ~4×, with a resolution of 60-80 nm. We have recently developed X10 microscopy, which uses a gel that achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide a step-by-step protocol for X10 expansion microscopy. A typical experiment consists of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization, (iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol presented here includes recommendations for optimization, pitfalls and their solutions, and detailed guidelines that should increase reproducibility. Although our protocol focuses on X10 expansion microscopy, we detail which of these suggestions are also applicable to classic fourfold expansion microscopy. We exemplify our protocol using primary hippocampal neurons from rats, but our approach can be used with other primary cells or cultured cell lines of interest. This protocol will enable any researcher with basic experience in immunostainings and access to an epifluorescence microscope to perform super-resolution microscopy with X10. The procedure takes 3 d and requires ~5 h of actively handling the sample for labeling and expansion, and another ~3 h for imaging and analysis.
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38
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Molle J, Jakob L, Bohlen J, Raab M, Tinnefeld P, Grohmann D. Towards structural biology with super-resolution microscopy. NANOSCALE 2018; 10:16416-16424. [PMID: 30141803 DOI: 10.1039/c8nr03361g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Fluorescence resonance energy transfer (FRET) has been instrumental in determining the structure and dynamics of biomolecules but distances above 8 nanometers are not accessible. However, with the advent and rapid development of super-resolution (SR) microscopy, distances between two fluorescent dyes below 20 nanometers can be resolved, which hitherto has been inaccessible for fluorescence microscopy approaches due to the limited resolving power of an optical imaging system that is determined by the fundamental laws of light diffraction (referred to as the diffraction limit). Therefore, the question arises whether SR microscopy can ultimately close the resolution gap between FRET and the diffraction limit and whether SR microscopy can be employed for the structural interrogation of proteins in the sub-20 nm range? Here, we show that the combination of DNA nanotechnology and single-molecule biochemistry allows the first step towards the investigation of the structural organization of a protein via SR microscopy. Limiting factors and possible future directions for the full implementation of SR microscopy as a structural tool are discussed.
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Affiliation(s)
- Julia Molle
- Institute for Physical and Theoretical Chemistry, and Braunschweig Institute for Integrated Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA), TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
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39
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Asano SM, Gao R, Wassie AT, Tillberg P, Chen F, Boyden ES. Expansion Microscopy: Protocols for Imaging Proteins and RNA in Cells and Tissues. CURRENT PROTOCOLS IN CELL BIOLOGY 2018; 80:e56. [PMID: 30070431 PMCID: PMC6158110 DOI: 10.1002/cpcb.56] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Expansion microscopy (ExM) is a recently developed technique that enables nanoscale-resolution imaging of preserved cells and tissues on conventional diffraction-limited microscopes via isotropic physical expansion of the specimens before imaging. In ExM, biomolecules and/or fluorescent labels in the specimen are linked to a dense, expandable polymer matrix synthesized evenly throughout the specimen, which undergoes 3-dimensional expansion by ∼4.5 fold linearly when immersed in water. Since our first report, versions of ExM optimized for visualization of proteins, RNA, and other biomolecules have emerged. Here we describe best-practice, step-by-step ExM protocols for performing analysis of proteins (protein retention ExM, or proExM) as well as RNAs (expansion fluorescence in situ hybridization, or ExFISH), using chemicals and hardware found in a typical biology lab. Furthermore, a detailed protocol for handling and mounting expanded samples and for imaging them with confocal and light-sheet microscopes is provided. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Shoh M. Asano
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
- McGovern Institute, MIT, Cambridge, Massachusetts, USA
- Internal Medicine Research Unit, Pfizer Inc., Cambridge, Massachusetts, USA
| | - Ruixuan Gao
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
- McGovern Institute, MIT, Cambridge, Massachusetts, USA
| | - Asmamaw T. Wassie
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
- McGovern Institute, MIT, Cambridge, Massachusetts, USA
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
| | | | - Fei Chen
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Edward S. Boyden
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
- McGovern Institute, MIT, Cambridge, Massachusetts, USA
- Internal Medicine Research Unit, Pfizer Inc., Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA
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40
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Alon S, Huynh GH, Boyden ES. Expansion microscopy: enabling single cell analysis in intact biological systems. FEBS J 2018; 286:1482-1494. [PMID: 29938896 DOI: 10.1111/febs.14597] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/23/2018] [Accepted: 06/21/2018] [Indexed: 12/17/2022]
Abstract
There is a need for single cell analysis methods that enable the identification and localization of different kinds of biomolecules throughout cells and intact tissues, thereby allowing characterization and classification of individual cells and their relationships to each other within intact systems. Expansion microscopy (ExM) is a technology that physically magnifies tissues in an isotropic way, thereby achieving super-resolution microscopy on diffraction-limited microscopes, enabling rapid image acquisition and large field of view. As a result, ExM is well-positioned to integrate molecular content and cellular morphology, with the spatial precision sufficient to resolve individual biological building blocks, and the scale and accessibility required to deploy over extended 3-D objects like tissues and organs.
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Affiliation(s)
- Shahar Alon
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.,McGovern Institute, MIT, Cambridge, MA, USA
| | - Grace H Huynh
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.,McGovern Institute, MIT, Cambridge, MA, USA.,Microsoft Research, Seattle, WA, USA
| | - Edward S Boyden
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.,McGovern Institute, MIT, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.,Koch Institute, MIT, Cambridge, MA, USA
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Truckenbrodt S, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10 expansion microscopy enables 25-nm resolution on conventional microscopes. EMBO Rep 2018; 19:embr.201845836. [PMID: 29987134 PMCID: PMC6123658 DOI: 10.15252/embr.201845836] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 06/08/2018] [Accepted: 06/18/2018] [Indexed: 01/01/2023] Open
Abstract
Expansion microscopy is a recently introduced imaging technique that achieves super‐resolution through physically expanding the specimen by ~4×, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately fourfold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20–30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10× in each dimension, which corresponds to an expansion of the sample volume by more than 1,000‐fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm on conventional epifluorescence microscopes. X10 provides multi‐color images similar or even superior to those produced with more challenging methods, such as STED, STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest and easiest option for high‐quality super‐resolution imaging currently available. X10 should be usable in any laboratory, irrespective of the machinery owned or of the technical knowledge.
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Affiliation(s)
- Sven Truckenbrodt
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany .,International Max Planck Research School for Molecular Biology, Göttingen, Germany
| | - Manuel Maidorn
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany.,International Max Planck Research School for Molecular Biology, Göttingen, Germany
| | - Dagmar Crzan
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
| | - Hanna Wildhagen
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
| | - Selda Kabatas
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
| | - Silvio O Rizzoli
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
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Karagiannis ED, Boyden ES. Expansion microscopy: development and neuroscience applications. Curr Opin Neurobiol 2018; 50:56-63. [PMID: 29316506 PMCID: PMC5984670 DOI: 10.1016/j.conb.2017.12.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/30/2017] [Accepted: 12/16/2017] [Indexed: 01/01/2023]
Abstract
Many neuroscience questions center around understanding how the molecules and wiring in neural circuits mechanistically yield behavioral functions, or go awry in disease states. However, mapping the molecules and wiring of neurons across the large scales of neural circuits has posed a great challenge. We recently developed expansion microscopy (ExM), a process in which we physically magnify biological specimens such as brain circuits. We synthesize throughout preserved brain specimens a dense, even mesh of a swellable polymer such as sodium polyacrylate, anchoring key biomolecules such as proteins and nucleic acids to the polymer. After mechanical homogenization of the specimen-polymer composite, we add water, and the polymer swells, pulling biomolecules apart. Due to the larger separation between molecules, ordinary microscopes can then perform nanoscale resolution imaging. We here review the ExM technology as well as applications to the mapping of synapses, cells, and circuits, including deployment in species such as Drosophila, mouse, non-human primate, and human.
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Affiliation(s)
| | - Edward S Boyden
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Witte R, Andriasyan V, Georgi F, Yakimovich A, Greber UF. Concepts in Light Microscopy of Viruses. Viruses 2018; 10:E202. [PMID: 29670029 PMCID: PMC5923496 DOI: 10.3390/v10040202] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022] Open
Abstract
Viruses threaten humans, livestock, and plants, and are difficult to combat. Imaging of viruses by light microscopy is key to uncover the nature of known and emerging viruses in the quest for finding new ways to treat viral disease and deepening the understanding of virus–host interactions. Here, we provide an overview of recent technology for imaging cells and viruses by light microscopy, in particular fluorescence microscopy in static and live-cell modes. The review lays out guidelines for how novel fluorescent chemical probes and proteins can be used in light microscopy to illuminate cells, and how they can be used to study virus infections. We discuss advantages and opportunities of confocal and multi-photon microscopy, selective plane illumination microscopy, and super-resolution microscopy. We emphasize the prevalent concepts in image processing and data analyses, and provide an outlook into label-free digital holographic microscopy for virus research.
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Affiliation(s)
- Robert Witte
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Artur Yakimovich
- MRC Laboratory for Molecular Cell Biology, University College London, Gower St., London WC1E 6BT, UK.
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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