1
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Gilbert MAG, Fatima N, Jenkins J, O'Sullivan TJ, Schertel A, Halfon Y, Wilkinson M, Morrema THJ, Geibel M, Read RJ, Ranson NA, Radford SE, Hoozemans JJM, Frank RAW. CryoET of β-amyloid and tau within postmortem Alzheimer's disease brain. Nature 2024; 631:913-919. [PMID: 38987603 PMCID: PMC11269202 DOI: 10.1038/s41586-024-07680-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 06/06/2024] [Indexed: 07/12/2024]
Abstract
A defining pathological feature of most neurodegenerative diseases is the assembly of proteins into amyloid that form disease-specific structures1. In Alzheimer's disease, this is characterized by the deposition of β-amyloid and tau with disease-specific conformations. The in situ structure of amyloid in the human brain is unknown. Here, using cryo-fluorescence microscopy-targeted cryo-sectioning, cryo-focused ion beam-scanning electron microscopy lift-out and cryo-electron tomography, we determined in-tissue architectures of β-amyloid and tau pathology in a postmortem Alzheimer's disease donor brain. β-amyloid plaques contained a mixture of fibrils, some of which were branched, and protofilaments, arranged in parallel arrays and lattice-like structures. Extracellular vesicles and cuboidal particles defined the non-amyloid constituents of β-amyloid plaques. By contrast, tau inclusions formed parallel clusters of unbranched filaments. Subtomogram averaging a cluster of 136 tau filaments in a single tomogram revealed the polypeptide backbone conformation and filament polarity orientation of paired helical filaments within tissue. Filaments within most clusters were similar to each other, but were different between clusters, showing amyloid heterogeneity that is spatially organized by subcellular location. The in situ structural approaches outlined here for human donor tissues have applications to a broad range of neurodegenerative diseases.
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Affiliation(s)
- Madeleine A G Gilbert
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Nayab Fatima
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Joshua Jenkins
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Thomas J O'Sullivan
- Astbury Biostructure Laboratory CryoEM facility, Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Andreas Schertel
- ZEISS Microscopy Customer Center Europe, Carl Zeiss Microscopy GmbH, Oberkochen, Germany
| | - Yehuda Halfon
- Astbury Biostructure Laboratory CryoEM facility, Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Tjado H J Morrema
- Department of Pathology, Unit Neuropathology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Mirjam Geibel
- ZEISS Microscopy Customer Center Europe, Carl Zeiss Microscopy GmbH, Oberkochen, Germany
| | - Randy J Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Jeroen J M Hoozemans
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - René A W Frank
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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2
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Galaz-Montoya JG. The advent of preventive high-resolution structural histopathology by artificial-intelligence-powered cryogenic electron tomography. Front Mol Biosci 2024; 11:1390858. [PMID: 38868297 PMCID: PMC11167099 DOI: 10.3389/fmolb.2024.1390858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/08/2024] [Indexed: 06/14/2024] Open
Abstract
Advances in cryogenic electron microscopy (cryoEM) single particle analysis have revolutionized structural biology by facilitating the in vitro determination of atomic- and near-atomic-resolution structures for fully hydrated macromolecular complexes exhibiting compositional and conformational heterogeneity across a wide range of sizes. Cryogenic electron tomography (cryoET) and subtomogram averaging are rapidly progressing toward delivering similar insights for macromolecular complexes in situ, without requiring tags or harsh biochemical purification. Furthermore, cryoET enables the visualization of cellular and tissue phenotypes directly at molecular, nanometric resolution without chemical fixation or staining artifacts. This forward-looking review covers recent developments in cryoEM/ET and related technologies such as cryogenic focused ion beam milling scanning electron microscopy and correlative light microscopy, increasingly enhanced and supported by artificial intelligence algorithms. Their potential application to emerging concepts is discussed, primarily the prospect of complementing medical histopathology analysis. Machine learning solutions are poised to address current challenges posed by "big data" in cryoET of tissues, cells, and macromolecules, offering the promise of enabling novel, quantitative insights into disease processes, which may translate into the clinic and lead to improved diagnostics and targeted therapeutics.
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Affiliation(s)
- Jesús G. Galaz-Montoya
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, United States
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3
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Van Veen D, Galaz-Montoya JG, Shen L, Baldwin P, Chaudhari AS, Lyumkis D, Schmid MF, Chiu W, Pauly J. Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. Int J Mol Sci 2024; 25:5473. [PMID: 38791508 PMCID: PMC11121946 DOI: 10.3390/ijms25105473] [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: 04/10/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input projections. This eliminates the need for pretraining, reducing reconstruction runtime by 3-20× compared to supervised methods. Our in silico results show improved shape completion and reduction of missing wedge artifacts, assessed through several voxel-based image quality metrics in real space and a novel directional Fourier Shell Correlation (FSC) metric. Our study illuminates benefits and considerations of both supervised and unsupervised approaches, guiding the development of improved reconstruction strategies.
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Affiliation(s)
- Dave Van Veen
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA;
| | - Jesús G. Galaz-Montoya
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; (J.G.G.-M.); (W.C.)
| | - Liyue Shen
- Department of Electrical and Computer Engineering, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Philip Baldwin
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Genetics, The Salk Institute of Biological Sciences, La Jolla, CA 92037, USA;
| | | | - Dmitry Lyumkis
- Department of Genetics, The Salk Institute of Biological Sciences, La Jolla, CA 92037, USA;
- Graduate School of Biological Sciences, University of California San Diego, La Jolla, CA 92037, USA
| | - Michael F. Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA;
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; (J.G.G.-M.); (W.C.)
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA;
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John Pauly
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA;
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4
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Chen J, Stephan T, Gaedke F, Liu T, Li Y, Schauss A, Chen P, Wulff V, Jakobs S, Jüngst C, Chen Z. An aldehyde-crosslinking mitochondrial probe for STED imaging in fixed cells. Proc Natl Acad Sci U S A 2024; 121:e2317703121. [PMID: 38687792 PMCID: PMC11087744 DOI: 10.1073/pnas.2317703121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/22/2024] [Indexed: 05/02/2024] Open
Abstract
Fluorescence labeling of chemically fixed specimens, especially immunolabeling, plays a vital role in super-resolution imaging as it offers a convenient way to visualize cellular structures like mitochondria or the distribution of biomolecules with high detail. Despite the development of various distinct probes that enable super-resolved stimulated emission depletion (STED) imaging of mitochondria in live cells, most of these membrane-potential-dependent fluorophores cannot be retained well in mitochondria after chemical fixation. This lack of suitable mitochondrial probes has limited STED imaging of mitochondria to live cell samples. In this study, we introduce a mitochondria-specific probe, PK Mito Orange FX (PKMO FX), which features a fixation-driven cross-linking motif and accumulates in the mitochondrial inner membrane. It exhibits high fluorescence retention after chemical fixation and efficient depletion at 775 nm, enabling nanoscopic imaging both before and after aldehyde fixation. We demonstrate the compatibility of this probe with conventional immunolabeling and other strategies commonly used for fluorescence labeling of fixed samples. Moreover, we show that PKMO FX facilitates correlative super-resolution light and electron microscopy, enabling the correlation of multicolor fluorescence images and transmission EM images via the characteristic mitochondrial pattern. Our probe further expands the mitochondrial toolkit for multimodal microscopy at nanometer resolutions.
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Affiliation(s)
- Jingting Chen
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing100871, China
| | - Till Stephan
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen37077, Germany
- Clinic of Neurology, University Medical Center Göttingen, Göttingen37075, Germany
| | - Felix Gaedke
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Tianyan Liu
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Yiyan Li
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Astrid Schauss
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Peng Chen
- Peking University-Nanjing Institute of Translational Medicine, Nanjing211800, China
- Genvivo Biotech (PuHaiJingShan), Nanjing211800, China
| | - Veronika Wulff
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen37077, Germany
- Clinic of Neurology, University Medical Center Göttingen, Göttingen37075, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology Translational, Neuroinflammation and Automated Microscopy, Göttingen37075, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells”, University of Göttingen, Göttingen37099, Germany
| | - Christian Jüngst
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Zhixing Chen
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
- Peking University-Nanjing Institute of Translational Medicine, Nanjing211800, China
- Genvivo Biotech (PuHaiJingShan), Nanjing211800, China
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5
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Van Veen D, Galaz-Montoya JG, Shen L, Baldwin P, Chaudhari AS, Lyumkis D, Schmid MF, Chiu W, Pauly J. Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589090. [PMID: 38712113 PMCID: PMC11071277 DOI: 10.1101/2024.04.12.589090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input projections. This eliminates the need for pretraining, reducing reconstruction runtime by 3 - 20× compared to supervised methods. Our in silico results show improved shape completion and reduction of missing wedge artifacts, assessed through several voxel-based image quality metrics in real space and a novel directional Fourier Shell Correlation (FSC) metric. Our study illuminates benefits and considerations of both supervised and unsupervised approaches, guiding the development of improved reconstruction strategies.
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Affiliation(s)
- Dave Van Veen
- Dept. of Electrical Engineering, Stanford University
| | | | - Liyue Shen
- Dept. of Electrical and Computer Engineering, University of Michigan
| | - Philip Baldwin
- Dept. of Biochemistry and Molecular Pharmacology, Baylor College of Medicine
- Dept. of Genetics, The Salk Institute for Biological Sciences
| | | | - Dmitry Lyumkis
- Dept. of Genetics, The Salk Institute for Biological Sciences
- Graduate School of Biological Sciences, University of California San Diego
| | - Michael F. Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory
| | - Wah Chiu
- Dept. of Bioengineering, Stanford University
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory
- Dept. of Microbiology and Immunology, Stanford University
| | - John Pauly
- Dept. of Electrical Engineering, Stanford University
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6
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Franzkoch R, Wilkening S, Liss V, Holtmannspötter M, Kurre R, Psathaki OE, Hensel M. Rapid in-EPON CLEM: Combining fast and efficient labeling of self-labeling enzyme tags with EM-resistant Janelia Fluor dyes and StayGold. Heliyon 2024; 10:e28055. [PMID: 38560224 PMCID: PMC10981041 DOI: 10.1016/j.heliyon.2024.e28055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Correlative light and electron microscopy (CLEM) combines light microscopy (LM) of fluorescent samples to ultrastructural analyses by electron microscopy (EM). Pre-embedding CLEM often suffers from inaccurate correlation between LM and EM modalities. Post-embedding CLEM enables precise registration of structures directly on EM sections, but requires fluorescent markers withstanding EM sample preparation, especially osmium tetroxide fixation, dehydration and EPON embedding. Most fluorescent proteins (FPs) lose their fluorescence during such conventional embedding (CE), but synthetic dyes represent promising alternatives as their stability exceeds those of FP. We analyzed various Janelia Fluor dyes and TMR conjugated to ligands for self-labeling enzymes, such as HaloTag, for fluorescence preservation after CE. We show that TMR, JF525, JF549, JFX549 and JFX554 retain fluorescence, with JFX549 and JFX554 yielding best results overall, also allowing integration of high-pressure freezing and freeze substitution. Furthermore, we found the recently published FP StayGold to resist CE, facilitating dual-fluorescence in-resin CLEM.
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Affiliation(s)
- Rico Franzkoch
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- IBiOs – Integrated Bioimaging Facility Osnabrück, Germany
| | | | - Viktoria Liss
- IBiOs – Integrated Bioimaging Facility Osnabrück, Germany
| | - Michael Holtmannspötter
- IBiOs – Integrated Bioimaging Facility Osnabrück, Germany
- CellNanOs – Center for Cellular Nanoanalytics Osnabrück, Germany
| | - Rainer Kurre
- IBiOs – Integrated Bioimaging Facility Osnabrück, Germany
- CellNanOs – Center for Cellular Nanoanalytics Osnabrück, Germany
| | - Olympia E. Psathaki
- IBiOs – Integrated Bioimaging Facility Osnabrück, Germany
- CellNanOs – Center for Cellular Nanoanalytics Osnabrück, Germany
| | - Michael Hensel
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- CellNanOs – Center for Cellular Nanoanalytics Osnabrück, Germany
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7
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Nogales E, Mahamid J. Bridging structural and cell biology with cryo-electron microscopy. Nature 2024; 628:47-56. [PMID: 38570716 PMCID: PMC11211576 DOI: 10.1038/s41586-024-07198-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/13/2024] [Indexed: 04/05/2024]
Abstract
Most life scientists would agree that understanding how cellular processes work requires structural knowledge about the macromolecules involved. For example, deciphering the double-helical nature of DNA revealed essential aspects of how genetic information is stored, copied and repaired. Yet, being reductionist in nature, structural biology requires the purification of large amounts of macromolecules, often trimmed off larger functional units. The advent of cryogenic electron microscopy (cryo-EM) greatly facilitated the study of large, functional complexes and generally of samples that are hard to express, purify and/or crystallize. Nevertheless, cryo-EM still requires purification and thus visualization outside of the natural context in which macromolecules operate and coexist. Conversely, cell biologists have been imaging cells using a number of fast-evolving techniques that keep expanding their spatial and temporal reach, but always far from the resolution at which chemistry can be understood. Thus, structural and cell biology provide complementary, yet unconnected visions of the inner workings of cells. Here we discuss how the interplay between cryo-EM and cryo-electron tomography, as a connecting bridge to visualize macromolecules in situ, holds great promise to create comprehensive structural depictions of macromolecules as they interact in complex mixtures or, ultimately, inside the cell itself.
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Affiliation(s)
- Eva Nogales
- Molecular and Cell Biology Department, Institute for Quantitative Biomedicine, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Howard Hughes Medical Institute, Berkeley, CA, USA.
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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8
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Tranfield EM, Fabig G, Kurth T, Müller-Reichert T. How to apply the broad toolbox of correlative light and electron microscopy to address a specific biological question. Methods Cell Biol 2024; 187:1-41. [PMID: 38705621 DOI: 10.1016/bs.mcb.2024.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Correlative light and electron microscopy (CLEM) is an approach that combines the strength of multiple imaging techniques to obtain complementary information about a given specimen. The "toolbox" for CLEM is broad, making it sometimes difficult to choose an appropriate approach for a given biological question. In this chapter, we provide experimental details for three CLEM approaches that can help the interested reader in designing a personalized CLEM strategy for obtaining ultrastructural data by using transmission electron microscopy (TEM). First, we describe chemical fixation of cells grown on a solid support (broadest approach). Second, we apply high-pressure freezing/freeze substitution to describe cellular ultrastructure (cryo-immobilization approach). Third, we give a protocol for a ultrastructural labeling by immuno-electron microscopy (immuno-EM approach). In addition, we also describe how to overlay fluorescence and electron microscopy images, an approach that is applicable to each of the reported different CLEM strategies. Here we provide step-by step descriptions prior to discussing possible technical problems and variations of these three general schemes to suit different models or different biological questions. This chapter is written for electron microscopists that are new to CLEM and unsure how to begin. Therefore, our protocols are meant to provide basic information with further references that should help the reader get started with applying a tailored strategy for a specific CLEM experiment.
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Affiliation(s)
- Erin M Tranfield
- Electron Microscopy Facility, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Gunar Fabig
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Thomas Kurth
- Core Facility Electron Microscopy and Histology Facility, Technology Platform, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Thomas Müller-Reichert
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
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9
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Franzkoch R, Anand A, Breitsprecher L, Psathaki OE, Barisch C. Resolving exit strategies of mycobacteria in Dictyostelium discoideum by combining high-pressure freezing with 3D-correlative light and electron microscopy. Mol Microbiol 2024; 121:593-604. [PMID: 38063129 DOI: 10.1111/mmi.15205] [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: 05/15/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 03/12/2024]
Abstract
The infection course of Mycobacterium tuberculosis is highly dynamic and comprises sequential stages that require damaging and crossing of several membranes to enable the translocation of the bacteria into the cytosol or their escape from the host. Many important breakthroughs such as the restriction of mycobacteria by the autophagy pathway and the recruitment of sophisticated host repair machineries to the Mycobacterium-containing vacuole have been gained in the Dictyostelium discoideum/M. marinum system. Despite the availability of well-established light and advanced electron microscopy techniques in this system, a correlative approach integrating both methods with near-native ultrastructural preservation is currently lacking. This is most likely due to the low ability of D. discoideum to adhere to surfaces, which results in cell loss even after fixation. To address this problem, we improved the adhesion of cells and developed a straightforward and convenient workflow for 3D-correlative light and electron microscopy. This approach includes high-pressure freezing, which is an excellent technique for preserving membranes. Thus, our method allows to monitor the ultrastructural aspects of vacuole escape which is of central importance for the survival and dissemination of bacterial pathogens.
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Affiliation(s)
- Rico Franzkoch
- iBiOs-integrated Bioimaging Facility, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics, Osnabrück, Germany
- Division of Microbiology, Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Aby Anand
- Center of Cellular Nanoanalytics, Osnabrück, Germany
- Division of Molecular Infection Biology, Department of Biology, University of Osnabrück, Osnabrück, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Division of Host-Microbe Interactome, Research Center Borstel - Leibniz Lung Center (FZB), Borstel, Germany
- Department of Biology, University of Hamburg, Hamburg, Germany
| | - Leonhard Breitsprecher
- iBiOs-integrated Bioimaging Facility, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics, Osnabrück, Germany
- Division of Microbiology, Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Olympia E Psathaki
- iBiOs-integrated Bioimaging Facility, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics, Osnabrück, Germany
| | - Caroline Barisch
- Center of Cellular Nanoanalytics, Osnabrück, Germany
- Division of Molecular Infection Biology, Department of Biology, University of Osnabrück, Osnabrück, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Division of Host-Microbe Interactome, Research Center Borstel - Leibniz Lung Center (FZB), Borstel, Germany
- Department of Biology, University of Hamburg, Hamburg, Germany
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10
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Mäntylä E, Verkade P. Some tips and tricks for a Correlative Light Electron Microscopy workflow using stable expression of fluorescent proteins. Methods Cell Biol 2024; 187:43-56. [PMID: 38705629 DOI: 10.1016/bs.mcb.2024.02.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Correlative Light Electron Microscopy (CLEM) encompasses a wide range of experimental approaches with different degrees of complexity and technical challenges where the attributes of both light and electron microscopy are combined in a single experiment. Although the biological question always determines what technology is the most appropriate, we generally set out to apply the simplest workflow possible. For 2D cell cultures expressing fluorescently tagged molecules, we report on a simple and very powerful CLEM approach by using gridded finder imaging dishes. We first determine the gross localization of the fluorescence using light microscopy and subsequently we retrace the origin/localization of the fluorescence by projecting it onto the ultrastructural reference space obtained by transmission electron microscopy (TEM). Here we describe this workflow and highlight some basic principles of the sample preparation for such a simple CLEM experiment. We will specifically focus on the steps following the resin embedding for TEM and the introduction of the sample in the electron microscope.
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Affiliation(s)
- Elina Mäntylä
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, United Kingdom.
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11
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Berkamp S, Daviran D, Smeets M, Caignard A, Jani RA, Sundermeyer P, Jonker C, Gerlach S, Hoffmann B, Lau K, Sachse C. Correlative Light and Electron Cryo-Microscopy Workflow Combining Micropatterning, Ice Shield, and an In-Chamber Fluorescence Light Microscope. Bio Protoc 2023; 13:e4901. [PMID: 38156035 PMCID: PMC10751236 DOI: 10.21769/bioprotoc.4901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 12/30/2023] Open
Abstract
In situ cryo-electron tomography (cryo-ET) is the most current, state-of-the-art technique to study cell machinery in its hydrated near-native state. The method provides ultrastructural details at sub-nanometer resolution for many components within the cellular context. Making use of recent advances in sample preparation techniques and combining this method with correlative light and electron microscopy (CLEM) approaches have enabled targeted molecular visualization. Nevertheless, the implementation has also added to the complexity of the workflow and introduced new obstacles in the way of streamlining and achieving high throughput, sample yield, and sample quality. Here, we report a detailed protocol by combining multiple newly available technologies to establish an integrated, high-throughput, optimized, and streamlined cryo-CLEM workflow for improved sample yield. Key features • PRIMO micropatterning allows precise cell positioning and maximum number of cell targets amenable to thinning with cryo focused-ion-beam-scanning electron microscopy. • CERES ice shield ensures that the lamellae remain free of ice contamination during the batch milling process. • METEOR in-chamber fluorescence microscope facilitates the targeted cryo focused-ion-beam (cryo FIB) milling of these targets. • Combining the three technologies into one cryo-CLEM workflow maximizes sample yield, throughput, and efficiency. Graphical overview.
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Affiliation(s)
- Sabrina Berkamp
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing, IBI-6: Structural Cell Biology, Forschungszentrum Jülich, Jülich, Germany
| | | | | | | | | | - Pia Sundermeyer
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing, IBI-6: Structural Cell Biology, Forschungszentrum Jülich, Jülich, Germany
| | | | - Sven Gerlach
- Institute of Biological Information Processing, IBI-2: Mechanobiology Forschungszentrum Jülich, Jülich, Germany
| | - Bernd Hoffmann
- Institute of Biological Information Processing, IBI-2: Mechanobiology Forschungszentrum Jülich, Jülich, Germany
| | | | - Carsten Sachse
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing, IBI-6: Structural Cell Biology, Forschungszentrum Jülich, Jülich, Germany
- Department of Biology, Heinrich Heine University, Düsseldorf, Germany
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12
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Mazal H, Wieser FF, Sandoghdar V. Insights into protein structure using cryogenic light microscopy. Biochem Soc Trans 2023; 51:2041-2059. [PMID: 38015555 PMCID: PMC10754291 DOI: 10.1042/bst20221246] [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: 08/26/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Fluorescence microscopy has witnessed many clever innovations in the last two decades, leading to new methods such as structured illumination and super-resolution microscopies. The attainable resolution in biological samples is, however, ultimately limited by residual motion within the sample or in the microscope setup. Thus, such experiments are typically performed on chemically fixed samples. Cryogenic light microscopy (Cryo-LM) has been investigated as an alternative, drawing on various preservation techniques developed for cryogenic electron microscopy (Cryo-EM). Moreover, this approach offers a powerful platform for correlative microscopy. Another key advantage of Cryo-LM is the strong reduction in photobleaching at low temperatures, facilitating the collection of orders of magnitude more photons from a single fluorophore. This results in much higher localization precision, leading to Angstrom resolution. In this review, we discuss the general development and progress of Cryo-LM with an emphasis on its application in harnessing structural information on proteins and protein complexes.
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Affiliation(s)
- Hisham Mazal
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
| | - Franz-Ferdinand Wieser
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
- Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
- Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
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13
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Markert SM. Studying zebrafish nervous system structure and function in health and disease with electron microscopy. Dev Growth Differ 2023; 65:502-516. [PMID: 37740826 DOI: 10.1111/dgd.12890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 09/25/2023]
Abstract
Zebrafish (Danio rerio) is a well-established model for studying the nervous system. Findings in zebrafish often inform studies on human diseases of the nervous system and provide crucial insight into disease mechanisms. The functions of the nervous system often rely on communication between neurons. Signal transduction is achieved via release of signaling molecules in the form of neuropeptides or neurotransmitters at synapses. Snapshots of membrane dynamics of these processes are imaged by electron microscopy. Electron microscopy can reveal ultrastructure and thus synaptic processes. This is crucial both for mapping synaptic connections and for investigating synaptic functions. In addition, via volumetric electron microscopy, the overall architecture of the nervous system becomes accessible, where structure can inform function. Electron microscopy is thus of particular value for studying the nervous system. However, today a plethora of electron microscopy techniques and protocols exist. Which technique is most suitable highly depends on the research question and scope as well as on the type of tissue that is examined. This review gives an overview of the electron microcopy techniques used on the zebrafish nervous system. It aims to give researchers a guide on which techniques are suitable for their specific questions and capabilities as well as an overview of the capabilities of electron microscopy in neurobiological research in the zebrafish model.
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14
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Liu Y, Zhai H, Alemayehu H, Boulanger J, Hopkins LJ, Borgeaud AC, Heroven C, Howe JD, Leigh KE, Bryant CE, Modis Y. Cryo-electron tomography of NLRP3-activated ASC complexes reveals organelle co-localization. Nat Commun 2023; 14:7246. [PMID: 37945612 PMCID: PMC10636019 DOI: 10.1038/s41467-023-43180-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
NLRP3 induces caspase-1-dependent pyroptotic cell death to drive inflammation. Aberrant activity of NLRP3 occurs in many human diseases. NLRP3 activation induces ASC polymerization into a single, micron-scale perinuclear punctum. Higher resolution imaging of this signaling platform is needed to understand how it induces pyroptosis. Here, we apply correlative cryo-light microscopy and cryo-electron tomography to visualize ASC/caspase-1 in NLRP3-activated cells. The puncta are composed of branched ASC filaments, with a tubular core formed by the pyrin domain. Ribosomes and Golgi-like or endosomal vesicles permeate the filament network, consistent with roles for these organelles in NLRP3 activation. Mitochondria are not associated with ASC but have outer-membrane discontinuities the same size as gasdermin D pores, consistent with our data showing gasdermin D associates with mitochondria and contributes to mitochondrial depolarization.
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Affiliation(s)
- Yangci Liu
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
| | - Haoming Zhai
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
| | - Helen Alemayehu
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
| | - Jérôme Boulanger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Lee J Hopkins
- Department of Medicine, University of Cambridge, Box 157, Level 5, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
- Wren Therapeutics, Clarendon House, Clarendon Road, Cambridge, CB2 8FH, UK
| | - Alicia C Borgeaud
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
| | - Christina Heroven
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Division of Structural Biology, University of Oxford, Oxford, OX3 7BN, UK
| | - Jonathan D Howe
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Kendra E Leigh
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
| | - Clare E Bryant
- Department of Medicine, University of Cambridge, Box 157, Level 5, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK.
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Yorgo Modis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK.
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15
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Schmidt N, Ganskih S, Wei Y, Gabel A, Zielinski S, Keshishian H, Lareau CA, Zimmermann L, Makroczyova J, Pearce C, Krey K, Hennig T, Stegmaier S, Moyon L, Horlacher M, Werner S, Aydin J, Olguin-Nava M, Potabattula R, Kibe A, Dölken L, Smyth RP, Caliskan N, Marsico A, Krempl C, Bodem J, Pichlmair A, Carr SA, Chlanda P, Erhard F, Munschauer M. SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9. Cell 2023; 186:4834-4850.e23. [PMID: 37794589 PMCID: PMC10617981 DOI: 10.1016/j.cell.2023.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 07/13/2023] [Accepted: 09/01/2023] [Indexed: 10/06/2023]
Abstract
Regulation of viral RNA biogenesis is fundamental to productive SARS-CoV-2 infection. To characterize host RNA-binding proteins (RBPs) involved in this process, we biochemically identified proteins bound to genomic and subgenomic SARS-CoV-2 RNAs. We find that the host protein SND1 binds the 5' end of negative-sense viral RNA and is required for SARS-CoV-2 RNA synthesis. SND1-depleted cells form smaller replication organelles and display diminished virus growth kinetics. We discover that NSP9, a viral RBP and direct SND1 interaction partner, is covalently linked to the 5' ends of positive- and negative-sense RNAs produced during infection. These linkages occur at replication-transcription initiation sites, consistent with NSP9 priming viral RNA synthesis. Mechanistically, SND1 remodels NSP9 occupancy and alters the covalent linkage of NSP9 to initiating nucleotides in viral RNA. Our findings implicate NSP9 in the initiation of SARS-CoV-2 RNA synthesis and unravel an unsuspected role of a cellular protein in orchestrating viral RNA production.
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Affiliation(s)
- Nora Schmidt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Sabina Ganskih
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Yuanjie Wei
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Alexander Gabel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Sebastian Zielinski
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | | | - Caleb A Lareau
- Program in Computational and System Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Liv Zimmermann
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jana Makroczyova
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Karsten Krey
- School of Medicine, Institute of Virology, Technical University of Munich, Munich, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Sebastian Stegmaier
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Lambert Moyon
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Marc Horlacher
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Simone Werner
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Jens Aydin
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Marco Olguin-Nava
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Ramya Potabattula
- Institute of Human Genetics, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Anuja Kibe
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Annalisa Marsico
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Christine Krempl
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Jochen Bodem
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Andreas Pichlmair
- School of Medicine, Institute of Virology, Technical University of Munich, Munich, Germany; German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Petr Chlanda
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany; Faculty for Computer and Data Science, University of Regensburg, Regensburg, Germany
| | - Mathias Munschauer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany; Faculty of Medicine, Julius-Maximilians-University Würzburg, Würzburg, Germany.
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16
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Prischich D, Camarero N, Encinar del Dedo J, Cambra-Pellejà M, Prat J, Nevola L, Martín-Quirós A, Rebollo E, Pastor L, Giralt E, Geli MI, Gorostiza P. Light-dependent inhibition of clathrin-mediated endocytosis in yeast unveils conserved functions of the AP2 complex. iScience 2023; 26:107899. [PMID: 37766990 PMCID: PMC10520943 DOI: 10.1016/j.isci.2023.107899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/04/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Clathrin-mediated endocytosis (CME) is an essential cellular process, conserved among eukaryotes. Yeast constitutes a powerful genetic model to dissect the complex endocytic machinery, yet there is a lack of specific pharmacological agents to interfere with CME in these organisms. TL2 is a light-regulated peptide inhibitor targeting the AP2-β-adaptin/β-arrestin interaction and that can photocontrol CME with high spatiotemporal precision in mammalian cells. Here, we study endocytic protein dynamics by live-cell imaging of the fluorescently tagged coat-associated protein Sla1-GFP, demonstrating that TL2 retains its inhibitory activity in S. cerevisiae spheroplasts. This is despite the β-adaptin/β-arrestin interaction not being conserved in yeast. Our data indicate that the AP2 α-adaptin is the functional target of activated TL2. We identified as interacting partners for the α-appendage, the Eps15 and epsin homologues Ede1 and Ent1. This demonstrates that endocytic cargo loading and sensing can be executed by conserved molecular interfaces, regardless of the proteins involved.
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Affiliation(s)
- Davia Prischich
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red – Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
| | - Núria Camarero
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red – Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
| | - Javier Encinar del Dedo
- Department of Cell Biology, Institute for Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Maria Cambra-Pellejà
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Judit Prat
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Laura Nevola
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrés Martín-Quirós
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elena Rebollo
- Molecular Imaging Platform, Institute for Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Laura Pastor
- Department of Cell Biology, Institute for Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Inorganic and Organic Chemistry, University of Barcelona (UB), Barcelona, Spain
| | - María Isabel Geli
- Department of Cell Biology, Institute for Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Pau Gorostiza
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red – Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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17
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Andrian T, Muela Y, Delgado L, Albertazzi L, Pujals S. A super-resolution and transmission electron microscopy correlative approach to study intracellular trafficking of nanoparticles. NANOSCALE 2023; 15:14615-14627. [PMID: 37614108 DOI: 10.1039/d3nr02838k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Nanoparticles (NPs) are used to encapsulate therapeutic cargos and deliver them specifically to the target site. The intracellular trafficking of NPs dictates the NP-cargo distribution within different cellular compartments, and thus governs their efficacy and safety. Knowledge in this field is crucial to understand their biological fate and improve their rational design. However, there is a lack of methods that allow precise localization and quantification of individual NPs within distinct cellular compartments simultaneously. Here, we address this issue by proposing a correlative light and electron microscopy (CLEM) method combining direct stochastic optical reconstruction microscopy (dSTORM) and transmission electron microscopy (TEM). We aim at combining the advantages of both techniques to precisely address NP localization in the context of the cell ultrastructure. Individual fluorescently-labelled poly(lactide-co-glycolide)-poly(ethylene glycol) (PLGA-PEG) NPs were directly visualized by dSTORM and assigned to cellular compartments by TEM. We first tracked NPs along the endo-lysosomal pathway at different time points, then demonstrated the effect of chloroquine on their intracellular distribution (i.e. endosomal escape). The proposed protocol can be applied to fluorescently labelled NPs and/or cargo, including those not detectable by TEM alone. Our studies are of great relevance to obtain important information on NP trafficking, and crucial for the design of more complex nanomaterials aimed at cytoplasmic/nucleic drug delivery.
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Affiliation(s)
- Teodora Andrian
- Institute for Bioengineering of Catalonia (IBEC), Carrer Baldiri Reixac 15-21, 08024 Barcelona, Spain.
| | - Yolanda Muela
- Electron Cryomicroscopy Unit, Centres Científics i Tecnològics de la Universitat de Barcelona (CCiTUB), Carrer Baldiri i Reixac 10-12, 08028 Barcelona, Spain
| | - Lidia Delgado
- Electron Cryomicroscopy Unit, Centres Científics i Tecnològics de la Universitat de Barcelona (CCiTUB), Carrer Baldiri i Reixac 10-12, 08028 Barcelona, Spain
| | - Lorenzo Albertazzi
- Institute for Bioengineering of Catalonia (IBEC), Carrer Baldiri Reixac 15-21, 08024 Barcelona, Spain.
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Silvia Pujals
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Carrer Jordi Girona 18-26, 08034 Barcelona, Spain.
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18
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Mocaer K, Mizzon G, Gunkel M, Halavatyi A, Steyer A, Oorschot V, Schorb M, Le Kieffre C, Yee DP, Chevalier F, Gallet B, Decelle J, Schwab Y, Ronchi P. Targeted volume correlative light and electron microscopy of an environmental marine microorganism. J Cell Sci 2023; 136:jcs261355. [PMID: 37455654 PMCID: PMC10445747 DOI: 10.1242/jcs.261355] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Photosynthetic microalgae are responsible for an important fraction of CO2 fixation and O2 production on Earth. Three-dimensional (3D) ultrastructural characterization of these organisms in their natural environment can contribute to a deeper understanding of their cell biology. However, the low throughput of volume electron microscopy (vEM) methods along with the complexity and heterogeneity of environmental samples pose great technical challenges. In the present study, we used a workflow based on a specific electron microscopy sample preparation method compatible with both light and vEM imaging in order to target one cell among a complex natural community. This method revealed the 3D subcellular landscape of a photosynthetic dinoflagellate, which we identified as Ensiculifera tyrrhenica, with quantitative characterization of multiple organelles. We show that this cell contains a single convoluted chloroplast and show the arrangement of the flagellar apparatus with its associated photosensitive elements. Moreover, we observed partial chromatin unfolding, potentially associated with transcription activity in these organisms, in which chromosomes are permanently condensed. Together with providing insights in dinoflagellate biology, this proof-of-principle study illustrates an efficient tool for the targeted ultrastructural analysis of environmental microorganisms in heterogeneous mixes.
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Affiliation(s)
- Karel Mocaer
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between the European Molecular Biology Laboratory and the Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Giulia Mizzon
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Department of Infectious Diseases, Molecular Virology, CIID, 69120 Heidelberg, Germany
- German Center for Infection Research, Heidelberg partner site, 69120 Heidelberg, Germany
| | - Manuel Gunkel
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Aliaksandr Halavatyi
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Anna Steyer
- EMBL Imaging Centre, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Viola Oorschot
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Martin Schorb
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Daniel P. Yee
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38054 Grenoble, France
| | - Fabien Chevalier
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38054 Grenoble, France
| | - Benoit Gallet
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France
| | - Johan Decelle
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38054 Grenoble, France
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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19
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Leistner C, Wilkinson M, Burgess A, Lovatt M, Goodbody S, Xu Y, Deuchars S, Radford SE, Ranson NA, Frank RAW. The in-tissue molecular architecture of β-amyloid pathology in the mammalian brain. Nat Commun 2023; 14:2833. [PMID: 37198197 PMCID: PMC10192217 DOI: 10.1038/s41467-023-38495-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 05/04/2023] [Indexed: 05/19/2023] Open
Abstract
Amyloid plaques composed of Aβ fibrils are a hallmark of Alzheimer's disease (AD). However, the molecular architecture of amyloid plaques in the context of fresh mammalian brain tissue is unknown. Here, using cryogenic correlated light and electron tomography we report the in situ molecular architecture of Aβ fibrils in the AppNL-G-F familial AD mouse model containing the Arctic mutation and an atomic model of ex vivo purified Arctic Aβ fibrils. We show that in-tissue Aβ fibrils are arranged in a lattice or parallel bundles, and are interdigitated by subcellular compartments, extracellular vesicles, extracellular droplets and extracellular multilamellar bodies. The Arctic Aβ fibril differs significantly from an earlier AppNL-F fibril structure, indicating a striking effect of the Arctic mutation. These structural data also revealed an ensemble of additional fibrillar species, including thin protofilament-like rods and branched fibrils. Together, these results provide a structural model for the dense network architecture that characterises β-amyloid plaque pathology.
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Affiliation(s)
- Conny Leistner
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Ailidh Burgess
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Megan Lovatt
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Stanley Goodbody
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Susan Deuchars
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - René A W Frank
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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20
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Chen L, He C. Single probes and resonant four-wave-mixing enabling novel correlative light electron microscopy workflow. LIGHT, SCIENCE & APPLICATIONS 2023; 12:111. [PMID: 37156768 PMCID: PMC10167341 DOI: 10.1038/s41377-023-01154-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Correlative light electron microscopy prefers single probes with stable performance in both optical and electron microscopy. Now researchers have shown how to harness gold nanoparticles featuring exceptional photostability and four-wave-mixing nonlinearity to realize a new correlation imaging approach.
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Affiliation(s)
- Long Chen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
| | - Chao He
- Department of Engineering Science, University of Oxford, Oxford, OX1 3PJ, UK.
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21
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Pazos I, Puig‐Tintó M, Betancur L, Cordero J, Jiménez‐Menéndez N, Abella M, Hernández AC, Duran AG, Adachi‐Fernández E, Belmonte‐Mateos C, Sabido‐Bozo S, Tosi S, Nezu A, Oliva B, Colombelli J, Graham TR, Yoshimori T, Muñiz M, Hamasaki M, Gallego O. The P4-ATPase Drs2 interacts with and stabilizes the multisubunit tethering complex TRAPPIII in yeast. EMBO Rep 2023; 24:e56134. [PMID: 36929574 PMCID: PMC10157312 DOI: 10.15252/embr.202256134] [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: 09/16/2022] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 03/17/2023] Open
Abstract
Multisubunit Tethering Complexes (MTCs) are a set of conserved protein complexes that tether vesicles at the acceptor membrane. Interactions with other components of the trafficking machinery regulate MTCs through mechanisms that are partially understood. Here, we systematically investigate the interactome that regulates MTCs. We report that P4-ATPases, a family of lipid flippases, interact with MTCs that participate in the anterograde and retrograde transport at the Golgi, such as TRAPPIII. We use the P4-ATPase Drs2 as a paradigm to investigate the mechanism and biological relevance of this interplay during transport of Atg9 vesicles. Binding of Trs85, the sole-specific subunit of TRAPPIII, to the N-terminal tail of Drs2 stabilizes TRAPPIII on membranes loaded with Atg9 and is required for Atg9 delivery during selective autophagy, a role that is independent of P4-ATPase canonical functions. This mechanism requires a conserved I(S/R)TTK motif that also mediates the interaction of the P4-ATPases Dnf1 and Dnf2 with MTCs, suggesting a broader role of P4-ATPases in MTC regulation.
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Affiliation(s)
- Irene Pazos
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Marta Puig‐Tintó
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Laura Betancur
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Jorge Cordero
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | | | - Marc Abella
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Altair C Hernández
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Ana G Duran
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Emi Adachi‐Fernández
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Carla Belmonte‐Mateos
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Susana Sabido‐Bozo
- Department of Cell BiologyUniversity of SevilleSevilleSpain
- Instituto de Biomedicina de Sevilla (IBiS)Hospital Universitario Virgen del Rocío/CSIC/Universidad de SevillaSevilleSpain
| | - Sébastien Tosi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Akiko Nezu
- Department of Genetics, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
| | - Baldomero Oliva
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
- Structural Bioinformatics Lab (GRIB‐IMIM)BarcelonaSpain
| | - Julien Colombelli
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Todd R Graham
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
| | - Manuel Muñiz
- Department of Cell BiologyUniversity of SevilleSevilleSpain
- Instituto de Biomedicina de Sevilla (IBiS)Hospital Universitario Virgen del Rocío/CSIC/Universidad de SevillaSevilleSpain
| | - Maho Hamasaki
- Department of Genetics, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
| | - Oriol Gallego
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
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22
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Wang T, Shi P, Luo D, Guo J, Liu H, Yuan J, Jin H, Wu X, Zhang Y, Xiong Z, Zhu J, Zhou R, Zhang R. A Convenient All-Cell Optical Imaging Method Compatible with Serial SEM for Brain Mapping. Brain Sci 2023; 13:711. [PMID: 37239183 PMCID: PMC10216590 DOI: 10.3390/brainsci13050711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
The mammalian brain, with its complexity and intricacy, poses significant challenges for researchers aiming to understand its inner workings. Optical multilayer interference tomography (OMLIT) is a novel, promising imaging technique that enables the mapping and reconstruction of mesoscale all-cell brain atlases and is seamlessly compatible with tape-based serial scanning electron microscopy (SEM) for microscale mapping in the same tissue. However, currently, OMLIT suffers from imperfect coatings, leading to background noise and image contamination. In this study, we introduced a new imaging configuration using carbon spraying to eliminate the tape-coating step, resulting in reduced noise and enhanced imaging quality. We demonstrated the improved imaging quality and validated its applicability through a correlative light-electron imaging workflow. Our method successfully reconstructed all cells and vasculature within a large OMLIT dataset, enabling basic morphological classification and analysis. We also show that this approach can perform effectively on thicker sections, extending its applicability to sub-micron scale slices, saving sample preparation and imaging time, and increasing imaging throughput. Consequently, this method emerges as a promising candidate for high-speed, high-throughput brain tissue reconstruction and analysis. Our findings open new avenues for exploring the structure and function of the brain using OMLIT images.
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Affiliation(s)
- Tianyi Wang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou 215163, China
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Peiyao Shi
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Dingsan Luo
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Jun Guo
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
| | - Hui Liu
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Jinyun Yuan
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Haiqun Jin
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
| | - Xiaolong Wu
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
| | - Yueyi Zhang
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
| | - Zhiwei Xiong
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
| | - Jinlong Zhu
- State Key Laboratory of Digital Manufacturing Equipment and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Renjie Zhou
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Ruobing Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou 215163, China
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
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23
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D'Imprima E, Garcia Montero M, Gawrzak S, Ronchi P, Zagoriy I, Schwab Y, Jechlinger M, Mahamid J. Light and electron microscopy continuum-resolution imaging of 3D cell cultures. Dev Cell 2023; 58:616-632.e6. [PMID: 36990090 PMCID: PMC10114294 DOI: 10.1016/j.devcel.2023.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/14/2022] [Accepted: 03/02/2023] [Indexed: 03/30/2023]
Abstract
3D cell cultures, in particular organoids, are emerging models in the investigation of healthy or diseased tissues. Understanding the complex cellular sociology in organoids requires integration of imaging modalities across spatial and temporal scales. We present a multi-scale imaging approach that traverses millimeter-scale live-cell light microscopy to nanometer-scale volume electron microscopy by performing 3D cell cultures in a single carrier that is amenable to all imaging steps. This allows for following organoids' growth, probing their morphology with fluorescent markers, identifying areas of interest, and analyzing their 3D ultrastructure. We demonstrate this workflow on mouse and human 3D cultures and use automated image segmentation to annotate and quantitatively analyze subcellular structures in patient-derived colorectal cancer organoids. Our analyses identify local organization of diffraction-limited cell junctions in compact and polarized epithelia. The continuum-resolution imaging pipeline is thus suited to fostering basic and translational organoid research by simultaneously exploiting the advantages of light and electron microscopy.
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Affiliation(s)
- Edoardo D'Imprima
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Marta Garcia Montero
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Sylwia Gawrzak
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Electron Microscopy Core Facility, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Martin Jechlinger
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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24
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Pope I, Tanner H, Masia F, Payne L, Arkill KP, Mantell J, Langbein W, Borri P, Verkade P. Correlative light-electron microscopy using small gold nanoparticles as single probes. LIGHT, SCIENCE & APPLICATIONS 2023; 12:80. [PMID: 36977682 PMCID: PMC10050153 DOI: 10.1038/s41377-023-01115-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/09/2023] [Accepted: 02/21/2023] [Indexed: 05/25/2023]
Abstract
Correlative light-electron microscopy (CLEM) requires the availability of robust probes which are visible both in light and electron microscopy. Here we demonstrate a CLEM approach using small gold nanoparticles as a single probe. Individual gold nanoparticles bound to the epidermal growth factor protein were located with nanometric precision background-free in human cancer cells by light microscopy using resonant four-wave mixing (FWM), and were correlatively mapped with high accuracy to the corresponding transmission electron microscopy images. We used nanoparticles of 10 nm and 5 nm radius, and show a correlation accuracy below 60 nm over an area larger than 10 µm size, without the need for additional fiducial markers. Correlation accuracy was improved to below 40 nm by reducing systematic errors, while the localisation precision is below 10 nm. Polarisation-resolved FWM correlates with nanoparticle shapes, promising for multiplexing by shape recognition in future applications. Owing to the photostability of gold nanoparticles and the applicability of FWM microscopy to living cells, FWM-CLEM opens up a powerful alternative to fluorescence-based methods.
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Affiliation(s)
- Iestyn Pope
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Hugh Tanner
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK
- Department of Chemistry, Umeå University, Umeå, 90187, Sweden
| | - Francesco Masia
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Lukas Payne
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Kenton Paul Arkill
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK
- School of Medicine, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Judith Mantell
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK
| | - Wolfgang Langbein
- School of Physics and Astronomy, Cardiff University, The Parade, Cardiff, CF24 3AA, UK
| | - Paola Borri
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK.
| | - Paul Verkade
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK.
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25
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Tanner H, Sherwin O, Verkade P. Labelling strategies for correlative light electron microscopy. Microsc Res Tech 2023. [PMID: 36846978 DOI: 10.1002/jemt.24304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 03/01/2023]
Abstract
Imaging is one of the key technologies underpinning discoveries in biomedical research. Each imaging technique however usually only provides a specific type of information. For instance, live-cell imaging using fluorescent tags can show us the dynamics of a system. On the other hand, electron microscopy (EM) gives us better resolution combined with the structural reference space. By applying a combination of light and electron microscopy modalities to a single sample one can exploit the advantages of both techniques in correlative light electron microscopy (CLEM). Although CLEM approaches can generate additional insights into the sample that cannot be gained by either technique in isolation, the visualization of the object of interest via markers or probes is still one of the bottlenecks in a Correlative Microscopy workflow. Whereas fluorescence is not directly visible in a standard electron microscope, gold particles, as the most common choice of probe for EM can also only be visualized using specialized light microscopes. In this review we will discuss some of the latest developments of probes for CLEM and some strategies how to choose a probe, discussing pros and cons of specific probes, and ensuring that they function as a dual modality marker.
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Affiliation(s)
- Hugh Tanner
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, UK.,Department of Chemistry, KBC Building, Umeå University, Umeå, Sweden
| | - Olivia Sherwin
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, UK
| | - Paul Verkade
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, UK
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26
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Mironov AA, Beznoussenko GV. Algorithm for Modern Electron Microscopic Examination of the Golgi Complex. Methods Mol Biol 2022; 2557:161-209. [PMID: 36512216 DOI: 10.1007/978-1-0716-2639-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Golgi complex (GC) is an essential organelle of the eukaryotic exocytic pathway. It has a very complexed structure and thus localization of its resident proteins is not trivial. Fast development of microscopic methods generates a huge difficulty for Golgi researchers to select the best protocol to use. Modern methods of light microscopy, such as super-resolution light microscopy (SRLM) and electron microscopy (EM), open new possibilities in analysis of various biological structures at organelle, cell, and organ levels. Nowadays, new generation of EM methods became available for the study of the GC; these include three-dimensional EM (3DEM), correlative light-EM (CLEM), immune EM, and new estimators within stereology that allow realization of maximal goal of any morphological study, namely, to achieve a three-dimensional model of the sample with optimal level of resolution and quantitative determination of its chemical composition. Methods of 3DEM have partially overlapping capabilities. This requires a careful comparison of these methods, identification of their strengths and weaknesses, and formulation of recommendations for their application to cell or tissue samples. Here, we present an overview of 3DEM methods for the study of the GC and some basics for how the images are formed and how the image quality can be improved.
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27
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Lovatt M, Leistner C, Frank RAW. Bridging length scales from molecules to the whole organism by cryoCLEM and cryoET. Faraday Discuss 2022; 240:114-126. [PMID: 35959706 PMCID: PMC9642002 DOI: 10.1039/d2fd00081d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/17/2022] [Indexed: 01/09/2023]
Abstract
Resolving atomic structures of isolated proteins has uncovered mechanisms and fundamental processes in biology. However, many functions can only be tested in the context of intact cells and tissues that are many orders of magnitude larger than the macromolecules on which they depend. Therefore, methods that interrogate macromolecular structure in situ provide a means of directly relating structure to function across length scales. Here, we developed several workflows using cryogenic correlated light and electron microscopy (cryoCLEM) and electron tomography (cryoET) that can bridge this gap to reveal the molecular infrastructure that underlies higher order functions within cells and tissues. We also describe experimental design considerations, including cryoCLEM labelling, sample preparation, and quality control, for determining the in situ molecular architectures within native, hydrated cells and tissues.
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Affiliation(s)
- Megan Lovatt
- Astbury Centre of Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
| | - Conny Leistner
- Astbury Centre of Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
| | - René A W Frank
- Astbury Centre of Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
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28
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Melero A, Boulanger J, Kukulski W, Miller EA. Ultrastructure of COPII vesicle formation in yeast characterized by correlative light and electron microscopy. Mol Biol Cell 2022; 33:ar122. [PMID: 36001360 PMCID: PMC9634970 DOI: 10.1091/mbc.e22-03-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Traffic of proteins out of the endoplasmic reticulum (ER) is driven by the COPII coat, a layered protein scaffold that mediates the capture of cargo proteins and the remodeling of the ER membrane into spherical vesicular carriers. Although the components of this machinery have been genetically defined, and the mechanisms of coat assembly extensively explored in vitro, understanding the physical mechanisms of membrane remodeling in cells remains a challenge. Here we use correlative light and electron microscopy (CLEM) to visualize the nanoscale ultrastructure of membrane remodeling at ER exit sites (ERES) in yeast cells. Using various COPII mutants, we have determined the broad contribution that each layer of the coat makes to membrane remodeling. Our data suggest that inner coat components define the radius of curvature, whereas outer coat components facilitate membrane fission. The organization of the coat in conjunction with membrane biophysical properties determines the ultrastructure of vesicles and thus the efficiency of protein transport.
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Affiliation(s)
- Alejandro Melero
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- *Address correspondence to: Elizabeth A. Miller (); Alejandro Melero ()
| | - Jerome Boulanger
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Wanda Kukulski
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Elizabeth A. Miller
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- *Address correspondence to: Elizabeth A. Miller (); Alejandro Melero ()
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29
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Dahmane S, Kerviel A, Morado DR, Shankar K, Ahlman B, Lazarou M, Altan-Bonnet N, Carlson LA. Membrane-assisted assembly and selective secretory autophagy of enteroviruses. Nat Commun 2022; 13:5986. [PMID: 36216808 PMCID: PMC9550805 DOI: 10.1038/s41467-022-33483-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
Abstract
Enteroviruses are non-enveloped positive-sense RNA viruses that cause diverse diseases in humans. Their rapid multiplication depends on remodeling of cytoplasmic membranes for viral genome replication. It is unknown how virions assemble around these newly synthesized genomes and how they are then loaded into autophagic membranes for release through secretory autophagy. Here, we use cryo-electron tomography of infected cells to show that poliovirus assembles directly on replication membranes. Pharmacological untethering of capsids from membranes abrogates RNA encapsidation. Our data directly visualize a membrane-bound half-capsid as a prominent virion assembly intermediate. Assembly progression past this intermediate depends on the class III phosphatidylinositol 3-kinase VPS34, a key host-cell autophagy factor. On the other hand, the canonical autophagy initiator ULK1 is shown to restrict virion production since its inhibition leads to increased accumulation of virions in vast intracellular arrays, followed by an increased vesicular release at later time points. Finally, we identify multiple layers of selectivity in virus-induced autophagy, with a strong selection for RNA-loaded virions over empty capsids and the segregation of virions from other types of autophagosome contents. These findings provide an integrated structural framework for multiple stages of the poliovirus life cycle.
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Affiliation(s)
- Selma Dahmane
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Adeline Kerviel
- Laboratory of Host-Pathogen Dynamics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dustin R Morado
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Kasturika Shankar
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Björn Ahlman
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Michael Lazarou
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Nihal Altan-Bonnet
- Laboratory of Host-Pathogen Dynamics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lars-Anders Carlson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden. .,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden. .,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.
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30
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Direct Capsid Labeling of Infectious HIV-1 by Genetic Code Expansion Allows Detection of Largely Complete Nuclear Capsids and Suggests Nuclear Entry of HIV-1 Complexes via Common Routes. mBio 2022; 13:e0195922. [PMID: 35972146 PMCID: PMC9600849 DOI: 10.1128/mbio.01959-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The cone-shaped mature HIV-1 capsid is the main orchestrator of early viral replication. After cytosolic entry, it transports the viral replication complex along microtubules toward the nucleus. While it was initially believed that the reverse transcribed genome is released from the capsid in the cytosol, recent observations indicate that a high amount of capsid protein (CA) remains associated with subviral complexes during import through the nuclear pore complex (NPC). Observation of postentry events via microscopic detection of HIV-1 CA is challenging, since epitope shielding limits immunodetection and the genetic fragility of CA hampers direct labeling approaches. Here, we present a minimally invasive strategy based on genetic code expansion and click chemistry that allows for site-directed fluorescent labeling of HIV-1 CA, while retaining virus morphology and infectivity. Thereby, we could directly visualize virions and subviral complexes using advanced microscopy, including nanoscopy and correlative imaging. Quantification of signal intensities of subviral complexes revealed an amount of CA associated with nuclear complexes in HeLa-derived cells and primary T cells consistent with a complete capsid and showed that treatment with the small molecule inhibitor PF74 did not result in capsid dissociation from nuclear complexes. Cone-shaped objects detected in the nucleus by electron tomography were clearly identified as capsid-derived structures by correlative microscopy. High-resolution imaging revealed dose-dependent clustering of nuclear capsids, suggesting that incoming particles may follow common entry routes.
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31
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Peddie CJ, Genoud C, Kreshuk A, Meechan K, Micheva KD, Narayan K, Pape C, Parton RG, Schieber NL, Schwab Y, Titze B, Verkade P, Aubrey A, Collinson LM. Volume electron microscopy. NATURE REVIEWS. METHODS PRIMERS 2022; 2:51. [PMID: 37409324 PMCID: PMC7614724 DOI: 10.1038/s43586-022-00131-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 07/07/2023]
Abstract
Life exists in three dimensions, but until the turn of the century most electron microscopy methods provided only 2D image data. Recently, electron microscopy techniques capable of delving deep into the structure of cells and tissues have emerged, collectively called volume electron microscopy (vEM). Developments in vEM have been dubbed a quiet revolution as the field evolved from established transmission and scanning electron microscopy techniques, so early publications largely focused on the bioscience applications rather than the underlying technological breakthroughs. However, with an explosion in the uptake of vEM across the biosciences and fast-paced advances in volume, resolution, throughput and ease of use, it is timely to introduce the field to new audiences. In this Primer, we introduce the different vEM imaging modalities, the specialized sample processing and image analysis pipelines that accompany each modality and the types of information revealed in the data. We showcase key applications in the biosciences where vEM has helped make breakthrough discoveries and consider limitations and future directions. We aim to show new users how vEM can support discovery science in their own research fields and inspire broader uptake of the technology, finally allowing its full adoption into mainstream biological imaging.
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Affiliation(s)
- Christopher J. Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Christel Genoud
- Electron Microscopy Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Anna Kreshuk
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kimberly Meechan
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Present address: Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Kristina D. Micheva
- Department of Molecular and Cellular Physiology, Stanford University, Palo Alto, CA, USA
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Constantin Pape
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Robert G. Parton
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicole L. Schieber
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Yannick Schwab
- Cell Biology and Biophysics Unit/ Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Aubrey Aubrey
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Lucy M. Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
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32
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Abstract
The three-dimensional organization of biomolecules important for the functioning of all living systems can be determined by cryo-electron tomography imaging under native biological contexts. Cryo-electron tomography is continually expanding and evolving, and the development of new methods that use the latest technology for sample thinning is enabling the visualization of ever larger and more complex biological systems, allowing imaging across scales. Quantitative cryo-electron tomography possesses the capability of visualizing the impact of molecular and environmental perturbations in subcellular structure and function to understand fundamental biological processes. This review provides an overview of current hardware and software developments that allow quantitative cryo-electron tomography studies and their limitations and how overcoming them may allow us to unleash the full power of cryo-electron tomography.
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Affiliation(s)
- Paula P. Navarro
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
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33
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Heiligenstein X, Lucas MS. One for All, All for One: A Close Look at In-Resin Fluorescence Protocols for CLEM. Front Cell Dev Biol 2022; 10:866472. [PMID: 35846358 PMCID: PMC9280628 DOI: 10.3389/fcell.2022.866472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Sample preparation is the novel bottleneck for high throughput correlative light and electron microscopy (CLEM). Protocols suitable for both imaging methods must therefore balance the requirements of each technique. For fluorescence light microscopy, a structure of interest can be targeted using: 1) staining, which is often structure or tissue specific rather than protein specific, 2) dye-coupled proteins or antibodies, or 3) genetically encoded fluorescent proteins. Each of these three methods has its own advantages. For ultrastructural investigation by electron microscopy (EM) resin embedding remains a significant sample preparation approach, as it stabilizes the sample such that it withstands the vacuum conditions of the EM, and enables long-term storage. Traditionally, samples are treated with heavy metal salts prior to resin embedding, in order to increase imaging contrast for EM. This is particularly important for volume EM (vEM) techniques. Yet, commonly used contrasting agents (e.g., osmium tetroxide, uranyl acetate) tend to impair fluorescence. The discovery that fluorescence can be preserved in resin-embedded specimens after mild heavy metal staining was a game changer for CLEM. These so-called in-resin fluorescence protocols present a significant leap forward for CLEM approaches towards high precision localization of a fluorescent signal in (volume) EM data. Integrated microscopy approaches, combining LM and EM detection into a single instrument certainly require such an “all in one” sample preparation. Preserving, or adding, dedicated fluorescence prior to resin embedding requires a compromise, which often comes at the expense of EM imaging contrast and membrane visibility. Especially vEM can be strongly hampered by a lack of heavy metal contrasting. This review critically reflects upon the fundamental aspects of resin embedding with regard to 1) specimen fixation and the physics and chemistry underlying the preservation of protein structure with respect to fluorescence and antigenicity, 2) optimization of EM contrast for transmission or scanning EM, and 3) the choice of embedding resin. On this basis, various existing workflows employing in-resin fluorescence are described, highlighting their common features, discussing advantages and disadvantages of the respective approach, and finally concluding with promising future developments for in-resin CLEM.
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Affiliation(s)
| | - Miriam S. Lucas
- Scientific Center for Light and Electron Microscopy (ScopeM), ETH Zurich, Zurich, Switzerland
- *Correspondence: Miriam S. Lucas,
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34
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van den Dries K, Fransen J, Cambi A. Fluorescence CLEM in biology: historic developments and current super-resolution applications. FEBS Lett 2022; 596:2486-2496. [PMID: 35674424 DOI: 10.1002/1873-3468.14421] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/12/2022]
Abstract
Correlative light and electron microscopy (CLEM) is a powerful imaging approach that allows the direct correlation of information obtained on a light and an electron microscope. There is a growing interest in the application of CLEM in biology, mainly attributable to technical advances in field of fluorescence microscopy in the past two decades. In this review, we summarize the important developments in CLEM for biological applications, focusing on the combination of fluorescence microscopy and electron microscopy. We first provide a brief overview of the early days of fluorescence CLEM usage starting with the initial rise in the late 1970s and the subsequent optimization of CLEM workflows during the following two decades. Next, we describe how the engineering of fluorescent proteins and the development of super-resolution fluorescence microscopy have significantly renewed the interest in CLEM resulting in the present application of fluorescence CLEM in many different areas of cellular and molecular biology. Lastly, we present the promises and challenges for the future of fluorescence CLEM discussing novel workflows, probe development and quantification possibilities.
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Affiliation(s)
- Koen van den Dries
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Jack Fransen
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands.,Microscopic Imaging Center, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Alessandra Cambi
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
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35
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Fermie J, de Jager L, Foster HE, Veenendaal T, de Heus C, van Dijk S, ten Brink C, Oorschot V, Yang L, Li W, Müller WH, Howes S, Carter AP, Förster F, Posthuma G, Gerritsen HC, Klumperman J, Liv N. Bimodal endocytic probe for three-dimensional correlative light and electron microscopy. CELL REPORTS METHODS 2022; 2:100220. [PMID: 35637912 PMCID: PMC9142762 DOI: 10.1016/j.crmeth.2022.100220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 02/04/2022] [Accepted: 04/26/2022] [Indexed: 12/03/2022]
Abstract
We present a bimodal endocytic tracer, fluorescent BSA-gold (fBSA-Au), as a fiducial marker for 2D and 3D correlative light and electron microscopy (CLEM) applications. fBSA-Au consists of colloidal gold (Au) particles stabilized with fluorescent BSA. The conjugate is efficiently endocytosed and distributed throughout the 3D endolysosomal network of cells and has an excellent visibility in both fluorescence microscopy (FM) and electron microscopy (EM). We demonstrate that fBSA-Au facilitates rapid registration in several 2D and 3D CLEM applications using Tokuyasu cryosections, resin-embedded material, and cryoelectron microscopy (cryo-EM). Endocytosed fBSA-Au benefits from a homogeneous 3D distribution throughout the endosomal system within the cell, does not obscure any cellular ultrastructure, and enables accurate (50-150 nm) correlation of fluorescence to EM data. The broad applicability and visibility in both modalities makes fBSA-Au an excellent endocytic fiducial marker for 2D and 3D (cryo)CLEM applications.
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Affiliation(s)
- Job Fermie
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands
| | - Leanne de Jager
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Helen E. Foster
- Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Cambridge, UK
| | - Tineke Veenendaal
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Cecilia de Heus
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Suzanne van Dijk
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Corlinda ten Brink
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Viola Oorschot
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Lin Yang
- Institute of Genetics & Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- Institute of Genetics & Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wally H. Müller
- Microbiology, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Stuart Howes
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Andrew P. Carter
- Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Cambridge, UK
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - George Posthuma
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Hans C. Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands
| | - Judith Klumperman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Nalan Liv
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
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36
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Parallel gold enhancement of quantum dots 565/655 for double-labelling correlative light and electron microscopy on human autopsied samples. Sci Rep 2022; 12:6113. [PMID: 35413968 PMCID: PMC9005520 DOI: 10.1038/s41598-022-09849-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/23/2022] [Indexed: 11/24/2022] Open
Abstract
Cadmium selenide quantum dots (QDs) are fluorescent and electron-dense nanoparticles. When used as reporter of immunolabeling, this dual visibility is essential for direct comparison of its fluorescent signals on light microscopy (LM) and their ultrastructrual counterparts on electron microscopy (EM) as correlative light and electron microscopy (CLEM). To facilitate EM recognition, QDs on EM grid were gold enhanced, which increased their size and electron density. On histological sections as well, gold-enhanced QDs, used as a reporter of immunolabeling, were easily recognized on EM. Because target structures are visible on bright field microscopy, gold enhancement facilitated trimming the target structures into final EM sections. Furthermore, gold enhancement of rod-shaped QD655 on EM grid was accentuated on their tips while spherical QD565 was gold-enhanced as sphere in contrast. This EM distinction was evident on histological sections where QD565 (green fluorescence) and QD655 (red fluorescence) were used as a reporter pair for double immunolabeling. Double-labeled immuno-fluorescent images, initially captured before EM processing, are now compared with their respective immuno EM counterparts. Specific labeling of each epitope was corroborated by mutual comparison between LM and EM. Although fluoronanogold may be a candidate reporter partner with QDs for gold-enhanced, double-labeling CLEM, its limited penetration into fixed tissue hampers universal use for thick histological sections. Gold-enhancement of QD immunolabeling, now expanded to double-labeling CLEM for human brain samples, will pave the way to translate molecular events into ultrastructural morphopathogenesis in situ.
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37
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Morgado-Palacin L. Ori Avinoam: Mind, body, and membranes in shape. J Biophys Biochem Cytol 2022; 221:213085. [PMID: 35319769 PMCID: PMC8952800 DOI: 10.1083/jcb.202203049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Ori Avinoam studies membrane remodeling with a focus on cell-to-cell fusion through the lens of correlative light and electron microscopy.
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38
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Improved Fluorescent Proteins for Dual-Colour Post-Embedding CLEM. Cells 2022; 11:cells11071077. [PMID: 35406640 PMCID: PMC8997867 DOI: 10.3390/cells11071077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 02/04/2023] Open
Abstract
Post-embedding correlative light and electron microscopy (CLEM) has the advantage of high-precision registration and enables light and electron microscopy imaging of the same slice. However, its broad application has been hampered by the limited available fluorescent proteins (FPs) and a low signal-to-background ratio (SBR). Here, we developed a green photoswitchable FP, mEosEM-E with substantially high on/off contrast in EM samples embedded in Epon resin, which maximally preserves cellular structures but quenches the fluorescence of FPs. Taking advantage of the photoswitching property of mEosEM-E, the autofluorescence background from the resin was significantly reduced by a subtraction-based CLEM (sCLEM) method. Meanwhile, we identified a red fluorescent protein (RFP) mScarlet-H that exhibited higher brightness and SBR in resin than previously reported RFPs. With mEosEM-E and mScarlet-H, dual-colour post-Epon-embedding CLEM images with high SBR and no cross-talk signal were successfully performed to reveal the organization of nucleolar proteins. Moreover, a dissection of the influences of different EM sample preparation steps on the fluorescence preservation for several RFPs provides useful guidance for further probe development.
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39
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Membrane-associated cytoplasmic granules carrying the Argonaute protein WAGO-3 enable paternal epigenetic inheritance in Caenorhabditis elegans. Nat Cell Biol 2022; 24:217-229. [PMID: 35132225 PMCID: PMC9973253 DOI: 10.1038/s41556-021-00827-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/03/2021] [Indexed: 01/04/2023]
Abstract
Epigenetic inheritance describes the transmission of gene regulatory information across generations without altering DNA sequences, enabling offspring to adapt to environmental conditions. Small RNAs have been implicated in this, through both the oocyte and the sperm. However, as much of the cellular content is extruded during spermatogenesis, it is unclear whether cytoplasmic small RNAs can contribute to epigenetic inheritance through sperm. Here we identify a sperm-specific germ granule, termed the paternal epigenetic inheritance (PEI) granule, that mediates paternal epigenetic inheritance by retaining the cytoplasmic Argonaute protein WAGO-3 during spermatogenesis in Caenorhabditis elegans. We identify the PEI granule proteins PEI-1 and PEI-2, which have distinct functions in this process: granule formation, Argonaute selectivity and subcellular localization. We show that PEI granule segregation is coupled to the transport of sperm-specific secretory vesicles through PEI-2 in an S-palmitoylation-dependent manner. PEI-like proteins are found in humans, suggesting that the identified mechanism may be conserved.
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40
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Lane R, Wolters AHG, Giepmans BNG, Hoogenboom JP. Integrated Array Tomography for 3D Correlative Light and Electron Microscopy. Front Mol Biosci 2022; 8:822232. [PMID: 35127826 PMCID: PMC8809480 DOI: 10.3389/fmolb.2021.822232] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/15/2021] [Indexed: 12/22/2022] Open
Abstract
Volume electron microscopy (EM) of biological systems has grown exponentially in recent years due to innovative large-scale imaging approaches. As a standalone imaging method, however, large-scale EM typically has two major limitations: slow rates of acquisition and the difficulty to provide targeted biological information. We developed a 3D image acquisition and reconstruction pipeline that overcomes both of these limitations by using a widefield fluorescence microscope integrated inside of a scanning electron microscope. The workflow consists of acquiring large field of view fluorescence microscopy (FM) images, which guide to regions of interest for successive EM (integrated correlative light and electron microscopy). High precision EM-FM overlay is achieved using cathodoluminescent markers. We conduct a proof-of-concept of our integrated workflow on immunolabelled serial sections of tissues. Acquisitions are limited to regions containing biological targets, expediting total acquisition times and reducing the burden of excess data by tens or hundreds of GBs.
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Affiliation(s)
- Ryan Lane
- Imaging Physics, Delft University of Technology, Delft, Netherlands
| | - Anouk H. G. Wolters
- Department of Biomedical Sciences of Cells and Systems, University Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ben N. G. Giepmans
- Department of Biomedical Sciences of Cells and Systems, University Groningen, University Medical Center Groningen, Groningen, Netherlands
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41
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Siddiqui H, Yevstigneyev N, Madani G, McCormick S. Approaches to Visualising Endocytosis of LDL-Related Lipoproteins. Biomolecules 2022; 12:biom12020158. [PMID: 35204658 PMCID: PMC8961563 DOI: 10.3390/biom12020158] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/20/2021] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
Endocytosis is the process by which molecules are actively transported into cells. It can take on a variety of forms depending on the cellular machinery involved ranging from specific receptor-mediated endocytosis to the less selective and actin-driven macropinocytosis. The plasma lipoproteins, which deliver lipids and other cargo to cells, have been intensely studied with respect to their endocytic uptake. One of the first molecules to be visualised undergoing endocytosis via a receptor-mediated, clathrin-dependent pathway was low-density lipoprotein (LDL). The LDL molecule has subsequently been shown to be internalised through multiple endocytic pathways. Dissecting the pathways of lipoprotein endocytosis has been crucial to understanding the regulation of plasma lipid levels and how lipids enter cells in the arterial wall to promote atherosclerosis. It has also aided understanding of the dysregulation that occurs in plasma lipid levels when molecules involved in uptake are defective, as is the case in familial hypercholesterolemia (FH). The aim of this review is to outline the many endocytic pathways utilised for lipoprotein uptake. It explores the various experimental approaches that have been applied to visualise lipoprotein endocytosis with an emphasis on LDL and its more complex counterpart, lipoprotein(a) [Lp(a)]. Finally, we look at new developments in lipoprotein visualisation that hold promise for scrutinising endocytic pathways to finer detail in the future.
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Affiliation(s)
- Halima Siddiqui
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand; (H.S.); (N.Y.); (G.M.)
- HeartOtago, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
| | - Nikita Yevstigneyev
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand; (H.S.); (N.Y.); (G.M.)
- HeartOtago, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
| | - Golnoush Madani
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand; (H.S.); (N.Y.); (G.M.)
- HeartOtago, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
| | - Sally McCormick
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand; (H.S.); (N.Y.); (G.M.)
- HeartOtago, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
- Correspondence:
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42
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Baatsen P, Gabarre S, Vints K, Wouters R, Vandael D, Goodchild R, Munck S, Gounko NV. Preservation of Fluorescence Signal and Imaging Optimization for Integrated Light and Electron Microscopy. Front Cell Dev Biol 2022; 9:737621. [PMID: 34977003 PMCID: PMC8715528 DOI: 10.3389/fcell.2021.737621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Life science research often needs to define where molecules are located within the complex environment of a cell or tissue. Genetically encoded fluorescent proteins and or fluorescence affinity-labeling are the go-to methods. Although recent fluorescent microscopy methods can provide localization of fluorescent molecules with relatively high resolution, an ultrastructural context is missing. This is solved by imaging a region of interest with correlative light and electron microscopy (CLEM). We have adopted a protocol that preserves both genetically-encoded and antibody-derived fluorescent signals in resin-embedded cell and tissue samples and provides high-resolution electron microscopy imaging of the same thin section. This method is particularly suitable for dedicated CLEM instruments that combine fluorescence and electron microscopy optics. In addition, we optimized scanning EM imaging parameters for samples of varying thicknesses. These protocols will enable rapid acquisition of CLEM information from samples and can be adapted for three-dimensional EM.
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Affiliation(s)
- Pieter Baatsen
- VIB-KU Leuven Center for Brain and Disease Research, Electron Microscopy Platform and VIB-Bioimaging Core, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Sergio Gabarre
- VIB-KU Leuven Center for Brain and Disease Research, Electron Microscopy Platform and VIB-Bioimaging Core, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium.,VIB-KU Leuven Center for Brain and Disease Research, Light Microscopy Expertise Unit and VIB Bioimaging Core, Leuven, Belgium
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain and Disease Research, Electron Microscopy Platform and VIB-Bioimaging Core, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Rosanne Wouters
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium.,VIB-KU Leuven Center for Brain and Disease Research, Laboratory for Membrane Trafficking, Leuven, Belgium
| | - Dorien Vandael
- VIB-KU Leuven Center for Brain and Disease Research, Electron Microscopy Platform and VIB-Bioimaging Core, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Rose Goodchild
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium.,VIB-KU Leuven Center for Brain and Disease Research, Laboratory for Dystonia Research, Leuven, Belgium
| | - Sebastian Munck
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium.,VIB-KU Leuven Center for Brain and Disease Research, Light Microscopy Expertise Unit and VIB Bioimaging Core, Leuven, Belgium
| | - Natalia V Gounko
- VIB-KU Leuven Center for Brain and Disease Research, Electron Microscopy Platform and VIB-Bioimaging Core, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
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43
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Bragulat-Teixidor H, Hossain MJ, Otsuka S. Visualizing Nuclear Pore Complex Assembly In Situ in Human Cells at Nanometer Resolution by Correlating Live Imaging with Electron Microscopy. Methods Mol Biol 2022; 2502:493-512. [PMID: 35412258 DOI: 10.1007/978-1-0716-2337-4_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In eukaryotic cells that undergo open mitosis, nuclear pore complex assembly proceeds via two distinct pathways: postmitotic and interphase assembly. Studying both assembly processes is challenging because postmitotic assembly is fast, interphase assembly is rare and sporadic, and assembly intermediates in both pathways are very small with a diameter below 100 nm. Here, we present a protocol for studying nuclear pore complex biogenesis in situ in cultured human cells in a spatiotemporally resolved and quantitative manner by combining live imaging with three-dimensional electron microscopy. The method described here can also be applied for studying other cell cycle-associated events with high spatiotemporal resolution.
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Affiliation(s)
- Helena Bragulat-Teixidor
- Max Perutz Labs, a joint venture of the University of Vienna and the Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - M Julius Hossain
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shotaro Otsuka
- Max Perutz Labs, a joint venture of the University of Vienna and the Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
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44
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Parlanti P, Cappello V. Microscopes, tools, probes, and protocols: A guide in the route of correlative microscopy for biomedical investigation. Micron 2021; 152:103182. [PMID: 34801960 DOI: 10.1016/j.micron.2021.103182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/12/2021] [Accepted: 11/14/2021] [Indexed: 12/11/2022]
Abstract
In the last decades, the advancements of microscopes technology, together with the development of new imaging approaches, are trying to address some biological questions that have been unresolved in the past: the need to combine in the same analysis temporal, functional and morphological information on the biological sample has become pressing. For this reason, the use of correlative microscopy, in which two or more imaging techniques are combined in the same analysis, is getting increasingly widespread. In fact, correlative microscopy can overcome limitations of a single imaging method, giving access to a larger amount of information from the same specimen. However, correlative microscopy can be challenging, and appropriate protocols for sample preparation and imaging methods must be selected. Here we review the state of the art of correlating electron microscopy with different imaging methods, focusing on sample preparation, tools, and labeling methods, with the aim to provide a comprehensive guide for those scientists who are approaching the field of correlative methods.
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Affiliation(s)
- Paola Parlanti
- Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography, Viale Rinaldo Piaggio 34, I-56025, Pontedera (PI), Italy.
| | - Valentina Cappello
- Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography, Viale Rinaldo Piaggio 34, I-56025, Pontedera (PI), Italy.
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45
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Simon CS, Funaya C, Bauer J, Voβ Y, Machado M, Penning A, Klaschka D, Cyrklaff M, Kim J, Ganter M, Guizetti J. An extended DNA-free intranuclear compartment organizes centrosome microtubules in malaria parasites. Life Sci Alliance 2021; 4:e202101199. [PMID: 34535568 PMCID: PMC8473725 DOI: 10.26508/lsa.202101199] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 11/24/2022] Open
Abstract
Proliferation of Plasmodium falciparum in red blood cells is the cause of malaria and is underpinned by an unconventional cell division mode, called schizogony. Contrary to model organisms, P. falciparum replicates by multiple rounds of nuclear divisions that are not interrupted by cytokinesis. Organization and dynamics of critical nuclear division factors remain poorly understood. Centriolar plaques, the centrosomes of P. falciparum, serve as microtubule organizing centers and have an acentriolar, amorphous structure. The small size of parasite nuclei has precluded detailed analysis of intranuclear microtubule organization by classical fluorescence microscopy. We apply recently developed super-resolution and time-lapse imaging protocols to describe microtubule reconfiguration during schizogony. Analysis of centrin, nuclear pore, and microtubule positioning reveals two distinct compartments of the centriolar plaque. Whereas centrin is extranuclear, we confirm by correlative light and electron tomography that microtubules are nucleated in a previously unknown and extended intranuclear compartment, which is devoid of chromatin but protein-dense. This study generates a working model for an unconventional centrosome and enables a better understanding about the diversity of eukaryotic cell division.
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Affiliation(s)
- Caroline S Simon
- Centre for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Charlotta Funaya
- Electron Microscopy Core Facility, Heidelberg University, Heidelberg, Germany
| | - Johanna Bauer
- Centre for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Yannik Voβ
- Centre for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Marta Machado
- Centre for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
- Graduate Program in Areas of Basic and Applied Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Alexander Penning
- Centre for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Darius Klaschka
- Centre for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Marek Cyrklaff
- Centre for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Juyeop Kim
- Centre for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus Ganter
- Centre for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Julien Guizetti
- Centre for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
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46
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Schifferer M, Snaidero N, Djannatian M, Kerschensteiner M, Misgeld T. Niwaki Instead of Random Forests: Targeted Serial Sectioning Scanning Electron Microscopy With Reimaging Capabilities for Exploring Central Nervous System Cell Biology and Pathology. Front Neuroanat 2021; 15:732506. [PMID: 34720890 PMCID: PMC8548362 DOI: 10.3389/fnana.2021.732506] [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: 06/29/2021] [Accepted: 09/24/2021] [Indexed: 11/13/2022] Open
Abstract
Ultrastructural analysis of discrete neurobiological structures by volume scanning electron microscopy (SEM) often constitutes a "needle-in-the-haystack" problem and therefore relies on sophisticated search strategies. The appropriate SEM approach for a given relocation task not only depends on the desired final image quality but also on the complexity and required accuracy of the screening process. Block-face SEM techniques like Focused Ion Beam or serial block-face SEM are "one-shot" imaging runs by nature and, thus, require precise relocation prior to acquisition. In contrast, "multi-shot" approaches conserve the sectioned tissue through the collection of serial sections onto solid support and allow reimaging. These tissue libraries generated by Array Tomography or Automated Tape Collecting Ultramicrotomy can be screened at low resolution to target high resolution SEM. This is particularly useful if a structure of interest is rare or has been predetermined by correlated light microscopy, which can assign molecular, dynamic and functional information to an ultrastructure. As such approaches require bridging mm to nm scales, they rely on tissue trimming at different stages of sample processing. Relocation is facilitated by endogenous or exogenous landmarks that are visible by several imaging modalities, combined with appropriate registration strategies that allow overlaying images of various sources. Here, we discuss the opportunities of using multi-shot serial sectioning SEM approaches, as well as suitable trimming and registration techniques, to slim down the high-resolution imaging volume to the actual structure of interest and hence facilitate ambitious targeted volume SEM projects.
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Affiliation(s)
- Martina Schifferer
- Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Nicolas Snaidero
- Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
- Hertie Institute for Clinical Brain Research, Tübingen, Germany
| | - Minou Djannatian
- Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
| | - Martin Kerschensteiner
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
- Faculty of Medicine, Biomedical Center (BMC), Ludwig-Maximilians-University Munich, Munich, Germany
| | - Thomas Misgeld
- Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
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47
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Abstract
Fluorescence imaging techniques play a pivotal role in our understanding of the nervous system. The emergence of various super-resolution microscopy methods and specialized fluorescent probes enables direct insight into neuronal structure and protein arrangements in cellular subcompartments with so far unmatched resolution. Super-resolving visualization techniques in neurons unveil a novel understanding of cytoskeletal composition, distribution, motility, and signaling of membrane proteins, subsynaptic structure and function, and neuron-glia interaction. Well-defined molecular targets in autoimmune and neurodegenerative disease models provide excellent starting points for in-depth investigation of disease pathophysiology using novel and innovative imaging methodology. Application of super-resolution microscopy in human brain samples and for testing clinical biomarkers is still in its infancy but opens new opportunities for translational research in neurology and neuroscience. In this review, we describe how super-resolving microscopy has improved our understanding of neuronal and brain function and dysfunction in the last two decades.
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Affiliation(s)
- Christian Werner
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Christian Geis
- Section Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
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48
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Ronchi P, Mizzon G, Machado P, D’Imprima E, Best BT, Cassella L, Schnorrenberg S, Montero MG, Jechlinger M, Ephrussi A, Leptin M, Mahamid J, Schwab Y. High-precision targeting workflow for volume electron microscopy. J Cell Biol 2021; 220:e202104069. [PMID: 34160561 PMCID: PMC8225610 DOI: 10.1083/jcb.202104069] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/27/2021] [Accepted: 06/06/2021] [Indexed: 02/07/2023] Open
Abstract
Cells are 3D objects. Therefore, volume EM (vEM) is often crucial for correct interpretation of ultrastructural data. Today, scanning EM (SEM) methods such as focused ion beam (FIB)-SEM are frequently used for vEM analyses. While they allow automated data acquisition, precise targeting of volumes of interest within a large sample remains challenging. Here, we provide a workflow to target FIB-SEM acquisition of fluorescently labeled cells or subcellular structures with micrometer precision. The strategy relies on fluorescence preservation during sample preparation and targeted trimming guided by confocal maps of the fluorescence signal in the resin block. Laser branding is used to create landmarks on the block surface to position the FIB-SEM acquisition. Using this method, we acquired volumes of specific single cells within large tissues such as 3D cultures of mouse mammary gland organoids, tracheal terminal cells in Drosophila melanogaster larvae, and ovarian follicular cells in adult Drosophila, discovering ultrastructural details that could not be appreciated before.
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Affiliation(s)
- Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Giulia Mizzon
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Pedro Machado
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Edoardo D’Imprima
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Benedikt T. Best
- Directors’ Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Lucia Cassella
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sebastian Schnorrenberg
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marta G. Montero
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin Jechlinger
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maria Leptin
- Directors’ Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Yannick Schwab
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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49
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TomoAlign: A novel approach to correcting sample motion and 3D CTF in CryoET. J Struct Biol 2021; 213:107778. [PMID: 34416376 DOI: 10.1016/j.jsb.2021.107778] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/16/2021] [Accepted: 08/08/2021] [Indexed: 11/23/2022]
Abstract
TomoAlign is a software package that integrates tools to mitigate two important resolution limiting factors in cryoET, namely the beam-induced sample motion and the contrast transfer function (CTF) of the microscope. The package is especially focused on cryoET of thick specimens where fiducial markers are required for accurate tilt-series alignment and sample motion estimation. TomoAlign models the beam-induced sample motion undergone during the tilt-series acquisition. The motion models are used to produce motion-corrected subtilt-series centered on the particles of interest. In addition, the defocus of each particle at each tilt image is determined and can be corrected, resulting in motion-corrected and CTF-corrected subtilt-series from which the subtomograms can be computed. Alternatively, the CTF information can be passed on so that CTF correction can be carried out entirely within external packages like Relion. TomoAlign serves as a versatile tool that can streamline the cryoET workflow from initial alignment of tilt-series to final subtomogram averaging during in situ structure determination.
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50
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Regulation of microtubule dynamics, mechanics and function through the growing tip. Nat Rev Mol Cell Biol 2021; 22:777-795. [PMID: 34408299 DOI: 10.1038/s41580-021-00399-x] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 02/07/2023]
Abstract
Microtubule dynamics and their control are essential for the normal function and division of all eukaryotic cells. This plethora of functions is, in large part, supported by dynamic microtubule tips, which can bind to various intracellular targets, generate mechanical forces and couple with actin microfilaments. Here, we review progress in the understanding of microtubule assembly and dynamics, focusing on new information about the structure of microtubule tips. First, we discuss evidence for the widely accepted GTP cap model of microtubule dynamics. Next, we address microtubule dynamic instability in the context of structural information about assembly intermediates at microtubule tips. Three currently discussed models of microtubule assembly and dynamics are reviewed. These are considered in the context of established facts and recent data, which suggest that some long-held views must be re-evaluated. Finally, we review structural observations about the tips of microtubules in cells and describe their implications for understanding the mechanisms of microtubule regulation by associated proteins, by mechanical forces and by microtubule-targeting drugs, prominently including cancer chemotherapeutics.
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