1
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Konopová B, Týč J. Minimal resin embedding of SBF-SEM samples reduces charging and facilitates finding a surface-linked region of interest. Front Zool 2023; 20:29. [PMID: 37641135 PMCID: PMC10463905 DOI: 10.1186/s12983-023-00507-x] [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: 03/06/2023] [Accepted: 08/02/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND For decoding the mechanism of how cells and organs function information on their ultrastructure is essential. High-resolution 3D imaging has revolutionized morphology. Serial block face scanning electron microscopy (SBF-SEM) offers non-laborious, automated imaging in 3D of up to ~ 1 mm3 large biological objects at nanometer-scale resolution. For many samples there are obstacles. Quality imaging is often hampered by charging effects, which originate in the nonconductive resin used for embedding. Especially, if the imaged region of interest (ROI) includes the surface of the sample and neighbours the empty resin, which insulates the object. This extra resin also obscures the sample's morphology, thus making navigation to the ROI difficult. RESULTS Using the example of small arthropods and a fish roe we describe a workflow to prepare samples for SBF-SEM using the minimal resin (MR) embedding method. We show that for imaging of surface structures this simple approach conveniently tackles and solves both of the two major problems-charging and ROI localization-that complicate imaging of SBF-SEM samples embedded in an excess of overlying resin. As the surface ROI is not masked by the resin, samples can be precisely trimmed before they are placed into the imaging chamber. The initial approaching step is fast and easy. No extra trimming inside the microscope is necessary. Importantly, charging is absent or greatly reduced meaning that imaging can be accomplished under good vacuum conditions, typically at the optimal high vacuum. This leads to better resolution, better signal to noise ratio, and faster image acquisition. CONCLUSIONS In MR embedded samples charging is minimized and ROI easily targeted. MR embedding does not require any special equipment or skills. It saves effort, microscope time and eventually leads to high quality data. Studies on surface-linked ROIs, or any samples normally surrounded by the excess of resin, would benefit from adopting the technique.
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Affiliation(s)
- Barbora Konopová
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic.
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
| | - Jiří Týč
- Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic.
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2
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Stempinski ES, Pagano L, Riesterer JL, Adamou SK, Thibault G, Song X, Chang YH, López CS. Automated large volume sample preparation for vEM. Methods Cell Biol 2023; 177:1-32. [PMID: 37451763 DOI: 10.1016/bs.mcb.2023.01.009] [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] [Indexed: 07/18/2023]
Abstract
New developments in electron microscopy technology, improved efficiency of detectors, and artificial intelligence applications for data analysis over the past decade have increased the use of volume electron microscopy (vEM) in the life sciences field. Moreover, sample preparation methods are continuously being modified by investigators to improve final sample quality, increase electron density, combine imaging technologies, and minimize the introduction of artifacts into specimens under study. There are a variety of conventional bench protocols that a researcher can utilize, though most of these protocols require several days. In this work, we describe the utilization of an automated specimen processor, the mPrep™ ASP-2000™, to prepare samples for vEM that are compatible with focused ion beam scanning electron microscopy (FIB-SEM), serial block face scanning electron microscopy (SBF-SEM), and array tomography (AT). The protocols described here aimed for methods that are completed in a much shorter period of time while minimizing the exposure of the operator to hazardous and toxic chemicals and improving the reproducibility of the specimens' heavy metal staining, all without compromising the quality of the data acquired using backscattered electrons during SEM imaging. As a control, we have included a widely used sample bench protocol and have utilized it as a comparator for image quality analysis, both qualitatively and using image quality analysis metrics.
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Affiliation(s)
- Erin S Stempinski
- Multiscale Microscopy Core, Oregon Health & Science University, Portland, OR, United States
| | - Lucas Pagano
- Knight Cancer Institute-CEDAR, Oregan Health & Science University, Portland, OR, United States
| | - Jessica L Riesterer
- Multiscale Microscopy Core, Oregon Health & Science University, Portland, OR, United States; Knight Cancer Institute-CEDAR, Oregan Health & Science University, Portland, OR, United States
| | - Steven K Adamou
- Multiscale Microscopy Core, Oregon Health & Science University, Portland, OR, United States
| | - Guillaume Thibault
- Knight Cancer Institute-CEDAR, Oregan Health & Science University, Portland, OR, United States; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, United States
| | - Xubo Song
- Knight Cancer Institute-CEDAR, Oregan Health & Science University, Portland, OR, United States
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, United States
| | - Claudia S López
- Multiscale Microscopy Core, Oregon Health & Science University, Portland, OR, United States; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, United States; Pacific Northwest Center for Cryo-EM, Oregon Health & Science University, Portland, OR, United States.
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3
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Mangione F, Titlow J, Maclachlan C, Gho M, Davis I, Collinson L, Tapon N. Co-option of epidermal cells enables touch sensing. Nat Cell Biol 2023; 25:540-549. [PMID: 36959505 PMCID: PMC10104782 DOI: 10.1038/s41556-023-01110-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 02/20/2023] [Indexed: 03/25/2023]
Abstract
The epidermis is equipped with specialized mechanosensory organs that enable the detection of tactile stimuli. Here, by examining the differentiation of the tactile bristles, mechanosensory organs decorating the Drosophila adult epidermis, we show that neighbouring epidermal cells are essential for touch perception. Each mechanosensory bristle signals to the surrounding epidermis to co-opt a single epidermal cell, which we named the F-Cell. Once specified, the F-Cell adopts a specialized morphology to ensheath each bristle. Functional assays reveal that adult mechanosensory bristles require association with the epidermal F-Cell for touch sensing. Our findings underscore the importance of resident epidermal cells in the assembly of functional touch-sensitive organs.
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Affiliation(s)
- Federica Mangione
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, London, UK.
| | - Joshua Titlow
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Catherine Maclachlan
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Michel Gho
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement, Institut de Biologie Paris Seine (LBD-IBPS), Paris, France
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Nicolas Tapon
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, London, UK.
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4
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McClain ML, Nowotarski SH. Serial block-face scanning electron microscopy of Schmidtea mediterranea. Methods Cell Biol 2023; 177:213-240. [PMID: 37451768 DOI: 10.1016/bs.mcb.2023.01.013] [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: 02/27/2023]
Abstract
The flatworm planarian, Schmidtea mediterranea (Smed) is a master at regenerating and rebuilding whole animals from fragments. A full understanding of Smed's regenerative capabilities requires a high-resolution characterization of organs, tissues, and the adult stem cells necessary for regeneration in their native environment. Here, we describe a serial block face scanning electron microscopy (SBF-SEM) protocol, optimized for Smed specifically, for visualizing the ultrastructure of membranes and condensed chromosomes in this model organism.
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Affiliation(s)
| | - Stephanie H Nowotarski
- Stowers Institute for Medical Research, Kansas City, MO, United States; Howard Hughes Medical Institute, Chevy Chase, MD, United States.
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5
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Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila melanogaster after Rapid Cryofixation. Int J Mol Sci 2023; 24:ijms24032128. [PMID: 36768451 PMCID: PMC9917252 DOI: 10.3390/ijms24032128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations.
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Affiliation(s)
- Achmed Mrestani
- Department of Neurophysiology, Institute for Physiology, University of Würzburg, 97070 Würzburg, Germany
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
- Department of Neurology, Leipzig University Medical Center, 04103 Leipzig, Germany
| | - Katharina Lichter
- Department of Neurophysiology, Institute for Physiology, University of Würzburg, 97070 Würzburg, Germany
- Department of Neurosurgery, University Hospital of Würzburg, 97080 Würzburg, Germany
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Anna-Leena Sirén
- Department of Neurophysiology, Institute for Physiology, University of Würzburg, 97070 Würzburg, Germany
- Department of Neurosurgery, University Hospital of Würzburg, 97080 Würzburg, Germany
- Correspondence:
| | - Manfred Heckmann
- Department of Neurophysiology, Institute for Physiology, University of Würzburg, 97070 Würzburg, Germany
| | - Mila M. Paul
- Department of Neurophysiology, Institute for Physiology, University of Würzburg, 97070 Würzburg, Germany
- Department of Orthopaedic Trauma, Hand, Plastic and Reconstructive Surgery, University Hospital of Würzburg, 97080 Wurzburg, Germany
| | - Martin Pauli
- Department of Neurophysiology, Institute for Physiology, University of Würzburg, 97070 Würzburg, Germany
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6
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Three-dimensional SEM, TEM, and STEM for analysis of large-scale biological systems. Histochem Cell Biol 2022; 158:203-211. [PMID: 35829815 PMCID: PMC9399040 DOI: 10.1007/s00418-022-02117-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2022] [Indexed: 12/12/2022]
Abstract
A major aim in structural cell biology is to analyze intact cells in three dimensions, visualize subcellular structures, and even localize proteins at the best possible resolution in three dimensions. Though recently developed electron microscopy tools such as electron tomography, or three-dimensional (3D) scanning electron microscopy, offer great resolution in three dimensions, the challenge is that, the better the resolution, usually the smaller the volume under investigation. Several different approaches to overcome this challenge were presented at the Microscopy Conference in Vienna in 2021. These tools include array tomography, batch tomography, or scanning transmission electron tomography, all of which can nowadays be extended toward correlative light and electron tomography, with greatly increased 3D information. Here, we review these tools, describe the underlying procedures, and discuss their advantages and limits.
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7
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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] [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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8
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Loginov SV, Fermie J, Fokkema J, Agronskaia AV, De Heus C, Blab GA, Klumperman J, Gerritsen HC, Liv N. Correlative Organelle Microscopy: Fluorescence Guided Volume Electron Microscopy of Intracellular Processes. Front Cell Dev Biol 2022; 10:829545. [PMID: 35478966 PMCID: PMC9035751 DOI: 10.3389/fcell.2022.829545] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/04/2022] [Indexed: 01/19/2023] Open
Abstract
Intracellular processes depend on a strict spatial and temporal organization of proteins and organelles. Therefore, directly linking molecular to nanoscale ultrastructural information is crucial in understanding cellular physiology. Volume or three-dimensional (3D) correlative light and electron microscopy (volume-CLEM) holds unique potential to explore cellular physiology at high-resolution ultrastructural detail across cell volumes. However, the application of volume-CLEM is hampered by limitations in throughput and 3D correlation efficiency. In order to address these limitations, we describe a novel pipeline for volume-CLEM that provides high-precision (<100 nm) registration between 3D fluorescence microscopy (FM) and 3D electron microscopy (EM) datasets with significantly increased throughput. Using multi-modal fiducial nanoparticles that remain fluorescent in epoxy resins and a 3D confocal fluorescence microscope integrated into a Focused Ion Beam Scanning Electron Microscope (FIB.SEM), our approach uses FM to target extremely small volumes of even single organelles for imaging in volume EM and obviates the need for post-correlation of big 3D datasets. We extend our targeted volume-CLEM approach to include live-cell imaging, adding information on the motility of intracellular membranes selected for volume-CLEM. We demonstrate the power of our approach by targeted imaging of rare and transient contact sites between the endoplasmic reticulum (ER) and lysosomes within hours rather than days. Our data suggest that extensive ER-lysosome and mitochondria-lysosome interactions restrict lysosome motility, highlighting the unique capabilities of our integrated CLEM pipeline for linking molecular dynamic data to high-resolution ultrastructural detail in 3D.
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Affiliation(s)
- Sergey V. Loginov
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Job Fermie
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Jantina Fokkema
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Alexandra V. Agronskaia
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Cilia De Heus
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Gerhard A. Blab
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Judith Klumperman
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Hans C. Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Nalan Liv
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- *Correspondence: Nalan Liv,
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9
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Meschkat M, Steyer AM, Weil MT, Kusch K, Jahn O, Piepkorn L, Agüi-Gonzalez P, Phan NTN, Ruhwedel T, Sadowski B, Rizzoli SO, Werner HB, Ehrenreich H, Nave KA, Möbius W. White matter integrity in mice requires continuous myelin synthesis at the inner tongue. Nat Commun 2022; 13:1163. [PMID: 35246535 PMCID: PMC8897471 DOI: 10.1038/s41467-022-28720-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 01/24/2022] [Indexed: 12/18/2022] Open
Abstract
Myelin, the electrically insulating sheath on axons, undergoes dynamic changes over time. However, it is composed of proteins with long lifetimes. This raises the question how such a stable structure is renewed. Here, we study the integrity of myelinated tracts after experimentally preventing the formation of new myelin in the CNS of adult mice, using an inducible Mbp null allele. Oligodendrocytes survive recombination, continue to express myelin genes, but they fail to maintain compacted myelin sheaths. Using 3D electron microscopy and mass spectrometry imaging we visualize myelin-like membranes failing to incorporate adaxonally, most prominently at juxta-paranodes. Myelinoid body formation indicates degradation of existing myelin at the abaxonal side and the inner tongue of the sheath. Thinning of compact myelin and shortening of internodes result in the loss of about 50% of myelin and axonal pathology within 20 weeks post recombination. In summary, our data suggest that functional axon-myelin units require the continuous incorporation of new myelin membranes. Myelin is formed of proteins of long half-lives. The mechanisms of renewal of such a stable structure are unclear. Here, the authors show that myelin integrity requires continuous myelin synthesis at the inner tongue, contributing to the maintenance of a functional axon-myelin unit.
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Affiliation(s)
- Martin Meschkat
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,Electron Microscopy Core Unit, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,Göttingen Graduate Center for Neurosciences, Biophysics, and Molecular Biosciences (GGNB), Göttingen, Germany.,DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany.,Abberior Instruments GmbH, Göttingen, Germany
| | - Anna M Steyer
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,Electron Microscopy Core Unit, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany.,Imaging Centre, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Marie-Theres Weil
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,Electron Microscopy Core Unit, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Kathrin Kusch
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Olaf Jahn
- DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany.,Proteomics Group, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,Translational Neuroproteomics Group, Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Lars Piepkorn
- Proteomics Group, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,Translational Neuroproteomics Group, Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Paola Agüi-Gonzalez
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Center for Biostructural Imaging of Neurodegeneration, Göttingen, Germany
| | - Nhu Thi Ngoc Phan
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Center for Biostructural Imaging of Neurodegeneration, Göttingen, Germany.,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Torben Ruhwedel
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,Electron Microscopy Core Unit, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Boguslawa Sadowski
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,Electron Microscopy Core Unit, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Silvio O Rizzoli
- DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany.,Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Center for Biostructural Imaging of Neurodegeneration, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Hauke B Werner
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Hannelore Ehrenreich
- DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany.,Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Klaus-Armin Nave
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Wiebke Möbius
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany. .,Electron Microscopy Core Unit, Max Planck Institute of Experimental Medicine, Göttingen, Germany. .,DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany. .,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
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10
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So C, Menelaou K, Uraji J, Harasimov K, Steyer AM, Seres KB, Bucevičius J, Lukinavičius G, Möbius W, Sibold C, Tandler-Schneider A, Eckel H, Moltrecht R, Blayney M, Elder K, Schuh M. Mechanism of spindle pole organization and instability in human oocytes. Science 2022; 375:eabj3944. [PMID: 35143306 DOI: 10.1126/science.abj3944] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human oocytes are prone to assembling meiotic spindles with unstable poles, which can favor aneuploidy in human eggs. The underlying causes of spindle instability are unknown. We found that NUMA (nuclear mitotic apparatus protein)-mediated clustering of microtubule minus ends focused the spindle poles in human, bovine, and porcine oocytes and in mouse oocytes depleted of acentriolar microtubule-organizing centers (aMTOCs). However, unlike human oocytes, bovine, porcine, and aMTOC-free mouse oocytes have stable spindles. We identified the molecular motor KIFC1 (kinesin superfamily protein C1) as a spindle-stabilizing protein that is deficient in human oocytes. Depletion of KIFC1 recapitulated spindle instability in bovine and aMTOC-free mouse oocytes, and the introduction of exogenous KIFC1 rescued spindle instability in human oocytes. Thus, the deficiency of KIFC1 contributes to spindle instability in human oocytes.
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Affiliation(s)
- Chun So
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Katerina Menelaou
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Bourn Hall Clinic, Cambridge, UK
| | - Julia Uraji
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Bourn Hall Clinic, Cambridge, UK
| | - Katarina Harasimov
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Anna M Steyer
- Electron Microscopy Core Unit, Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - K Bianka Seres
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Bourn Hall Clinic, Cambridge, UK
| | - Jonas Bucevičius
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Wiebke Möbius
- Electron Microscopy Core Unit, Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | | | | | - Heike Eckel
- Kinderwunschzentrum Göttingen, Göttingen, Germany
| | | | | | | | - Melina Schuh
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
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11
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Britz S, Markert SM, Witvliet D, Steyer AM, Tröger S, Mulcahy B, Kollmannsberger P, Schwab Y, Zhen M, Stigloher C. Structural Analysis of the Caenorhabditis elegans Dauer Larval Anterior Sensilla by Focused Ion Beam-Scanning Electron Microscopy. Front Neuroanat 2021; 15:732520. [PMID: 34819841 PMCID: PMC8607169 DOI: 10.3389/fnana.2021.732520] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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
At the end of the first larval stage, the nematode Caenorhabditis elegans developing in harsh environmental conditions is able to choose an alternative developmental path called the dauer diapause. Dauer larvae exhibit different physiology and behaviors from non-dauer larvae. Using focused ion beam-scanning electron microscopy (FIB-SEM), we volumetrically reconstructed the anterior sensory apparatus of C. elegans dauer larvae with unprecedented precision. We provide a detailed description of some neurons, focusing on structural details that were unknown or unresolved by previously published studies. They include the following: (1) dauer-specific branches of the IL2 sensory neurons project into the periphery of anterior sensilla and motor or putative sensory neurons at the sub-lateral cords; (2) ciliated endings of URX sensory neurons are supported by both ILso and AMso socket cells near the amphid openings; (3) variability in amphid sensory dendrites among dauers; and (4) somatic RIP interneurons maintain their projection into the pharyngeal nervous system. Our results support the notion that dauer larvae structurally expand their sensory system to facilitate searching for more favorable environments.
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Affiliation(s)
- Sebastian Britz
- Imaging Core Facility of the Biocenter, Theodor-Boveri-Institute, Julius-Maximilians-University, Würzburg, Germany
| | - Sebastian Matthias Markert
- Imaging Core Facility of the Biocenter, Theodor-Boveri-Institute, Julius-Maximilians-University, Würzburg, Germany
| | - Daniel Witvliet
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, Physiology and Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Anna Maria Steyer
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany
| | - Sarah Tröger
- Imaging Core Facility of the Biocenter, Theodor-Boveri-Institute, Julius-Maximilians-University, Würzburg, Germany
| | - Ben Mulcahy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, Physiology and Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Philip Kollmannsberger
- Center for Computational and Theoretical Biology, Julius-Maximilians-University, Würzburg, Germany
| | - Yannick Schwab
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany
| | - Mei Zhen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, Physiology and Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Christian Stigloher
- Imaging Core Facility of the Biocenter, Theodor-Boveri-Institute, Julius-Maximilians-University, Würzburg, Germany
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12
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Whole-body integration of gene expression and single-cell morphology. Cell 2021; 184:4819-4837.e22. [PMID: 34380046 PMCID: PMC8445025 DOI: 10.1016/j.cell.2021.07.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/05/2021] [Accepted: 07/14/2021] [Indexed: 01/10/2023]
Abstract
Animal bodies are composed of cell types with unique expression programs that implement their distinct locations, shapes, structures, and functions. Based on these properties, cell types assemble into specific tissues and organs. To systematically explore the link between cell-type-specific gene expression and morphology, we registered an expression atlas to a whole-body electron microscopy volume of the nereid Platynereis dumerilii. Automated segmentation of cells and nuclei identifies major cell classes and establishes a link between gene activation, chromatin topography, and nuclear size. Clustering of segmented cells according to gene expression reveals spatially coherent tissues. In the brain, genetically defined groups of neurons match ganglionic nuclei with coherent projections. Besides interneurons, we uncover sensory-neurosecretory cells in the nereid mushroom bodies, which thus qualify as sensory organs. They furthermore resemble the vertebrate telencephalon by molecular anatomy. We provide an integrated browser as a Fiji plugin for remote exploration of all available multimodal datasets. A cellular atlas integrates gene expression and ultrastructure for an entire annelid Morphometry of all segmented cells, nuclei, and chromatin categorizes cell classes Molecular anatomy and projectome of head ganglionic nuclei and mushroom bodies An open-source browser for multimodal big image data exploration and analysis
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13
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Peloggia J, Münch D, Meneses-Giles P, Romero-Carvajal A, Lush ME, Lawson ND, McClain M, Pan YA, Piotrowski T. Adaptive cell invasion maintains lateral line organ homeostasis in response to environmental changes. Dev Cell 2021; 56:1296-1312.e7. [PMID: 33878346 DOI: 10.1016/j.devcel.2021.03.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/21/2021] [Accepted: 03/24/2021] [Indexed: 10/21/2022]
Abstract
Mammalian inner ear and fish lateral line sensory hair cells (HCs) detect fluid motion to transduce environmental signals. Actively maintained ionic homeostasis of the mammalian inner ear endolymph is essential for HC function. In contrast, fish lateral line HCs are exposed to the fluctuating ionic composition of the aqueous environment. Using lineage labeling, in vivo time-lapse imaging and scRNA-seq, we discovered highly motile skin-derived cells that invade mature mechanosensory organs of the zebrafish lateral line and differentiate into Neuromast-associated (Nm) ionocytes. This invasion is adaptive as it is triggered by environmental fluctuations. Our discovery of Nm ionocytes challenges the notion of an entirely placodally derived lateral line and identifies Nm ionocytes as likely regulators of HC function possibly by modulating the ionic microenvironment. Nm ionocytes provide an experimentally accessible in vivo system to study cell invasion and migration, as well as the physiological adaptation of vertebrate organs to changing environmental conditions.
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Affiliation(s)
- Julia Peloggia
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Daniela Münch
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Andrés Romero-Carvajal
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Pontificia Universidad Católica del Ecuador, Escuela de Ciencias Biológicas, Quito, Ecuador
| | - Mark E Lush
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Nathan D Lawson
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester 01605, USA
| | - Melainia McClain
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Y Albert Pan
- Center for Neurobiology Research, Fralin Biomedical Research Institute at Virginia Tech Carilion, Virginia Tech, Roanoke, VA 24016, USA; Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA; Department of Psychiatry and Behavioral Medicine, Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA
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14
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Photonic-chip assisted correlative light and electron microscopy. Commun Biol 2020; 3:739. [PMID: 33288833 PMCID: PMC7721707 DOI: 10.1038/s42003-020-01473-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 11/10/2020] [Indexed: 11/23/2022] Open
Abstract
Correlative light and electron microscopy (CLEM) unifies the versatility of light microscopy (LM) with the high resolution of electron microscopy (EM), allowing one to zoom into the complex organization of cells. Here, we introduce photonic chip assisted CLEM, enabling multi-modal total internal reflection fluorescence (TIRF) microscopy over large field of view and high precision localization of the target area of interest within EM. The photonic chips are used as a substrate to hold, to illuminate and to provide landmarking of the sample through specially designed grid-like numbering systems. Using this approach, we demonstrate its applicability for tracking the area of interest, imaging the three-dimensional (3D) structural organization of nano-sized morphological features on liver sinusoidal endothelial cells such as fenestrations (trans-cytoplasmic nanopores), and correlating specific endo-lysosomal compartments with its cargo protein upon endocytosis. Tinguely et al. develop a photonic chip-based correlative light-electron microscopy system to generate co-registered multi-modal total internal reflection fluorescence microscopy (TIRF) and electron microscopy (EM) images of biological samples at nanometer scale.
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15
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Luo T, Deng L, Li A, Zhou C, Shao S, Sun Q, Gong H, Yang X, Li X. Scalable Resin Embedding Method for Large-Volume Brain Tissues with High Fluorescence Preservation Capacity. iScience 2020; 23:101717. [PMID: 33196032 PMCID: PMC7645060 DOI: 10.1016/j.isci.2020.101717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/06/2020] [Accepted: 10/16/2020] [Indexed: 01/15/2023] Open
Abstract
Resin embedding is widely used to dissect the fine structure of bio-tissue with electron and optical microscopy. However, it is difficult to embed large-volume tissues with resin. Here, we modified the formula of LR-White resin to prevent the sample cracking during polymerization process and applied this method to the intact brains of mouse, ferret, and macaque. Meanwhile, we increased the fluorescence preservation rate for green fluorescent protein (GFP) from 73 ± 4.0% to 126 ± 3.0% and tdTomato from 60 ± 3.3% to 117 ± 2.8%. Combined with the whole-brain imaging system, we acquired the cytoarchitectonic information and the circuit information such as individual axon and boutons which were labeled with multiple fluorescent proteins. This method shows great potential in the study of continuous fine microstructure information in large-volume tissues from different species, which can facilitate the neuroscience research and help the understanding of the structure-function relationship in complex bio-tissues. Modified LR-White resin embedding was proposed to embed large-volume tissues Retarder α-methyl-styrene was added to prevent cracking during polymerization Resin formula was modified to preserve multiple fluorescent proteins Microstructure information was acquired from the brains of different species
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Affiliation(s)
- Ting Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Lei Deng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,HUST-Suzhou Institute for Brainsmatics, Suzhou 215125, China
| | - Can Zhou
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shuai Shao
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Qingtao Sun
- HUST-Suzhou Institute for Brainsmatics, Suzhou 215125, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,HUST-Suzhou Institute for Brainsmatics, Suzhou 215125, China
| | - Xiaoquan Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,HUST-Suzhou Institute for Brainsmatics, Suzhou 215125, China
| | - Xiangning Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, #1037, Luoyu Road, Wuhan, Hubei 430074, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,HUST-Suzhou Institute for Brainsmatics, Suzhou 215125, China
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16
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Abstract
Correlative light and electron microscopy (CLEM) combines the strengths of light microscopy (LM) and electron microscopy (EM) to pin-point and visualize cellular or macromolecular structures. However, there are many different imaging modalities that can be combined in a CLEM workflow, creating a vast number of combinations that can overwhelm new-comers to the field. Here, we offer a conceptual framework to help guide the decision-making process for choosing the CLEM workflow that can best address your research question, based on the answer to five questions.
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17
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So C, Seres KB, Steyer AM, Mönnich E, Clift D, Pejkovska A, Möbius W, Schuh M. A liquid-like spindle domain promotes acentrosomal spindle assembly in mammalian oocytes. Science 2020; 364:364/6447/eaat9557. [PMID: 31249032 DOI: 10.1126/science.aat9557] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/02/2019] [Indexed: 12/22/2022]
Abstract
Mammalian oocytes segregate chromosomes with a microtubule spindle that lacks centrosomes, but the mechanisms by which acentrosomal spindles are organized and function are largely unclear. In this study, we identify a conserved subcellular structure in mammalian oocytes that forms by phase separation. This structure, which we term the liquid-like meiotic spindle domain (LISD), permeates the spindle poles and forms dynamic protrusions that extend well beyond the spindle. The LISD selectively concentrates multiple microtubule regulatory factors and allows them to diffuse rapidly within the spindle volume. Disruption of the LISD via different means disperses these factors and leads to severe spindle assembly defects. Our data suggest a model whereby the LISD promotes meiotic spindle assembly by serving as a reservoir that sequesters and mobilizes microtubule regulatory factors in proximity to spindle microtubules.
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Affiliation(s)
- Chun So
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - K Bianka Seres
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.,Bourn Hall Clinic, Cambridge CB23 2TN, UK
| | - Anna M Steyer
- Electron Microscopy Core Unit, Department of Neurogenetics, Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany.,Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37073 Göttingen, Germany
| | - Eike Mönnich
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Dean Clift
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Anastasija Pejkovska
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Wiebke Möbius
- Electron Microscopy Core Unit, Department of Neurogenetics, Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany.,Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37073 Göttingen, Germany
| | - Melina Schuh
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany. .,Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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18
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AMST: Alignment to Median Smoothed Template for Focused Ion Beam Scanning Electron Microscopy Image Stacks. Sci Rep 2020; 10:2004. [PMID: 32029771 PMCID: PMC7004979 DOI: 10.1038/s41598-020-58736-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/14/2020] [Indexed: 12/20/2022] Open
Abstract
Alignment of stacks of serial images generated by Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) is generally performed using translations only, either through slice-by-slice alignments with SIFT or alignment by template matching. However, limitations of these methods are two-fold: the introduction of a bias along the dataset in the z-direction which seriously alters the morphology of observed organelles and a missing compensation for pixel size variations inherent to the image acquisition itself. These pixel size variations result in local misalignments and jumps of a few nanometers in the image data that can compromise downstream image analysis. We introduce a novel approach which enables affine transformations to overcome local misalignments while avoiding the danger of introducing a scaling, rotation or shearing trend along the dataset. Our method first computes a template dataset with an alignment method restricted to translations only. This pre-aligned dataset is then smoothed selectively along the z-axis with a median filter, creating a template to which the raw data is aligned using affine transformations. Our method was applied to FIB-SEM datasets and showed clear improvement of the alignment along the z-axis resulting in a significantly more accurate automatic boundary segmentation using a convolutional neural network.
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19
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Abstract
Focused ion beam-scanning electron microscopy (FIB-SEM) has become a widely used technique in life sciences. To achieve the best data quality, sample preparation is important and has to be adapted to the specimen and the specific application. Here we illustrate three preparation procedures for mouse nervous tissue: First, the use of high-pressure freezing followed by direct imaging of vitrified tissue without any staining in the FIB-SEM under cryo-conditions as direct and fast procedure. Second, a slow procedure involving freeze substitution of frozen samples combined with additional staining for enhanced contrast and plastic embedding. Third, a fast preparation applying microwave-assisted chemical fixation and processing for resin embedding. All three methods of sample preparation are suitable for obtaining data stacks by FIB-SEM acquisition and 3D reconstruction.
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20
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Clearance by Microglia Depends on Packaging of Phagosomes into a Unique Cellular Compartment. Dev Cell 2019; 49:77-88.e7. [DOI: 10.1016/j.devcel.2019.02.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 11/23/2018] [Accepted: 02/13/2019] [Indexed: 11/19/2022]
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21
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Luckner M, Wanner G. From Light Microscopy to Analytical Scanning Electron Microscopy (SEM) and Focused Ion Beam (FIB)/SEM in Biology: Fixed Coordinates, Flat Embedding, Absolute References. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2018; 24:526-544. [PMID: 30246679 PMCID: PMC6378657 DOI: 10.1017/s1431927618015015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/05/2018] [Accepted: 07/16/2018] [Indexed: 05/07/2023]
Abstract
Correlative light and electron microscopy (CLEM) has been in use for several years, however it has remained a costly method with difficult sample preparation. Here, we report a series of technical improvements developed for precise and cost-effective correlative light and scanning electron microscopy (SEM) and focused ion beam (FIB)/SEM microscopy of single cells, as well as large tissue sections. Customized coordinate systems for both slides and coverslips were established for thin and ultra-thin embedding of a wide range of biological specimens. Immobilization of biological samples was examined with a variety of adhesives. For histological sections, a filter system for flat embedding was developed. We validated ultra-thin embedding on laser marked slides for efficient, high-resolution CLEM. Target cells can be re-located within minutes in SEM without protracted searching and correlative investigations were reduced to a minimum of preparation steps, while still reaching highest resolution. The FIB/SEM milling procedure is facilitated and significantly accelerated as: (i) milling a ramp becomes needless, (ii) significant re-deposition of milled material does not occur; and (iii) charging effects are markedly reduced. By optimizing all technical parameters FIB/SEM stacks with 2 nm iso-voxels were achieved over thousands of sections, in a wide range of biological samples.
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Affiliation(s)
- Manja Luckner
- Department Biology I, Ultrastructural Research, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Gerhard Wanner
- Department Biology I, Ultrastructural Research, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
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22
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Luckner M, Burgold S, Filser S, Scheungrab M, Niyaz Y, Hummel E, Wanner G, Herms J. Label-free 3D-CLEM Using Endogenous Tissue Landmarks. iScience 2018; 6:92-101. [PMID: 30240628 PMCID: PMC6137285 DOI: 10.1016/j.isci.2018.07.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/20/2018] [Accepted: 07/16/2018] [Indexed: 01/09/2023] Open
Abstract
Emerging 3D correlative light and electron microscopy approaches enable studying neuronal structure-function relations at unprecedented depth and precision. However, established protocols for the correlation of light and electron micrographs rely on the introduction of artificial fiducial markers, such as polymer beads or near-infrared brandings, which might obscure or even damage the structure under investigation. Here, we report a general applicable "flat embedding" preparation, enabling high-precision overlay of light and scanning electron micrographs, using exclusively endogenous landmarks in the brain: blood vessels, nuclei, and myelinated axons. Furthermore, we demonstrate feasibility of the workflow by combining in vivo 2-photon microscopy and focused ion beam scanning electron microscopy to dissect the role of astrocytic coverage in the persistence of dendritic spines.
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Affiliation(s)
- Manja Luckner
- Department of Biology I, Biocenter Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany; German Center for Neurodegenerative Diseases (DZNE), Translational Brain Research, Munich 81377, Germany
| | - Steffen Burgold
- German Center for Neurodegenerative Diseases (DZNE), Translational Brain Research, Munich 81377, Germany; Center for Neuropathology, Ludwig-Maximilians-University Munich, Munich 81377, Germany; Carl Zeiss Microscopy, Oberkochen 73447, Germany
| | - Severin Filser
- German Center for Neurodegenerative Diseases (DZNE), Translational Brain Research, Munich 81377, Germany
| | - Maximilian Scheungrab
- Department of Biology I, Biocenter Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany
| | - Yilmaz Niyaz
- Carl Zeiss Microscopy, Oberkochen 73447, Germany
| | - Eric Hummel
- Carl Zeiss Microscopy, Oberkochen 73447, Germany
| | - Gerhard Wanner
- Department of Biology I, Biocenter Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany
| | - Jochen Herms
- Department of Biology I, Biocenter Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany; German Center for Neurodegenerative Diseases (DZNE), Translational Brain Research, Munich 81377, Germany; Center for Neuropathology, Ludwig-Maximilians-University Munich, Munich 81377, Germany; Munich Cluster of Systems Neurology (SyNergy), Munich 81377, Germany.
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23
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Abstract
A portfolio is presented documenting economic, high-resolution correlative focused ion beam scanning electron microscopy (FIB/SEM) in routine, comprising: (i) the use of custom-labeled slides and coverslips, (ii) embedding of cells in thin, or ultra-thin resin layers for correlative light and electron microscopy (CLEM) and (iii) the claim to reach the highest resolution possible with FIB/SEM in xyz. Regions of interest (ROIs) defined in light microscope (LM), can be relocated quickly and precisely in SEM. As proof of principle, HeLa cells were investigated in 3D context at all stages of the cell cycle, documenting ultrastructural changes during mitosis: nuclear envelope breakdown and reassembly, Golgi degradation and reconstitution and the formation of the midzone and midbody.
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24
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VAN Donselaar EG, Dorresteijn B, Popov-Čeleketić D, VAN DE Wetering WJ, Verrips TC, Boekhout T, Schneijdenberg CTWM, Xenaki AT, VAN DER Krift TP, Müller WH. Extremely thin layer plastification for focused-ion beam scanning electron microscopy: an improved method to study cell surfaces and organelles of cultured cells. J Microsc 2018; 270:359-373. [PMID: 29574724 DOI: 10.1111/jmi.12694] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 02/16/2018] [Accepted: 02/17/2018] [Indexed: 02/01/2023]
Abstract
Since the recent boost in the usage of electron microscopy in life-science research, there is a great need for new methods. Recently minimal resin embedding methods have been successfully introduced in the sample preparation for focused-ion beam scanning electron microscopy (FIB-SEM). In these methods several possibilities are given to remove as much resin as possible from the surface of cultured cells or multicellular organisms. Here we introduce an alternative way in the minimal resin embedding method to remove excess of resin from two widely different cell types by the use of Mascotte filter paper. Our goal in correlative light and electron microscopic studies of immunogold-labelled breast cancer SKBR3 cells was to visualise gold-labelled HER2 plasma membrane proteins as well as the intracellular structures of flat and round cells. We found a significant difference (p < 0.001) in the number of gold particles of selected cells per 0.6 μm2 cell surface: on average a flat cell contained 2.46 ± 1.98 gold particles, and a round cell 5.66 ± 2.92 gold particles. Moreover, there was a clear difference in the subcellular organisation of these two cells. The round SKBR3 cell contained many organelles, such as mitochondria, Golgi and endoplasmic reticulum, when compared with flat SKBR3 cells. Our next goal was to visualise crosswall associated organelles, septal pore caps, of Rhizoctonia solani fungal cells by the combined use of a heavy metal staining and our extremely thin layer plastification (ETLP) method. At low magnifications this resulted into easily finding septa which appeared as bright crosswalls in the back-scattered electron mode in the scanning electron microscope. Then, a septum was selected for FIB-SEM. Cross-sectioned views clearly revealed the perforate septal pore cap of R. solani next to other structures, such as mitochondria, endoplasmic reticulum, lipid bodies, dolipore septum, and the pore channel. As the ETLP method was applied on two widely different cell types, the use of the ETLP method will be beneficial to correlative studies of other cell model systems and multicellular organisms.
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Affiliation(s)
- E G VAN Donselaar
- Department of Cell Biology, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
| | - B Dorresteijn
- Science Faculty, Biology Department, Utrecht University, Utrecht, the Netherlands
| | - D Popov-Čeleketić
- Science Faculty, Biology Department, Utrecht University, Utrecht, the Netherlands.,Visuals Consulting, Utrecht, the Netherlands
| | - W J VAN DE Wetering
- Science Faculty, Biology Department, Utrecht University, Utrecht, the Netherlands.,QVQ, Utrecht, the Netherlands
| | | | - T Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht Science Park, Utrecht, the Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
| | | | - A T Xenaki
- Science Faculty, Biology Department, Utrecht University, Utrecht, the Netherlands
| | - T P VAN DER Krift
- Science Faculty, Chemistry Department, Utrecht University, Utrecht, the Netherlands
| | - W H Müller
- Science Faculty, Chemistry Department, Utrecht University, Utrecht, the Netherlands
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