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Munck S, De Bo C, Cawthorne C, Colombelli J. Innovating in a bioimaging core through instrument development. J Microsc 2024; 294:319-337. [PMID: 38683038 DOI: 10.1111/jmi.13312] [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: 03/01/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
Developing devices and instrumentation in a bioimaging core facility is an important part of the innovation mandate inherent in the core facility model but is a complex area due to the required skills and investments, and the impossibility of a universally applicable model. Here, we seek to define technological innovation in microscopy and situate it within the wider core facility innovation portfolio, highlighting how strategic development can accelerate access to innovative imaging modalities and increase service range, and thus maintain the cutting edge needed for sustainability. We consider technology development from the perspective of core facility staff and their stakeholders as well as their research environment and aim to present a practical guide to the 'Why, When, and How' of developing and integrating innovative technology in the core facility portfolio. Core facilities need to innovate to stay up to date. However, how to carry out the innovation is not very obvious. One area of innovation in imaging core facilities is the building of optical setups. However, the creation of optical setups requires specific skill sets, time, and investments. Consequently, the topic of whether a core facility should develop optical devices is discussed as controversial. Here, we provide resources that should help get into this topic, and we discuss different options when and how it makes sense to build optical devices in core facilities. We discuss various aspects, including consequences for staff and the relation of the core to the institute, and also broaden the scope toward other areas of innovation.
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Affiliation(s)
- Sebastian Munck
- Neuroscience Department, KU Leuven, Leuven, Belgium
- VIB BioImaging Core, VIB, Leuven, Belgium
| | | | - Christopher Cawthorne
- Department of Imaging and Pathology, Nuclear Medicine and Molecular Imaging, KU Leuven, Leuven, Belgium
| | - Julien Colombelli
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
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2
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Sitarska E, Almeida SD, Beckwith MS, Stopp J, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt M, Kreshuk A, Erzberger A, Diz-Muñoz A. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nat Commun 2023; 14:5644. [PMID: 37704612 PMCID: PMC10499897 DOI: 10.1038/s41467-023-41173-1] [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: 10/18/2022] [Accepted: 08/22/2023] [Indexed: 09/15/2023] Open
Abstract
To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells' capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment.
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Affiliation(s)
- Ewa Sitarska
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany
| | - Silvia Dias Almeida
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
- Division of Medical Image Computing, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | | | - Julian Stopp
- Institute of Science and Technology Austria, 3400, Klosterneuburg, Austria
| | - Jakub Czuchnowski
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Marc Siggel
- EMBL Hamburg, European Molecular Biology Laboratory, 22607, Hamburg, Germany
- Centre for Structural Systems Biology, 22607, Hamburg, Germany
| | - Rita Roessner
- EMBL Hamburg, European Molecular Biology Laboratory, 22607, Hamburg, Germany
- Centre for Structural Systems Biology, 22607, Hamburg, Germany
| | - Aline Tschanz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany
| | - Christer Ejsing
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Jan Kosinski
- EMBL Hamburg, European Molecular Biology Laboratory, 22607, Hamburg, Germany
- Centre for Structural Systems Biology, 22607, Hamburg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Michael Sixt
- Institute of Science and Technology Austria, 3400, Klosterneuburg, Austria
| | - Anna Kreshuk
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Anna Erzberger
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Alba Diz-Muñoz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
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3
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Jiao W, Chatton JY, Genoud C. Mitochondria morphometry in 3D datasets obtained from mouse brains with serial block-face scanning electron microscopy. Methods Cell Biol 2023; 177:197-211. [PMID: 37451767 DOI: 10.1016/bs.mcb.2023.01.021] [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: 07/18/2023]
Abstract
The dysfunction of mitochondria is linked with many diseases. In the nervous system, evidence of their implication in neurodegenerative disease is growing. Mitochondria health is assessed by their impact on cellular metabolism but alterations in their morphologies and locations in the cells can also be markers of dysfunctions. Light microscopy techniques allow us to look at mitochondria in vivo in cells or tissue. But in the case of the nervous system, in order to assess the precise location of mitochondria in different cell types and neuronal compartments (cell bodies, dendrites or axons), electron microscopy is required. While the percentage of volume occupied by mitochondria can be assessed on 2D images, alterations in length, branching, and interactions with other organelles require three-dimensional (3D) segmentation of mitochondria in volumes imaged at ultrastructural level. Nowadays three-dimensional volume electron microscopy (vEM) imaging techniques such as serial block face scanning electron microscopy (SBF-SEM) enable us to image 3D volumes of tissue at ultrastructural level and can be done routinely. Segmentation of all the neuropil is also successfully achieved at a large scale in the nervous system. Here, we show a workflow based on open access resources, which allows us to image, segment, and analyze mitochondria in 3D volumes of regions of interest in the mouse brain. Taking advantage of recent developments, e.g., pre-trained models for mitochondria, we speed up the reconstruction and analysis. We also critically assess the impact on the results of the different reconstruction methods chosen and the level of manual corrections invested.
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Affiliation(s)
- Wei Jiao
- Electron Microscopy Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Jean-Yves Chatton
- Department of Fundamental Neurosciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Christel Genoud
- Electron Microscopy Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
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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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Paganos P, Ronchi P, Carl J, Mizzon G, Martinez P, Benvenuto G, Arnone MI. Integrating single cell transcriptomics and volume electron microscopy confirms the presence of pancreatic acinar-like cells in sea urchins. Front Cell Dev Biol 2022; 10:991664. [PMID: 36060803 PMCID: PMC9437490 DOI: 10.3389/fcell.2022.991664] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 07/21/2022] [Indexed: 01/11/2023] Open
Abstract
The identity and function of a given cell type relies on the differential expression of gene batteries that promote diverse phenotypes and functional specificities. Therefore, the identification of the molecular and morphological fingerprints of cell types across taxa is essential for untangling their evolution. Here we use a multidisciplinary approach to identify the molecular and morphological features of an exocrine, pancreas-like cell type harbored within the sea urchin larval gut. Using single cell transcriptomics, we identify various cell populations with a pancreatic-like molecular fingerprint that are enriched within the S. purpuratus larva digestive tract. Among these, in the region where they reside, the midgut/stomach domain, we find that populations of exocrine pancreas-like cells have a unique regulatory wiring distinct from the rest the of the cell types of the same region. Furthermore, Serial Block-face scanning Electron Microscopy (SBEM) of the exocrine cells shows that this reported molecular diversity is associated to distinct morphological features that reflect the physiological and functional properties of this cell type. Therefore, we propose that these sea urchin exocrine cells are homologous to the well-known mammalian pancreatic acinar cells and thus we trace the origin of this particular cell type to the time of deuterostome diversification. Overall, our approach allows a thorough characterization of a complex cell type and shows how both the transcriptomic and morphological information contribute to disentangling the evolution of cell types and organs such as the pancreatic cells and pancreas.
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Affiliation(s)
| | - Paolo Ronchi
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jil Carl
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Giulia Mizzon
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Pedro Martinez
- Institut Català de Recerca i Estudis Avancats (ICREA), Barcelona, Spain,Genetics Department, University of Barcelona, Barcelona, Spain
| | | | - Maria Ina Arnone
- Stazione Zoologica Anton Dohrn (SZN), Naples, Italy,*Correspondence: Maria Ina Arnone,
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6
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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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7
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Ayuso-Jimeno IP, Ronchi P, Wang T, Gallori CE, Gross CT. Identifying long-range synaptic inputs using genetically encoded labels and volume electron microscopy. Sci Rep 2022; 12:10213. [PMID: 35715545 PMCID: PMC9205864 DOI: 10.1038/s41598-022-14309-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 06/06/2022] [Indexed: 11/08/2022] Open
Abstract
Enzymes that facilitate the local deposition of electron dense reaction products have been widely used as labels in electron microscopy (EM) for the identification of synaptic contacts in neural tissue. Peroxidases, in particular, can efficiently metabolize 3,3'-diaminobenzidine tetrahydrochloride hydrate (DAB) to produce precipitates with high contrast under EM following heavy metal staining, and can be genetically encoded to facilitate the labeling of specific cell-types or organelles. Nevertheless, the peroxidase/DAB method has so far not been reported to work in a multiplexed manner in combination with 3D volume EM techniques (e.g. Serial blockface electron microscopy, SBEM; Focused ion beam electron microscopy, FIBSEM) that are favored for the large-scale ultrastructural assessment of synaptic architecture However, a recently described peroxidase with enhanced enzymatic activity (dAPEX2) can efficienty deposit EM-visible DAB products in thick tissue without detergent treatment opening the possibility for the multiplex labeling of genetically defined cell-types in combination with volume EM methods. Here we demonstrate that multiplexed dAPEX2/DAB tagging is compatible with both FIBSEM and SBEM volume EM approaches and use them to map long-range genetically identified synaptic inputs from the anterior cingulate cortex to the periaqueductal gray in the mouse brain.
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Affiliation(s)
- Irene P Ayuso-Jimeno
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Via Ramarini 32, 00015, Monterotondo, RM, Italy
| | - Paolo Ronchi
- Electron Microscopy Core Facility (EMCF), European Molecular Biology Laboratory (EMBL), 69117, Meyerhofstr, Germany
| | - Tianzi Wang
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Via Ramarini 32, 00015, Monterotondo, RM, Italy
| | - Catherine E Gallori
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Via Ramarini 32, 00015, Monterotondo, RM, Italy
| | - Cornelius T Gross
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Via Ramarini 32, 00015, Monterotondo, RM, Italy.
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8
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Application of the mirror technique for block-face scanning electron microscopy. Brain Struct Funct 2022; 227:1933-1947. [PMID: 35643821 PMCID: PMC9232443 DOI: 10.1007/s00429-022-02506-w] [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: 10/03/2021] [Accepted: 05/04/2022] [Indexed: 11/29/2022]
Abstract
The mirror technique adapted for electron microscopy allows correlating neuronal structures across the cutting plane of adjoining light microscopic sections which, however, have a limited thickness, typically less than 100 µm (Talapka et al. in Front Neuroanat, 2021, 10.3389/fnana.2021.652422). Here, we extend the mirror technique for tissue blocks in the millimeter range and demonstrate compatibility with serial block-face electron microscopy (SBEM). An essential step of the methodological improvement regards the recognition that unbound resin must be removed from the tissue surface to gain visibility of surface structures. To this, the tissue block was placed on absorbent paper during the curing process. In this way, neuronal cell bodies could be unequivocally identified using epi-illumination and confocal microscopy. Thus, the layout of cell bodies which were cut by the sectioning plane can be correlated with the layout of their complementary part in the adjoining section processed for immunohistochemistry. The modified mirror technique obviates the spatial limit in investigating synaptology of neurochemically identified structures such as neuronal processes, dendrites and axons.
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9
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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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10
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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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11
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Goggin P, Ho EML, Gnaegi H, Searle S, Oreffo ROC, Schneider P. Development of protocols for the first serial block-face scanning electron microscopy (SBF SEM) studies of bone tissue. Bone 2020; 131:115107. [PMID: 31669251 PMCID: PMC6961117 DOI: 10.1016/j.bone.2019.115107] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/27/2019] [Accepted: 10/09/2019] [Indexed: 11/28/2022]
Abstract
There is an unmet need for a high-resolution three-dimensional (3D) technique to simultaneously image osteocytes and the matrix in which these cells reside. In serial block-face scanning electron microscopy (SBF SEM), an ultramicrotome mounted within the vacuum chamber of a microscope repeatedly sections a resin-embedded block of tissue. Backscattered electron scans of the block face provide a stack of high-resolution two-dimensional images, which can be used to visualise and quantify cells and organelles in 3D. High-resolution 3D images of biological tissues from SBF SEM have been exploited considerably to date in the neuroscience field. However, non-brain samples, in particular hard biological tissues, have appeared more challenging to image by SBF SEM due to the difficulties of sectioning and rendering the samples conductive. We have developed and propose protocols for bone tissue preparation using SBF SEM, for imaging simultaneously soft and hard bone tissue components in 3D. We review the state of the art in high-resolution imaging of osteocytes, provide a historical perspective of SBF SEM, and we present first SBF SEM proof-of-concept studies for murine and human tissue. The application of SBF SEM to hard tissues will facilitate qualitative and quantitative 3D studies of tissue microstructure and ultrastructure in bone development, ageing and pathologies such as osteoporosis and osteoarthritis.
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Affiliation(s)
- Patricia Goggin
- Bioengineering Science Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
| | - Elaine M L Ho
- Bioengineering Science Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
| | | | | | - Richard O C Oreffo
- Bone and Joint Research Group, Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Philipp Schneider
- Bioengineering Science Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK.
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12
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Nguyen HB, Thai TQ, Sui Y, Azuma M, Fujiwara K, Ohno N. Methodological Improvements With Conductive Materials for Volume Imaging of Neural Circuits by Electron Microscopy. Front Neural Circuits 2018; 12:108. [PMID: 30532696 PMCID: PMC6265348 DOI: 10.3389/fncir.2018.00108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 11/13/2018] [Indexed: 12/29/2022] Open
Abstract
Recent advancements in electron microscope volume imaging, such as serial imaging using scanning electron microscopy (SEM), have facilitated the acquisition of three-dimensional ultrastructural information of biological samples. These advancements help build a comprehensive understanding of the functional structures in entire organelles, cells, organs and organisms, including large-scale wiring maps of neural circuitry in various species. Advanced volume imaging of biological specimens has often been limited by artifacts and insufficient contrast, which are partly caused by problems in staining, serial sectioning and electron beam irradiation. To address these issues, methods of sample preparation have been modified and improved in order to achieve better resolution and higher signal-to-noise ratios (SNRs) in large tissue volumes. These improvements include the development of new embedding media for electron microscope imaging that have desirable physical properties such as less deformation in the electron beam and higher stability for sectioning. The optimization of embedding media involves multiple resins and filler materials including biological tissues, metallic particles and conductive carbon black. These materials alter the physical properties of the embedding media, such as conductivity, which reduces specimen charge, ameliorates damage to sections, reduces image deformation and results in better ultrastructural data. These improvements and further studies to improve electron microscope volume imaging methods provide options for better scale, quality and throughput in the three-dimensional ultrastructural analyses of biological samples. These efforts will enable a deeper understanding of neuronal circuitry and the structural foundation of basic and higher brain functions.
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Affiliation(s)
- Huy Bang Nguyen
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences (NIPS), Okazaki, Japan
- Department of Anatomy and Structural Biology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Japan
- Department of Anatomy, Faculty of Medicine, University of Medicine and Pharmacy (UMP), Ho Chi Minh City, Vietnam
| | - Truc Quynh Thai
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences (NIPS), Okazaki, Japan
- Department of Anatomy and Structural Biology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Japan
| | - Yang Sui
- Department of Anatomy and Structural Biology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Japan
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Morio Azuma
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Ken Fujiwara
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Nobuhiko Ohno
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences (NIPS), Okazaki, Japan
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, Shimotsuke, Japan
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Kubota Y, Sohn J, Kawaguchi Y. Large Volume Electron Microscopy and Neural Microcircuit Analysis. Front Neural Circuits 2018; 12:98. [PMID: 30483066 PMCID: PMC6240581 DOI: 10.3389/fncir.2018.00098] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/17/2018] [Indexed: 12/23/2022] Open
Abstract
One recent technical innovation in neuroscience is microcircuit analysis using three-dimensional reconstructions of neural elements with a large volume Electron microscopy (EM) data set. Large-scale data sets are acquired with newly-developed electron microscope systems such as automated tape-collecting ultramicrotomy (ATUM) with scanning EM (SEM), serial block-face EM (SBEM) and focused ion beam-SEM (FIB-SEM). Currently, projects are also underway to develop computer applications for the registration and segmentation of the serially-captured electron micrographs that are suitable for analyzing large volume EM data sets thoroughly and efficiently. The analysis of large volume data sets can bring innovative research results. These recently available techniques promote our understanding of the functional architecture of the brain.
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Affiliation(s)
- Yoshiyuki Kubota
- Division of Cerebral Circuitry, National Institute for Physiological Sciences (NIPS), Okazaki, Japan
- Department of Physiological Sciences, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
| | - Jaerin Sohn
- Division of Cerebral Circuitry, National Institute for Physiological Sciences (NIPS), Okazaki, Japan
- Research Fellow of Japan Society for the Promotion of Science (JSPS), Tokyo, Japan
| | - Yasuo Kawaguchi
- Division of Cerebral Circuitry, National Institute for Physiological Sciences (NIPS), Okazaki, Japan
- Department of Physiological Sciences, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
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14
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Genoud C, Titze B, Graff-Meyer A, Friedrich RW. Fast Homogeneous En Bloc Staining of Large Tissue Samples for Volume Electron Microscopy. Front Neuroanat 2018; 12:76. [PMID: 30323746 PMCID: PMC6172304 DOI: 10.3389/fnana.2018.00076] [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: 06/20/2018] [Accepted: 08/29/2018] [Indexed: 11/15/2022] Open
Abstract
Fixation and staining of large tissue samples are critical for the acquisition of volumetric electron microscopic image datasets and the subsequent reconstruction of neuronal circuits. Efficient protocols exist for the staining of small samples, but uniform contrast is often difficult to achieve when the sample diameter exceeds a few hundred micrometers. Recently, a protocol (BROPA, brain-wide reduced-osmium staining with pyrogallol-mediated amplification) was developed that achieves homogeneous staining of the entire mouse brain but requires very long sample preparation times. By exploring modifications of this protocol we developed a substantially faster procedure, fBROPA, that allows for reliable high-quality staining of tissue blocks on the millimeter scale. Modifications of the original BROPA protocol include drastically reduced incubation times and a lead aspartate incubation to increase sample conductivity. Using this procedure, whole brains from adult zebrafish were stained within 4 days. Homogenous high-contrast staining was achieved throughout the brain. High-quality image stacks with voxel sizes of 10 × 10 × 25 nm3 were obtained by serial block-face imaging using an electron dose of ~15 e−/nm2. No obvious reduction in staining quality was observed in comparison to smaller samples stained by other state-of-the-art procedures. Furthermore, high-quality images with minimal charging artifacts were obtained from non-neural tissues with low membrane density. fBROPA is therefore likely to be a versatile and efficient sample preparation protocol for a wide range of applications in volume electron microscopy.
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Affiliation(s)
- Christel Genoud
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Benjamin Titze
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Rainer W Friedrich
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, Switzerland
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