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Regmi KC, Ghosh S, Koch B, Neumann U, Stein B, O'Connell RJ, Innes RW. Three-Dimensional Ultrastructure of Arabidopsis Cotyledons Infected with Colletotrichum higginsianum. Mol Plant Microbe Interact 2024; 37:396-406. [PMID: 38148303 DOI: 10.1094/mpmi-05-23-0068-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
We used serial block-face scanning electron microscopy (SBF-SEM) to study the host-pathogen interface between Arabidopsis cotyledons and the hemibiotrophic fungus Colletotrichum higginsianum. By combining high-pressure freezing and freeze-substitution with SBF-SEM, followed by segmentation and reconstruction of the imaging volume using the freely accessible software IMOD, we created 3D models of the series of cytological events that occur during the Colletotrichum-Arabidopsis susceptible interaction. We found that the host cell membranes underwent massive expansion to accommodate the rapidly growing intracellular hypha. As the fungal infection proceeded from the biotrophic to the necrotrophic stage, the host cell membranes went through increasing levels of disintegration culminating in host cell death. Intriguingly, we documented autophagosomes in proximity to biotrophic hyphae using transmission electron microscopy (TEM) and a concurrent increase in autophagic flux between early to mid/late biotrophic phase of the infection process. Occasionally, we observed osmiophilic bodies in the vicinity of biotrophic hyphae using TEM only and near necrotrophic hyphae under both TEM and SBF-SEM. Overall, we established a method for obtaining serial SBF-SEM images, each with a lateral (x-y) pixel resolution of 10 nm and an axial (z) resolution of 40 nm, that can be reconstructed into interactive 3D models using the IMOD. Application of this method to the Colletotrichum-Arabidopsis pathosystem allowed us to more fully understand the spatial arrangement and morphological architecture of the fungal hyphae after they penetrate epidermal cells of Arabidopsis cotyledons and the cytological changes the host cell undergoes as the infection progresses toward necrotrophy. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Kamesh C Regmi
- Indiana University, Department of Biology, Bloomington, IN 47405, U.S.A
| | - Suchismita Ghosh
- Indiana University, Department of Biology, Bloomington, IN 47405, U.S.A
| | - Benjamin Koch
- Indiana University, Department of Biology, Bloomington, IN 47405, U.S.A
| | - Ulla Neumann
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Barry Stein
- Indiana University, Department of Biology, Bloomington, IN 47405, U.S.A
| | | | - Roger W Innes
- Indiana University, Department of Biology, Bloomington, IN 47405, U.S.A
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Chaudhary P, Lockwood H, Stowell C, Bushong E, Reynaud J, Yang H, Gardiner SK, Wiliams G, Williams I, Ellisman M, Marsh-Armstrong N, Burgoyne C. Retrolaminar Demyelination of Structurally Intact Axons in Nonhuman Primate Experimental Glaucoma. Invest Ophthalmol Vis Sci 2024; 65:36. [PMID: 38407858 PMCID: PMC10902877 DOI: 10.1167/iovs.65.2.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/28/2024] [Indexed: 02/27/2024] Open
Abstract
Purpose To determine if structurally intact, retrolaminar optic nerve (RON) axons are demyelinated in nonhuman primate (NHP) experimental glaucoma (EG). Methods Unilateral EG NHPs (n = 3) were perfusion fixed, EG and control eyes were enucleated, and foveal Bruch's membrane opening (FoBMO) 30° sectoral axon counts were estimated. Optic nerve heads were trephined; serial vibratome sections (VSs) were imaged and colocalized to a fundus photograph establishing their FoBMO location. The peripheral neural canal region within n = 5 EG versus control eye VS comparisons was targeted for scanning block-face electron microscopic reconstruction (SBEMR) using micro-computed tomographic reconstructions (µCTRs) of each VS. Posterior laminar beams within each µCTR were segmented, allowing a best-fit posterior laminar surface (PLS) to be colocalized into its respective SBEMR. Within each SBEMR, up to 300 axons were randomly traced until they ended (nonintact) or left the block (intact). For each intact axon, myelin onset was identified and myelin onset distance (MOD) was measured relative to the PLS. For each EG versus control SBEMR comparison, survival analyses compared EG and control MOD. Results MOD calculations were successful in three EG and five control eye SBEMRs. Within each SBEMR comparison, EG versus control eye axon loss was -32.9%, -8.3%, and -15.2% (respectively), and MOD was increased in the EG versus control SBEMR (P < 0.0001 for each EG versus control SBEMR comparison). When data from all three EG eye SBEMRs were compared to all five control eye SBEMRs, MOD was increased within the EG eyes. Conclusions Structurally intact, RON axons are demyelinated in NHP early to moderate EG. Studies to determine their functional status are indicated.
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Affiliation(s)
- Priya Chaudhary
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Howard Lockwood
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Cheri Stowell
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Eric Bushong
- National Center for Microscopy & Imaging Research, UCSD, La Jolla, California, United States
| | - Juan Reynaud
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Hongli Yang
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Stuart K Gardiner
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Galen Wiliams
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Imee Williams
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
| | - Mark Ellisman
- National Center for Microscopy & Imaging Research, UCSD, La Jolla, California, United States
| | - Nick Marsh-Armstrong
- Department of Ophthalmology, University of California, Davis, California, United States
| | - Claude Burgoyne
- Optic Nerve Head Research Laboratory, Legacy Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
- Discoveries in Sight, Devers Eye Institute, Legacy Research Institute, Portland, Oregon, United States
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Knoblauch J, Waadt R, Cousins AB, Kunz HH. Probing the in situ volumes of Arabidopsis leaf plastids using three-dimensional confocal and scanning electron microscopy. Plant J 2024; 117:332-341. [PMID: 37985241 DOI: 10.1111/tpj.16554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/31/2023] [Accepted: 11/08/2023] [Indexed: 11/22/2023]
Abstract
Leaf plastids harbor a plethora of biochemical reactions including photosynthesis, one of the most important metabolic pathways on Earth. Scientists are eager to unveil the physiological processes within the organelle but also their interconnection with the rest of the plant cell. An increasingly important feature of this venture is to use experimental data in the design of metabolic models. A remaining obstacle has been the limited in situ volume information of plastids and other cell organelles. To fill this gap for chloroplasts, we established three microscopy protocols delivering in situ volumes based on: (i) chlorophyll fluorescence emerging from the thylakoid membrane, (ii) a CFP marker embedded in the envelope, and (iii) calculations from serial block-face scanning electron microscopy (SBFSEM). The obtained data were corroborated by comparing wild-type data with two mutant lines affected in the plastid division machinery known to produce small and large mesophyll chloroplasts, respectively. Furthermore, we also determined the volume of the much smaller guard cell plastids. Interestingly, their volume is not governed by the same components of the division machinery which defines mesophyll plastid size. Based on our three approaches, the average volume of a mature Col-0 wild-type mesophyll chloroplasts is 93 μm3 . Wild-type guard cell plastids are approximately 18 μm3 . Lastly, our comparative analysis shows that the chlorophyll fluorescence analysis can accurately determine chloroplast volumes, providing an important tool to research groups without access to transgenic marker lines expressing genetically encoded fluorescence proteins or costly SBFSEM equipment.
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Affiliation(s)
- Jan Knoblauch
- School of Biological Sciences, Washington State University, P.O. Box 644236, Pullman, Washington, 99164-4236, USA
| | - Rainer Waadt
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, 48149, Münster, Germany
| | - Asaph B Cousins
- School of Biological Sciences, Washington State University, P.O. Box 644236, Pullman, Washington, 99164-4236, USA
| | - Hans-Henning Kunz
- School of Biological Sciences, Washington State University, P.O. Box 644236, Pullman, Washington, 99164-4236, USA
- LMU Munich, Plant Biochemistry, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
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MANTANI Y, OHNO N, HARUTA T, NAKANISHI S, MORISHITA R, MURASE S, YOKOYAMA T, HOSHI N. Histological study on the reginal difference in the localization of mucosal enteric glial cells and their sheath structure in the rat intestine. J Vet Med Sci 2023; 85:1034-1039. [PMID: 37612064 PMCID: PMC10600526 DOI: 10.1292/jvms.23-0266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023] Open
Abstract
The present study aimed to histologically clarify the regional specificity of the mucosal enteric glial cells (mEGCs) in the rat intestine with serial block-face scanning electron microscopy (SBF-SEM). SBF-SEM analysis with the ileum, the cecum and the descending colon revealed that mEGC nuclei were more abundant in the data stacks from the apical portion of the villus and the lateral portion of the crypt of the ileum. mEGCs exhibited a high rate of coverage over the nerve bundle around the lateral portion of the ileal crypt, but showed an extremely low level of coverage in the luminal portion of the cecum. These findings evidenced regional differences in the localization of mEGCs and in their sheath structure in the rat intestine.
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Affiliation(s)
- Youhei MANTANI
- Laboratory of Histophysiology, Department of Bioresource
Science, Graduate School of Agricultural Science, Kobe University, Hyogo, Japan
| | - Nobuhiko OHNO
- Department of Anatomy, Division of Histology and Cell
Biology, School of Medicine, Jichi Medical University, Tochigi, Japan
- Division of Ultrastructural Research, National Institute for
Physiological Sciences, Aichi, Japan
| | - Tomohiro HARUTA
- Bio 3D Promotion Group, Application Management Department,
JEOL Ltd., Tokyo, Japan
| | - Satoki NAKANISHI
- Laboratory of Histophysiology, Department of Bioresource
Science, Graduate School of Agricultural Science, Kobe University, Hyogo, Japan
| | - Rinako MORISHITA
- Laboratory of Histophysiology, Department of Bioresource
Science, Graduate School of Agricultural Science, Kobe University, Hyogo, Japan
| | - Shota MURASE
- Laboratory of Histophysiology, Department of Bioresource
Science, Graduate School of Agricultural Science, Kobe University, Hyogo, Japan
| | - Toshifumi YOKOYAMA
- Laboratory of Animal Molecular Morphology, Department of
Bioresource Science, Graduate School of Agricultural Science, Kobe University, Hyogo,
Japan
| | - Nobuhiko HOSHI
- Laboratory of Animal Molecular Morphology, Department of
Bioresource Science, Graduate School of Agricultural Science, Kobe University, Hyogo,
Japan
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Bains KK, Young RD, Koudouna E, Lewis PN, Quantock AJ. Cell-Cell and Cell-Matrix Interactions at the Presumptive Stem Cell Niche of the Chick Corneal Limbus. Cells 2023; 12:2334. [PMID: 37830548 PMCID: PMC10571731 DOI: 10.3390/cells12192334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 10/14/2023] Open
Abstract
(1) Background: Owing to its ready availability and ease of acquisition, developing chick corneal tissue has long been used for research purposes. Here, we seek to ascertain the three-dimensional microanatomy and spatiotemporal interrelationships of the cells (epithelial and stromal), extracellular matrix, and vasculature at the corneo-scleral limbus as the site of the corneal stem cell niche of the chicken eye. (2) Methods: The limbus of developing (i.e., embryonic days (E) 16 and 18, just prior to hatch) and mature chicken eyes was imaged using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and the volume electron microscopy technique, serial-block face SEM (SBF-SEM), the latter technique allowing us to generate three-dimensional reconstructions from data sets of up to 1000 serial images; (3) Results: Data revealed that miniature limbal undulations of the embryonic basement membrane, akin to Palisades of Vogt (PoV), matured into distinct invaginations of epithelial cells that extended proximally into a vascularized limbal stroma. Basal limbal epithelial cells, moreover, occasionally exhibited a high nuclear:cytoplasmic ratio, which is a characteristic feature of stem cells. SBF-SEM identified direct cell-cell associations between corneal epithelial and stromal cells at the base of structures akin to limbal crypts (LCs), with cord-like projections of extracellular matrix extending from the basal epithelial lamina into the subjacent stroma, where they made direct contact with stomal cells in the immature limbus. (4) Conclusion: Similarities with human tissue suggest that the corneal limbus of the mature chicken eye is likely the site of a corneal stem cell niche. The ability to study embryonic corneas pre-hatch, where we see characteristic niche-like features emerge, thus provides an opportunity to chart the development of the limbal stem cell niche of the cornea.
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Affiliation(s)
| | | | | | | | - Andrew J. Quantock
- Structural Biophysics Group, School of Optometry and Vision Sciences, Cardiff University, Maindy Road, Cardiff CF10 3AT, UK; (K.K.B.); (R.D.Y.); (E.K.); (P.N.L.)
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Inoue T, Ohno N, Oishi N, Mochizuki K, Katoh R, Kondo T. Three-dimensional structural analysis of papillary thyroid carcinoma nuclei with serial block-face scanning electron microscopy (SBF-SEM). Pathol Int 2023; 73:341-350. [PMID: 37154498 DOI: 10.1111/pin.13329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/21/2023] [Indexed: 05/10/2023]
Abstract
Nuclear morphology of carcinoma cells is critical for the pathological diagnosis of papillary thyroid carcinoma (PTC). However, three-dimensional architecture of PTC nuclei is still elusive. In this study, we analyzed the three-dimensional ultrastructure of PTC nuclei using serial block-face scanning electron microscopy which takes advantage of the high-throughput acquisition of serial electron microscopic images and three-dimensional reconstruction of subcellular structures. En bloc-stained and resin-embedded specimens were prepared from surgically removed PTCs and normal thyroid tissues. We acquired two-dimensional images from serial block-face scanning electron microscopy and reconstructed three-dimensional nuclear structures. Quantitative comparisons showed that the nuclei of carcinoma cells were larger and more complex than those of normal follicular cells. The three-dimensional reconstruction of carcinoma nuclei divided intranuclear cytoplasmic inclusions into "open intranuclear cytoplasmic inclusions" connecting to cytoplasm outside the nucleus and "closed intranuclear cytoplasmic inclusions" without that connection. Cytoplasm with abundant organelles was observed in open inclusions, but closed inclusions contained fewer organelles with or without degeneration. Granules with a dense core were only observed in closed inclusions. Our observations suggested that open inclusions originate from nuclear invaginations, and disconnection from cytoplasm leads to closed inclusions.
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Affiliation(s)
- Tomohiro Inoue
- Department of Pathology, University of Yamanashi, Chuo, Japan
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, Jichi Medical University, Shimotsuke, Japan
- Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, Japan
| | - Naoki Oishi
- Department of Pathology, University of Yamanashi, Chuo, Japan
| | - Kunio Mochizuki
- Department of Pathology, University of Yamanashi, Chuo, Japan
| | - Ryohei Katoh
- Department of Pathology, Ito Hospital, Tokyo, Japan
| | - Tetsuo Kondo
- Department of Pathology, University of Yamanashi, Chuo, Japan
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Riley KC, Koleilat A, Dugdale JA, Cooper SA, Christensen TA, Schimmenti LA. Three-Dimensional Structure of Inner Ear Hair Cell Ribbon Synapses in a Zebrafish Model of Usher Syndrome Type 1B. Zebrafish 2023; 20:47-54. [PMID: 37071854 DOI: 10.1089/zeb.2022.0049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
Our understanding of inner ear hair cell ultrastructure has heretofore relied upon two-dimensional imaging; however, serial block-face scanning electron microscopy (SBFSEM) changes this paradigm allowing for three-dimensional evaluation. We compared inner ear hair cells of the apical cristae in myo7aa-/- null zebrafish, a model of human Usher Syndrome type 1B, to hair cells in wild-type zebrafish by SBFSEM to investigate possible ribbon synapse ultrastructural differences. Previously, it has been shown that compared to wild type, myo7aa-/- zebrafish neuromast hair cells have fewer ribbon synapses yet similar ribbon areas. We expect the recapitulation of these results within the inner ear apical crista hair cells furthering the knowledge of three-dimensional ribbon synapse structure while resolving the feasibility of therapeutically targeting myo7aa-/- mutant ribbons. In this report, we evaluated ribbon synapse number, volume, surface area, and sphericity. Localization of ribbons and their distance from the nearest innervation were also evaluated. We determined that myo7aa-/- mutant ribbon synapses are smaller in volume and surface area; however, all other measurements were not significantly different from wild-type zebrafish. Because the ribbon synapses are nearly indistinguishable between the myo7aa-/- mutant and wild type, it suggests that the ribbons are structurally receptive, supporting that therapeutic intervention may be feasible.
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Affiliation(s)
- Kenneth C Riley
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Alaa Koleilat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Joseph A Dugdale
- Department of Otorhinolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Shawna A Cooper
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Trace A Christensen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
- Microscopy and Cell Analysis Core, and Mayo Clinic, Rochester, Minnesota, USA
| | - Lisa A Schimmenti
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
- Department of Otorhinolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
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Czymmek KJ, Duncan KE, Berg H. Realizing the Full Potential of Advanced Microscopy Approaches for Interrogating Plant-Microbe Interactions. Mol Plant Microbe Interact 2023; 36:245-255. [PMID: 36947723 DOI: 10.1094/mpmi-10-22-0208-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Microscopy has served as a fundamental tool for insight and discovery in plant-microbe interactions for centuries. From classical light and electron microscopy to corresponding specialized methods for sample preparation and cellular contrasting agents, these approaches have become routine components in the toolkit of plant and microbiology scientists alike to visualize, probe and understand the nature of host-microbe relationships. Over the last three decades, three-dimensional perspectives led by the development of electron tomography, and especially, confocal techniques continue to provide remarkable clarity and spatial detail of tissue and cellular phenomena. Confocal and electron microscopy provide novel revelations that are now commonplace in medium and large institutions. However, many other cutting-edge technologies and sample preparation workflows are relatively unexploited yet offer tremendous potential for unprecedented advancement in our understanding of the inner workings of pathogenic, beneficial, and symbiotic plant-microbe interactions. Here, we highlight key applications, benefits, and challenges of contemporary advanced imaging platforms for plant-microbe systems with special emphasis on several recently developed approaches, such as light-sheet, single molecule, super-resolution, and adaptive optics microscopy, as well as ambient and cryo-volume electron microscopy, X-ray microscopy, and cryo-electron tomography. Furthermore, the potential for complementary sample preparation methodologies, such as optical clearing, expansion microscopy, and multiplex imaging, will be reviewed. Our ultimate goal is to stimulate awareness of these powerful cutting-edge technologies and facilitate their appropriate application and adoption to solve important and unresolved biological questions in the field. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Kirk J Czymmek
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
- Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
| | - Keith E Duncan
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
| | - Howard Berg
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, U.S.A
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van Opbergen CJM, Sall J, Petzold C, Dancel-Manning K, Delmar M, Liang FX. "Orphan" Connexin43 in Plakophilin-2 Deficient Hearts Revealed by Volume Electron Microscopy. Front Cell Dev Biol 2022; 10:843687. [PMID: 35663385 PMCID: PMC9159532 DOI: 10.3389/fcell.2022.843687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Previous studies revealed an abundance of functional Connexin43 (Cx43) hemichannels consequent to loss of plakophilin-2 (PKP2) expression in adult murine hearts. The increased Cx43-mediated membrane permeability is likely responsible for excess entry of calcium into the cells, leading to an arrhythmogenic/cardiomyopathic phenotype. The latter has translational implications to the molecular mechanisms of inheritable arrhythmogenic right ventricular cardiomyopathy (ARVC). Despite functional evidence, visualization of these "orphan" (i.e., non-paired in a gap junction configuration) Cx43 hemichannels remains lacking. Immuno-electron microscopy (IEM) remains an extremely powerful tool to localize, with nanometric resolution, a protein within its native structural landscape. Yet, challenges for IEM are to preserve the antigenicity of the molecular target and to provide access for antibodies to reach their target, while maintaining the cellular/tissue ultrastructure. Fixation is important for maintaining cell structure, but strong fixation and vigorous dehydration (as it is routine for EM) can alter protein structure, thus impairing antigen-antibody binding. Here, we implemented a method to combine pre-embedding immunolabeling (pre-embedding) with serial block-face scanning electron microscopy (SBF-SEM). We utilized a murine model of cardiomyocyte-specific, Tamoxifen (TAM) activated knockout of PKP2. Adult hearts were harvested 14 days post-TAM, at this time hearts present a phenotype of concealed ARVC (i.e., an arrhythmogenic phenotype but no overt structural disease). Thick (200 µm) vibratome slices were immunolabelled for Cx43 and treated with nanogold or FluoroNanogold, coupled with a silver enhancement. Left or right ventricular free walls were dissected and three-dimensional (3D) localization of Cx43 in cardiac muscle was performed using SBF-SEM. Reconstructed images allowed us to visualize the entire length of gap junction plaques, seen as two parallel, closely packed strings of Cx43-immunoreactive beads at the intercalated disc. In contrast, in PKP2-deficient hearts we observed bulging of the intercellular space, and entire areas where only one of the two strings could be observed, indicating the presence of orphan Cx43. We conclude that pre-embedding and SBF-SEM allowed visualization of cardiac Cx43 plaques in their native environment, providing for the first time a visual complement of functional data indicating the presence of orphan Cx43 hemichannels resulting from loss of desmosomal integrity in the heart.
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Affiliation(s)
- Chantal J M van Opbergen
- The Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, New York, NY, United States
| | - Joseph Sall
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, United States
| | - Chris Petzold
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, United States
| | - Kristen Dancel-Manning
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, United States
| | - Mario Delmar
- The Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, New York, NY, United States
| | - Feng-Xia Liang
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, United States
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Hirashima S, Ohta K, Rikimaru-Nishi Y, Togo A, Funatsu T, Tsuneyoshi R, Shima Y, Nakamura KI. Correlative volume-imaging using combined array tomography and FIB-SEM tomography with beam deceleration for 3D architecture visualization in tissue. Microscopy (Oxf) 2022; 71:187-192. [PMID: 35325180 PMCID: PMC9169539 DOI: 10.1093/jmicro/dfac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/27/2022] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
Focused ion beamed (FIB) SEM has a higher spatial resolution than other volume-imaging methods owing to the use of ion beams. However, in this method, it is challenging to analyse entire biological structures buried deep in the resin block. We developed a novel volume-imaging method by combining array tomography and FIB-SEM tomography and investigated the chondrocyte ultrastructure. Our method imparts certainty in determining the analysis area such that cracks or areas with poor staining within the block are avoided. The chondrocyte surface showed fine dendritic processes that were thinner than ultrathin sections. Upon combination with immunostaining, this method holds promise for analysing mesoscopic architectures.
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Affiliation(s)
- Shingo Hirashima
- Department of Anatomy, Division of Microscopic and Developmental Anatomy, Kurume University School of Medicine, Kurume 830-0011, Japan
- Dental and Oral Medical Center, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Keisuke Ohta
- Department of Anatomy, Division of Microscopic and Developmental Anatomy, Kurume University School of Medicine, Kurume 830-0011, Japan
- Advanced Imaging Research Center, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Yukiko Rikimaru-Nishi
- Department of Anatomy, Division of Microscopic and Developmental Anatomy, Kurume University School of Medicine, Kurume 830-0011, Japan
- Department of Plastic and Reconstructive Surgery and Maxillofacial Surgery, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Akinobu Togo
- Advanced Imaging Research Center, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Takashi Funatsu
- Advanced Imaging Research Center, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Risa Tsuneyoshi
- Department of Anatomy, Division of Microscopic and Developmental Anatomy, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Yuichi Shima
- Department of Anatomy, Division of Microscopic and Developmental Anatomy, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Kei-ichiro Nakamura
- Department of Anatomy, Division of Microscopic and Developmental Anatomy, Kurume University School of Medicine, Kurume 830-0011, Japan
- Cognitive and Molecular Research Institute of Brain Diseases, Kurume University School of Medicine, Kurume 830-0011, Japan
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11
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Mursalimov S, Ohno N, Matsumoto M, Bayborodin S, Deineko E. Corrigendum: Serial Block-Face Scanning Electron Microscopy Reveals That Intercellular Nuclear Migration Occurs in Most Normal Tobacco Male Meiocytes. Front Plant Sci 2022; 13:847408. [PMID: 35145540 PMCID: PMC8822320 DOI: 10.3389/fpls.2022.847408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2021.672642.].
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Affiliation(s)
- Sergey Mursalimov
- Laboratory of Plant Bioengineering, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, Shimotsuke, Japan
- Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, Japan
| | - Mami Matsumoto
- Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Japan
| | - Sergey Bayborodin
- Laboratory of Plant Bioengineering, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena Deineko
- Laboratory of Plant Bioengineering, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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12
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Appuhn SV, Siebert S, Myti D, Wrede C, Surate Solaligue DE, Pérez-Bravo D, Brandenberger C, Schipke J, Morty RE, Grothausmann R, Mühlfeld C. Capillary Changes Precede Disordered Alveolarization in a Mouse Model of Bronchopulmonary Dysplasia. Am J Respir Cell Mol Biol 2021; 65:81-91. [PMID: 33784484 DOI: 10.1165/rcmb.2021-0004oc] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bronchopulmonary dysplasia (BPD), the most common sequela of preterm birth, is a severe disorder of the lung that is often associated with long-lasting morbidity. A hallmark of BPD is the disruption of alveolarization, whose pathogenesis is incompletely understood. Here, we tested the vascular hypothesis that disordered vascular development precedes the decreased alveolarization associated with BPD. Neonatal mouse pups were exposed to 7, 14, or 21 days of normoxia (21% O2) or hyperoxia (85% O2) with n = 8-11 for each group. The right lungs were fixed by vascular perfusion and investigated by design-based stereology or three-dimensional reconstruction of data sets obtained by serial block-face scanning EM. The alveolar capillary network of hyperoxia-exposed mice was characterized by rarefaction, partially altered geometry, and widening of capillary segments as shown by three-dimensional reconstruction. Stereology revealed that the development of alveolar epithelium and capillary endothelium was decreased in hyperoxia-exposed mice; however, the time course of these effects was different. That the surface area of the alveolar epithelium was smaller in hyperoxia-exposed mice first became evident at Day 14. In contrast, the surface area of the endothelium was reduced in hyperoxia-exposed mouse pups at Day 7. The thickness of the air-blood barrier decreased during postnatal development in normoxic mice, whereas it increased in hyperoxic mice. The endothelium and the septal connective tissue made appreciable contributions to the thickened septa. In conclusion, the present study provides clear support for the idea that the stunted alveolarization follows the disordered microvascular development, thus supporting the vascular hypothesis of BPD.
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Affiliation(s)
- Svenja V Appuhn
- Institute of Functional and Applied Anatomy and.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover, Member of the German Center for Lung Research (DZL), Hannover, Germany
| | - Sara Siebert
- Institute of Functional and Applied Anatomy and.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover, Member of the German Center for Lung Research (DZL), Hannover, Germany
| | - Despoina Myti
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), Member of the German Center for Lung Research (DZL), University of Giessen and Marburg Lung Center, Giessen, Germany; and
| | - Christoph Wrede
- Institute of Functional and Applied Anatomy and.,Research Core Unit Electron Microscopy, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover, Member of the German Center for Lung Research (DZL), Hannover, Germany
| | - David E Surate Solaligue
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), Member of the German Center for Lung Research (DZL), University of Giessen and Marburg Lung Center, Giessen, Germany; and
| | - David Pérez-Bravo
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), Member of the German Center for Lung Research (DZL), University of Giessen and Marburg Lung Center, Giessen, Germany; and
| | - Christina Brandenberger
- Institute of Functional and Applied Anatomy and.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover, Member of the German Center for Lung Research (DZL), Hannover, Germany
| | - Julia Schipke
- Institute of Functional and Applied Anatomy and.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover, Member of the German Center for Lung Research (DZL), Hannover, Germany
| | - Rory E Morty
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), Member of the German Center for Lung Research (DZL), University of Giessen and Marburg Lung Center, Giessen, Germany; and
| | - Roman Grothausmann
- Institute of Functional and Applied Anatomy and.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover, Member of the German Center for Lung Research (DZL), Hannover, Germany.,Faculty of Engineering and Health, HAWK University of Applied Sciences and Arts, Göttingen, Germany
| | - Christian Mühlfeld
- Institute of Functional and Applied Anatomy and.,Research Core Unit Electron Microscopy, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover, Member of the German Center for Lung Research (DZL), Hannover, Germany
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13
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Courson JA, Landry PT, Do T, Spehlmann E, Lafontant PJ, Patel N, Rumbaut RE, Burns AR. Serial Block-Face Scanning Electron Microscopy (SBF-SEM) of Biological Tissue Samples. J Vis Exp 2021:10.3791/62045. [PMID: 33843931 PMCID: PMC8225236 DOI: 10.3791/62045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Serial block-face scanning electron microscopy (SBF-SEM) allows for the collection of hundreds to thousands of serially-registered ultrastructural images, offering an unprecedented three-dimensional view of tissue microanatomy. While SBF-SEM has seen an exponential increase in use in recent years, technical aspects such as proper tissue preparation and imaging parameters are paramount for the success of this imaging modality. This imaging system benefits from the automated nature of the device, allowing one to leave the microscope unattended during the imaging process, with the automated collection of hundreds of images possible in a single day. However, without appropriate tissue preparation cellular ultrastructure can be altered in such a way that incorrect or misleading conclusions might be drawn. Additionally, images are generated by scanning the block-face of a resin-embedded biological sample and this often presents challenges and considerations that must be addressed. The accumulation of electrons within the block during imaging, known as "tissue charging," can lead to a loss of contrast and an inability to appreciate cellular structure. Moreover, while increasing electron beam intensity/voltage or decreasing beam-scanning speed can increase image resolution, this can also have the unfortunate side effect of damaging the resin block and distorting subsequent images in the imaging series. Here we present a routine protocol for the preparation of biological tissue samples that preserves cellular ultrastructure and diminishes tissue charging. We also provide imaging considerations for the rapid acquisition of high-quality serial-images with minimal damage to the tissue block.
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Affiliation(s)
- Justin A. Courson
- University of Houston, College of Optometry, Houston, TX,
United States of America
| | - Paul T. Landry
- University of Houston, College of Optometry, Houston, TX,
United States of America
| | - Thao Do
- University of Houston, College of Optometry, Houston, TX,
United States of America
| | - Eric Spehlmann
- DePauw University, Department of Biology, Greencastle, IN,
United States of America
| | - Pascal J. Lafontant
- DePauw University, Department of Biology, Greencastle, IN,
United States of America
| | - Nimesh Patel
- University of Houston, College of Optometry, Houston, TX,
United States of America
| | - Rolando E. Rumbaut
- Center for Translational Research on Inflammatory Diseases
(CTRID), Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, United
States of America,Baylor College of Medicine, Children’s Nutrition
Center, Houston, TX, United States of America
| | - Alan R. Burns
- University of Houston, College of Optometry, Houston, TX,
United States of America,Baylor College of Medicine, Children’s Nutrition
Center, Houston, TX, United States of America
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14
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Mursalimov S, Ohno N, Matsumoto M, Bayborodin S, Deineko E. Serial Block-Face Scanning Electron Microscopy Reveals That Intercellular Nuclear Migration Occurs in Most Normal Tobacco Male Meiocytes. Front Plant Sci 2021; 12:672642. [PMID: 34025709 PMCID: PMC8138938 DOI: 10.3389/fpls.2021.672642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/07/2021] [Indexed: 05/14/2023]
Abstract
Serial block-face scanning electron microscopy (SBF-SEM) was used here to study tobacco male meiosis. Three-dimensional ultrastructural analyses revealed that intercellular nuclear migration (INM) occurs in 90-100% of tobacco meiocytes. At the very beginning of meiosis, every meiocyte connected with neighboring cells by more than 100 channels was capable of INM. At leptotene and zygotene, the nucleus in most tobacco meiocytes approached the cell wall and formed nuclear protuberances (NPs) that crossed the cell wall through the channels and extended into the cytoplasm of a neighboring cell. The separation of NPs from the migrating nuclei and micronuclei formation were not observed. In some cases, the NPs and nuclei of neighboring cells appeared apposed to each other, and the gap between their nuclear membranes became invisible. At pachytene, NPs retracted into their own cells. After that, the INM stopped. We consider INM a normal part of tobacco meiosis, but the reason for such behavior of nuclei is unclear. The results obtained by SBF-SEM suggest that there are still many unexplored features of plant meiosis hidden by limitations of common types of microscopy and that SBF-SEM can turn over a new leaf in plant meiosis research.
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Affiliation(s)
- Sergey Mursalimov
- Laboratory of Plant Bioengineering, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- *Correspondence: Sergey Mursalimov
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, Shimotsuke, Japan
- Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, Japan
| | - Mami Matsumoto
- Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Japan
| | - Sergey Bayborodin
- Laboratory of Plant Bioengineering, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena Deineko
- Laboratory of Plant Bioengineering, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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15
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Hwang YS, Maclachlan C, Blanc J, Dubois A, Petersen CCH, Knott G, Lee SH. 3D Ultrastructure of Synaptic Inputs to Distinct GABAergic Neurons in the Mouse Primary Visual Cortex. Cereb Cortex 2020; 31:2610-2624. [PMID: 33350443 PMCID: PMC8023854 DOI: 10.1093/cercor/bhaa378] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/13/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022] Open
Abstract
Synapses are the fundamental elements of the brain’s complicated neural networks. Although the ultrastructure of synapses has been extensively studied, the difference in how synaptic inputs are organized onto distinct neuronal types is not yet fully understood. Here, we examined the cell-type-specific ultrastructure of proximal processes from the soma of parvalbumin-positive (PV+) and somatostatin-positive (SST+) GABAergic neurons in comparison with a pyramidal neuron in the mouse primary visual cortex (V1), using serial block-face scanning electron microscopy. Interestingly, each type of neuron organizes excitatory and inhibitory synapses in a unique way. First, we found that a subset of SST+ neurons are spiny, having spines on both soma and dendrites. Each of those spines has a highly complicated structure that has up to eight synaptic inputs. Next, the PV+ and SST+ neurons receive more robust excitatory inputs to their perisoma than does the pyramidal neuron. Notably, excitatory synapses on GABAergic neurons were often multiple-synapse boutons, making another synapse on distal dendrites. On the other hand, inhibitory synapses near the soma were often single-targeting multiple boutons. Collectively, our data demonstrate that synaptic inputs near the soma are differentially organized across cell types and form a network that balances inhibition and excitation in the V1.
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Affiliation(s)
- Yang-Sun Hwang
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Catherine Maclachlan
- Biological Electron Microscopy Facility, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Jérôme Blanc
- Biological Electron Microscopy Facility, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Anaëlle Dubois
- Biological Electron Microscopy Facility, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Carl C H Petersen
- Laboratory of Sensory Processing, Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Graham Knott
- Biological Electron Microscopy Facility, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Seung-Hee Lee
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
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16
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Wrede C, Hegermann J, Mühlfeld C. Novel cell contact between podocyte microprojections and parietal epithelial cells analyzed by volume electron microscopy. Am J Physiol Renal Physiol 2020; 318:F1246-F1251. [PMID: 32249613 DOI: 10.1152/ajprenal.00097.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Podocytes are highly specialized cells with a clear cell polarity. It is known that in health and disease, microvilli protrude from the apical surface of the podocytes into the urinary space. As a basis to better understand the podocyte microprojections/microvilli, the present study analyzed their spatial localization, extension, and contact site with parietal epithelial cells (PECs). Using different electron microscopic (EM) techniques, we analyzed renal corpuscles of healthy young adult male C57BL/6 mice fixed by vascular perfusion. Serial block-face scanning EM was used to visualize entire corpuscles, focused ion beam scanning EM was performed to characterize microprojection/microvilli-rich regions at higher magnification, and transmission EM of serial sections was used to analyze the contact zone between podocyte microprojections and PECs. Numerous microprojections originating from the primary processes of podocytes were present in the urinary space in all regions of the corpuscle. They often reached the apical surface of the PEC but did not make junctional contacts. At high resolution, it was observed that the glycocalyx of both cells was in contact. Depending on the distance between podocytes and PECs, these microprojections had a stretched or coiled state. The present study shows that microprojections/microvilli of podocytes are a physiological feature of healthy mouse kidneys and are frequently in contact with the apical surface of PECs, thus spanning the urinary space. It is proposed that podocyte microprojections serve mechanosensory or communicative functions between podocytes and PECs.
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Affiliation(s)
- Christoph Wrede
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany.,Research Core Unit Electron Microscopy, Hannover Medical School, Hannover, Germany
| | - Jan Hegermann
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany.,Research Core Unit Electron Microscopy, Hannover Medical School, Hannover, Germany
| | - Christian Mühlfeld
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany.,Research Core Unit Electron Microscopy, Hannover Medical School, Hannover, Germany
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17
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Buchacker T, Mühlfeld C, Wrede C, Wagner WL, Beare R, McCormick M, Grothausmann R. Assessment of the Alveolar Capillary Network in the Postnatal Mouse Lung in 3D Using Serial Block-Face Scanning Electron Microscopy. Front Physiol 2019; 10:1357. [PMID: 31824323 PMCID: PMC6881265 DOI: 10.3389/fphys.2019.01357] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 10/14/2019] [Indexed: 12/20/2022] Open
Abstract
The alveolar capillary network (ACN) has a large surface area that provides the basis for an optimized gas exchange in the lung. It needs to adapt to morphological changes during early lung development and alveolarization. Structural alterations of the pulmonary vasculature can lead to pathological functional conditions such as in bronchopulmonary dysplasia and various other lung diseases. To understand the development of the ACN and its impact on the pathogenesis of lung diseases, methods are needed that enable comparative analyses of the complex three-dimensional structure of the ACN at different developmental stages and under pathological conditions. In this study a newborn mouse lung was imaged with serial block-face scanning electron microscopy (SBF-SEM) to investigate the ACN and its surrounding structures before the alveolarization process begins. Most parts but not all of the examined ACN contain two layers of capillaries, which were repeatedly connected with each other. A path from an arteriole to a venule was extracted and straightened to allow cross-sectional visualization of the data along the path within a plane. This allows a qualitative characterization of the structures that erythrocytes pass on their way through the ACN. One way to define regions of the ACN supplied by specific arterioles is presented and used for analyses. Pillars, possibly intussusceptive, were found in the vasculature but no specific pattern was observed in regard to parts of the saccular septa. This study provides 3D information with a resolution of about 150 nm on the microscopic structure of a newborn mouse lung and outlines some of the potentials and challenges of SBF-SEM for 3D analyses of the ACN.
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Affiliation(s)
- Tobias Buchacker
- Institute of Functional and Applied Anatomy, Medizinische Hochschule Hannover, Hanover, Germany.,Biomedical Research in Endstage and Obstructive Lung Research (BREATH), Member of the German Center for Lung Research, Hanover, Germany
| | - Christian Mühlfeld
- Institute of Functional and Applied Anatomy, Medizinische Hochschule Hannover, Hanover, Germany.,Biomedical Research in Endstage and Obstructive Lung Research (BREATH), Member of the German Center for Lung Research, Hanover, Germany.,REBIRTH Cluster of Excellence, Hanover, Germany
| | - Christoph Wrede
- Institute of Functional and Applied Anatomy, Medizinische Hochschule Hannover, Hanover, Germany.,Biomedical Research in Endstage and Obstructive Lung Research (BREATH), Member of the German Center for Lung Research, Hanover, Germany.,Research Core Unit Electron Microscopy, Hannover Medical School, Hanover, Germany
| | - Willi L Wagner
- Department of Diagnostic and Interventional Radiology (DIR), University of Heidelberg, Heidelberg, Germany.,Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany
| | - Richard Beare
- Department of Medicine, Monash University, Melbourne, VIC, Australia.,Developmental Imaging, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | | | - Roman Grothausmann
- Institute of Functional and Applied Anatomy, Medizinische Hochschule Hannover, Hanover, Germany.,Biomedical Research in Endstage and Obstructive Lung Research (BREATH), Member of the German Center for Lung Research, Hanover, Germany
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18
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Safa BN, Peloquin JM, Natriello JR, Caplan JL, Elliott DM. Helical fibrillar microstructure of tendon using serial block-face scanning electron microscopy and a mechanical model for interfibrillar load transfer. J R Soc Interface 2019; 16:20190547. [PMID: 31744419 DOI: 10.1098/rsif.2019.0547] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Tendon's hierarchical structure allows for load transfer between its fibrillar elements at multiple length scales. Tendon microstructure is particularly important, because it includes the cells and their surrounding collagen fibrils, where mechanical interactions can have potentially important physiological and pathological contributions. However, the three-dimensional (3D) microstructure and the mechanisms of load transfer in that length scale are not known. It has been postulated that interfibrillar matrix shear or direct load transfer via the fusion/branching of small fibrils are responsible for load transfer, but the significance of these mechanisms is still unclear. Alternatively, the helical fibrils that occur at the microstructural scale in tendon may also mediate load transfer; however, these structures are not well studied due to the lack of a three-dimensional visualization of tendon microstructure. In this study, we used serial block-face scanning electron microscopy to investigate the 3D microstructure of fibrils in rat tail tendon. We found that tendon fibrils have a complex architecture with many helically wrapped fibrils. We studied the mechanical implications of these helical structures using finite-element modelling and found that frictional contact between helical fibrils can induce load transfer even in the absence of matrix bonding or fibril fusion/branching. This study is significant in that it provides a three-dimensional view of the tendon microstructure and suggests friction between helically wrapped fibrils as a mechanism for load transfer, which is an important aspect of tendon biomechanics.
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Affiliation(s)
- Babak N Safa
- Department of Biomedical Engineering, University of Delaware, Newark, DE, USA.,Department of Mechanical Engineering, University of Delaware, Newark, DE, USA
| | - John M Peloquin
- Department of Biomedical Engineering, University of Delaware, Newark, DE, USA
| | - Jessica R Natriello
- Department of Biomedical Engineering, University of Delaware, Newark, DE, USA
| | - Jeffrey L Caplan
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.,Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Dawn M Elliott
- Department of Biomedical Engineering, University of Delaware, Newark, DE, USA
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19
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Melia CE, Peddie CJ, de Jong AWM, Snijder EJ, Collinson LM, Koster AJ, van der Schaar HM, van Kuppeveld FJM, Bárcena M. Origins of Enterovirus Replication Organelles Established by Whole-Cell Electron Microscopy. mBio 2019; 10:e00951-19. [PMID: 31186324 PMCID: PMC6561026 DOI: 10.1128/mbio.00951-19] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/06/2019] [Indexed: 11/24/2022] Open
Abstract
Enterovirus genome replication occurs at virus-induced structures derived from cellular membranes and lipids. However, the origin of these replication organelles (ROs) remains uncertain. Ultrastructural evidence of the membrane donor is lacking, suggesting that the sites of its transition into ROs are rare or fleeting. To overcome this challenge, we combined live-cell imaging and serial block-face scanning electron microscopy of whole cells to capture emerging enterovirus ROs. The first foci of fluorescently labeled viral protein correlated with ROs connected to the endoplasmic reticulum (ER) and preceded the appearance of ROs stemming from the trans-Golgi network. Whole-cell data sets further revealed striking contact regions between ROs and lipid droplets that may represent a route for lipid shuttling to facilitate RO proliferation and genome replication. Our data provide direct evidence that enteroviruses use ER and then Golgi membranes to initiate RO formation, demonstrating the remarkable flexibility with which enteroviruses usurp cellular organelles.IMPORTANCE Enteroviruses are causative agents of a range of human diseases. The replication of these viruses within cells relies on specialized membranous structures termed replication organelles (ROs) that form during infection but whose origin remains elusive. To capture the emergence of enterovirus ROs, we use correlative light and serial block-face scanning electron microscopy, a powerful method to pinpoint rare events in their whole-cell ultrastructural context. RO biogenesis was found to occur first at ER and then at Golgi membranes. Extensive contacts were found between early ROs and lipid droplets (LDs), which likely serve to provide LD-derived lipids required for replication. Together, these data establish the dual origin of enterovirus ROs and the chronology of their biogenesis at different supporting cellular membranes.
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Affiliation(s)
- Charlotte E Melia
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Anja W M de Jong
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Lucy M Collinson
- Electron Microscopy STP, The Francis Crick Institute, London, United Kingdom
| | - Abraham J Koster
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hilde M van der Schaar
- Virology Division, Faculty of Veterinary Medicine, Department of Infectious Diseases & Immunology, Utrecht University, Utrecht, The Netherlands
| | - Frank J M van Kuppeveld
- Virology Division, Faculty of Veterinary Medicine, Department of Infectious Diseases & Immunology, Utrecht University, Utrecht, The Netherlands
| | - Montserrat Bárcena
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
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20
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Mantani Y, Haruta T, Nishida M, Yokoyama T, Hoshi N, Kitagawa H. Three-dimensional analysis of fibroblast-like cells in the lamina propria of the rat ileum using serial block-face scanning electron microscopy. J Vet Med Sci 2019; 81:454-465. [PMID: 30700677 PMCID: PMC6451913 DOI: 10.1292/jvms.18-0654] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Serial block-face scanning electron microscopy (SBF-SEM) is useful for three-dimensional observation of tissues or cells at high-resolution. In this study, SBF-SEM was used to
three-dimensionally analyze the characteristics of fibroblast-like cells (FBLCs) in the rat ileal lamina propria (LP). The results revealed that FBLCs in LP could be divided into four types,
tentatively named FBLC type I-IV, based on the external cellular appearance, abundance or shape of each organelle, detailed distribution in the LP and relationship with surrounding cells.
FBLC-I and -II localized around the intestinal crypt (InC), FBLC-III localized from the lateral portion of InC to the apical portion of the intestinal villus (InV), and FBLC-IV localized in
the InV. FBLC-I, -II and -III, but not FBLC-IV, localized beneath the epithelium. FBLC-II possessed thin lamellar-shaped endoplasmic reticula, whereas FBLC-I possessed expanded endoplasmic
reticula that occasionally showed a spherical shape. FBLC-III and -IV possessed a cytoplasmic region with high-electron density and no organelles immediately beneath the cellular membrane;
this region was found at the epithelial sides in FBLC-III and scattered in FBLC-IV. FBLC-IV were in constant close proximity to villous myocytes throughout the InV and also in contact with
FBLC-III especially in the apical portion of the InV. FBLC-I, -II and -IV, but not -III, were constantly found to be in contact with various immunocompetent cells in the LP.
Three-dimensional analysis using SBF-SEM indicates that four types of FBLC localized in the rat ileal LP.
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Affiliation(s)
- Youhei Mantani
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Tomohiro Haruta
- Bio 3D Promotion Group, Application Management Department, JEOL Ltd., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Miho Nishida
- Laboratory of Animal Molecular Morphology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Toshifumi Yokoyama
- Laboratory of Animal Molecular Morphology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Nobuhiko Hoshi
- Laboratory of Animal Molecular Morphology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Hiroshi Kitagawa
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
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21
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Tsang TK, Bushong EA, Boassa D, Hu J, Romoli B, Phan S, Dulcis D, Su CY, Ellisman MH. High-quality ultrastructural preservation using cryofixation for 3D electron microscopy of genetically labeled tissues. eLife 2018; 7:35524. [PMID: 29749931 PMCID: PMC5988420 DOI: 10.7554/elife.35524] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/09/2018] [Indexed: 02/06/2023] Open
Abstract
Electron microscopy (EM) offers unparalleled power to study cell substructures at the nanoscale. Cryofixation by high-pressure freezing offers optimal morphological preservation, as it captures cellular structures instantaneously in their near-native state. However, the applicability of cryofixation is limited by its incompatibility with diaminobenzidine labeling using genetic EM tags and the high-contrast en bloc staining required for serial block-face scanning electron microscopy (SBEM). In addition, it is challenging to perform correlated light and electron microscopy (CLEM) with cryofixed samples. Consequently, these powerful methods cannot be applied to address questions requiring optimal morphological preservation. Here, we developed an approach that overcomes these limitations; it enables genetically labeled, cryofixed samples to be characterized with SBEM and 3D CLEM. Our approach is broadly applicable, as demonstrated in cultured cells, Drosophila olfactory organ and mouse brain. This optimization exploits the potential of cryofixation, allowing for quality ultrastructural preservation for diverse EM applications.
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Affiliation(s)
- Tin Ki Tsang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Eric A Bushong
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States
| | - Daniela Boassa
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States
| | - Junru Hu
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States
| | - Benedetto Romoli
- Department of Psychiatry, School of Medicine, University of California, San Diego, La Jolla, United States
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States
| | - Davide Dulcis
- Department of Psychiatry, School of Medicine, University of California, San Diego, La Jolla, United States
| | - Chih-Ying Su
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States.,Department of Neurosciences, School of Medicine, University of California, San Diego, La Jolla, United States
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22
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Napper RMA. Total Number Is Important: Using the Disector Method in Design-Based Stereology to Understand the Structure of the Rodent Brain. Front Neuroanat 2018; 12:16. [PMID: 29556178 PMCID: PMC5844935 DOI: 10.3389/fnana.2018.00016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 02/15/2018] [Indexed: 12/15/2022] Open
Abstract
The advantages of using design-based stereology in the collection of quantitative data, have been highlighted, in numerous publications, since the description of the disector method by Sterio (1984). This review article discusses the importance of total number derived with the disector method, as a key variable that must continue to be used to understand the rodent brain and that such data can be used to develop quantitative networks of the brain. The review article will highlight the huge impact total number has had on our understanding of the rodent brain and it will suggest that neuroscientists need to be aware of the increasing number of studies where density, not total number, is the quantitative measure used. It will emphasize that density can result in data that is misleading, most often in an unknown direction, and that we run the risk of this type of data being accepted into the collective neuroscience knowledge database. It will also suggest that design-based stereology using the disector method, can be used alongside recent developments in electron microscopy, such as serial block-face scanning electron microscopy (SEM), to obtain total number data very efficiently at the ultrastructural level. Throughout the article total number is discussed as a key parameter in understanding the micro-networks of the rodent brain as they can be represented as both anatomical and quantitative networks.
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Affiliation(s)
- Ruth M A Napper
- Brain Health Research Centre, Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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23
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Büsse S, Hörnschemeyer T, Fischer C. Three-dimensional reconstruction on cell level: case study elucidates the ultrastructure of the spinning apparatus of Embia sp. (Insecta: Embioptera). R Soc Open Sci 2016; 3:160563. [PMID: 27853574 PMCID: PMC5098999 DOI: 10.1098/rsos.160563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/09/2016] [Indexed: 06/06/2023]
Abstract
Spinning is a phenomenon not only present in spiders, but also in many other arthropods. The functional morphology and complexity of spinning organs is often poorly understood. Their elements are minute and studying them poses substantial methodological difficulties. This study presents a three-dimensional reconstruction of a silk gland of Embia sp. on cellular level, based on serial sections acquired with serial block-face scanning electron microscopy (SBFSEM) to showcase the power of this method. Previous studies achieved either high resolution to elucidate the ultrastructure or satisfying three-dimensional representations. The high-resolution achieved by SBFSEM can be easily used to reconstruct the three-dimensional ultrastructural organization of cellular structures. The herein investigated spinning apparatus of Embioptera can be taken as an example demonstrating the potential of this method. It was possible to reconstruct a multinucleated silk gland containing 63 nuclei. We focused on the applicability of this method in the field of morphological research and provide a step-by-step guide to the methodology. This will help in applying the method to other arthropod taxa and will help significantly in adapting the method to other animals, animal parts and tissues.
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Affiliation(s)
- Sebastian Büsse
- Department of Functional Morphology and Biomechanics, Institute of Zoology, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1–9, 24118 Kiel, Germany
- Department of Morphology, Systematics and Evolutionary Biology, J.- F.- Blumenbach Institute for Zoology and Anthropology, Georg-August-Universität Göttingen, Berliner Strasse 28, 37073 Göttingen, Germany
| | - Thomas Hörnschemeyer
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt, Germany
- Department of Morphology, Systematics and Evolutionary Biology, J.- F.- Blumenbach Institute for Zoology and Anthropology, Georg-August-Universität Göttingen, Berliner Strasse 28, 37073 Göttingen, Germany
| | - Christian Fischer
- Department of Morphology, Systematics and Evolutionary Biology, J.- F.- Blumenbach Institute for Zoology and Anthropology, Georg-August-Universität Göttingen, Berliner Strasse 28, 37073 Göttingen, Germany
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24
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Kremer A, Lippens S, Bartunkova S, Asselbergh B, Blanpain C, Fendrych M, Goossens A, Holt M, Janssens S, Krols M, Larsimont JC, Mc Guire C, Nowack MK, Saelens X, Schertel A, Schepens B, Slezak M, Timmerman V, Theunis C, VAN Brempt R, Visser Y, Guérin CJ. Developing 3D SEM in a broad biological context. J Microsc 2015; 259:80-96. [PMID: 25623622 PMCID: PMC4670703 DOI: 10.1111/jmi.12211] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/28/2014] [Indexed: 12/25/2022]
Abstract
When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions.
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Affiliation(s)
- A Kremer
- VIB Bio Imaging Core, Gent, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - S Lippens
- VIB Bio Imaging Core, Gent, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - S Bartunkova
- VIB Bio Imaging Core, Gent, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - B Asselbergh
- VIB Department of Molecular Genetics, Antwerp University, Antwerpen 2020, Belgium
| | - C Blanpain
- IRIBHM, Université Libre de Bruxelles, Brussels, B-1070, Belgium
| | - M Fendrych
- Department of Plant Systems Biology, VIB, Ghent, 9052, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.,Institute of Science and Technology (IST) Austria, Klosterneuburg, 3400, Austria
| | - A Goossens
- Department of Plant Systems Biology, VIB, Ghent, 9052, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - M Holt
- Center for the Biology of Disease, VIB, Leuven, Belgium.,Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - S Janssens
- Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Respiratory Medicine, Ghent University, Ghent, Belgium.,GROUP-ID Consortium, Ghent University and University Hospital, Ghent, Belgium
| | - M Krols
- Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,VIB Department of Molecular Genetics, Antwerp University, Antwerpen 2020, Belgium
| | - J-C Larsimont
- IRIBHM, Université Libre de Bruxelles, Brussels, B-1070, Belgium
| | - C Mc Guire
- Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - M K Nowack
- Department of Plant Systems Biology, VIB, Ghent, 9052, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - X Saelens
- Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - A Schertel
- Carl Zeiss Microscopy, GmbH, Oberkochen, Germany
| | - B Schepens
- Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - M Slezak
- Center for the Biology of Disease, VIB, Leuven, Belgium
| | - V Timmerman
- VIB Department of Molecular Genetics, Antwerp University, Antwerpen 2020, Belgium
| | - C Theunis
- Department of Intensive Care, Leiden University Medical Center, Leiden, The Netherlands.,Johnson and Johnson Pharmaceutical Research and Development, Beerse, Belgium
| | - R VAN Brempt
- Department of Intensive Care, Leiden University Medical Center, Leiden, The Netherlands.,Johnson and Johnson Pharmaceutical Research and Development, Beerse, Belgium
| | - Y Visser
- Department of Intensive Care, Leiden University Medical Center, Leiden, The Netherlands.,Johnson and Johnson Pharmaceutical Research and Development, Beerse, Belgium
| | - C J Guérin
- VIB Bio Imaging Core, Gent, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Inflammation Research Center, VIB, Technologiepark 927, Gent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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25
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Perez AJ, Seyedhosseini M, Deerinck TJ, Bushong EA, Panda S, Tasdizen T, Ellisman MH. A workflow for the automatic segmentation of organelles in electron microscopy image stacks. Front Neuroanat 2014; 8:126. [PMID: 25426032 PMCID: PMC4224098 DOI: 10.3389/fnana.2014.00126] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 10/19/2014] [Indexed: 11/13/2022] Open
Abstract
Electron microscopy (EM) facilitates analysis of the form, distribution, and functional status of key organelle systems in various pathological processes, including those associated with neurodegenerative disease. Such EM data often provide important new insights into the underlying disease mechanisms. The development of more accurate and efficient methods to quantify changes in subcellular microanatomy has already proven key to understanding the pathogenesis of Parkinson's and Alzheimer's diseases, as well as glaucoma. While our ability to acquire large volumes of 3D EM data is progressing rapidly, more advanced analysis tools are needed to assist in measuring precise three-dimensional morphologies of organelles within data sets that can include hundreds to thousands of whole cells. Although new imaging instrument throughputs can exceed teravoxels of data per day, image segmentation and analysis remain significant bottlenecks to achieving quantitative descriptions of whole cell structural organellomes. Here, we present a novel method for the automatic segmentation of organelles in 3D EM image stacks. Segmentations are generated using only 2D image information, making the method suitable for anisotropic imaging techniques such as serial block-face scanning electron microscopy (SBEM). Additionally, no assumptions about 3D organelle morphology are made, ensuring the method can be easily expanded to any number of structurally and functionally diverse organelles. Following the presentation of our algorithm, we validate its performance by assessing the segmentation accuracy of different organelle targets in an example SBEM dataset and demonstrate that it can be efficiently parallelized on supercomputing resources, resulting in a dramatic reduction in runtime.
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Affiliation(s)
- Alex J Perez
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA ; Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Mojtaba Seyedhosseini
- Scientific Computing and Imaging Institute, University of Utah Salt Lake City, UT, USA
| | - Thomas J Deerinck
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA
| | - Eric A Bushong
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA
| | - Satchidananda Panda
- Regulatory Biology Laboratory, Salk Institute for Biological Studies La Jolla, CA, USA
| | - Tolga Tasdizen
- Scientific Computing and Imaging Institute, University of Utah Salt Lake City, UT, USA
| | - Mark H Ellisman
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA ; Department of Bioengineering, University of California San Diego, La Jolla, CA, USA ; Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
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