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Zhao J, Yu X, Shentu X, Li D. The application and development of electron microscopy for three-dimensional reconstruction in life science: a review. Cell Tissue Res 2024; 396:1-18. [PMID: 38416172 DOI: 10.1007/s00441-024-03878-7] [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: 10/17/2023] [Accepted: 02/13/2024] [Indexed: 02/29/2024]
Abstract
Imaging technologies have played a pivotal role in advancing biological research by enabling visualization of biological structures and processes. While traditional electron microscopy (EM) produces two-dimensional images, emerging techniques now allow high-resolution three-dimensional (3D) characterization of specimens in situ, meeting growing needs in molecular and cellular biology. Combining transmission electron microscopy (TEM) with serial sectioning inaugurated 3D imaging, attracting biologists seeking to explore cell ultrastructure and driving advancement of 3D EM reconstruction. By comprehensively and precisely rendering internal structure and distribution, 3D TEM reconstruction provides unparalleled ultrastructural insights into cells and molecules, holding tremendous value for elucidating structure-function relationships and broadly propelling structural biology. Here, we first introduce the principle of 3D reconstruction of cells and tissues by classical approaches in TEM and then discuss modern technologies utilizing TEM and on new SEM-based as well as cryo-electron microscope (cryo-EM) techniques. 3D reconstruction techniques from serial sections, electron tomography (ET), and the recent single-particle analysis (SPA) are examined; the focused ion beam scanning electron microscopy (FIB-SEM), the serial block-face scanning electron microscopy (SBF-SEM), and automatic tape-collecting lathe ultramicrotome (ATUM-SEM) for 3D reconstruction of large volumes are discussed. Finally, we review the challenges and development prospects of these technologies in life science. It aims to provide an informative reference for biological researchers.
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Affiliation(s)
- Jingjing Zhao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China
| | - Xuping Shentu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China
| | - Danting Li
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China.
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2
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Hayashi S, Ohno N, Knott G, Molnár Z. Correlative light and volume electron microscopy to study brain development. Microscopy (Oxf) 2023; 72:279-286. [PMID: 36620906 DOI: 10.1093/jmicro/dfad002] [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: 11/30/2022] [Accepted: 01/06/2023] [Indexed: 01/10/2023] Open
Abstract
Recent advances in volume electron microscopy (EM) have been driving our thorough understanding of the brain architecture. Volume EM becomes increasingly powerful when cells and their subcellular structures that are imaged in light microscopy are correlated to those in ultramicrographs obtained with EM. This correlative approach, called correlative light and volume electron microscopy (vCLEM), is used to link three-dimensional ultrastructural information with physiological data such as intracellular Ca2+ dynamics. Genetic tools to express fluorescent proteins and/or an engineered form of a soybean ascorbate peroxidase allow us to perform vCLEM using natural landmarks including blood vessels without immunohistochemical staining. This immunostaining-free vCLEM has been successfully employed in two-photon Ca2+ imaging in vivo as well as in studying complex synaptic connections in thalamic neurons that receive a variety of specialized inputs from the cerebral cortex. In this mini-review, we overview how volume EM and vCLEM have contributed to studying the developmental processes of the brain. We also discuss potential applications of genetic manipulation of target cells using clustered regularly interspaced short palindromic repeats-associated protein 9 and subsequent volume EM to the analysis of protein localization as well as to loss-of-function studies of genes regulating brain development. We give examples for the combinatorial usage of genetic tools with vCLEM that will further enhance our understanding of regulatory mechanisms underlying brain development.
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Affiliation(s)
- Shuichi Hayashi
- Department of Anatomy, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
- Division of Ultrastructural Research, National Institute for Physiological Sciences, 5-1 Higashiyama Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Graham Knott
- Biological Electron Microscopy Facility, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, Lausanne CH-1015, Switzerland
| | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK
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3
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Electron tomography unravels new insights into fiber cell wall nanostructure; exploring 3D macromolecular biopolymeric nano-architecture of spruce fiber secondary walls. Sci Rep 2023; 13:2350. [PMID: 36759530 PMCID: PMC9911387 DOI: 10.1038/s41598-023-29113-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Lignocellulose biomass has a tremendous potential as renewable biomaterials for fostering the "bio-based society" and circular bioeconomy paradigm. It requires efficient use and breakdown of fiber cell walls containing mainly cellulose, hemicellulose and lignin biopolymers. Despite their great importance, there is an extensive debate on the true structure of fiber walls and knowledge on the macromolecular nano-organization is limited and remains elusive in 3D. We employed dual-axis electron tomography that allows visualization of previously unseen 3D macromolecular organization/biopolymeric nano-architecture of the secondary S2 layer of Norway spruce fiber wall. Unprecedented 3D nano-structural details with novel insights into cellulose microfibrils (~ 2 nm diameter), macrofibrils, nano-pore network and cell wall chemistry (volume %) across the S2 were explored and quantified including simulation of structure related permeability. Matrix polymer association with cellulose varied between microfibrils and macrofibrils with lignin directly associated with MFs. Simulated bio-nano-mechanical properties revealed stress distribution within the S2 and showed similar properties between the idealized 3D model and the native S2 (actual tomogram). Present work has great potential for significant advancements in lignocellulose research on nano-scale understanding of cell wall assembly/disassembly processes leading to more efficient industrial processes of functionalization, valorization and target modification technologies.
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Rajagopal V, Pinali C, Shiels HA. New revelations on the interplay between cardiomyocyte architecture and cardiomyocyte function in growth, health, and disease: a brief introduction. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210315. [PMID: 36189809 PMCID: PMC9527918 DOI: 10.1098/rstb.2021.0315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/26/2022] Open
Affiliation(s)
- Vijay Rajagopal
- Department of Biomedical Engineering, Faculty of Engineering and IT, The University of Melbourne, Victoria 3010, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Christian Pinali
- Division of Cardiovascular Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9NT, UK
| | - Holly A. Shiels
- Division of Cardiovascular Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9NT, UK
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5
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Weiner E, Pinskey JM, Nicastro D, Otegui MS. Electron microscopy for imaging organelles in plants and algae. PLANT PHYSIOLOGY 2022; 188:713-725. [PMID: 35235662 PMCID: PMC8825266 DOI: 10.1093/plphys/kiab449] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/23/2021] [Indexed: 05/31/2023]
Abstract
Recent developments in both instrumentation and image analysis algorithms have allowed three-dimensional electron microscopy (3D-EM) to increase automated image collections through large tissue volumes using serial block-face scanning EM (SEM) and to achieve near-atomic resolution of macromolecular complexes using cryo-electron tomography (cryo-ET) and sub-tomogram averaging. In this review, we discuss applications of cryo-ET to cell biology research on plant and algal systems and the special opportunities they offer for understanding the organization of eukaryotic organelles with unprecedently resolution. However, one of the most challenging aspects for cryo-ET is sample preparation, especially for multicellular organisms. We also discuss correlative light and electron microscopy (CLEM) approaches that have been developed for ET at both room and cryogenic temperatures.
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Affiliation(s)
- Ethan Weiner
- Department of Botany, University of Wisconsin, Madison 53706, Wisconsin
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison 53706, Wisconsin
| | - Justine M Pinskey
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas 75390, Texas
| | - Daniela Nicastro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas 75390, Texas
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin, Madison 53706, Wisconsin
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison 53706, Wisconsin
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6
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Electron tomography and immunogold labeling of plant cells. Methods Cell Biol 2020; 160:21-36. [PMID: 32896317 DOI: 10.1016/bs.mcb.2020.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Electron microscopy enables the imaging of organelles and macromolecular complexes within cells at nanometer scale resolution. Electron tomography of biological samples, either in vitrified ice or fixed and embedded in resin, provides three-dimensional structural information of relatively small volumes (a few cubic microns) of cells at axial resolutions of 1-7nm. This chapter discusses approaches for plant sample preparation by high-pressure freezing/freeze-substitution and resin-embedding for electron tomography and immunogold labeling using transmission electron microscopy.
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7
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Juneau M, Liu R, Peng Y, Malge A, Ma Z, Porosoff MD. Characterization of Metal‐zeolite Composite Catalysts: Determining the Environment of the Active Phase. ChemCatChem 2020. [DOI: 10.1002/cctc.201902039] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Mitchell Juneau
- Department of Chemical EngineeringUniversity of Rochester Rochester NY-14627 USA
| | - Renjie Liu
- Department of Chemical EngineeringUniversity of Rochester Rochester NY-14627 USA
| | - Yikang Peng
- Department of Chemical EngineeringUniversity of Rochester Rochester NY-14627 USA
| | - Akhilesh Malge
- Department of Chemical EngineeringUniversity of Rochester Rochester NY-14627 USA
| | - Zhiqiang Ma
- Department of Chemical EngineeringUniversity of Rochester Rochester NY-14627 USA
| | - Marc D. Porosoff
- Department of Chemical EngineeringUniversity of Rochester Rochester NY-14627 USA
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8
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Czymmek K, Sawant A, Goodman K, Pennington J, Pedersen P, Hoon M, Otegui MS. Imaging Plant Cells by High-Pressure Freezing and Serial block-face scanning electron microscopy. Methods Mol Biol 2020; 2177:69-81. [PMID: 32632806 DOI: 10.1007/978-1-0716-0767-1_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This chapter describes methods to enhanced contrast of plant material processed by high-pressure freezing and freeze substitution for improved visualization by serial block-face scanning electron microscopy (SBEM). The contrast enhancing steps are based on a protocol involving the sequential incubation of samples in heavy metals and sodium thiocarbohydrazide (OTO staining). We also describe the pipeline for imaging plant tissues in a commercial SBEM system (Gatan 3View®) and routines for the image analysis and three-dimensional reconstructions using open-source and commercial software packages.
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Affiliation(s)
- Kirk Czymmek
- Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Abhilash Sawant
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Kaija Goodman
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Janice Pennington
- Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Pal Pedersen
- Carl Zeiss Microscopy, LLC, White Plains, NY, USA
| | - Mrinalini Hoon
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA.
- Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, WI, USA.
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Guo J, Larabell CA. Soft X-ray tomography: virtual sculptures from cell cultures. Curr Opin Struct Biol 2019; 58:324-332. [PMID: 31495562 PMCID: PMC6791522 DOI: 10.1016/j.sbi.2019.06.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/24/2019] [Accepted: 06/27/2019] [Indexed: 12/20/2022]
Abstract
Cellular complexity is represented best in high-spatial resolution, three-dimensional (3D) reconstructions. Soft X-ray tomography (SXT) generates detailed volumetric reconstructions of cells preserved in a near-to-native, frozen-hydrated state. SXT is broadly applicable and can image specimens ranging from bacteria to large mammalian cells. As a reference, we summarize light and electron microscopic methods. We then present an overview of SXT and discuss its role in cellular imaging. We detail the methods used to image biological specimens and present recent highlights that illustrate the capabilities of the technique. We conclude by discussing correlative imaging, specifically the combination of SXT and fluorescence microscopy performed on the same specimen. This correlated approach combines the structural morphology of a cell with its physiological characteristics to build a deeply informative composite view.
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Affiliation(s)
- Jessica Guo
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Carolyn A Larabell
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
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10
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Otegui MS, Pennington JG. Electron tomography in plant cell biology. Microscopy (Oxf) 2019; 68:69-79. [PMID: 30452668 DOI: 10.1093/jmicro/dfy133] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/15/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022] Open
Abstract
Electron tomography (ET) approaches are based on the imaging of a biological specimen at different tilt angles by transmission electron microscopy (TEM). ET can be applied to both plastic-embedded and frozen samples. Technological advancements in TEM, direct electron detection, automated image collection, and imaging processing algorithms allow for 2-7-nm scale axial resolution in tomographic reconstructions of cells and organelles. In this review, we discussed the application of ET in plant cell biology and new opportunities for imaging plant cells by cryo-ET and other 3D electron microscopy approaches.
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Affiliation(s)
- Marisa S Otegui
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison WI, USA.,Laboratory of Molecular and Cellular Biology, University of Wisconsin-Madison, 1525 Linden Drive, Madison WI, USA.,Department of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison WI, USA
| | - Jannice G Pennington
- Institute for Molecular Virology, University of Wisconsin-Madison, 1525 Linden Drive, Madison WI, USA.,Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, USA
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11
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Drescher D, Büchner T, Guttmann P, Werner S, Schneider G, Kneipp J. X-ray tomography shows the varying three-dimensional morphology of gold nanoaggregates in the cellular ultrastructure. NANOSCALE ADVANCES 2019; 1:2937-2945. [PMID: 36133586 PMCID: PMC9418343 DOI: 10.1039/c9na00198k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/08/2019] [Indexed: 05/28/2023]
Abstract
The processing of nanoparticles inside eukaryotic cells is a key step in many wanted and unwanted nano-bio-interactions. In order to understand the effects and functions of the intracellular aggregates that are formed, their properties and their interaction with the biological matrix must be characterized. High quality synchrotron soft X-ray tomography (SXT) data were obtained from cells containing gold nanoparticles that are commonly applied as tools for optical probing or drug delivery. 3D volume rendering of both cellular organelles and the nanoparticle aggregates of different sizes in the intact cells of two cell lines reveals variation in localization, size, shape and density of the intracellular gold nanoaggregates. The dependence of such variation on incubation time and cell type, as well as on the influence of pre-aggregation of primary nanoparticles is shown. The SXT results provide a detailed picture of intracellular aggregation and will improve the design of safe and efficient nanoparticle platforms for biomedical use.
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Affiliation(s)
- Daniela Drescher
- Humboldt-Universität zu Berlin, Department of Chemistry Brook-Taylor-Str. 2 12489 Berlin Germany
| | - Tina Büchner
- Humboldt-Universität zu Berlin, Department of Chemistry Brook-Taylor-Str. 2 12489 Berlin Germany
| | - Peter Guttmann
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Research Group X-ray Microscopy Albert-Einstein-Str. 15 12489 Berlin Germany
| | - Stephan Werner
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Research Group X-ray Microscopy Albert-Einstein-Str. 15 12489 Berlin Germany
| | - Gerd Schneider
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Research Group X-ray Microscopy Albert-Einstein-Str. 15 12489 Berlin Germany
| | - Janina Kneipp
- Humboldt-Universität zu Berlin, Department of Chemistry Brook-Taylor-Str. 2 12489 Berlin Germany
- School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin Albert-Einstein-Str. 5-9 12489 Berlin Germany
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12
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Application of iterative reconstruction algorithms to mitigate CT-artefacts when measuring fiber reinforced polymer materials. POLYMER 2019. [DOI: 10.1016/j.polymer.2019.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Xie L, Song XJ, Liao ZF, Wu B, Yang J, Zhang H, Hong J. Endoplasmic reticulum remodeling induced by Wheat yellow mosaic virus infection studied by transmission electron microscopy. Micron 2019; 120:80-90. [PMID: 30807983 DOI: 10.1016/j.micron.2019.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/16/2019] [Accepted: 01/22/2019] [Indexed: 11/28/2022]
Abstract
Plant virus was a kind of organism lived depending on infecting viable host cell and propagated their posterity by replicating its hereditary nucleotide, transcripting into protein, assembling protein and nucleotide into virion (Ortín and Parra, 2006; Sanfaçon, 2005). Viral infection usually induces remodeling of host cell, especially endoplasmic reticulum (ER) for generating membrane packed viral factory. During the infection of Bymovirus, a kind of membranous body (MB) was generated in host cells, which is thought as an ER aggregate. In present study we performed a study on Wheat yellow mosaic virus (WYMV) induced MB by several transmission electron microscopy (TEM) based methods, including cytological observation, component analysis by immuno-gold labeling and structural analysis by electron tomography (ET). WYMV infection induced at least two morphologies of MB, including the lamella dominated morphology (lamella-MB) looked like sprawling cirrus, and the tubule dominated morphology (tubule-MB) looked like latticed network. MB was verified composing of ER as revealed by immuno-gold labeling by antibody against endoplasmic reticulum (ER) retention signal as well as by detailed observation of MB construction modules as double layer membrane. By immuno-gold labeling, both two MB morphologies (lamella-MB and tubule-MB) had same components in viral derived protein and membrane origination (from ER). Structural analysis by ET reconstruction revealed the organization of ER in MB. Lamella-MB was composed of cesER like structures arranged irregularly whereas tubule-MB was composed of tubER like structures arranged regularly. This study provided insights into the structural details in how Bymovirus utilizing host membrane system.
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Affiliation(s)
- Li Xie
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Xi-Jiao Song
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Zhen-Feng Liao
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Bin Wu
- Institute of plant protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
| | - Jian Yang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Hengmu Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Jian Hong
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou 310058, China.
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Vanhecke D, Rodríguez-Lorenzo L, Kinnear C, Durantie E, Rothen-Rutishauser B, Petri-Fink A. Assumption-free morphological quantification of single anisotropic nanoparticles and aggregates. NANOSCALE 2017; 9:4918-4927. [PMID: 28358404 DOI: 10.1039/c6nr07884b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Characterizing the morphometric parameters of noble metal nanoparticles for sensing and catalysis is a persistent challenge due to their small size and complex shape. Herein, we present an approach to determine the volume, surface area, and curvature of non-symmetric anisotropic nanoparticles using electron tomography and design-based stereology without the use of segmentation tools or modeling of the particles. Finally, we apply these tools to aggregates to estimate their fractal dimension.
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Affiliation(s)
- Dimitri Vanhecke
- University of Fribourg, Adolphe Merkle Institute, Ch. des Verdiers 4, Fribourg, Switzerland.
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15
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Mapping brain structure and function: cellular resolution, global perspective. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2017; 203:245-264. [PMID: 28341866 DOI: 10.1007/s00359-017-1163-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 12/23/2022]
Abstract
A comprehensive understanding of the brain requires analysis, although from a global perspective, with cellular, and even subcellular, resolution. An important step towards this goal involves the establishment of three-dimensional high-resolution brain maps, incorporating brain-wide information about the cells and their connections, as well as the chemical architecture. The progress made in such anatomical brain mapping in recent years has been paralleled by the development of physiological techniques that enable investigators to generate global neural activity maps, also with cellular resolution, while simultaneously recording the organism's behavioral activity. Combination of the high-resolution anatomical and physiological maps, followed by theoretical systems analysis of the deduced network, will offer unprecedented opportunities for a better understanding of how the brain, as a whole, processes sensory information and generates behavior.
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16
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Structure and components of the globular and filamentous viroplasms induced by Rice black-streaked dwarf virus. Micron 2017; 98:12-23. [PMID: 28359957 DOI: 10.1016/j.micron.2017.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 02/18/2017] [Accepted: 03/02/2017] [Indexed: 01/15/2023]
Abstract
Viroplasms of members of the family Reoviridae are considered to be viral factories for genome replication and virion assembly. Globular and filamentous phenotypes have different components and probably have different functions. We used transmission electron microscopy and electron tomography to examine the structure and components of the two viroplasm phenotypes induced by Rice black-streaked dwarf virus (RBSDV). Immuno-gold labeling was used to localize each of the 13 RBSDV encoded proteins as well as double-stranded RNA, host cytoskeleton actin-11 and α-tubulin. Ten of the RBSDV proteins were localized in one or both types of viroplasm. P5-1, P6 and P9-1 were localized on both viroplasm phenotypes but P5-1 was preferentially associated with filaments and P9-1 with the matrix. Structural analysis by electron tomography showed that osmiophilic granules 6-8nm in diameter served as the fundamental unit for constructing both of the viroplasm phenotypes but were more densely packed in the filamentous phenotype.
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17
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Hauser M, Wojcik M, Kim D, Mahmoudi M, Li W, Xu K. Correlative Super-Resolution Microscopy: New Dimensions and New Opportunities. Chem Rev 2017; 117:7428-7456. [PMID: 28045508 DOI: 10.1021/acs.chemrev.6b00604] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Correlative microscopy, the integration of two or more microscopy techniques performed on the same sample, produces results that emphasize the strengths of each technique while offsetting their individual weaknesses. Light microscopy has historically been a central method in correlative microscopy due to its widespread availability, compatibility with hydrated and live biological samples, and excellent molecular specificity through fluorescence labeling. However, conventional light microscopy can only achieve a resolution of ∼300 nm, undercutting its advantages in correlations with higher-resolution methods. The rise of super-resolution microscopy (SRM) over the past decade has drastically improved the resolution of light microscopy to ∼10 nm, thus creating exciting new opportunities and challenges for correlative microscopy. Here we review how these challenges are addressed to effectively correlate SRM with other microscopy techniques, including light microscopy, electron microscopy, cryomicroscopy, atomic force microscopy, and various forms of spectroscopy. Though we emphasize biological studies, we also discuss the application of correlative SRM to materials characterization and single-molecule reactions. Finally, we point out current limitations and discuss possible future improvements and advances. We thus demonstrate how a correlative approach adds new dimensions of information and provides new opportunities in the fast-growing field of SRM.
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Affiliation(s)
- Meghan Hauser
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Michal Wojcik
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Doory Kim
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Morteza Mahmoudi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Wan Li
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California , Berkeley, California 94720, United States.,Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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18
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Xie L, Shang W, Liu C, Zhang Q, Sunter G, Hong J, Zhou X. Mutual association of Broad bean wilt virus 2 VP37-derived tubules and plasmodesmata obtained from cytological observation. Sci Rep 2016; 6:21552. [PMID: 26903400 PMCID: PMC4763251 DOI: 10.1038/srep21552] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/19/2016] [Indexed: 01/25/2023] Open
Abstract
The movement protein VP37 of broad bean wilt virus 2 (BBWV 2) forms tubules in the plasmodesmata (PD) for the transport of virions between cells. This paper reports a mutual association between the BBWV 2 VP37-tubule complex and PD at the cytological level as determined by transmission electron microscopy. The generation of VP37-tubules within different PD leads to a different occurrence frequency as well as different morphology lines of virus-like particles. In addition, the frequency of VP37-tubules was different between PD found at different cellular interfaces, as well as between single-lined PD and branched PD. VP37-tubule generation also induced structural alterations of PD as well as modifications to the cell wall (CW) in the vicinity of the PD. A structural comparison using three-dimensional (3D) electron tomography (ET), determined that desmotubule structures found in the center of normal PD were absent in PD containing VP37-tubules. Using gold labeling, modification of the CW by callose deposition and cellulose reduction was observable on PD containing VP37-tubule. These cytological observations provide evidence of a mutual association of MP-derived tubules and PD in a natural host, improving our fundamental understanding of interactions between viral MP and PD that result in intercellular movement of virus particles.
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Affiliation(s)
- Li Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.,Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Weina Shang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chengke Liu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qinfen Zhang
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Garry Sunter
- Department of Biology, University of Texas at San Antonio, San Antonio TX 78249, USA
| | - Jian Hong
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.,Center of Analysis and Measurement, Zhejiang University, Hangzhou 310029, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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19
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Efficient Extraction of Macromolecular Complexes from Electron Tomograms Based on Reduced Representation Templates. COMPUTER ANALYSIS OF IMAGES AND PATTERNS : PROCEEDINGS OF THE ... INTERNATIONAL CONFERENCE ON AUTOMATIC IMAGE PROCESSING. INTERNATIONAL CONFERENCE ON AUTOMATIC IMAGE PROCESSING 2015; 9256:423-431. [PMID: 30058003 DOI: 10.1007/978-3-319-23192-1_35] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Electron tomography is the most widely applicable method for obtaining 3D information by electron microscopy. In the field of biology it has been realized that electron tomography is capable of providing a complete, molecular resolution three-dimensional mapping of entire proteoms. However, to realize this goal, information needs to be extracted efficiently from these tomograms. Owing to extremely low signal-to-noise ratios, this task is mostly carried out manually. Standard template matching approaches tend to generate large amounts of false positives. We developed an alternative method for feature extraction in biological electron tomography based on reduced representation templates, approximating the search model by a small number of anchor points used to calculate the scoring function. Using this approach we see a reduction of about 50% false positives with matched-filter approaches to below 5%. At the same time, false negatives stay below 5%, thus essentially matching the performance one would expect from human operators.
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20
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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] [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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21
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Paridaen JT, Huttner WB, Wilsch-Bräuninger M. Analysis of primary cilia in the developing mouse brain. Methods Cell Biol 2015; 127:93-129. [DOI: 10.1016/bs.mcb.2014.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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22
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Compensation of missing wedge effects with sequential statistical reconstruction in electron tomography. PLoS One 2014; 9:e108978. [PMID: 25279759 PMCID: PMC4184818 DOI: 10.1371/journal.pone.0108978] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 08/25/2014] [Indexed: 11/19/2022] Open
Abstract
Electron tomography (ET) of biological samples is used to study the organization and the structure of the whole cell and subcellular complexes in great detail. However, projections cannot be acquired over full tilt angle range with biological samples in electron microscopy. ET image reconstruction can be considered an ill-posed problem because of this missing information. This results in artifacts, seen as the loss of three-dimensional (3D) resolution in the reconstructed images. The goal of this study was to achieve isotropic resolution with a statistical reconstruction method, sequential maximum a posteriori expectation maximization (sMAP-EM), using no prior morphological knowledge about the specimen. The missing wedge effects on sMAP-EM were examined with a synthetic cell phantom to assess the effects of noise. An experimental dataset of a multivesicular body was evaluated with a number of gold particles. An ellipsoid fitting based method was developed to realize the quantitative measures elongation and contrast in an automated, objective, and reliable way. The method statistically evaluates the sub-volumes containing gold particles randomly located in various parts of the whole volume, thus giving information about the robustness of the volume reconstruction. The quantitative results were also compared with reconstructions made with widely-used weighted backprojection and simultaneous iterative reconstruction technique methods. The results showed that the proposed sMAP-EM method significantly suppresses the effects of the missing information producing isotropic resolution. Furthermore, this method improves the contrast ratio, enhancing the applicability of further automatic and semi-automatic analysis. These improvements in ET reconstruction by sMAP-EM enable analysis of subcellular structures with higher three-dimensional resolution and contrast than conventional methods.
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23
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Xie L, Lv MF, Zhang HM, Yang J, Li JM, Chen JP. Tumours induced by a plant virus are derived from vascular tissue and have multiple intercellular gateways that facilitate virus movement. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4873-4886. [PMID: 24987015 DOI: 10.1093/jxb/eru254] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Structural studies showed that tumours induced by Southern rice black-streaked dwarf virus (SRBSDV; genus Fijivirus, family Reoviridae) were highly organized, modified phloem, composed of sclerenchyma, vessels, hyperplastic phloem parenchyma and sieve elements (SEs). Only parenchyma and SEs were invaded by the virus. There was a special region that consisted exclusively of SEs without the usual companion cells and a new flexible type of intercellular gateway was observed on all SE-SE interfaces in this region. These flexible gateways significantly increased the intercellular contacts and thus enhanced potential symplastic transport in the tumour. Flexible gateways were structurally similar to compressed plasmodesmata but were able to accommodate complete SRBSDV virions (~80 nm diameter). Virions were also found in sieve-pore gateways, providing strong evidence for the movement of a virus with large virions within phloem tissue and suggesting that the unusual neovascularization of plant virus-induced tumours facilitated virus spread. A working model for the spread of tumour-inducing reoviruses in plants is presented.
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Affiliation(s)
- Li Xie
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Plant Protection and Biotechnology, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ming-Fang Lv
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Plant Protection and Biotechnology, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Heng-Mu Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Plant Protection and Biotechnology, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Yang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Plant Protection and Biotechnology, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jun-Min Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Plant Protection and Biotechnology, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian-Ping Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Plant Protection and Biotechnology, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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24
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Peddie CJ, Collinson LM. Exploring the third dimension: Volume electron microscopy comes of age. Micron 2014; 61:9-19. [DOI: 10.1016/j.micron.2014.01.009] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/30/2014] [Accepted: 01/30/2014] [Indexed: 12/12/2022]
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25
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Doroquez DB, Berciu C, Anderson JR, Sengupta P, Nicastro D. A high-resolution morphological and ultrastructural map of anterior sensory cilia and glia in Caenorhabditis elegans. eLife 2014; 3:e01948. [PMID: 24668170 PMCID: PMC3965213 DOI: 10.7554/elife.01948] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 02/17/2014] [Indexed: 12/22/2022] Open
Abstract
Many primary sensory cilia exhibit unique architectures that are critical for transduction of specific sensory stimuli. Although basic ciliogenic mechanisms are well described, how complex ciliary structures are generated remains unclear. Seminal work performed several decades ago provided an initial but incomplete description of diverse sensory cilia morphologies in C. elegans. To begin to explore the mechanisms that generate these remarkably complex structures, we have taken advantage of advances in electron microscopy and tomography, and reconstructed three-dimensional structures of fifty of sixty sensory cilia in the C. elegans adult hermaphrodite at high resolution. We characterize novel axonemal microtubule organization patterns, clarify structural features at the ciliary base, describe new aspects of cilia-glia interactions, and identify structures suggesting novel mechanisms of ciliary protein trafficking. This complete ultrastructural description of diverse cilia in C. elegans provides the foundation for investigations into underlying ciliogenic pathways, as well as contributions of defined ciliary structures to specific neuronal functions. DOI: http://dx.doi.org/10.7554/eLife.01948.001.
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Affiliation(s)
- David B Doroquez
- Department of Biology, Brandeis University, Waltham, United States
- National Center for Behavioral Genomics, Brandeis University, Waltham, United States
| | - Cristina Berciu
- Department of Biology, Brandeis University, Waltham, United States
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States
| | - James R Anderson
- Department of Ophthalmology, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, United States
| | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, United States
- National Center for Behavioral Genomics, Brandeis University, Waltham, United States
| | - Daniela Nicastro
- Department of Biology, Brandeis University, Waltham, United States
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States
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26
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Redemann S, Weber B, Möller M, Verbavatz JM, Hyman AA, Baum D, Prohaska S, Müller-Reichert T. The segmentation of microtubules in electron tomograms using Amira. Methods Mol Biol 2014; 1136:261-278. [PMID: 24633801 DOI: 10.1007/978-1-4939-0329-0_12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The development of automatic tools for the three-dimensional reconstruction of the microtubule cytoskeleton is crucial for large-scale analysis of mitotic spindles. Recently, we have published a method for the semiautomatic tracing of microtubules based on 3D template matching (Weber et al., J Struct Biol 178:129-138, 2012). Here, we give step-by-step instructions for the automatic tracing of microtubules emanating from centrosomes in the early mitotic Caenorhabditis elegans embryo. This approach, integrated in the visualization and data analysis software Amira, is applicable to tomographic data sets from other model systems.
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Affiliation(s)
- Stefanie Redemann
- Experimental Center, Medical Faculty Carl Gustav Carus , Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
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27
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Dynamical Aspects of Biomacromolecular Multi-resolution Modelling Using the UltraScan Solution Modeler (US-SOMO) Suite. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/978-94-017-8550-1_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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28
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Nunez-Iglesias J, Vitaladevuni S, Scheffer L, Bolorizadeh M, Hess H, Fetter R, Chklovskii DB. Electron Microscopy Reconstruction of Brain Structure Using Sparse Representations Over Learned Dictionaries. IEEE TRANSACTIONS ON MEDICAL IMAGING 2013; 32:2179-2188. [PMID: 23925366 DOI: 10.1109/tmi.2013.2276018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A central problem in neuroscience is reconstructing neuronal circuits on the synapse level. Due to a wide range of scales in brain architecture such reconstruction requires imaging that is both high-resolution and high-throughput. Existing electron microscopy (EM) techniques possess required resolution in the lateral plane and either high-throughput or high depth resolution but not both. Here, we exploit recent advances in unsupervised learning and signal processing to obtain high depth-resolution EM images computationally without sacrificing throughput. First, we show that the brain tissue can be represented as a sparse linear combination of localized basis functions that are learned using high-resolution datasets. We then develop compressive sensing-inspired techniques that can reconstruct the brain tissue from very few (typically five) tomographic views of each section. This enables tracing of neuronal processes and, hence, high throughput reconstruction of neural circuits on the level of individual synapses.
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29
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Brookes E, Pérez J, Cardinali B, Profumo A, Vachette P, Rocco M. Fibrinogen species as resolved by HPLC-SAXS data processing within the UltraScan Solution Modeler ( US-SOMO) enhanced SAS module. J Appl Crystallogr 2013; 46:1823-1833. [PMID: 24282333 PMCID: PMC3831300 DOI: 10.1107/s0021889813027751] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/09/2013] [Indexed: 12/04/2022] Open
Abstract
Fibrinogen is a large heterogeneous aggregation/degradation-prone protein playing a central role in blood coagulation and associated pathologies, whose structure is not completely resolved. When a high-molecular-weight fraction was analyzed by size-exclusion high-performance liquid chromatography/small-angle X-ray scattering (HPLC-SAXS), several composite peaks were apparent and because of the stickiness of fibrinogen the analysis was complicated by severe capillary fouling. Novel SAS analysis tools developed as a part of the UltraScan Solution Modeler (US-SOMO; http://somo.uthscsa.edu/), an open-source suite of utilities with advanced graphical user interfaces whose initial goal was the hydrodynamic modeling of biomacromolecules, were implemented and applied to this problem. They include the correction of baseline drift due to the accumulation of material on the SAXS capillary walls, and the Gaussian decomposition of non-baseline-resolved HPLC-SAXS elution peaks. It was thus possible to resolve at least two species co-eluting under the fibrinogen main monomer peak, probably resulting from in-column degradation, and two others under an oligomers peak. The overall and cross-sectional radii of gyration, molecular mass and mass/length ratio of all species were determined using the manual or semi-automated procedures available within the US-SOMO SAS module. Differences between monomeric species and linear and sideways oligomers were thus identified and rationalized. This new US-SOMO version additionally contains several computational and graphical tools, implementing functionalities such as the mapping of residues contributing to particular regions of P(r), and an advanced module for the comparison of primary I(q) versus q data with model curves computed from atomic level structures or bead models. It should be of great help in multi-resolution studies involving hydrodynamics, solution scattering and crystallographic/NMR data.
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Affiliation(s)
- Emre Brookes
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA
| | - Javier Pérez
- Beamline SWING, Synchrotron SOLEIL, L’Orme des Merisiers, BP48, Saint-Aubin, Gif sur Yvette, France
| | - Barbara Cardinali
- Biopolimeri e Proteomica, IRCCS AOU San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aldo Profumo
- Biopolimeri e Proteomica, IRCCS AOU San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Patrice Vachette
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, CNRS UMR 8619, UPS 11, Orsay, France
- Université Paris-Sud 11, Bâtiment 430, Orsay, France
| | - Mattia Rocco
- Biopolimeri e Proteomica, IRCCS AOU San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
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30
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Cougot N, Molza AE, Delesques J, Giudice E, Cavalier A, Rolland JP, Ermel G, Blanco C, Thomas D, Gillet R. Visualizing compaction of polysomes in bacteria. J Mol Biol 2013; 426:377-88. [PMID: 24095898 DOI: 10.1016/j.jmb.2013.09.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 09/25/2013] [Accepted: 09/25/2013] [Indexed: 10/26/2022]
Abstract
During protein synthesis, many translating ribosomes are bound together with an mRNA molecule to form polysomes (or polyribosomes). While the spatial organization of bacterial polysomes has been well studied in vitro, little is known about how they cluster when cellular conditions are highly constrained. To better understand this, we used electron tomography, template matching, and three-dimensional modeling to analyze the supramolecular network of ribosomes after induction of translational pauses. In Escherichia coli, we overexpressed an mRNA carrying a polyproline motif known to induce pausing during translation. When working with a strain lacking transfer-messenger RNA, the principle actor in the "trans-translation" rescuing system, the cells survived the hijacking of the translation machinery but this resulted in a sharp modification of the ribosomal network. The results of our experiments demonstrate that single ribosomes are replaced with large amounts of compacted polysomes. These polysomes are highly organized, principally forming hairpins and dimers of hairpins that stack together. We propose that these spatial arrangements help maintain translation efficiency when the rescue systems are absent or overwhelmed.
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Affiliation(s)
- Nicolas Cougot
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Anne-Elisabeth Molza
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Jérémy Delesques
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Emmanuel Giudice
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Annie Cavalier
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Jean-Paul Rolland
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Gwennola Ermel
- Université de Rennes 1, EA 1254, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Carlos Blanco
- Université de Rennes 1, EA 1254, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Daniel Thomas
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Reynald Gillet
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France; Institut Universitaire de France.
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31
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Cougot N, Molza AE, Giudice E, Cavalier A, Thomas D, Gillet R. Structural organization of the polysomes adjacent to mammalian processing bodies (P-bodies). RNA Biol 2013; 10:314-20. [PMID: 23324601 DOI: 10.4161/rna.23342] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A finely tuned balance of translation, storage and decay of mRNAs (mRNAs) is important for the regulation of gene expression. In eukaryotic cells, this takes place in dynamic cytoplasmic RNA-protein granules termed Processing bodies (P-bodies). In this study, by using immunoelectron tomography, 3D modeling and template matching, we analyze the size and the organization of the polysomes in the vicinity of human P-bodies. Our results show the presence of several polysomes that are compatible with a translational activity around P-bodies. Therefore, movement of mRNAs between polysomes and P-bodies can take place when the two compartments are in close contact. The presence of initiation factors in the proximity of P-bodies also suggests that translation of mRNAs can resume at the periphery of these granules.
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Affiliation(s)
- Nicolas Cougot
- Université de Rennes 1, UMR, CNRS 6290 IGDR, Translation and Folding Team, Campus de Beaulieu, Rennes Cedex, France
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Strunk KM, Wang K, Ke D, Gray JL, Zhang P. Thinning of large mammalian cells for cryo-TEM characterization by cryo-FIB milling. J Microsc 2013; 247:220-7. [PMID: 22906009 DOI: 10.1111/j.1365-2818.2012.03635.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Focused ion beam milling at cryogenic temperatures (cryo-FIB) is a valuable tool that can be used to thin vitreous biological specimens for subsequent imaging and analysis by cryo-transmission electron microscopy (cryo-TEM) in a frozen-hydrated state. This technique offers the potential benefit of eliminating the mechanical artefacts that are typically found with cryo-ultramicrotomy. However, due to the additional complexity in transferring samples in and out of the FIB, contamination and devitrification of the amorphous ice is commonly encountered. To address these problems, we have designed a sample cryo-shuttle that directly and specifically accepts Polara TEM cartridges to simplify the transfer process between FIB and TEM. We optimized several parameters in the cryo-FIB and cryo-TEM processes using the quality of the samples' ice as an indicator and demonstrated high-quality milling with large mammalian cells. By comparing the results from HeLa cells to those from Escherichia coli cells, we discuss some of the artefacts and challenges we have encountered using this technique.
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Affiliation(s)
- K M Strunk
- Department of Mechanical Engineering and Materials Science, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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Chakravadhanula VSK, Kübel C, Hrkac T, Zaporojtchenko V, Strunskus T, Faupel F, Kienle L. Surface segregation in TiO2-based nanocomposite thin films. NANOTECHNOLOGY 2012; 23:495701. [PMID: 23150221 DOI: 10.1088/0957-4484/23/49/495701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The morphology of nanocomposites plays a pivotal role in understanding their functionality and determines their capabilities for applications. The use of nanocomposite coatings requires a study of the size effects on their functional properties. Noble metal nanoparticles are promising candidates for nanocomposite thin film applications due to their antibacterial, plasmonic and photocatalytic properties. In this contribution, the morphology of Ag-TiO(2) and Au-TiO(2) nanocomposite thin films has been investigated experimentally using electron tomography in transmission electron microscopy in combination with UV/vis spectroscopy. Based on the additional 3D information obtained from tomography, we propose a two-step model towards the observed bimodal particle size in these nanocomposite thin films prepared by co-sputtering from two different sources. Furthermore, we show that the optical properties exhibit a well-defined relation with the morphology of the nanocomposite thin films. The present investigations demonstrate the potential of electron tomography for revealing the complex structure and formation processes of functional nanocomposites.
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Affiliation(s)
- Venkata Sai Kiran Chakravadhanula
- Institute for Materials Science, Synthesis and Real Structure, Faculty of Engineering, Christian Albrechts University of Kiel, Kiel, Germany
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34
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Immuno EM–OM correlative microscopy in solution by atmospheric scanning electron microscopy (ASEM). J Struct Biol 2012; 180:259-70. [DOI: 10.1016/j.jsb.2012.08.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 08/01/2012] [Accepted: 08/07/2012] [Indexed: 12/12/2022]
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35
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You YW, Chang HY, Liao HY, Kao WL, Yen GJ, Chang CJ, Tsai MH, Shyue JJ. Electron tomography of HEK293T cells using scanning electron microscope-based scanning transmission electron microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2012; 18:1037-1042. [PMID: 23026379 DOI: 10.1017/s1431927612001158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Based on a scanning electron microscope operated at 30 kV with a homemade specimen holder and a multiangle solid-state detector behind the sample, low-kV scanning transmission electron microscopy (STEM) is presented with subsequent electron tomography for three-dimensional (3D) volume structure. Because of the low acceleration voltage, the stronger electron-atom scattering leads to a stronger contrast in the resulting image than standard TEM, especially for light elements. Furthermore, the low-kV STEM yields less radiation damage to the specimen, hence the structure can be preserved. In this work, two-dimensional STEM images of a 1-μm-thick cell section with projection angles between ±50° were collected, and the 3D volume structure was reconstructed using the simultaneous iterative reconstructive technique algorithm with the TomoJ plugin for ImageJ, which are both public domain software. Furthermore, the cross-sectional structure was obtained with the Volume Viewer plugin in ImageJ. Although the tilting angle is constrained and limits the resulting structural resolution, slicing the reconstructed volume generated the depth profile of the thick specimen with sufficient resolution to examine cellular uptake of Au nanoparticles, and the final position of these nanoparticles inside the cell was imaged.
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Affiliation(s)
- Yun-Wen You
- Research Center for Applied Sciences, Academia Sinica, Taipei 115, Taiwan
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36
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Badia-Martinez D, Peralta B, Andrés G, Guerra M, Gil-Carton D, Abrescia NG. Three-dimensional visualization of forming Hepatitis C virus-like particles by electron-tomography. Virology 2012; 430:120-6. [DOI: 10.1016/j.virol.2012.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/02/2012] [Accepted: 05/06/2012] [Indexed: 12/17/2022]
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3D structure determination of native mammalian cells using cryo-FIB and cryo-electron tomography. J Struct Biol 2012; 180:318-26. [PMID: 22796867 DOI: 10.1016/j.jsb.2012.07.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 07/02/2012] [Accepted: 07/03/2012] [Indexed: 11/23/2022]
Abstract
Cryo-electron tomography (cryo-ET) has enabled high resolution three-dimensional(3D) structural analysis of virus and host cell interactions and many cell signaling events; these studies, however, have largely been limited to very thin, peripheral regions of eukaryotic cells or to small prokaryotic cells. Recent efforts to make thin, vitreous sections using cryo-ultramicrotomy have been successful, however,this method is technically very challenging and with many artifacts. Here, we report a simple and robust method for creating in situ, frozen-hydrated cell lamellas using a focused ion beam at cryogenic temperature (cryo-FIB), allowing access to any interior cellular regions of interest. We demonstrate the utility of cryo-FIB with high resolution 3D cellular structures from both bacterial cells and large mammalian cells. The method will not only facilitate high-throughput 3D structural analysis of biological specimens, but is also broadly applicable to sample preparation of thin films and surface materials without the need for FIB "lift-out".
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38
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Jiménez N, Post JA. A Novel Approach for Intracellular 3D Immuno-Labeling for Electron Tomography. Traffic 2012; 13:926-33. [DOI: 10.1111/j.1600-0854.2012.01363.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 04/04/2012] [Accepted: 04/09/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Nuria Jiménez
- Department of Biomolecular Imaging; Institute of Biomembranes, Utrecht University; Padualaan 8; Utrecht; 3584 CH; The Netherlands
| | - Jan Andries Post
- Department of Biomolecular Imaging; Institute of Biomembranes, Utrecht University; Padualaan 8; Utrecht; 3584 CH; The Netherlands
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Alloyeau D. Transmission Electron Microscopy: A Multifunctional Tool for the Atomic-scale Characterization of Nanoalloys. NANOALLOYS 2012. [DOI: 10.1007/978-1-4471-4014-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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D-CAT: Density and Clustering Annotation Tool for three dimensional electron microscopic volumes. J Struct Biol 2011; 177:571-7. [PMID: 22173221 DOI: 10.1016/j.jsb.2011.11.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 11/28/2011] [Accepted: 11/30/2011] [Indexed: 11/21/2022]
Abstract
Three dimensional (3D) electron microscopy techniques have become valuable tools for investigating cellular architecture and the processes that govern it. A vast amount of information is available in every 3D tomogram but the options for presenting this information in a clear and visually appealing way are limited. To address this, we developed D-CAT; a MatLab-application to accurately visualize the distribution of membrane proteins and/or membrane-bound structures. Presence (density) and distribution (clustering, depletion) are presented as color-coded areas on membranes. By using IMOD models both as input and output format, we ensure that the application fits within workflows common in the field of 3D electron microscopy.
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Eshar S, Dahan-Pasternak N, Weiner A, Dzikowski R. High resolution 3D perspective of Plasmodium biology: advancing into a new era. Trends Parasitol 2011; 27:548-54. [DOI: 10.1016/j.pt.2011.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/01/2011] [Accepted: 08/03/2011] [Indexed: 11/30/2022]
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Fogarty KH, Zhang W, Grigsby IF, Johnson JL, Chen Y, Mueller JD, Mansky LM. New insights into HTLV-1 particle structure, assembly, and Gag-Gag interactions in living cells. Viruses 2011; 3:770-93. [PMID: 21994753 PMCID: PMC3185773 DOI: 10.3390/v3060770] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 05/20/2011] [Accepted: 05/20/2011] [Indexed: 11/16/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) has a reputation for being extremely difficult to study in cell culture. The challenges in propagating HTLV-1 has prevented a rigorous analysis of how these viruses replicate in cells, including the detailed steps involved in virus assembly. The details for how retrovirus particle assembly occurs are poorly understood, even for other more tractable retroviral systems. Recent studies on HTLV-1 using state-of-the-art cryo-electron microscopy and fluorescence-based biophysical approaches explored questions related to HTLV-1 particle size, Gag stoichiometry in virions, and Gag-Gag interactions in living cells. These results provided new and exciting insights into fundamental aspects of HTLV-1 particle assembly-which are distinct from those of other retroviruses, including HIV-1. The application of these and other novel biophysical approaches promise to provide exciting new insights into HTLV-1 replication.
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Affiliation(s)
- Keir H. Fogarty
- Institute for Molecular Virology, University of Minnesota, Minneapolis, 18-242 Moos Tower, 515 Delaware St. SE, Minneapolis, MN 55455, USA; E-Mails: (K.H.F.); (W.Z.); (I.F.G.); (Y.C.); (J.D.M.)
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; E-Mail: (J.L.J.)
| | - Wei Zhang
- Institute for Molecular Virology, University of Minnesota, Minneapolis, 18-242 Moos Tower, 515 Delaware St. SE, Minneapolis, MN 55455, USA; E-Mails: (K.H.F.); (W.Z.); (I.F.G.); (Y.C.); (J.D.M.)
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Iwen F. Grigsby
- Institute for Molecular Virology, University of Minnesota, Minneapolis, 18-242 Moos Tower, 515 Delaware St. SE, Minneapolis, MN 55455, USA; E-Mails: (K.H.F.); (W.Z.); (I.F.G.); (Y.C.); (J.D.M.)
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jolene L. Johnson
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; E-Mail: (J.L.J.)
| | - Yan Chen
- Institute for Molecular Virology, University of Minnesota, Minneapolis, 18-242 Moos Tower, 515 Delaware St. SE, Minneapolis, MN 55455, USA; E-Mails: (K.H.F.); (W.Z.); (I.F.G.); (Y.C.); (J.D.M.)
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; E-Mail: (J.L.J.)
| | - Joachim D. Mueller
- Institute for Molecular Virology, University of Minnesota, Minneapolis, 18-242 Moos Tower, 515 Delaware St. SE, Minneapolis, MN 55455, USA; E-Mails: (K.H.F.); (W.Z.); (I.F.G.); (Y.C.); (J.D.M.)
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; E-Mail: (J.L.J.)
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Louis M. Mansky
- Institute for Molecular Virology, University of Minnesota, Minneapolis, 18-242 Moos Tower, 515 Delaware St. SE, Minneapolis, MN 55455, USA; E-Mails: (K.H.F.); (W.Z.); (I.F.G.); (Y.C.); (J.D.M.)
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Microbiology, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
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Telocytes in pleura: two- and three-dimensional imaging by transmission electron microscopy. Cell Tissue Res 2010; 343:389-97. [PMID: 21174125 PMCID: PMC3032227 DOI: 10.1007/s00441-010-1095-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 11/18/2010] [Indexed: 01/26/2023]
Abstract
Information about the ultrastructure of connective (interstitial) cells supporting the pleural mesothelium is scarce. Our aim has been to examine whether telocytes (TCs) are present in pleura, as in epicardium and mesentery. TCs are a distinct type of cell, characterized by specific prolongations named telopodes (Tp). We have used transmission electron microscopy (TEM) and electron tomography (ET) to determine whether ultrastructural diagnostic criteria accepted for TCs are fulfilled by any of the cell subpopulations existing in the sub-mesothelial layer in mouse and human pleura. TCs have been identified with TEM by their characteristic prolongations. Tp appear long and moniliform, because of the alternation of podomeres (thin segments of less than 0.2 μm) and podoms (small dilations accommodating caveolae, mitochondria, and endoplasmic reticulum). Tp ramifications follow a dichotomic pattern and establish specialized cell-to-cell junctional complexes. TCs, via their Tp, seem to form an interstitial network beneath the mesothelium, covering about two-thirds of the abluminal mesothelial layer. ET has revealed complex junctional structures and tight junctions connecting pleural TCs, and small vesicles at this level in Tp. Thus, pleural TCs share significant similarities with TCs described in other serosae. Whether TCs are a (major) player in mesothelial-cell-induced tissue repair remains to be established. Nevertheless, the extremely long thin Tp and complex junctional structures that they form and the release of vesicles (or exosomes) indicate the participation of TCs in long-distance homo- or heterocellular communication.
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45
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Three-dimensional reconstruction of nucleolar components by electron microscope tomography. Methods Mol Biol 2010; 463:137-58. [PMID: 18951166 DOI: 10.1007/978-1-59745-406-3_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
The nucleus is a complex volume constituted of numerous subcompartments in which specific functions take place due to a specific spatial organization of their molecular components. To understand how these molecules are spatially organized within these machineries, it is necessary to investigate their three-dimensional organization at high resolution. To reach this goal, electron tomography appears to be a method of choice; it can generate tomograms with a resolution of a few nanometers by using multiple projections of a tilted section several hundred to several thousand nanometers in thickness imaged by transmission electron microscopy (TEM).Specific identification of molecules of interest contained within such thick sections requires their specific immunocytochemical labelling using electron-dense markers. We recently demonstrated that electron tomography of proteins immunostained with nanogold particles before embedding, and subsequently amplified with silver, was very fruitful due to the inherently high spatial resolution of the medium-voltage scanning and transmission electron microscope (STEM). Here we describe this approach, which is very efficient for tracing the 3D organization of proteins within complex machineries by using antibodies raised against one of the proteins, or against GFP to analyse GFP-tagged proteins.
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46
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Structural evidence of glycoprotein assembly in cellular membrane compartments prior to Alphavirus budding. J Virol 2010; 84:11145-51. [PMID: 20739526 DOI: 10.1128/jvi.00036-10] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Membrane glycoproteins of alphavirus play a critical role in the assembly and budding of progeny virions. However, knowledge regarding transport of viral glycoproteins to the plasma membrane is obscure. In this study, we investigated the role of cytopathic vacuole type II (CPV-II) through in situ electron tomography of alphavirus-infected cells. The results revealed that CPV-II contains viral glycoproteins arranged in helical tubular arrays resembling the basic organization of glycoprotein trimers on the envelope of the mature virions. The location of CPV-II adjacent to the site of viral budding suggests a model for the transport of structural components to the site of budding. Thus, the structural characteristics of CPV-II can be used in evaluating the design of a packaging cell line for replicon production.
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47
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Bar Sadan M, Wolf SG, Houben L. Bright-field electron tomography of individual inorganic fullerene-like structures. NANOSCALE 2010; 2:423-428. [PMID: 20644827 DOI: 10.1039/b9nr00251k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS(2) or MoS(2) fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.
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Affiliation(s)
- Maya Bar Sadan
- Institute of Solid State Research, Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Research Centre Jülich GmbH, 52425 Jülich, Germany.
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Sander E, Stein A, Swickrath M, Barocas V. Out of Many, One: Modeling Schemes for Biopolymer and Biofibril Networks. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-1-4020-9785-0_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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49
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Volkmann N. Methods for segmentation and interpretation of electron tomographic reconstructions. Methods Enzymol 2010; 483:31-46. [PMID: 20888468 DOI: 10.1016/s0076-6879(10)83002-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Electron tomography has become a powerful tool for revealing the molecular architecture of biological cells and tissues. In principle, electron tomography can provide high-resolution mapping of entire proteomes. The achievable resolution (3-8 nm) is capable of bridging the gap between live-cell imaging and atomic resolution structures. However, the relevant information is not readily accessible from the data and needs to be identified, extracted, and processed before it can be used. Because electron tomography imaging and image acquisition technologies have enjoyed major advances in the last few years and continue to increase data throughput, the need for approaches that allow automatic and objective interpretation of electron tomograms becomes more and more urgent. This chapter provides an overview of the state of the art in this field and attempts to identify the major bottlenecks that prevent approaches for interpreting electron tomography data to develop their full potential.
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Affiliation(s)
- Niels Volkmann
- Sanford-Burnham Medical Research Institute, La Jolla, California, USA
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50
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Kobayashi A, Fujigaya T, Itoh M, Taguchi T, Takano H. Technical note: A tool for determining rotational tilt axis with or without fiducial markers. Ultramicroscopy 2009; 110:1-6. [DOI: 10.1016/j.ultramic.2009.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 07/27/2009] [Accepted: 08/18/2009] [Indexed: 10/20/2022]
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