1
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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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Markert SM. Studying zebrafish nervous system structure and function in health and disease with electron microscopy. Dev Growth Differ 2023; 65:502-516. [PMID: 37740826 DOI: 10.1111/dgd.12890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 09/25/2023]
Abstract
Zebrafish (Danio rerio) is a well-established model for studying the nervous system. Findings in zebrafish often inform studies on human diseases of the nervous system and provide crucial insight into disease mechanisms. The functions of the nervous system often rely on communication between neurons. Signal transduction is achieved via release of signaling molecules in the form of neuropeptides or neurotransmitters at synapses. Snapshots of membrane dynamics of these processes are imaged by electron microscopy. Electron microscopy can reveal ultrastructure and thus synaptic processes. This is crucial both for mapping synaptic connections and for investigating synaptic functions. In addition, via volumetric electron microscopy, the overall architecture of the nervous system becomes accessible, where structure can inform function. Electron microscopy is thus of particular value for studying the nervous system. However, today a plethora of electron microscopy techniques and protocols exist. Which technique is most suitable highly depends on the research question and scope as well as on the type of tissue that is examined. This review gives an overview of the electron microcopy techniques used on the zebrafish nervous system. It aims to give researchers a guide on which techniques are suitable for their specific questions and capabilities as well as an overview of the capabilities of electron microscopy in neurobiological research in the zebrafish model.
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3
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Su R, Wang S, McDargh Z, O'Shaughnessy B. Three membrane fusion pore families determine the pathway to pore dilation. Biophys J 2023; 122:3986-3998. [PMID: 37644721 PMCID: PMC10560699 DOI: 10.1016/j.bpj.2023.08.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/19/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023] Open
Abstract
During exocytosis secretory vesicles fuse with a target membrane and release neurotransmitters, hormones, or other bioactive molecules through a membrane fusion pore. The initially small pore may subsequently dilate for full contents release, as commonly observed in amperometric traces. The size, shape, and evolution of the pore is critical to the course of contents release, but exact fusion pore solutions accounting for membrane tension and bending energy constraints have not been available. Here, we obtained exact solutions for fusion pores between two membranes. We find three families: a narrow pore, a wide pore, and an intermediate tether-like pore. For high tensions these are close to the catenoidal and tether solutions recently reported for freely hinged membrane boundaries. We suggest membrane fusion initially generates a stable narrow pore, and the dilation pathway is a transition to the stable wide pore family. The unstable intermediate pore is the transition state that sets the energy barrier for this dilation pathway. Pore dilation is mechanosensitive, as the energy barrier is lowered by increased membrane tension. Finally, we study fusion pores in nanodiscs, powerful systems for the study of individual pores. We show that nanodiscs stabilize fusion pores by locking them into the narrow pore family.
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Affiliation(s)
- Rui Su
- Department of Chemical Engineering, Columbia University, New York City, New York
| | - Shuyuan Wang
- Department of Chemical Engineering, Columbia University, New York City, New York; Department of Physics, Columbia University, New York City, New York
| | - Zachary McDargh
- Department of Chemical Engineering, Columbia University, New York City, New York
| | - Ben O'Shaughnessy
- Department of Chemical Engineering, Columbia University, New York City, New York.
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4
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Sanders S, Jensen Y, Reimer R, Bosse JB. From the beginnings to multidimensional light and electron microscopy of virus morphogenesis. Adv Virus Res 2023; 116:45-88. [PMID: 37524482 DOI: 10.1016/bs.aivir.2023.05.001] [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: 08/02/2023]
Abstract
Individual functional viral morphogenesis events are often dynamic, short, and infrequent and might be obscured by other pathways and dead-end products. Volumetric live cell imaging has become an essential tool for studying viral morphogenesis events. It allows following entire dynamic processes while providing functional evidence that the imaged process is involved in viral production. Moreover, it allows to capture many individual events and allows quantitative analysis. Finally, the correlation of volumetric live-cell data with volumetric electron microscopy (EM) can provide crucial insights into the ultrastructure and mechanisms of viral morphogenesis events. Here, we provide an overview and discussion of suitable imaging methods for volumetric correlative imaging of viral morphogenesis and frame them in a historical summary of their development.
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Affiliation(s)
- Saskia Sanders
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Yannick Jensen
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | | | - Jens B Bosse
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
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5
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Ronchi P, Mizzon G, Machado P, D’Imprima E, Best BT, Cassella L, Schnorrenberg S, Montero MG, Jechlinger M, Ephrussi A, Leptin M, Mahamid J, Schwab Y. High-precision targeting workflow for volume electron microscopy. J Cell Biol 2021; 220:e202104069. [PMID: 34160561 PMCID: PMC8225610 DOI: 10.1083/jcb.202104069] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/27/2021] [Accepted: 06/06/2021] [Indexed: 02/07/2023] Open
Abstract
Cells are 3D objects. Therefore, volume EM (vEM) is often crucial for correct interpretation of ultrastructural data. Today, scanning EM (SEM) methods such as focused ion beam (FIB)-SEM are frequently used for vEM analyses. While they allow automated data acquisition, precise targeting of volumes of interest within a large sample remains challenging. Here, we provide a workflow to target FIB-SEM acquisition of fluorescently labeled cells or subcellular structures with micrometer precision. The strategy relies on fluorescence preservation during sample preparation and targeted trimming guided by confocal maps of the fluorescence signal in the resin block. Laser branding is used to create landmarks on the block surface to position the FIB-SEM acquisition. Using this method, we acquired volumes of specific single cells within large tissues such as 3D cultures of mouse mammary gland organoids, tracheal terminal cells in Drosophila melanogaster larvae, and ovarian follicular cells in adult Drosophila, discovering ultrastructural details that could not be appreciated before.
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Affiliation(s)
- Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Giulia Mizzon
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Pedro Machado
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Edoardo D’Imprima
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Benedikt T. Best
- Directors’ Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Lucia Cassella
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sebastian Schnorrenberg
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marta G. Montero
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin Jechlinger
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maria Leptin
- Directors’ Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Yannick Schwab
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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6
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Baena V, Conrad R, Friday P, Fitzgerald E, Kim T, Bernbaum J, Berensmann H, Harned A, Nagashima K, Narayan K. FIB-SEM as a Volume Electron Microscopy Approach to Study Cellular Architectures in SARS-CoV-2 and Other Viral Infections: A Practical Primer for a Virologist. Viruses 2021; 13:v13040611. [PMID: 33918371 PMCID: PMC8066521 DOI: 10.3390/v13040611] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 01/06/2023] Open
Abstract
The visualization of cellular ultrastructure over a wide range of volumes is becoming possible by increasingly powerful techniques grouped under the rubric “volume electron microscopy” or volume EM (vEM). Focused ion beam scanning electron microscopy (FIB-SEM) occupies a “Goldilocks zone” in vEM: iterative and automated cycles of milling and imaging allow the interrogation of microns-thick specimens in 3-D at resolutions of tens of nanometers or less. This bestows on FIB-SEM the unique ability to aid the accurate and precise study of architectures of virus-cell interactions. Here we give the virologist or cell biologist a primer on FIB-SEM imaging in the context of vEM and discuss practical aspects of a room temperature FIB-SEM experiment. In an in vitro study of SARS-CoV-2 infection, we show that accurate quantitation of viral densities and surface curvatures enabled by FIB-SEM imaging reveals SARS-CoV-2 viruses preferentially located at areas of plasma membrane that have positive mean curvatures.
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Affiliation(s)
- Valentina Baena
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (V.B.); (R.C.); (P.F.); (E.F.); (T.K.); (H.B.); (A.H.); (K.N.)
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Ryan Conrad
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (V.B.); (R.C.); (P.F.); (E.F.); (T.K.); (H.B.); (A.H.); (K.N.)
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Patrick Friday
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (V.B.); (R.C.); (P.F.); (E.F.); (T.K.); (H.B.); (A.H.); (K.N.)
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Ella Fitzgerald
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (V.B.); (R.C.); (P.F.); (E.F.); (T.K.); (H.B.); (A.H.); (K.N.)
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Taeeun Kim
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (V.B.); (R.C.); (P.F.); (E.F.); (T.K.); (H.B.); (A.H.); (K.N.)
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - John Bernbaum
- National Institute of Allergy and Infectious Diseases, Division of Clinical Research, Integrated Research Facility at Fort Detrick (IRF-Frederick), Frederick, MD 21702, USA;
| | - Heather Berensmann
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (V.B.); (R.C.); (P.F.); (E.F.); (T.K.); (H.B.); (A.H.); (K.N.)
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Adam Harned
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (V.B.); (R.C.); (P.F.); (E.F.); (T.K.); (H.B.); (A.H.); (K.N.)
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Kunio Nagashima
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (V.B.); (R.C.); (P.F.); (E.F.); (T.K.); (H.B.); (A.H.); (K.N.)
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (V.B.); (R.C.); (P.F.); (E.F.); (T.K.); (H.B.); (A.H.); (K.N.)
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Correspondence:
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7
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Abstract
Since its entry into biomedical research in the first half of the twentieth century, electron microscopy has been a valuable tool for lung researchers to explore the lung's delicate ultrastructure. Among others, it proved the existence of a continuous alveolar epithelium and demonstrated the surfactant lining layer. With the establishment of serial sectioning transmission electron microscopy, as the first "volume electron microscopic" technique, electron microscopy entered the third dimension and investigations of the lung's three-dimensional ultrastructure became possible. Over the years, further techniques, ranging from electron tomography over serial block-face and focused ion beam scanning electron microscopy to array tomography became available. All techniques cover different volumes and resolutions, and, thus, different scientific questions. This review gives an overview of these techniques and their application in lung research, focusing on their fields of application and practical implementation. Furthermore, an introduction is given how the output raw data are processed and the final three-dimensional models can be generated.
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Affiliation(s)
- Jan Philipp Schneider
- Institute of Functional and Applied Anatomy, Hannover Medical School, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Jan Hegermann
- Institute of Functional and Applied Anatomy, Hannover Medical School, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
- Research Core Unit Electron Microscopy, Hannover Medical School, 30625 Hannover, Germany
| | - Christoph Wrede
- Institute of Functional and Applied Anatomy, Hannover Medical School, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
- Research Core Unit Electron Microscopy, Hannover Medical School, 30625 Hannover, Germany
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8
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Kauscher U, Penders J, Nagelkerke A, Holme MN, Nele V, Massi L, Gopal S, Whittaker TE, Stevens MM. Gold Nanocluster Extracellular Vesicle Supraparticles: Self-Assembled Nanostructures for Three-Dimensional Uptake Visualization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:3912-3923. [PMID: 32250120 PMCID: PMC7161082 DOI: 10.1021/acs.langmuir.9b03479] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Extracellular vesicles (EVs) are secreted by the vast majority of cells and are being intensively studied due to their emerging involvement in a variety of cellular communication processes. However, the study of their cellular uptake and fate has been hampered by difficulty in imaging EVs against the cellular background. Here, we show that EVs combined with hydrophobic gold nanoclusters (AuNCs) can self-assemble into supraparticles, offering an excellent labeling strategy for high-resolution electron microscopic imaging in vitro. We have tracked and visualized the reuptake of breast cancer cell-derived EV AuNC supraparticles into their parent cells, from early endocytosis to lysosomal degradation, using focused ion beam-scanning electron microscopy (FIB-SEM). The presence of gold within the EVs and lysosomes was confirmed via DF-STEM EDX analysis of lift-out sections. The demonstrated formation of AuNC EV supraparticles will facilitate future applications in EV imaging as well as the EV-assisted cellular delivery of AuNCs.
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Affiliation(s)
- Ulrike Kauscher
- Department
of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jelle Penders
- Department
of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Anika Nagelkerke
- Department
of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- University
of Groningen, Groningen Research Institute
of Pharmacy, Pharmaceutical Analysis,
POB 196 XB20, NL-9700 AD Groningen, The Netherlands
| | - Margaret N. Holme
- Department
of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Valeria Nele
- Department
of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Lucia Massi
- Department
of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Sahana Gopal
- Department
of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Thomas E. Whittaker
- Department
of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Molly M. Stevens
- Department
of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm SE-171 77, Sweden
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9
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Riesterer JL, López CS, Stempinski ES, Williams M, Loftis K, Stoltz K, Thibault G, Lanicault C, Williams T, Gray JW. A workflow for visualizing human cancer biopsies using large-format electron microscopy. Methods Cell Biol 2020; 158:163-181. [PMID: 32423648 DOI: 10.1016/bs.mcb.2020.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Recent developments in large format electron microscopy have enabled generation of images that provide detailed ultrastructural information on normal and diseased cells and tissues. Analyses of these images increase our understanding of cellular organization and interactions and disease-related changes therein. In this manuscript, we describe a workflow for two-dimensional (2D) and three-dimensional (3D) imaging, including both optical and scanning electron microscopy (SEM) methods, that allow pathologists and cancer biology researchers to identify areas of interest from human cancer biopsies. The protocols and mounting strategies described in this workflow are compatible with 2D large format EM mapping, 3D focused ion beam-SEM and serial block face-SEM. The flexibility to use diverse imaging technologies available at most academic institutions makes this workflow useful and applicable for most life science samples. Volumetric analysis of the biopsies studied here revealed morphological, organizational and ultrastructural aspects of the tumor cells and surrounding environment that cannot be revealed by conventional 2D EM imaging. Our results indicate that although 2D EM is still an important tool in many areas of diagnostic pathology, 3D images of ultrastructural relationships between both normal and cancerous cells, in combination with their extracellular matrix, enables cancer researchers and pathologists to better understand the progression of the disease and identify potential therapeutic targets.
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Affiliation(s)
- Jessica L Riesterer
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States; Multiscale Microscopy Core, Oregon Health and Sciences University, Portland, OR, United States.
| | - Claudia S López
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States; Multiscale Microscopy Core, Oregon Health and Sciences University, Portland, OR, United States; Pacific Northwest Center for CryoEM, Oregon Health and Sciences University, Portland, OR, United States.
| | - Erin S Stempinski
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States; Multiscale Microscopy Core, Oregon Health and Sciences University, Portland, OR, United States
| | - Melissa Williams
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States; Multiscale Microscopy Core, Oregon Health and Sciences University, Portland, OR, United States
| | - Kevin Loftis
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States
| | - Kevin Stoltz
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States
| | - Guillaume Thibault
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States
| | - Christian Lanicault
- Department of Pathology, Oregon Health and Sciences University, Portland, OR, United States
| | - Todd Williams
- Department of Pathology, Oregon Health and Sciences University, Portland, OR, United States
| | - Joe W Gray
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States.
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10
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Almarshad HA, Madhavan M, Hoshino K. Focused Ion Beam-Based Milling, Imaging and Analysis of 3D Tumor Spheroids. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2018; 2018:4480-4483. [PMID: 30441346 DOI: 10.1109/embc.2018.8513165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We investigate the structural cellular alterations in breast cancer spheroids at various growth stages using transmission electron microscopy (TEM), focused ion beam (FIB), and scanning electron microscopy (SEM) imaging. Samples sliced by FIB milling were studied for 3D analysis and construction. The imaging results of different spheroid ages were compared for a better understanding of cancer spheroid models. This study will serve as a pilot study and reference control for further studies with the 3D tumor model including nanoparticles interaction and mechanical characterization.
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11
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Biological serial block face scanning electron microscopy at improved z-resolution based on Monte Carlo model. Sci Rep 2018; 8:12985. [PMID: 30154532 PMCID: PMC6113311 DOI: 10.1038/s41598-018-31231-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022] Open
Abstract
Serial block-face electron microscopy (SBEM) provides nanoscale 3D ultrastructure of embedded and stained cells and tissues in volumes of up to 107 µm3. In SBEM, electrons with 1–3 keV energies are incident on a specimen block, from which backscattered electron (BSE) images are collected with x, y resolution of 5–10 nm in the block-face plane, and successive layers are removed by an in situ ultramicrotome. Spatial resolution along the z-direction, however, is limited to around 25 nm by the minimum cutting thickness. To improve the z-resolution, we have extracted depth information from BSE images acquired at dual primary beam energies, using Monte Carlo simulations of electron scattering. The relationship between depth of stain and ratio of dual-energy BSE intensities enables us to determine 3D structure with a ×2 improvement in z-resolution. We demonstrate the technique by sub-slice imaging of hepatocyte membranes in liver tissue.
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12
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In vitro single-cell dissection revealing the interior structure of cable bacteria. Proc Natl Acad Sci U S A 2018; 115:8517-8522. [PMID: 30082405 DOI: 10.1073/pnas.1807562115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Filamentous Desulfobulbaceae bacteria were recently discovered as long-range transporters of electrons from sulfide to oxygen in marine sediments. The long-range electron transfer through these cable bacteria has created considerable interests, but it has also raised many questions, such as what structural basis will be required to enable micrometer-sized cells to build into centimeter-long continuous filaments? Here we dissected cable bacteria cells in vitro by atomic force microscopy and further explored the interior, which is normally hidden behind the outer membrane. Using nanoscale topographical and mechanical maps, different types of bacterial cell-cell junctions and strings along the cable length were identified. More important, these strings were found to be continuous along the bacterial cells passing through the cell-cell junctions. This indicates that the strings serve an important function in maintaining integrity of individual cable bacteria cells as a united filament. Furthermore, ridges in the outer membrane are found to envelop the individual strings at cell-cell junctions, and they are proposed to strengthen the junctions. Finally, we propose a model for the division and growth of the cable bacteria, which illustrate the possible structural requirements for the formation of centimeter-length filaments in the recently discovered cable bacteria.
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13
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Ayoub S, Tsai KC, Khalighi AH, Sacks MS. The Three-Dimensional Microenvironment of the Mitral Valve: Insights into the Effects of Physiological Loads. Cell Mol Bioeng 2018; 11:291-306. [PMID: 31719888 PMCID: PMC6816749 DOI: 10.1007/s12195-018-0529-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 05/14/2018] [Indexed: 10/24/2022] Open
Abstract
INTRODUCTION In the mitral valve (MV), numerous pathological factors, especially those resulting from changes in external loading, have been shown to affect MV structure and composition. Such changes are driven by the MV interstitial cell (MVIC) population via protein synthesis and enzymatic degradation of extracellular matrix (ECM) components. METHODS While cell phenotype, ECM composition and regulation, and tissue level changes in MVIC shape under stress have been studied, a detailed understanding of the three-dimensional (3D) microstructural mechanisms are lacking. As a first step in addressing this challenge, we applied focused ion beam scanning electron microscopy (FIB-SEM) to reveal novel details of the MV microenvironment in 3D. RESULTS We demonstrated that collagen is organized into large fibers consisting of an average of 605 ± 113 fibrils, with a mean diameter of 61.2 ± 9.8 nm. In contrast, elastin was organized into two distinct structural subtypes: (1) sheet-like lamellar elastin, and (2) circumferentially oriented elastin struts, based on both the aspect ratio and transmural tilt. MVICs were observed to have a large cytoplasmic volume, as evidenced by the large mean surface area to volume ratio 3.68 ± 0.35, which increased under physiological loading conditions to 4.98 ± 1.17. CONCLUSIONS Our findings suggest that each MVIC mechanically interacted only with the nearest 3-4 collagen fibers. This key observation suggests that in developing multiscale MV models, each MVIC can be considered a mechanically integral part of the local fiber ensemble and is unlikely to be influenced by more distant structures.
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Affiliation(s)
- Salma Ayoub
- Willerson Center for Cardiovascular Modeling and Simulation, Institute for Computational Engineering and Sciences and the Department of Biomedical Engineering, The University of Texas at Austin, 201 East 24th Street, POB 5.236, 1 University Station C0200, Austin, TX 78712 USA
| | - Karen C. Tsai
- Willerson Center for Cardiovascular Modeling and Simulation, Institute for Computational Engineering and Sciences and the Department of Biomedical Engineering, The University of Texas at Austin, 201 East 24th Street, POB 5.236, 1 University Station C0200, Austin, TX 78712 USA
| | - Amir H. Khalighi
- Willerson Center for Cardiovascular Modeling and Simulation, Institute for Computational Engineering and Sciences and the Department of Biomedical Engineering, The University of Texas at Austin, 201 East 24th Street, POB 5.236, 1 University Station C0200, Austin, TX 78712 USA
| | - Michael S. Sacks
- Willerson Center for Cardiovascular Modeling and Simulation, Institute for Computational Engineering and Sciences and the Department of Biomedical Engineering, The University of Texas at Austin, 201 East 24th Street, POB 5.236, 1 University Station C0200, Austin, TX 78712 USA
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14
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Expanding horizons of cryo-tomography to larger volumes. Curr Opin Microbiol 2018; 43:155-161. [DOI: 10.1016/j.mib.2018.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/02/2018] [Accepted: 01/03/2018] [Indexed: 12/18/2022]
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15
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Hasegawa T, Yamamoto T, Hongo H, Qiu Z, Abe M, Kanesaki T, Tanaka K, Endo T, de Freitas PHL, Li M, Amizuka N. Three-dimensional ultrastructure of osteocytes assessed by focused ion beam-scanning electron microscopy (FIB-SEM). Histochem Cell Biol 2018; 149:423-432. [DOI: 10.1007/s00418-018-1645-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2018] [Indexed: 10/18/2022]
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16
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Comparison of 3D cellular imaging techniques based on scanned electron probes: Serial block face SEM vs. Axial bright-field STEM tomography. J Struct Biol 2018; 202:216-228. [PMID: 29408702 DOI: 10.1016/j.jsb.2018.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/26/2018] [Accepted: 01/30/2018] [Indexed: 11/22/2022]
Abstract
Microscopies based on focused electron probes allow the cell biologist to image the 3D ultrastructure of eukaryotic cells and tissues extending over large volumes, thus providing new insight into the relationship between cellular architecture and function of organelles. Here we compare two such techniques: electron tomography in conjunction with axial bright-field scanning transmission electron microscopy (BF-STEM), and serial block face scanning electron microscopy (SBF-SEM). The advantages and limitations of each technique are illustrated by their application to determining the 3D ultrastructure of human blood platelets, by considering specimen geometry, specimen preparation, beam damage and image processing methods. Many features of the complex membranes composing the platelet organelles can be determined from both approaches, although STEM tomography offers a higher ∼3 nm isotropic pixel size, compared with ∼5 nm for SBF-SEM in the plane of the block face and ∼30 nm in the perpendicular direction. In this regard, we demonstrate that STEM tomography is advantageous for visualizing the platelet canalicular system, which consists of an interconnected network of narrow (∼50-100 nm) membranous cisternae. In contrast, SBF-SEM enables visualization of complete platelets, each of which extends ∼2 µm in minimum dimension, whereas BF-STEM tomography can typically only visualize approximately half of the platelet volume due to a rapid non-linear loss of signal in specimens of thickness greater than ∼1.5 µm. We also show that the limitations of each approach can be ameliorated by combining 3D and 2D measurements using a stereological approach.
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17
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Webb RI, Schieber NL. Volume Scanning Electron Microscopy: Serial Block-Face Scanning Electron Microscopy Focussed Ion Beam Scanning Electron Microscopy. BIOLOGICAL AND MEDICAL PHYSICS, BIOMEDICAL ENGINEERING 2018. [DOI: 10.1007/978-3-319-68997-5_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Li J, Kim Y, Liu B, Qin R, Li J, Fu J. Automated patterning and probing with multiple nanoscale tools for single-cell analysis. Micron 2017; 101:132-137. [PMID: 28772204 DOI: 10.1016/j.micron.2017.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/05/2017] [Accepted: 06/05/2017] [Indexed: 10/19/2022]
Abstract
The nano-manipulation approach that combines Focused Ion Beam (FIB) milling and various imaging and probing techniques enables researchers to investigate the cellular structures in three dimensions. Such fusion approach, however, requires extensive effort on locating and examining randomly-distributed targets due to limited Field of View (FOV) when high magnification is desired. In the present study, we present the development that automates 'pattern and probe' particularly for single-cell analysis, achieved by computer aided tools including feature recognition and geometric planning algorithms. Scheduling of serial FOVs for imaging and probing of multiple cells was considered as a rectangle covering problem, and optimal or near-optimal solutions were obtained with the heuristics developed. FIB milling was then employed automatically followed by downstream analysis using Atomic Force Microscopy (AFM) to probe the cellular interior. Our strategy was applied to examine bacterial cells (Klebsiella pneumoniae) and achieved high efficiency with limited human interference. The developed algorithms can be easily adapted and integrated with different imaging platforms towards high-throughput imaging analysis of single cells.
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Affiliation(s)
- Jiayao Li
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia.
| | - Yeonuk Kim
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Boyin Liu
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Ruwen Qin
- Department of Engineering Management and Systems Engineering, Missouri University of Science and Technology, Rolla, MO 65409, USA
| | - Jian Li
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Jing Fu
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia.
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19
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Guehrs E, Schneider M, Günther CM, Hessing P, Heitz K, Wittke D, López-Serrano Oliver A, Jakubowski N, Plendl J, Eisebitt S, Haase A. Quantification of silver nanoparticle uptake and distribution within individual human macrophages by FIB/SEM slice and view. J Nanobiotechnology 2017; 15:21. [PMID: 28327151 PMCID: PMC5359962 DOI: 10.1186/s12951-017-0255-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/08/2017] [Indexed: 11/25/2022] Open
Abstract
Background Quantification of nanoparticle (NP) uptake in cells or tissues is very important for safety assessment. Often, electron microscopy based approaches are used for this purpose, which allow imaging at very high resolution. However, precise quantification of NP numbers in cells and tissues remains challenging. The aim of this study was to present a novel approach, that combines precise quantification of NPs in individual cells together with high resolution imaging of their intracellular distribution based on focused ion beam/ scanning electron microscopy (FIB/SEM) slice and view approaches. Results We quantified cellular uptake of 75 nm diameter citrate stabilized silver NPs (Ag 75 Cit) into an individual human macrophage derived from monocytic THP-1 cells using a FIB/SEM slice and view approach. Cells were treated with 10 μg/ml for 24 h. We investigated a single cell and found in total 3138 ± 722 silver NPs inside this cell. Most of the silver NPs were located in large agglomerates, only a few were found in clusters of fewer than five NPs. Furthermore, we cross-checked our results by using inductively coupled plasma mass spectrometry and could confirm the FIB/SEM results. Conclusions Our approach based on FIB/SEM slice and view is currently the only one that allows the quantification of the absolute dose of silver NPs in individual cells and at the same time to assess their intracellular distribution at high resolution. We therefore propose to use FIB/SEM slice and view to systematically analyse the cellular uptake of various NPs as a function of size, concentration and incubation time.
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Affiliation(s)
- Erik Guehrs
- Institute for Optics and Atomic Physics, Technical University of Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Michael Schneider
- Institute for Optics and Atomic Physics, Technical University of Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.,Max-Born-Institute for Nonlinear Optics and Short Pulse Spectroscopy, Max-Born-Straße 2A, 12489, Berlin, Germany
| | - Christian M Günther
- Institute for Optics and Atomic Physics, Technical University of Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Piet Hessing
- Max-Born-Institute for Nonlinear Optics and Short Pulse Spectroscopy, Max-Born-Straße 2A, 12489, Berlin, Germany
| | - Karen Heitz
- Institute for Optics and Atomic Physics, Technical University of Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Doreen Wittke
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Ana López-Serrano Oliver
- Division 1.1 Inorganic Trace Analysis, Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Str. 11, 12489, Berlin, Germany
| | - Norbert Jakubowski
- Division 1.1 Inorganic Trace Analysis, Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Str. 11, 12489, Berlin, Germany
| | - Johanna Plendl
- Institute of Veterinary Anatomy, Free University Berlin, Koserstr. 20, 14195, Berlin, Germany
| | - Stefan Eisebitt
- Institute for Optics and Atomic Physics, Technical University of Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.,Max-Born-Institute for Nonlinear Optics and Short Pulse Spectroscopy, Max-Born-Straße 2A, 12489, Berlin, Germany
| | - Andrea Haase
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany.
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20
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Hasegawa T, Endo T, Tsuchiya E, Kudo A, Shen Z, Moritani Y, Abe M, Yamamoto T, Hongo H, Tsuboi K, Yoshida T, Nagai T, Khadiza N, Yokoyama A, Luiz de Freitas PH, Li M, Amizuka N. Biological application of focus ion beam-scanning electron microscopy (FIB-SEM) to the imaging of cartilaginous fibrils and osteoblastic cytoplasmic processes. J Oral Biosci 2017. [DOI: 10.1016/j.job.2016.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Hoang TV, Kizilyaprak C, Spehner D, Humbel BM, Schultz P. Automatic segmentation of high pressure frozen and freeze-substituted mouse retina nuclei from FIB-SEM tomograms. J Struct Biol 2017; 197:123-134. [DOI: 10.1016/j.jsb.2016.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 10/03/2016] [Accepted: 10/06/2016] [Indexed: 10/20/2022]
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22
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Visualization of HIV T Cell Virological Synapses and Virus-Containing Compartments by Three-Dimensional Correlative Light and Electron Microscopy. J Virol 2017; 91:JVI.01605-16. [PMID: 27847357 PMCID: PMC5215336 DOI: 10.1128/jvi.01605-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 10/31/2016] [Indexed: 11/20/2022] Open
Abstract
Virological synapses (VS) are adhesive structures that form between infected and uninfected cells to enhance the spread of HIV-1. During T cell VS formation, viral proteins are actively recruited to the site of cell-cell contact where the viral material is efficiently translocated to target cells into heterogeneous, protease-resistant, antibody-inaccessible compartments. Using correlative light and electron microscopy (CLEM), we define the membrane topography of the virus-containing compartments (VCC) where HIV is found following VS-mediated transfer. Focused ion beam scanning electron microscopy (FIB-SEM) and serial sectioning transmission electron microscopy (SS-TEM) were used to better resolve the fluorescent Gag-containing structures within the VCC. We found that small punctate fluorescent signals correlated with single viral particles in enclosed vesicular compartments or surface-localized virus particles and that large fluorescent signals correlated with membranous Gag-containing structures with unknown pathological function. CLEM imaging revealed distinct pools of newly deposited viral proteins within endocytic and nonendocytic compartments in VS target T cells. IMPORTANCE This study directly correlates individual virus-associated objects observed in light microscopy with ultrastructural features seen by electron microscopy in the HIV-1 virological synapse. This approach elucidates which infection-associated ultrastructural features represent bona fide HIV protein complexes. We define the morphology of some HIV cell-to-cell transfer intermediates as true endocytic compartments and resolve unique synapse-associated viral structures created by transfer across virological synapses.
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23
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Dirk BS, Van Nynatten LR, Dikeakos JD. Where in the Cell Are You? Probing HIV-1 Host Interactions through Advanced Imaging Techniques. Viruses 2016; 8:v8100288. [PMID: 27775563 PMCID: PMC5086620 DOI: 10.3390/v8100288] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/06/2016] [Accepted: 10/10/2016] [Indexed: 12/19/2022] Open
Abstract
Viruses must continuously evolve to hijack the host cell machinery in order to successfully replicate and orchestrate key interactions that support their persistence. The type-1 human immunodeficiency virus (HIV-1) is a prime example of viral persistence within the host, having plagued the human population for decades. In recent years, advances in cellular imaging and molecular biology have aided the elucidation of key steps mediating the HIV-1 lifecycle and viral pathogenesis. Super-resolution imaging techniques such as stimulated emission depletion (STED) and photoactivation and localization microscopy (PALM) have been instrumental in studying viral assembly and release through both cell-cell transmission and cell-free viral transmission. Moreover, powerful methods such as Forster resonance energy transfer (FRET) and bimolecular fluorescence complementation (BiFC) have shed light on the protein-protein interactions HIV-1 engages within the host to hijack the cellular machinery. Specific advancements in live cell imaging in combination with the use of multicolor viral particles have become indispensable to unravelling the dynamic nature of these virus-host interactions. In the current review, we outline novel imaging methods that have been used to study the HIV-1 lifecycle and highlight advancements in the cell culture models developed to enhance our understanding of the HIV-1 lifecycle.
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Affiliation(s)
- Brennan S Dirk
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
| | - Logan R Van Nynatten
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
| | - Jimmy D Dikeakos
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
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24
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Electron tomography of rabbit cardiomyocyte three-dimensional ultrastructure. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 121:77-84. [PMID: 27210305 PMCID: PMC4959512 DOI: 10.1016/j.pbiomolbio.2016.05.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/01/2016] [Indexed: 12/22/2022]
Abstract
The field of cardiovascular research has benefitted from rapid developments in imaging technology over the last few decades. Accordingly, an ever growing number of large, multidimensional data sets have begun to appear, often challenging existing pre-conceptions about structure and function of biological systems. For tissue and cell structure imaging, the move from 2D section-based microscopy to true 3D data collection has been a major driver of new insight. In the sub-cellular domain, electron tomography is a powerful technique for exploration of cellular structures in 3D with unparalleled fidelity at nanometer resolution. Electron tomography is particularly advantageous for studying highly compartmentalised cells such as cardiomyocytes, where elaborate sub-cellular structures play crucial roles in electrophysiology and mechanics. Although the anatomy of specific ultra-structures, such as dyadic couplons, has been extensively explored using 2D electron microscopy of thin sections, we still lack accurate, quantitative knowledge of true individual shape, volume and surface area of sub-cellular domains, as well as their 3D spatial interrelations; let alone of how these are reshaped during the cycle of contraction and relaxation. Here we discuss and illustrate the utility of ET for identification, visualisation, and analysis of 3D cardiomyocyte ultrastructures such as the T-tubular system, sarcoplasmic reticulum, mitochondria and microtubules.
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25
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Bykov YS, Cortese M, Briggs JAG, Bartenschlager R. Correlative light and electron microscopy methods for the study of virus-cell interactions. FEBS Lett 2016; 590:1877-95. [PMID: 27008928 DOI: 10.1002/1873-3468.12153] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 03/09/2016] [Accepted: 03/22/2016] [Indexed: 12/21/2022]
Abstract
Electron microscopy (EM) is an invaluable tool to study the interactions of viruses with cells, and the ultrastructural changes induced in host cells by virus infection. Light microscopy (LM) is a complementary tool with the potential to locate rare events, label specific components, and obtain dynamic information. The combination of LM and EM in correlative light and electron microscopy (CLEM) is particularly powerful. It can be used to complement a static EM image with dynamic data from live imaging, identify the ultrastructure observed in LM, or, conversely, provide molecular specificity data for a known ultrastructure. Here, we describe methods and strategies for CLEM, discuss their advantages and limitations, and review applications of CLEM to study virus-host interactions.
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Affiliation(s)
- Yury S Bykov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Germany
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Germany
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26
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Abstract
A quiet revolution is under way in technologies used for nanoscale cellular imaging. Focused ion beams, previously restricted to the materials sciences and semiconductor fields, are rapidly becoming powerful tools for ultrastructural imaging of biological samples. Cell and tissue architecture, as preserved in plastic-embedded resin or in plunge-frozen form, can be investigated in three dimensions by scanning electron microscopy imaging of freshly created surfaces that result from the progressive removal of material using a focused ion beam. The focused ion beam can also be used as a sculpting tool to create specific specimen shapes such as lamellae or needles that can be analyzed further by transmission electron microscopy or by methods that probe chemical composition. Here we provide an in-depth primer to the application of focused ion beams in biology, including a guide to the practical aspects of using the technology, as well as selected examples of its contribution to the generation of new insights into subcellular architecture and mechanisms underlying host-pathogen interactions.
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27
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Chang IYT, Joester D. Large Area Cryo-Planing of Vitrified Samples Using Broad-Beam Ion Milling. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2015; 21:1616-1621. [PMID: 26455924 DOI: 10.1017/s143192761501510x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
On account of its excellent resolution and high throughput, cryoSEM imaging has recently seen resurgence. In this work, we report on the development of cryogenic triple ion gun milling (CryoTIGM™), a broad ion beam milling technique for cryo-planing of vitrified, "frozen-hydrated" specimens. We find that sections prepared with CryoTIGM™ are smooth over exceptionally large areas (~700,000 µm2), and reveal ultrastructural details in similar or better quality than freeze-fractured samples.
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Affiliation(s)
- Irene Y T Chang
- Department of Materials Science and Engineering,Northwestern University,2220 Campus Drive,Evanston,IL 60208,USA
| | - Derk Joester
- Department of Materials Science and Engineering,Northwestern University,2220 Campus Drive,Evanston,IL 60208,USA
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28
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Cryo-planing of frozen-hydrated samples using cryo triple ion gun milling (CryoTIGM™). J Struct Biol 2015; 192:569-579. [PMID: 26549007 DOI: 10.1016/j.jsb.2015.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 11/23/2022]
Abstract
Cryo-SEM is a high throughput technique for imaging biological ultrastructure in its most pristine state, i.e. without chemical fixation, embedding, or drying. Freeze fracture is routinely used to prepare internal surfaces for cryo-SEM imaging. However, the propagation of the fracture plane is highly dependent on sample properties, and the resulting surface frequently shows substantial topography, which can complicate image analysis and interpretation. We have developed a broad ion beam milling technique, called cryogenic triple ion gun milling (CryoTIGM™ ['krī-ə-,tīm]), for cryo-planing frozen-hydrated biological specimens. Comparing sample preparation by CryoTIGM™ and freeze fracture in three model systems, Baker's yeast, mouse liver tissue, and whole sea urchin embryos, we find that CryoTIGM™ yields very large (∼700,000 μm(2)) and smooth sections that present ultrastructural details at similar or better quality than freeze-fractured samples. A particular strength of CryoTIGM™ is the ability to section samples with hard-soft contrast such as brittle calcite (CaCO3) spicules in the sea urchin embryo.
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29
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Bushong EA, Johnson DD, Kim KY, Terada M, Hatori M, Peltier ST, Panda S, Merkle A, Ellisman MH. X-ray microscopy as an approach to increasing accuracy and efficiency of serial block-face imaging for correlated light and electron microscopy of biological specimens. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2015; 21:231-8. [PMID: 25392009 PMCID: PMC4415271 DOI: 10.1017/s1431927614013579] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The recently developed three-dimensional electron microscopic (EM) method of serial block-face scanning electron microscopy (SBEM) has rapidly established itself as a powerful imaging approach. Volume EM imaging with this scanning electron microscopy (SEM) method requires intense staining of biological specimens with heavy metals to allow sufficient back-scatter electron signal and also to render specimens sufficiently conductive to control charging artifacts. These more extreme heavy metal staining protocols render specimens light opaque and make it much more difficult to track and identify regions of interest (ROIs) for the SBEM imaging process than for a typical thin section transmission electron microscopy correlative light and electron microscopy study. We present a strategy employing X-ray microscopy (XRM) both for tracking ROIs and for increasing the efficiency of the workflow used for typical projects undertaken with SBEM. XRM was found to reveal an impressive level of detail in tissue heavily stained for SBEM imaging, allowing for the identification of tissue landmarks that can be subsequently used to guide data collection in the SEM. Furthermore, specific labeling of individual cells using diaminobenzidine is detectable in XRM volumes. We demonstrate that tungsten carbide particles or upconverting nanophosphor particles can be used as fiducial markers to further increase the precision and efficiency of SBEM imaging.
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Affiliation(s)
- Eric A Bushong
- 1Center for Research in Biological Systems,National Center for Microscopy and Imaging Research,University of California at San Diego,9500 Gilman Drive,La Jolla,CA 92093,USA
| | - Donald D Johnson
- 1Center for Research in Biological Systems,National Center for Microscopy and Imaging Research,University of California at San Diego,9500 Gilman Drive,La Jolla,CA 92093,USA
| | - Keun-Young Kim
- 1Center for Research in Biological Systems,National Center for Microscopy and Imaging Research,University of California at San Diego,9500 Gilman Drive,La Jolla,CA 92093,USA
| | - Masako Terada
- 2Carl Zeiss X-ray Microscopy Inc.,4385 Hopyard Rd #100,Pleasanton,CA 94588,USA
| | - Megumi Hatori
- 3Salk Institute for Biological Sciences,10010 N Torrey Pines Rd,La Jolla,CA 92037,USA
| | - Steven T Peltier
- 1Center for Research in Biological Systems,National Center for Microscopy and Imaging Research,University of California at San Diego,9500 Gilman Drive,La Jolla,CA 92093,USA
| | - Satchidananda Panda
- 3Salk Institute for Biological Sciences,10010 N Torrey Pines Rd,La Jolla,CA 92037,USA
| | - Arno Merkle
- 2Carl Zeiss X-ray Microscopy Inc.,4385 Hopyard Rd #100,Pleasanton,CA 94588,USA
| | - Mark H Ellisman
- 1Center for Research in Biological Systems,National Center for Microscopy and Imaging Research,University of California at San Diego,9500 Gilman Drive,La Jolla,CA 92093,USA
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30
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Klingberg H, B. Oddershede L, Loeschner K, Larsen EH, Loft S, Møller P. Uptake of gold nanoparticles in primary human endothelial cells. Toxicol Res (Camb) 2015. [DOI: 10.1039/c4tx00061g] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Single-particle resolution techniques show that endothelial cells internalise 80 nm unmodified gold nanoparticles by endocytosis with subsequent transport to vesicles.
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Affiliation(s)
- Henrik Klingberg
- Department of Public Health
- Section of Environment Health
- University of Copenhagen
- Copenhagen
- Denmark
| | | | - Katrin Loeschner
- Division of Food Chemistry
- National Food Institute
- Technical University of Denmark
- Søborg
- Denmark
| | - Erik H. Larsen
- Division of Food Chemistry
- National Food Institute
- Technical University of Denmark
- Søborg
- Denmark
| | - Steffen Loft
- Department of Public Health
- Section of Environment Health
- University of Copenhagen
- Copenhagen
- Denmark
| | - Peter Møller
- Department of Public Health
- Section of Environment Health
- University of Copenhagen
- Copenhagen
- Denmark
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31
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Kim Y, Abuelfilat AY, Hoo SP, Al-Abboodi A, Liu B, Ng T, Chan P, Fu J. Tuning the surface properties of hydrogel at the nanoscale with focused ion irradiation. SOFT MATTER 2014; 10:8448-8456. [PMID: 25225831 DOI: 10.1039/c4sm01061b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
With the site-specific machining capability of Focused Ion Beam (FIB) irradiation, we aim to tailor the surface morphology and physical attributes of biocompatible hydrogel at the nano/micro scale particularly for tissue engineering and other biomedical studies. Thin films of Gtn-HPA/CMC-Tyr hydrogels were deposited on a gold-coated substrate and were subjected to irradiation with a kiloelectronvolt (keV) gallium ion beam. The sputtering yield, surface morphology and mechanical property changes were investigated using Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM) and Monte Carlo simulations. The sputtering yield of the hydrogel was found to be approximately 0.47 μm(3) nC(-1) compared with Monte-Carlo simulation results of 0.09 μm(3) nC(-1). Compared to the surface roughness of the pristine hydrogel at approximately 2 nm, the average surface roughness significantly increased with the increase of ion fluence with measurements extended to 20 nm at 100 pC μm(-2). Highly packed submicron porous patterns were also revealed with AFM, while significantly decreased pore sizes and increased porosity were found with ion irradiation at oblique incidence. The Young's modulus of irradiated hydrogel determined using AFM force spectroscopy was revealed to be dependent on ion fluence. Compared to the original Young's modulus value of 20 MPa, irradiation elevated the value to 250 MPa and 350 MPa at 1 pC μm(-2) and 100 pC μm(-2), respectively. Cell culture studies confirmed that the irradiated hydrogel samples were biocompatible, and the generated nanoscale patterns remained stable under physiological conditions.
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Affiliation(s)
- Y Kim
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia.
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32
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Ahlberg S, Antonopulos A, Diendorf J, Dringen R, Epple M, Flöck R, Goedecke W, Graf C, Haberl N, Helmlinger J, Herzog F, Heuer F, Hirn S, Johannes C, Kittler S, Köller M, Korn K, Kreyling WG, Krombach F, Lademann J, Loza K, Luther EM, Malissek M, Meinke MC, Nordmeyer D, Pailliart A, Raabe J, Rancan F, Rothen-Rutishauser B, Rühl E, Schleh C, Seibel A, Sengstock C, Treuel L, Vogt A, Weber K, Zellner R. PVP-coated, negatively charged silver nanoparticles: A multi-center study of their physicochemical characteristics, cell culture and in vivo experiments. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2014; 5:1944-65. [PMID: 25383306 PMCID: PMC4222445 DOI: 10.3762/bjnano.5.205] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 10/07/2014] [Indexed: 04/14/2023]
Abstract
PVP-capped silver nanoparticles with a diameter of the metallic core of 70 nm, a hydrodynamic diameter of 120 nm and a zeta potential of -20 mV were prepared and investigated with regard to their biological activity. This review summarizes the physicochemical properties (dissolution, protein adsorption, dispersability) of these nanoparticles and the cellular consequences of the exposure of a broad range of biological test systems to this defined type of silver nanoparticles. Silver nanoparticles dissolve in water in the presence of oxygen. In addition, in biological media (i.e., in the presence of proteins) the surface of silver nanoparticles is rapidly coated by a protein corona that influences their physicochemical and biological properties including cellular uptake. Silver nanoparticles are taken up by cell-type specific endocytosis pathways as demonstrated for hMSC, primary T-cells, primary monocytes, and astrocytes. A visualization of particles inside cells is possible by X-ray microscopy, fluorescence microscopy, and combined FIB/SEM analysis. By staining organelles, their localization inside the cell can be additionally determined. While primary brain astrocytes are shown to be fairly tolerant toward silver nanoparticles, silver nanoparticles induce the formation of DNA double-strand-breaks (DSB) and lead to chromosomal aberrations and sister-chromatid exchanges in Chinese hamster fibroblast cell lines (CHO9, K1, V79B). An exposure of rats to silver nanoparticles in vivo induced a moderate pulmonary toxicity, however, only at rather high concentrations. The same was found in precision-cut lung slices of rats in which silver nanoparticles remained mainly at the tissue surface. In a human 3D triple-cell culture model consisting of three cell types (alveolar epithelial cells, macrophages, and dendritic cells), adverse effects were also only found at high silver concentrations. The silver ions that are released from silver nanoparticles may be harmful to skin with disrupted barrier (e.g., wounds) and induce oxidative stress in skin cells (HaCaT). In conclusion, the data obtained on the effects of this well-defined type of silver nanoparticles on various biological systems clearly demonstrate that cell-type specific properties as well as experimental conditions determine the biocompatibility of and the cellular responses to an exposure with silver nanoparticles.
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33
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Liu B, Uddin MH, Ng TW, Paterson DL, Velkov T, Li J, Fu J. In situ probing the interior of single bacterial cells at nanometer scale. NANOTECHNOLOGY 2014; 25:415101. [PMID: 25257833 DOI: 10.1088/0957-4484/25/41/415101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report a novel approach to probe the interior of single bacterial cells at nanometre resolution by combining focused ion beam (FIB) and atomic force microscopy (AFM). After removing layers of pre-defined thickness in the order of 100 nm on the target bacterial cells with FIB milling, AFM of different modes can be employed to probe the cellular interior under both ambient and aqueous environments. Our initial investigations focused on the surface topology induced by FIB milling and the hydration effects on AFM measurements, followed by assessment of the sample protocols. With fine-tuning of the process parameters, in situ AFM probing beneath the bacterial cell wall was achieved for the first time. We further demonstrate the proposed method by performing a spatial mapping of intracellular elasticity and chemistry of the multi-drug resistant strain Klebsiella pneumoniae cells prior to and after it was exposed to the 'last-line' antibiotic polymyxin B. Our results revealed increased stiffness occurring in both surface and interior regions of the treated cells, suggesting loss of integrity of the outer membrane from polymyxin treatments. In addition, the hydrophobicity measurement using a functionalized AFM tip was able to highlight the evident hydrophobic portion of the cell such as the regions containing cell membrane. We expect that the proposed FIB-AFM platform will help in gaining deeper insights of bacteria-drug interactions to develop potential strategies for combating multi-drug resistance.
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34
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Patwardhan A, Ashton A, Brandt R, Butcher S, Carzaniga R, Chiu W, Collinson L, Doux P, Duke E, Ellisman MH, Franken E, Grünewald K, Heriche JK, Koster A, Kühlbrandt W, Lagerstedt I, Larabell C, Lawson CL, Saibil HR, Sanz-García E, Subramaniam S, Verkade P, Swedlow JR, Kleywegt GJ. A 3D cellular context for the macromolecular world. Nat Struct Mol Biol 2014; 21:841-5. [PMID: 25289590 PMCID: PMC4346196 DOI: 10.1038/nsmb.2897] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community.
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Affiliation(s)
- Ardan Patwardhan
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | | | | | - Sarah Butcher
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Raffaella Carzaniga
- Electron Microscopy Unit, Cancer Research UK London Research Institute, London, UK
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Lucy Collinson
- Electron Microscopy Unit, Cancer Research UK London Research Institute, London, UK
| | - Pascal Doux
- FEI Visualization Sciences Group, Mérignac, France
| | | | - Mark H Ellisman
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research (NCMIR), University of California, San Diego, San Diego, California, USA
| | - Erik Franken
- FEI Electron Optics B.V., Eindhoven, the Netherlands
| | - Kay Grünewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Jean-Karim Heriche
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Abraham Koster
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute for Biophysics, Frankfurt, Germany
| | - Ingvar Lagerstedt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Carolyn Larabell
- Department of Anatomy, University of California, San Francisco, San Francisco, California, USA
| | - Catherine L Lawson
- Research Collaboratory for Structural Bioinformatics, Rutgers University, Piscataway, New Jersey, USA
| | - Helen R Saibil
- Institute of Structural and Molecular Biology, Department of Crystallography, Birkbeck College, London, UK
| | - Eduardo Sanz-García
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Sriram Subramaniam
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Paul Verkade
- Wolfson Bioimaging Facility, School of Biochemistry, University of Bristol, Bristol, UK
| | - Jason R Swedlow
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Gerard J Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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35
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Do T, Murphy G, Earl LA, Del Prete GQ, Grandinetti G, Li GH, Estes JD, Rao P, Trubey CM, Thomas J, Spector J, Bliss D, Nath A, Lifson JD, Subramaniam S. Three-dimensional imaging of HIV-1 virological synapses reveals membrane architectures involved in virus transmission. J Virol 2014; 88:10327-39. [PMID: 24965444 PMCID: PMC4178837 DOI: 10.1128/jvi.00788-14] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 06/12/2014] [Indexed: 01/25/2023] Open
Abstract
UNLABELLED HIV transmission efficiency is greatly increased when viruses are transmitted at virological synapses formed between infected and uninfected cells. We have previously shown that virological synapses formed between HIV-pulsed mature dendritic cells (DCs) and uninfected T cells contain interdigitated membrane surfaces, with T cell filopodia extending toward virions sequestered deep inside invaginations formed on the DC membrane. To explore membrane structural changes relevant to HIV transmission across other types of intercellular conjugates, we used a combination of light and focused ion beam scanning electron microscopy (FIB-SEM) to determine the three-dimensional (3D) architectures of contact regions between HIV-1-infected CD4(+) T cells and either uninfected human CD4(+) T cells or human fetal astrocytes. We present evidence that in each case, membrane extensions that originate from the uninfected cells, either as membrane sheets or filopodial bridges, are present and may be involved in HIV transmission from infected to uninfected cells. We show that individual virions are distributed along the length of astrocyte filopodia, suggesting that virus transfer to the astrocytes is mediated, at least in part, by processes originating from the astrocyte itself. Mechanisms that selectively disrupt the polarization and formation of such membrane extensions could thus represent a possible target for reducing viral spread. IMPORTANCE Our findings lead to new insights into unique aspects of HIV transmission in the brain and at T cell-T cell synapses, which are thought to be a predominant mode of rapid HIV transmission early in the infection process.
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Affiliation(s)
- Thao Do
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gavin Murphy
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lesley A Earl
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gregory Q Del Prete
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland, USA
| | - Giovanna Grandinetti
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Guan-Han Li
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Jacob D Estes
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland, USA
| | - Prashant Rao
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Charles M Trubey
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland, USA
| | - James Thomas
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland, USA
| | - Jeffrey Spector
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Donald Bliss
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland, USA
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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36
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Abstract
Synaptic ribbons are presynaptic protein structures found at many synapses that convey graded, "analog" sensory signals in the visual, auditory, and vestibular pathways. Ribbons, typically anchored to the presynaptic membrane and surrounded by tethered synaptic vesicles, are thought to regulate or facilitate vesicle delivery to the presynaptic membrane. No direct evidence exists, however, to indicate how vesicles interact with the ribbon or, once attached, move along the ribbon's surface to reach the presynaptic release sites at its base. To address these questions, we have created, validated, and tested a passive vesicle diffusion model of retinal rod bipolar cell ribbon synapses. We used axial (bright-field) electron tomography in the scanning transmission electron microscopy to obtain 3D structures of rat rod bipolar cell terminals in 1-μm-thick sections of retinal tissue at an isotropic spatial resolution of ∼3 nm. The resulting structures were then incorporated with previously published estimates of vesicle diffusion dynamics into numerical simulations that accurately reproduced electrophysiologically measured vesicle release/replenishment rates and vesicle pool sizes. The simulations suggest that, under physiologically realistic conditions, diffusion of vesicles crowded on the ribbon surface gives rise to a flow field that enhances delivery of vesicles to the presynaptic membrane without requiring an active transport mechanism. Numerical simulations of ribbon-vesicle interactions predict that transient binding and unbinding of multiple tethers to each synaptic vesicle may achieve sufficiently tight association of vesicles to the ribbon while permitting the fast diffusion along the ribbon that is required to sustain high release rates.
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37
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Risco C, de Castro IF, Sanz-Sánchez L, Narayan K, Grandinetti G, Subramaniam S. Three-Dimensional Imaging of Viral Infections. Annu Rev Virol 2014; 1:453-73. [PMID: 26958730 DOI: 10.1146/annurev-virology-031413-085351] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Three-dimensional (3D) imaging technologies are beginning to have significant impact in the field of virology, as they are helping us understand how viruses take control of cells. In this article we review several methodologies for 3D imaging of cells and show how these technologies are contributing to the study of viral infections and the characterization of specialized structures formed in virus-infected cells. We include 3D reconstruction by transmission electron microscopy (TEM) using serial sections, electron tomography, and focused ion beam scanning electron microscopy (FIB-SEM). We summarize from these methods selected contributions to our understanding of viral entry, replication, morphogenesis, egress and propagation, and changes in the spatial architecture of virus-infected cells. In combination with live-cell imaging, correlative microscopy, and new techniques for molecular mapping in situ, the availability of these methods for 3D imaging is expected to provide deeper insights into understanding the structural and dynamic aspects of viral infection.
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Affiliation(s)
- Cristina Risco
- Cell Structure Laboratory, National Center for Biotechnology (CNB-CSIC), Madrid 28049, Spain;
| | | | - Laura Sanz-Sánchez
- Cell Structure Laboratory, National Center for Biotechnology (CNB-CSIC), Madrid 28049, Spain;
| | - Kedar Narayan
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, Maryland 20892;
| | - Giovanna Grandinetti
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, Maryland 20892;
| | - Sriram Subramaniam
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, Maryland 20892;
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38
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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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39
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Pascual García C, Burchardt AD, Carvalho RN, Gilliland D, C. António D, Rossi F, Lettieri T. Detection of silver nanoparticles inside marine diatom Thalassiosira pseudonana by electron microscopy and focused ion beam. PLoS One 2014; 9:e96078. [PMID: 24797958 PMCID: PMC4010438 DOI: 10.1371/journal.pone.0096078] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/03/2014] [Indexed: 11/19/2022] Open
Abstract
In the following article an electron/ion microscopy study will be presented which investigates the uptake of silver nanoparticles (AgNPs) by the marine diatom Thalassiosira pseudonana, a primary producer aquatic species. This organism has a characteristic silica exoskeleton that may represent a barrier for the uptake of some chemical pollutants, including nanoparticles (NPs), but that presents a technical challenge when attempting to use electron-microscopy (EM) methods to study NP uptake. Here we present a convenient method to detect the NPs interacting with the diatom cell. It is based on a fixation procedure involving critical point drying which, without prior slicing of the cell, allows its inspection using transmission electron microscopy. Employing a combination of electron and ion microscopy techniques to selectively cut the cell where the NPs were detected, we are able to demonstrate and visualize for the first time the presence of AgNPs inside the cell membrane.
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Affiliation(s)
- César Pascual García
- European Commission—Joint Research Centre, Institute for Health and Consumer Protection, Ispra (VA), Italy
- * E-mail: (CPG); (TL)
| | - Alina D. Burchardt
- European Commission—Joint Research Centre, Institute for Environment and Sustainability, Ispra (VA), Italy
- FU-Berlin, Fachbereich Biologie, Chemie, Pharmazie, Berlin, Germany
| | - Raquel N. Carvalho
- European Commission—Joint Research Centre, Institute for Environment and Sustainability, Ispra (VA), Italy
| | - Douglas Gilliland
- European Commission—Joint Research Centre, Institute for Health and Consumer Protection, Ispra (VA), Italy
| | - Diana C. António
- European Commission—Joint Research Centre, Institute for Health and Consumer Protection, Ispra (VA), Italy
- Departamento de Biologia and CESAM, Universidade de Aveiro, Aveiro, Portugal
| | - François Rossi
- European Commission—Joint Research Centre, Institute for Health and Consumer Protection, Ispra (VA), Italy
| | - Teresa Lettieri
- European Commission—Joint Research Centre, Institute for Environment and Sustainability, Ispra (VA), Italy
- * E-mail: (CPG); (TL)
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40
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KIZILYAPRAK C, DARASPE J, HUMBEL B. Focused ion beam scanning electron microscopy in biology. J Microsc 2014; 254:109-14. [DOI: 10.1111/jmi.12127] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 03/12/2014] [Indexed: 12/27/2022]
Affiliation(s)
- C. KIZILYAPRAK
- Electron Microscopy Facility; University of Lausanne; Biophore 1015 Lausanne Switzerland
| | - J. DARASPE
- Electron Microscopy Facility; University of Lausanne; Biophore 1015 Lausanne Switzerland
| | - B.M. HUMBEL
- Electron Microscopy Facility; University of Lausanne; Biophore 1015 Lausanne Switzerland
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41
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Liu B, Yu HH, Ng TW, Paterson DL, Velkov T, Li J, Fu J. Nanoscale focused ion beam tomography of single bacterial cells for assessment of antibiotic effects. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2014; 20:537-547. [PMID: 24589280 DOI: 10.1017/s1431927614000026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Antibiotic resistance is a major risk to human health, and to provide valuable insights into mechanisms of resistance, innovative methods are needed to examine the cellular responses to antibiotic treatment. Focused ion beam tomography is proposed to image and assess the detailed three-dimensional (3D) ultrastructure of single bacterial cells. By iteratively removing slices of thickness in the order of 10 nm, high magnification 2D images can be acquired by scanning electron microscopy at single-digit nanometer resolution. In this study, Klebsiella pneumoniae was treated with polymyxin B, and 3D models of both cell envelope and cytoplasm regions containing the nucleoid and ribosomes were reconstructed. The 3D volume containing the nucleoid and ribosomes was significantly smaller, and the cell length along the longitudinal axis was extended by 40% in the treated cells, implying stress responses to the drug treatment. More than a 200% increase in protrusions per unit surface area on the cell envelope was observed in the curvature analysis after treatment. Experiments by conventional transmission electron microscopy and atomic force microscopy were also performed, followed by comparison and discussions. In conclusion, the proposed 3D imaging method and associated analysis provide a unique tool for the assessment of antibiotic effects on multidrug-resistant bacteria at nanometer resolution.
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Affiliation(s)
- Boyin Liu
- 1 Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Heidi H Yu
- 2 Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Tuck Wah Ng
- 1 Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - David L Paterson
- 3 Centre for Clinical Research, University of Queensland, Brisbane, QLD 4072, Australia
| | - Tony Velkov
- 2 Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Jian Li
- 2 Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Jing Fu
- 1 Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
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42
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Abstract
Three-dimensional information is much easier to understand than a set of two-dimensional images. Therefore a layman is thrilled by the pseudo-3D image taken in a scanning electron microscope (SEM) while, when seeing a transmission electron micrograph, his imagination is challenged. First approaches to gain insight in the third dimension were to make serial microtome sections of a region of interest (ROI) and then building a model of the object. Serial microtome sectioning is a tedious and skill-demanding work and therefore seldom done. In the last two decades with the increase of computer power, sophisticated display options, and the development of new instruments, an SEM with a built-in microtome as well as a focused ion beam scanning electron microscope (FIB-SEM), serial sectioning, and 3D analysis has become far easier and faster.Due to the relief like topology of the microtome trimmed block face of resin-embedded tissue, the ROI can be searched in the secondary electron mode, and at the selected spot, the ROI is prepared with the ion beam for 3D analysis. For FIB-SEM tomography, a thin slice is removed with the ion beam and the newly exposed face is imaged with the electron beam, usually by recording the backscattered electrons. The process, also called "slice and view," is repeated until the desired volume is imaged.As FIB-SEM allows 3D imaging of biological fine structure at high resolution of only small volumes, it is crucial to perform slice and view at carefully selected spots. Finding the region of interest is therefore a prerequisite for meaningful imaging. Thin layer plastification of biofilms offers direct access to the original sample surface and allows the selection of an ROI for site-specific FIB-SEM tomography just by its pronounced topographic features.
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Affiliation(s)
- Caroline Kizilyaprak
- Electron Microscopy Facility, Biophore, University of Lausanne, Lausanne, Switzerland
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43
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Narayan K, Danielson CM, Lagarec K, Lowekamp BC, Coffman P, Laquerre A, Phaneuf MW, Hope TJ, Subramaniam S. Multi-resolution correlative focused ion beam scanning electron microscopy: applications to cell biology. J Struct Biol 2013; 185:278-84. [PMID: 24300554 DOI: 10.1016/j.jsb.2013.11.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 11/21/2013] [Accepted: 11/24/2013] [Indexed: 11/30/2022]
Abstract
Efficient correlative imaging of small targets within large fields is a central problem in cell biology. Here, we demonstrate a series of technical advances in focused ion beam scanning electron microscopy (FIB-SEM) to address this issue. We report increases in the speed, robustness and automation of the process, and achieve consistent z slice thickness of ∼3 nm. We introduce "keyframe imaging" as a new approach to simultaneously image large fields of view and obtain high-resolution 3D images of targeted sub-volumes. We demonstrate application of these advances to image post-fusion cytoplasmic intermediates of the HIV core. Using fluorescently labeled cell membranes, proteins and HIV cores, we first produce a "target map" of an HIV infected cell by fluorescence microscopy. We then generate a correlated 3D EM volume of the entire cell as well as high-resolution 3D images of individual HIV cores, achieving correlative imaging across a volume scale of 10(9) in a single automated experimental run.
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Affiliation(s)
- Kedar Narayan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Cindy M Danielson
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Ken Lagarec
- Fibics Incorporated, 556 Booth St., Suite 200, Ottawa, Ontario K1A 0G1, Canada
| | | | - Phil Coffman
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Alexandre Laquerre
- Fibics Incorporated, 556 Booth St., Suite 200, Ottawa, Ontario K1A 0G1, Canada
| | - Michael W Phaneuf
- Fibics Incorporated, 556 Booth St., Suite 200, Ottawa, Ontario K1A 0G1, Canada
| | - Thomas J Hope
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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44
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Remis JP, Wei D, Gorur A, Zemla M, Haraga J, Allen S, Witkowska HE, Costerton JW, Berleman JE, Auer M. Bacterial social networks: structure and composition of Myxococcus xanthus outer membrane vesicle chains. Environ Microbiol 2013; 16:598-610. [PMID: 23848955 DOI: 10.1111/1462-2920.12187] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 06/08/2013] [Indexed: 11/30/2022]
Abstract
The social soil bacterium, Myxococcus xanthus, displays a variety of complex and highly coordinated behaviours, including social motility, predatory rippling and fruiting body formation. Here we show that M. xanthus cells produce a network of outer membrane extensions in the form of outer membrane vesicle chains and membrane tubes that interconnect cells. We observed peritrichous display of vesicles and vesicle chains, and increased abundance in biofilms compared with planktonic cultures. By applying a range of imaging techniques, including three-dimensional (3D) focused ion beam scanning electron microscopy, we determined these structures to range between 30 and 60 nm in width and up to 5 μm in length. Purified vesicle chains consist of typical M. xanthus lipids, fucose, mannose, N-acetylglucosamine and N-acetylgalactoseamine carbohydrates and a small set of cargo protein. The protein content includes CglB and Tgl outer membrane proteins known to be transferable between cells in a contact-dependent manner. Most significantly, the 3D organization of cells within biofilms indicates that cells are connected via an extensive network of membrane extensions that may connect cells at the level of the periplasmic space. Such a network would allow the transfer of membrane proteins and other molecules between cells, and therefore could provide a mechanism for the coordination of social activities.
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Affiliation(s)
- Jonathan P Remis
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94025, USA
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Satori CP, Henderson MM, Krautkramer EA, Kostal V, Distefano MM, Arriaga EA. Bioanalysis of eukaryotic organelles. Chem Rev 2013; 113:2733-811. [PMID: 23570618 PMCID: PMC3676536 DOI: 10.1021/cr300354g] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Chad P. Satori
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Michelle M. Henderson
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Elyse A. Krautkramer
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Vratislav Kostal
- Tescan, Libusina trida 21, Brno, 623 00, Czech Republic
- Institute of Analytical Chemistry ASCR, Veveri 97, Brno, 602 00, Czech Republic
| | - Mark M. Distefano
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Edgar A. Arriaga
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
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McAughtrie S, Lau K, Faulds K, Graham D. 3D optical imaging of multiple SERS nanotags in cells. Chem Sci 2013. [DOI: 10.1039/c3sc51437d] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Abstract
Cellular energy homeostasis is a crucial function of oxidative tissues but becomes altered with obesity, a major health problem that is rising unabated and demands attention. Maintaining cardiac lipid homeostasis relies on complex processes and pathways that require concerted actions between lipid droplets (LDs) and mitochondria to prevent intracellular accumulation of bioactive or toxic lipids while providing an efficient supply of lipid for conversion into ATP. While cardiac mitochondria have been extensively studied, cardiac LDs and their role in heart function have not been fully characterized. The cardiac LD compartment is highly dynamic and individual LD is small, making their study challenging. Here, we describe a simple procedure to isolate cardiac LDs that provide sufficient amounts of highly enriched material to allow subsequent protein and lipid biochemical characterization. We also present a detailed protocol to image cardiac LDs by conventional transmission electronic microscopy to provide two-dimensional (2D) analyses of cardiac LDs and mitochondria. Finally, we discuss the potential advantages of dual ion beam and electron beam platform (FIB-SEM) technology to study the cardiac LDs and mitochondria by allowing 3D imaging analysis.
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Affiliation(s)
- Hong Wang
- Division of Endocrinology, Department of Medicine, School of Medicine, University of Maryland, Baltimore, Maryland, USA
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Novo S, Barrios L, Ibáñez E, Nogués C. The zona pellucida porosity: three-dimensional reconstruction of four types of mouse oocyte zona pellucida using a dual beam microscope. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2012; 18:1442-1449. [PMID: 23237572 DOI: 10.1017/s1431927612013487] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In the last decade, the applicability of focus ion beam-field emission scanning electron microscopy (FIB-FESEM) in the biological field has begun to get relevance. Among the possibilities offered by FIB-FESEM, high-resolution three-dimensional (3D) reconstruction of biological structures is one of the most interesting. Using this tool, the 3D porosity of four different types of mouse oocyte zona pellucida (ZP) was analyzed. A surface analysis of the mouse oocyte ZP was first performed by SEM. Next, one oocyte per ZP type was selected, and an area of its ZP was completely milled, using the cut and view mode, in the FIB-FESEM. Through a 3D reconstruction of the milled area, a map of the distribution of the pores across the ZP was established and the number and volume of pores were quantified, thus enabling for the first time the study of the inner porosity of the mouse ZP. Differences in ZP porosity observed among the four types analyzed allowed us to outline a model to explain the changes that the ZP undergoes through immature, mature, predegenerative, and degenerative stages.
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Affiliation(s)
- Sergi Novo
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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Wei D, Jacobs S, Modla S, Zhang S, Young CL, Cirino R, Caplan J, Czymmek K. High-resolution three-dimensional reconstruction of a whole yeast cell using focused-ion beam scanning electron microscopy. Biotechniques 2012; 53:41-8. [PMID: 22780318 DOI: 10.2144/000113850] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/29/2012] [Indexed: 11/23/2022] Open
Abstract
We developed an approach for focused gallium-ion beam scanning electron microscopy with energy filtered detection of backscattered electrons to create near isometric voxels for high-resolution whole cell visualization. Specifically, this method allowed us to create three-dimensional volumes of high-pressure frozen, freeze-substituted Saccharomyces cerevisiae yeast cells with pixel resolutions down to 3 nm/pixel in x, y, and z, supported by both empirical data and Monte Carlo simulations. As a result, we were able to segment and quantify data sets of numerous targeted subcellular structures/organelles at high-resolution, including the volume, volume percentage, and surface area of the endoplasmic reticulum, cell wall, vacuoles, and mitochondria from an entire cell. Sites of mitochondrial and endoplasmic reticulum interconnectivity were readily identified in rendered data sets. The ability to visualize, segment, and quantify entire eukaryotic cells at high-resolution (potentially sub-5 nanometers isotropic voxels) will provide new perspectives and insights of the inner workings of cells.
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Chojnacki J, Müller B. Investigation of HIV-1 assembly and release using modern fluorescence imaging techniques. Traffic 2012; 14:15-24. [PMID: 22957540 DOI: 10.1111/tra.12006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 09/04/2012] [Accepted: 09/07/2012] [Indexed: 12/17/2022]
Abstract
The replication of HIV-1, like that of all viruses, is intimately connected with cellular structures and pathways. For many years, bulk biochemical and cell biological methods were the main approaches employed to investigate interactions between HIV-1 and its host cell. However, during the past decade advancements in fluorescence imaging technologies opened new possibilities for the direct visualization of individual steps occurring throughout the viral replication cycle. Electron microscopy (EM) methods, which have traditionally been employed for the study of viruses, are complemented by fluorescence microscopy (FM) techniques that allow us to follow the dynamics of virus-cell interaction. Subdiffraction fluorescence microscopy, as well as correlative EM/FM approaches, are narrowing the fundamental gap between the high structural resolution provided by EM and the high temporal resolution and throughput accomplished by FM. The application of modern microscopy to the study of HIV-1-host cell interactions has provided insights into the biology of the virus which could not easily, or not at all, have been gained by other methods. Here, we review how modern fluorescence imaging techniques enhanced our knowledge of the dynamic and structural changes involved in HIV-1 particle formation.
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Affiliation(s)
- Jakub Chojnacki
- Department of Infectious Diseases, Virology, University Hospital of Heidelberg, Heidelberg, Germany
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