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Hayashi S, Ohno N, Knott G, Molnár Z. Correlative light and volume electron microscopy to study brain development. Microscopy (Oxf) 2023; 72:279-286. [PMID: 36620906 DOI: 10.1093/jmicro/dfad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/06/2023] [Indexed: 01/10/2023] Open
Abstract
Recent advances in volume electron microscopy (EM) have been driving our thorough understanding of the brain architecture. Volume EM becomes increasingly powerful when cells and their subcellular structures that are imaged in light microscopy are correlated to those in ultramicrographs obtained with EM. This correlative approach, called correlative light and volume electron microscopy (vCLEM), is used to link three-dimensional ultrastructural information with physiological data such as intracellular Ca2+ dynamics. Genetic tools to express fluorescent proteins and/or an engineered form of a soybean ascorbate peroxidase allow us to perform vCLEM using natural landmarks including blood vessels without immunohistochemical staining. This immunostaining-free vCLEM has been successfully employed in two-photon Ca2+ imaging in vivo as well as in studying complex synaptic connections in thalamic neurons that receive a variety of specialized inputs from the cerebral cortex. In this mini-review, we overview how volume EM and vCLEM have contributed to studying the developmental processes of the brain. We also discuss potential applications of genetic manipulation of target cells using clustered regularly interspaced short palindromic repeats-associated protein 9 and subsequent volume EM to the analysis of protein localization as well as to loss-of-function studies of genes regulating brain development. We give examples for the combinatorial usage of genetic tools with vCLEM that will further enhance our understanding of regulatory mechanisms underlying brain development.
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Affiliation(s)
- Shuichi Hayashi
- Department of Anatomy, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
- Division of Ultrastructural Research, National Institute for Physiological Sciences, 5-1 Higashiyama Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Graham Knott
- Biological Electron Microscopy Facility, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Route Cantonale, Lausanne CH-1015, Switzerland
| | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK
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2
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Tamada H. Three-dimensional ultrastructure analysis of organelles in injured motor neuron. Anat Sci Int 2023:10.1007/s12565-023-00720-y. [PMID: 37071350 DOI: 10.1007/s12565-023-00720-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/23/2023] [Indexed: 04/19/2023]
Abstract
Morphological analysis of organelles is one of the important clues for understanding the cellular conditions and mechanisms occurring in cells. In particular, nanoscale information within crowded intracellular organelles of tissues provide more direct implications when compared to analyses of cells in culture or isolation. However, there are some difficulties in detecting individual shape using light microscopy, including super-resolution microscopy. Transmission electron microscopy (TEM), wherein the ultrastructure can be imaged at the membrane level, cannot determine the whole structure, and analyze it quantitatively. Volume EM, such as focused ion beam/scanning electron microscopy (FIB/SEM), can be a powerful tool to explore the details of three-dimensional ultrastructures even within a certain volume, and to measure several parameters from them. In this review, the advantages of FIB/SEM analysis in organelle studies are highlighted along with the introduction of mitochondrial analysis in injured motor neurons. This would aid in understanding the morphological details of mitochondria, especially those distributed in the cell bodies as well as in the axon initial segment (AIS) in mouse tissues. These regions have not been explored thus far due to the difficulties encountered in accessing their images by conditional microscopies. Some mechanisms of nerve regeneration have also been discussed with reference to the obtained findings. Finally, future perspectives on FIB/SEM are introduced. The combination of biochemical and genetic understanding of organelle structures and a nanoscale understanding of their three-dimensional distribution and morphology will help to match achievements in genomics and structural biology.
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Affiliation(s)
- Hiromi Tamada
- Functional Anatomy and Neuroscience, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-Ku, Nagoya, Aichi, 466-8550, Japan.
- Anatomy, Graduate School of Medicines, University of Fukui, Matsuokashimoaizuki, Eiheiji-Cho, Yoshida-Gun, Fukui, 910-1193, Japan.
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3
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Proteomic mapping and optogenetic manipulation of membrane contact sites. Biochem J 2022; 479:1857-1875. [PMID: 36111979 PMCID: PMC9555801 DOI: 10.1042/bcj20220382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
Abstract
Membrane contact sites (MCSs) mediate crucial physiological processes in eukaryotic cells, including ion signaling, lipid metabolism, and autophagy. Dysregulation of MCSs is closely related to various diseases, such as type 2 diabetes mellitus (T2DM), neurodegenerative diseases, and cancers. Visualization, proteomic mapping and manipulation of MCSs may help the dissection of the physiology and pathology MCSs. Recent technical advances have enabled better understanding of the dynamics and functions of MCSs. Here we present a summary of currently known functions of MCSs, with a focus on optical approaches to visualize and manipulate MCSs, as well as proteomic mapping within MCSs.
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4
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Kievits AJ, Lane R, Carroll EC, Hoogenboom JP. How innovations in methodology offer new prospects for volume electron microscopy. J Microsc 2022; 287:114-137. [PMID: 35810393 PMCID: PMC9546337 DOI: 10.1111/jmi.13134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 11/29/2022]
Abstract
Detailed knowledge of biological structure has been key in understanding biology at several levels of organisation, from organs to cells and proteins. Volume electron microscopy (volume EM) provides high resolution 3D structural information about tissues on the nanometre scale. However, the throughput rate of conventional electron microscopes has limited the volume size and number of samples that can be imaged. Recent improvements in methodology are currently driving a revolution in volume EM, making possible the structural imaging of whole organs and small organisms. In turn, these recent developments in image acquisition have created or stressed bottlenecks in other parts of the pipeline, like sample preparation, image analysis and data management. While the progress in image analysis is stunning due to the advent of automatic segmentation and server‐based annotation tools, several challenges remain. Here we discuss recent trends in volume EM, emerging methods for increasing throughput and implications for sample preparation, image analysis and data management.
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Affiliation(s)
- Arent J. Kievits
- Imaging Physics Delft University of Technology Delft 2624CJ The Netherlands
| | - Ryan Lane
- Imaging Physics Delft University of Technology Delft 2624CJ The Netherlands
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5
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Guerin CJ, Lippens S. Correlative light and volume electron microscopy (vCLEM): How community participation can advance developing technologies. J Microsc 2021; 284:97-102. [PMID: 34476818 PMCID: PMC9291772 DOI: 10.1111/jmi.13056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/31/2021] [Accepted: 08/31/2021] [Indexed: 12/28/2022]
Abstract
Correlative light and electron microscopy is a valuable tool to image samples across resolution scales and link data on structure and function. While studies using this technique have been available since the 1960s, recent developments have enabled applying these workflows to large volumes of cells and tissues. Much of the development in this area has been facilitated through the collaborative efforts of microscopists and commercial companies to bring the methods, hardware and image processing technologies needed into laboratories and core imaging facilities. This is a prime example of how what was once a niche area can be brought into the mainstream of microscopy by the efforts of imaging pioneers who push the boundaries of possibility.
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Affiliation(s)
| | - Saskia Lippens
- VIB Bio Imaging Core, VIB - Ghent University, Ghent, Belgium
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6
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Phng LK, Belting HG. Endothelial cell mechanics and blood flow forces in vascular morphogenesis. Semin Cell Dev Biol 2021; 120:32-43. [PMID: 34154883 DOI: 10.1016/j.semcdb.2021.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/10/2021] [Accepted: 06/10/2021] [Indexed: 12/21/2022]
Abstract
The vertebrate cardiovascular system is made up by a hierarchically structured network of highly specialised blood vessels. This network emerges during early embryogenesis and evolves in size and complexity concomitant with embryonic growth and organ formation. Underlying this plasticity are actin-driven endothelial cell behaviours, which allow endothelial cells to change their shape and move within the vascular network. In this review, we discuss the cellular and molecular mechanisms involved in vascular network formation and how these intrinsic mechanisms are influenced by haemodynamic forces provided by pressurized blood flow. While most of this review focusses on in vivo evidence from zebrafish embryos, we also mention complementary findings obtained in other experimental systems.
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Affiliation(s)
- Li-Kun Phng
- Laboratory for Vascular Morphogenesis, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan.
| | - Heinz-Georg Belting
- Department of Cell Biology, Biozentrum, University of Basel, Basel 4056, Switzerland.
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7
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Ueda T, Morita K, Koyama F, Teramura Y, Nakagawa T, Nakamura S, Matsumoto Y, Inoue T, Nakamoto T, Sasaki Y, Kuge H, Takeda M, Ohbayashi C, Fujii H, Sho M. A detailed comparison between the endoscopic images using blue laser imaging and three-dimensional reconstructed pathological images of colonic lesions. PLoS One 2020; 15:e0235279. [PMID: 32598341 PMCID: PMC7323971 DOI: 10.1371/journal.pone.0235279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/12/2020] [Indexed: 01/18/2023] Open
Abstract
Blue laser/light imaging (BLI) is an image-enhanced endoscopy (IEE) technique that can provide an accurate diagnosis by closely observing the surface structure of various colonic lesions. However, complete correspondence between endoscopic images and pathological images has not been demonstrated. The aim of this study was to accurately compare endoscopic images and the pathological images using a three-dimensionally (3D) reconstructed pathological model. Continuous thin layer sections were prepared from colonic tissue specimens and immunohistochemically stained for CD34 and CAM5.2. Three-dimensional reconstructed images were created by superimposing immunohistochemically stained pathological images. The endoscopic image with magnifying BLI was compared with the top view of the 3D reconstructed image to identify any one-to-one correspondence between the endoscopic images and histopathological images using the gland orifices and microvessels as a guide. Using 3D reconstructed pathological images, we were able to identify the location on the endoscope image in cases of colonic adenocarcinoma, adenoma and normal mucosa. As a result, the horizontal plane of the endoscopic image and the vertical plane of the 2D pathological specimen were able to be compared, and we successfully determined the visible blood vessel depth and performed a detailed evaluation on magnifying BLI. Examples are as follows: (1) The median vasculature depth from the mucosal surface that could be recognized as vasculature on magnifying BLI was 29.4 μm. The median depth of unrecognizable vessels on magnifying BLI was 218.8 μm, which was significantly deeper than recognizable vessels. (2) Some brownish structures were suggested to potentially be not only dense vessels, vessel expansions, corrupted vessels but also bleeding or extravasation of erythrocytes. Overall, we demonstrated a new approach to matching endoscopic images and pathological findings using a 3D-reconstructed pathological model immunohistochemically stained for CD34 and CAM5.2. This approach may increase the overall understanding of endoscopic images and positively contribute to making more accurate endoscopic diagnoses.
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Affiliation(s)
- Takeshi Ueda
- Department of Surgery, Nara Medical University, Kashihara, Japan
- Department of Surgery, Minami-Nara General Medical center, Yoshino, Nara, Japan
| | - Kohei Morita
- Department of Diagnostic Pathology, Nara Medical University, Kashihara, Japan
| | - Fumikazu Koyama
- Department of Surgery, Nara Medical University, Kashihara, Japan
- Department of Endoscopy, Nara Medical University Hospital, Kashihara, Japan
| | - Yuichi Teramura
- Clinical Research Endoscopy System Division and Medical System Business Division, FUJIFILM Corporation, Tokyo, Japan
| | | | - Shinji Nakamura
- Department of Surgery, Takanohara Central Hospital, Nara, Japan
| | - Yayoi Matsumoto
- Department of Surgery, Nara Medical University, Kashihara, Japan
| | - Takashi Inoue
- Department of Surgery, Nara Medical University, Kashihara, Japan
| | - Takayuki Nakamoto
- Department of Surgery, Nara Medical University, Kashihara, Japan
- Department of Endoscopy, Nara Medical University Hospital, Kashihara, Japan
| | - Yoshiyuki Sasaki
- Department of Surgery, Nara Medical University, Kashihara, Japan
| | - Hiroyuki Kuge
- Department of Surgery, Nara Medical University, Kashihara, Japan
| | - Maiko Takeda
- Department of Diagnostic Pathology, Nara Medical University, Kashihara, Japan
| | - Chiho Ohbayashi
- Department of Diagnostic Pathology, Nara Medical University, Kashihara, Japan
| | - Hisao Fujii
- Gastrointestinal Endoscopy and IBD center, Yoshida Hospital, Nara, Japan
| | - Masayuki Sho
- Department of Surgery, Nara Medical University, Kashihara, Japan
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8
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Cheng D, Morsch M, Shami GJ, Chung RS, Braet F. Observation and characterisation of macrophages in zebrafish liver. Micron 2020; 132:102851. [PMID: 32092694 DOI: 10.1016/j.micron.2020.102851] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/12/2020] [Accepted: 02/12/2020] [Indexed: 01/22/2023]
Abstract
Kupffer cells are liver-resident macrophages that play an important role in mediating immune-related functions in mammals and humans. They are well-known for their capacity to phagocytose large amounts of waste complexes, cell debris, microbial particles and even malignant cells. Location, appearance and functional aspects are important features used to identify these characteristic cells of the liver sinusoid. To-date, there is limited information on the occurrence of macrophages in zebrafish liver. Therefore, we aimed to characterise the ultrastructural and functional aspects of liver-associated macrophages in the zebrafish model by taking advantage of the latest advances in zebrafish genetics and multimodal correlative imaging. Herein, we report on the occurrence of macrophages within the zebrafish liver exhibiting conventional ultrastructural features (e.g. presence of pseudopodia, extensive lysosomal apparatus, a phagolysosome and making up ∼3% of the liver volume). Intriguingly, these cells were not located within the sinusoidal vascular bed of hepatic tissue but instead resided between hepatocytes and lacked phagocytic function. While our results demonstrated the presence and structural similarities with liver macrophages from other experimental models, their functional characteristics were distinctly different from Kupffer cells that have been described in rodents and humans. These findings illustrate that the innate immune system of the zebrafish liver has some distinctly different characteristics compared to other animal experimental models. This conclusion underpins our call for future studies in order to have a better understanding of the physiological role of macrophages residing between the parenchymal cells of the zebrafish liver.
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Affiliation(s)
- Delfine Cheng
- School of Medical Sciences (Discipline of Anatomy and Histology) - The Bosch Institute, The University of Sydney, NSW 2006, Australia.
| | - Marco Morsch
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Gerald J Shami
- School of Medical Sciences (Discipline of Anatomy and Histology) - The Bosch Institute, The University of Sydney, NSW 2006, Australia.
| | - Roger S Chung
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Filip Braet
- School of Medical Sciences (Discipline of Anatomy and Histology) - The Bosch Institute, The University of Sydney, NSW 2006, Australia; Australian Centre for Microscopy & Microanalysis, The University of Sydney, NSW 2006, Australia; Charles Perkins Centre (Cellular Imaging Facility), The University of Sydney, NSW 2006, Australia.
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9
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O'Brown NM, Megason SG, Gu C. Suppression of transcytosis regulates zebrafish blood-brain barrier function. eLife 2019; 8:47326. [PMID: 31429822 PMCID: PMC6726461 DOI: 10.7554/elife.47326] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022] Open
Abstract
As an optically transparent model organism with an endothelial blood-brain barrier (BBB), zebrafish offer a powerful tool to study the vertebrate BBB. However, the precise developmental profile of functional zebrafish BBB acquisition and the subcellular and molecular mechanisms governing the zebrafish BBB remain poorly characterized. Here, we capture the dynamics of developmental BBB leakage using live imaging, revealing a combination of steady accumulation in the parenchyma and sporadic bursts of tracer leakage. Electron microscopy studies further reveal high levels of transcytosis in brain endothelium early in development that are suppressed later. The timing of this suppression of transcytosis coincides with the establishment of BBB function. Finally, we demonstrate a key mammalian BBB regulator Mfsd2a, which inhibits transcytosis, plays a conserved role in zebrafish, as mfsd2aa mutants display increased BBB permeability due to increased transcytosis. Our findings indicate a conserved developmental program of barrier acquisition between zebrafish and mice.
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Affiliation(s)
- Natasha M O'Brown
- Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Chenghua Gu
- Department of Neurobiology, Harvard Medical School, Boston, United States
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10
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Lippens S, Kremer A, Borghgraef P, Guérin CJ. Serial block face-scanning electron microscopy for volume electron microscopy. Methods Cell Biol 2019; 152:69-85. [PMID: 31326027 DOI: 10.1016/bs.mcb.2019.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
There are different technologies that can be used to obtain a 3D image at nanometer resolution. Over the past decade, there has been a growing interest in applying Serial Block Face Scanning Electron Microscopy (SBF-SEM) in different fields of life science research. This technology has the advantage that it can cover a range of volumes, going from monolayers to multiple tissue layers in all three dimensions. SBF-SEM was originally used in neuroscience and then expanded to other research domains. The whole process of sample preparation for SBF-SEM is very long and consists of many steps, which makes adjustment of a given workflow very challenging. Here we describe the SBF-SEM workflow and those steps in the process that can be tweaked for any sample.
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Affiliation(s)
- Saskia Lippens
- VIB BioImaging Core, VIB, Ghent, Belgium; VIB Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
| | - Anna Kremer
- VIB BioImaging Core, VIB, Ghent, Belgium; VIB Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Peter Borghgraef
- VIB BioImaging Core, VIB, Ghent, Belgium; VIB Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Christopher J Guérin
- VIB BioImaging Core, VIB, Ghent, Belgium; VIB Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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11
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Smith D, Starborg T. Serial block face scanning electron microscopy in cell biology: Applications and technology. Tissue Cell 2019; 57:111-122. [DOI: 10.1016/j.tice.2018.08.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/22/2018] [Accepted: 08/26/2018] [Indexed: 10/28/2022]
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12
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Mantani Y, Haruta T, Nishida M, Yokoyama T, Hoshi N, Kitagawa H. Three-dimensional analysis of fibroblast-like cells in the lamina propria of the rat ileum using serial block-face scanning electron microscopy. J Vet Med Sci 2019; 81:454-465. [PMID: 30700677 PMCID: PMC6451913 DOI: 10.1292/jvms.18-0654] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Serial block-face scanning electron microscopy (SBF-SEM) is useful for three-dimensional observation of tissues or cells at high-resolution. In this study, SBF-SEM was used to
three-dimensionally analyze the characteristics of fibroblast-like cells (FBLCs) in the rat ileal lamina propria (LP). The results revealed that FBLCs in LP could be divided into four types,
tentatively named FBLC type I-IV, based on the external cellular appearance, abundance or shape of each organelle, detailed distribution in the LP and relationship with surrounding cells.
FBLC-I and -II localized around the intestinal crypt (InC), FBLC-III localized from the lateral portion of InC to the apical portion of the intestinal villus (InV), and FBLC-IV localized in
the InV. FBLC-I, -II and -III, but not FBLC-IV, localized beneath the epithelium. FBLC-II possessed thin lamellar-shaped endoplasmic reticula, whereas FBLC-I possessed expanded endoplasmic
reticula that occasionally showed a spherical shape. FBLC-III and -IV possessed a cytoplasmic region with high-electron density and no organelles immediately beneath the cellular membrane;
this region was found at the epithelial sides in FBLC-III and scattered in FBLC-IV. FBLC-IV were in constant close proximity to villous myocytes throughout the InV and also in contact with
FBLC-III especially in the apical portion of the InV. FBLC-I, -II and -IV, but not -III, were constantly found to be in contact with various immunocompetent cells in the LP.
Three-dimensional analysis using SBF-SEM indicates that four types of FBLC localized in the rat ileal LP.
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Affiliation(s)
- Youhei Mantani
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Tomohiro Haruta
- Bio 3D Promotion Group, Application Management Department, JEOL Ltd., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Miho Nishida
- Laboratory of Animal Molecular Morphology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Toshifumi Yokoyama
- Laboratory of Animal Molecular Morphology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Nobuhiko Hoshi
- Laboratory of Animal Molecular Morphology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Hiroshi Kitagawa
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
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13
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Rosowski EE, Knox BP, Archambault LS, Huttenlocher A, Keller NP, Wheeler RT, Davis JM. The Zebrafish as a Model Host for Invasive Fungal Infections. J Fungi (Basel) 2018; 4:jof4040136. [PMID: 30551557 PMCID: PMC6308935 DOI: 10.3390/jof4040136] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 12/14/2022] Open
Abstract
The zebrafish has become a widely accepted model host for studies of infectious disease, including fungal infections. The species is genetically tractable, and the larvae are transparent and amenable to prolonged in vivo imaging and small molecule screening. The aim of this review is to provide a thorough introduction into the published studies of fungal infection in the zebrafish and the specific ways in which this model has benefited the field. In doing so, we hope to provide potential new zebrafish researchers with a snapshot of the current toolbox and prior results, while illustrating how the model has been used well and where the unfulfilled potential of this model can be found.
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Affiliation(s)
- Emily E Rosowski
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53716, USA.
| | - Benjamin P Knox
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53716, USA.
| | - Linda S Archambault
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA.
| | - Anna Huttenlocher
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53716, USA.
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53792, USA.
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53716, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Robert T Wheeler
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA.
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA.
| | - J Muse Davis
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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14
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Development Aspects of Zebrafish Myotendinous Junction: a Model System for Understanding Muscle Basement Membrane Formation and Failure. CURRENT PATHOBIOLOGY REPORTS 2017. [DOI: 10.1007/s40139-017-0140-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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15
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Janel S, Werkmeister E, Bongiovanni A, Lafont F, Barois N. CLAFEM: Correlative light atomic force electron microscopy. Methods Cell Biol 2017; 140:165-185. [PMID: 28528632 DOI: 10.1016/bs.mcb.2017.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Atomic force microscopy (AFM) is becoming increasingly used in the biology field. It can give highly accurate topography and biomechanical quantitative data, such as adhesion, elasticity, and viscosity, on living samples. Nowadays, correlative light electron microscopy is a must-have tool in the biology field that combines different microscopy techniques to spatially and temporally analyze the structure and function of a single sample. Here, we describe the combination of AFM with superresolution light microscopy and electron microscopy. We named this technique correlative light atomic force electron microscopy (CLAFEM) in which AFM can be used on fixed and living cells in association with superresolution light microscopy and further processed for transmission or scanning electron microscopy. We herein illustrate this approach to observe cellular bacterial infection and cytoskeleton. We show that CLAFEM brings complementary information at the cellular level, from on the one hand protein distribution and topography at the nanometer scale and on the other hand elasticity at the piconewton scales to fine ultrastructural details.
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Affiliation(s)
- Sébastien Janel
- Univ. Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Elisabeth Werkmeister
- Univ. Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Antonino Bongiovanni
- Univ. Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Frank Lafont
- Univ. Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Nicolas Barois
- Univ. Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille - CIIL - Center for Infection and Immunity of Lille, Lille, France
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16
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Labernadie A, Kato T, Brugués A, Serra-Picamal X, Derzsi S, Arwert E, Weston A, González-Tarragó V, Elosegui-Artola A, Albertazzi L, Alcaraz J, Roca-Cusachs P, Sahai E, Trepat X. A mechanically active heterotypic E-cadherin/N-cadherin adhesion enables fibroblasts to drive cancer cell invasion. Nat Cell Biol 2017; 19:224-237. [PMID: 28218910 PMCID: PMC5831988 DOI: 10.1038/ncb3478] [Citation(s) in RCA: 495] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/18/2017] [Indexed: 02/08/2023]
Abstract
Cancer-associated fibroblasts (CAFs) promote tumour invasion and metastasis. We show that CAFs exert a physical force on cancer cells that enables their collective invasion. Force transmission is mediated by a heterophilic adhesion involving N-cadherin at the CAF membrane and E-cadherin at the cancer cell membrane. This adhesion is mechanically active; when subjected to force it triggers β-catenin recruitment and adhesion reinforcement dependent on α-catenin/vinculin interaction. Impairment of E-cadherin/N-cadherin adhesion abrogates the ability of CAFs to guide collective cell migration and blocks cancer cell invasion. N-cadherin also mediates repolarization of the CAFs away from the cancer cells. In parallel, nectins and afadin are recruited to the cancer cell/CAF interface and CAF repolarization is afadin dependent. Heterotypic junctions between CAFs and cancer cells are observed in patient-derived material. Together, our findings show that a mechanically active heterophilic adhesion between CAFs and cancer cells enables cooperative tumour invasion.
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Affiliation(s)
- Anna Labernadie
- Institute for Bioengineering of Catalonia, Barcelona 08028,
Spain
| | - Takuya Kato
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT,
UK
| | - Agustí Brugués
- Institute for Bioengineering of Catalonia, Barcelona 08028,
Spain
| | - Xavier Serra-Picamal
- Institute for Bioengineering of Catalonia, Barcelona 08028,
Spain
- Unitat de Biofísica i Bioenginyeria, Facultat de Medicina,
Universitat de Barcelona, Barcelona 08036, Spain
| | - Stefanie Derzsi
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT,
UK
| | - Esther Arwert
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT,
UK
| | - Anne Weston
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT,
UK
| | | | | | | | - Jordi Alcaraz
- Unitat de Biofísica i Bioenginyeria, Facultat de Medicina,
Universitat de Barcelona, Barcelona 08036, Spain
| | - Pere Roca-Cusachs
- Institute for Bioengineering of Catalonia, Barcelona 08028,
Spain
- Unitat de Biofísica i Bioenginyeria, Facultat de Medicina,
Universitat de Barcelona, Barcelona 08036, Spain
| | - Erik Sahai
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT,
UK
| | - Xavier Trepat
- Institute for Bioengineering of Catalonia, Barcelona 08028,
Spain
- Unitat de Biofísica i Bioenginyeria, Facultat de Medicina,
Universitat de Barcelona, Barcelona 08036, Spain
- Institució Catalana de Recerca i Estudis Avançats
(ICREA), Barcelona 08010, Spain
- Centro de Investigación Biomédica en Red en
Bioingeniería, Biomateriales y Nanomedicina, Barcelona 08028, Spain
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17
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Russell MRG, Lerner TR, Burden JJ, Nkwe DO, Pelchen-Matthews A, Domart MC, Durgan J, Weston A, Jones ML, Peddie CJ, Carzaniga R, Florey O, Marsh M, Gutierrez MG, Collinson LM. 3D correlative light and electron microscopy of cultured cells using serial blockface scanning electron microscopy. J Cell Sci 2017; 130:278-291. [PMID: 27445312 PMCID: PMC5394779 DOI: 10.1242/jcs.188433] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 07/14/2016] [Indexed: 12/12/2022] Open
Abstract
The processes of life take place in multiple dimensions, but imaging these processes in even three dimensions is challenging. Here, we describe a workflow for 3D correlative light and electron microscopy (CLEM) of cell monolayers using fluorescence microscopy to identify and follow biological events, combined with serial blockface scanning electron microscopy to analyse the underlying ultrastructure. The workflow encompasses all steps from cell culture to sample processing, imaging strategy, and 3D image processing and analysis. We demonstrate successful application of the workflow to three studies, each aiming to better understand complex and dynamic biological processes, including bacterial and viral infections of cultured cells and formation of entotic cell-in-cell structures commonly observed in tumours. Our workflow revealed new insight into the replicative niche of Mycobacterium tuberculosis in primary human lymphatic endothelial cells, HIV-1 in human monocyte-derived macrophages, and the composition of the entotic vacuole. The broad application of this 3D CLEM technique will make it a useful addition to the correlative imaging toolbox for biomedical research.
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Affiliation(s)
- Matthew R G Russell
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Thomas R Lerner
- Host-pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Jemima J Burden
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - David O Nkwe
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Annegret Pelchen-Matthews
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Marie-Charlotte Domart
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Anne Weston
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Martin L Jones
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Christopher J Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Raffaella Carzaniga
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Mark Marsh
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Maximiliano G Gutierrez
- Host-pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Lucy M Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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18
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19
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Schieber NL, Machado P, Markert SM, Stigloher C, Schwab Y, Steyer AM. Minimal resin embedding of multicellular specimens for targeted FIB-SEM imaging. Methods Cell Biol 2017; 140:69-83. [DOI: 10.1016/bs.mcb.2017.03.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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20
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Abstract
Myelination by oligodendrocytes in the central nervous system (CNS) and Schwann cells in the peripheral nervous system is essential for nervous system function and health. Despite its importance, we have a relatively poor understanding of the molecular and cellular mechanisms that regulate myelination in the living animal, particularly in the CNS. This is partly due to the fact that myelination commences around birth in mammals, by which time the CNS is complex and largely inaccessible, and thus very difficult to image live in its intact form. As a consequence, in recent years much effort has been invested in the use of smaller, simpler, transparent model organisms to investigate mechanisms of myelination in vivo. Although the majority of such studies have employed zebrafish, the Xenopus tadpole also represents an important complementary system with advantages for investigating myelin biology in vivo. Here we review how the natural features of zebrafish embryos and larvae and Xenopus tadpoles make them ideal systems for experimentally interrogating myelination by live imaging. We outline common transgenic technologies used to generate zebrafish and Xenopus that express fluorescent reporters, which can be used to image myelination. We also provide an extensive overview of the imaging modalities most commonly employed to date to image the nervous system in these transparent systems, and also emerging technologies that we anticipate will become widely used in studies of zebrafish and Xenopus myelination in the near future.
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Affiliation(s)
- Jenea M Bin
- Centre for Neuroregeneration, MS Society Centre for Translational Research, Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
| | - David A Lyons
- Centre for Neuroregeneration, MS Society Centre for Translational Research, Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
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21
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Karreman MA, Hyenne V, Schwab Y, Goetz JG. Intravital Correlative Microscopy: Imaging Life at the Nanoscale. Trends Cell Biol 2016; 26:848-863. [DOI: 10.1016/j.tcb.2016.07.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/12/2016] [Accepted: 07/15/2016] [Indexed: 01/04/2023]
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22
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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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23
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Beckwith MS, Beckwith KS, Sikorski P, Skogaker NT, Flo TH, Halaas Ø. Seeing a Mycobacterium-Infected Cell in Nanoscale 3D: Correlative Imaging by Light Microscopy and FIB/SEM Tomography. PLoS One 2015; 10:e0134644. [PMID: 26406896 PMCID: PMC4583302 DOI: 10.1371/journal.pone.0134644] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/10/2015] [Indexed: 12/13/2022] Open
Abstract
Mycobacteria pose a threat to the world health today, with pathogenic and opportunistic bacteria causing tuberculosis and non-tuberculous disease in large parts of the population. Much is still unknown about the interplay between bacteria and host during infection and disease, and more research is needed to meet the challenge of drug resistance and inefficient vaccines. This work establishes a reliable and reproducible method for performing correlative imaging of human macrophages infected with mycobacteria at an ultra-high resolution and in 3D. Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) tomography is applied, together with confocal fluorescence microscopy for localization of appropriately infected cells. The method is based on an Aclar poly(chloro-tri-fluoro)ethylene substrate, micropatterned into an advantageous geometry by a simple thermomoulding process. The platform increases the throughput and quality of FIB/SEM tomography analyses, and was successfully applied to detail the intracellular environment of a whole mycobacterium-infected macrophage in 3D.
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Affiliation(s)
- Marianne Sandvold Beckwith
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Cancer Research and Molecular Medicine, NTNU, Trondheim, Norway
- * E-mail:
| | | | | | - Nan Tostrup Skogaker
- Department of Laboratory Medicine, Children’s and Women’s Health, NTNU, Trondheim, Norway
| | - Trude Helen Flo
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Cancer Research and Molecular Medicine, NTNU, Trondheim, Norway
| | - Øyvind Halaas
- Department of Cancer Research and Molecular Medicine, NTNU, Trondheim, Norway
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24
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de Boer P, Hoogenboom JP, Giepmans BNG. Correlated light and electron microscopy: ultrastructure lights up! Nat Methods 2015; 12:503-13. [PMID: 26020503 DOI: 10.1038/nmeth.3400] [Citation(s) in RCA: 281] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 04/15/2015] [Indexed: 12/15/2022]
Abstract
Microscopy has gone hand in hand with the study of living systems since van Leeuwenhoek observed living microorganisms and cells in 1674 using his light microscope. A spectrum of dyes and probes now enable the localization of molecules of interest within living cells by fluorescence microscopy. With electron microscopy (EM), cellular ultrastructure has been revealed. Bridging these two modalities, correlated light microscopy and EM (CLEM) opens new avenues. Studies of protein dynamics with fluorescent proteins (FPs), which leave the investigator 'in the dark' concerning cellular context, can be followed by EM examination. Rare events can be preselected at the light microscopy level before EM analysis. Ongoing development-including of dedicated probes, integrated microscopes, large-scale and three-dimensional EM and super-resolution fluorescence microscopy-now paves the way for broad CLEM implementation in biology.
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Affiliation(s)
- Pascal de Boer
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jacob P Hoogenboom
- Faculty of Applied Sciences, Delft University of Technology, Delft, the Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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25
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Bazmara H, Soltani M, Sefidgar M, Bazargan M, Mousavi Naeenian M, Rahmim A. The Vital Role of Blood Flow-Induced Proliferation and Migration in Capillary Network Formation in a Multiscale Model of Angiogenesis. PLoS One 2015; 10:e0128878. [PMID: 26047145 PMCID: PMC4457864 DOI: 10.1371/journal.pone.0128878] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/01/2015] [Indexed: 01/16/2023] Open
Abstract
Sprouting angiogenesis and capillary network formation are tissue scale phenomena. There are also sub-scale phenomena involved in angiogenesis including at the cellular and intracellular (molecular) scales. In this work, a multiscale model of angiogenesis spanning intracellular, cellular, and tissue scales is developed in detail. The key events that are considered at the tissue scale are formation of closed flow path (that is called loop in this article) and blood flow initiation in the loop. At the cellular scale, growth, migration, and anastomosis of endothelial cells (ECs) are important. At the intracellular scale, cell phenotype determination as well as alteration due to blood flow is included, having pivotal roles in the model. The main feature of the model is to obtain the physical behavior of a closed loop at the tissue scale, relying on the events at the cellular and intracellular scales, and not by imposing physical behavior upon it. Results show that, when blood flow is considered in the loop, the anastomosed sprouts stabilize and elongate. By contrast, when the loop is modeled without consideration of blood flow, the loop collapses. The results obtained in this work show that proper determination of EC phenotype is the key for its survival.
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Affiliation(s)
- Hossein Bazmara
- Department of Mechanical Engineering, K. N. T. University of Technology, Tehran, Iran
| | - Madjid Soltani
- Department of Mechanical Engineering, K. N. T. University of Technology, Tehran, Iran
- Division of Nuclear Medicine, Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, Baltimore, MD, United States of America
- * E-mail:
| | - Mostafa Sefidgar
- Department of Mechanical Engineering, K. N. T. University of Technology, Tehran, Iran
| | - Majid Bazargan
- Department of Mechanical Engineering, K. N. T. University of Technology, Tehran, Iran
| | | | - Arman Rahmim
- Division of Nuclear Medicine, Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, Baltimore, MD, United States of America
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26
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Mourik MJ, Faas FGA, Zimmermann H, Eikenboom J, Koster AJ. Towards the imaging of Weibel-Palade body biogenesis by serial block face-scanning electron microscopy. J Microsc 2015; 259:97-104. [PMID: 25644989 PMCID: PMC4670698 DOI: 10.1111/jmi.12222] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 12/23/2014] [Indexed: 12/25/2022]
Abstract
Electron microscopy is used in biological research to study the ultrastructure at high resolution to obtain information on specific cellular processes. Serial block face-scanning electron microscopy is a relatively novel electron microscopy imaging technique that allows three-dimensional characterization of the ultrastructure in both tissues and cells by measuring volumes of thousands of cubic micrometres yet at nanometre-scale resolution. In the scanning electron microscope, repeatedly an image is acquired followed by the removal of a thin layer resin embedded biological material by either a microtome or a focused ion beam. In this way, each recorded image contains novel structural information which can be used for three-dimensional analysis. Here, we explore focused ion beam facilitated serial block face-scanning electron microscopy to study the endothelial cell–specific storage organelles, the Weibel–Palade bodies, during their biogenesis at the Golgi apparatus. Weibel–Palade bodies predominantly contain the coagulation protein Von Willebrand factor which is secreted by the cell upon vascular damage. Using focused ion beam facilitated serial block face-scanning electron microscopy we show that the technique has the sensitivity to clearly reveal subcellular details like mitochondrial cristae and small vesicles with a diameter of about 50 nm. Also, we reveal numerous associations between Weibel–Palade bodies and Golgi stacks which became conceivable in large-scale three-dimensional data. We demonstrate that serial block face-scanning electron microscopy is a promising tool that offers an alternative for electron tomography to study subcellular organelle interactions in the context of a complete cell.
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Affiliation(s)
- M J Mourik
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - F G A Faas
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - J Eikenboom
- Department of Thrombosis and Hemostasis, Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - A J Koster
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
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27
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Karreman MA, Mercier L, Schieber NL, Shibue T, Schwab Y, Goetz JG. Correlating intravital multi-photon microscopy to 3D electron microscopy of invading tumor cells using anatomical reference points. PLoS One 2014; 9:e114448. [PMID: 25479106 PMCID: PMC4257674 DOI: 10.1371/journal.pone.0114448] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/06/2014] [Indexed: 01/24/2023] Open
Abstract
Correlative microscopy combines the advantages of both light and electron microscopy to enable imaging of rare and transient events at high resolution. Performing correlative microscopy in complex and bulky samples such as an entire living organism is a time-consuming and error-prone task. Here, we investigate correlative methods that rely on the use of artificial and endogenous structural features of the sample as reference points for correlating intravital fluorescence microscopy and electron microscopy. To investigate tumor cell behavior in vivo with ultrastructural accuracy, a reliable approach is needed to retrieve single tumor cells imaged deep within the tissue. For this purpose, fluorescently labeled tumor cells were subcutaneously injected into a mouse ear and imaged using two-photon-excitation microscopy. Using near-infrared branding, the position of the imaged area within the sample was labeled at the skin level, allowing for its precise recollection. Following sample preparation for electron microscopy, concerted usage of the artificial branding and anatomical landmarks enables targeting and approaching the cells of interest while serial sectioning through the specimen. We describe here three procedures showing how three-dimensional (3D) mapping of structural features in the tissue can be exploited to accurately correlate between the two imaging modalities, without having to rely on the use of artificially introduced markers of the region of interest. The methods employed here facilitate the link between intravital and nanoscale imaging of invasive tumor cells, enabling correlating function to structure in the study of tumor invasion and metastasis.
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Affiliation(s)
- Matthia A. Karreman
- European Molecular Biology Laboratory Heidelberg, Heidelberg, 69117, Germany
| | - Luc Mercier
- Inserm U1109, MN3T, Strasbourg, F-67200, France
- Université de Strasbourg, Strasbourg, F-67000, France
- LabEx Medalis, Université de Strasbourg, Strasbourg, F-67000, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, F-67000, France
| | - Nicole L. Schieber
- European Molecular Biology Laboratory Heidelberg, Heidelberg, 69117, Germany
| | - Tsukasa Shibue
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Yannick Schwab
- European Molecular Biology Laboratory Heidelberg, Heidelberg, 69117, Germany
- * E-mail: (YS); (JGG)
| | - Jacky G. Goetz
- Inserm U1109, MN3T, Strasbourg, F-67200, France
- Université de Strasbourg, Strasbourg, F-67000, France
- LabEx Medalis, Université de Strasbourg, Strasbourg, F-67000, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, F-67000, France
- * E-mail: (YS); (JGG)
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28
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Peddie CJ, Blight K, Wilson E, Melia C, Marrison J, Carzaniga R, Domart MC, O'Toole P, Larijani B, Collinson LM. Correlative and integrated light and electron microscopy of in-resin GFP fluorescence, used to localise diacylglycerol in mammalian cells. Ultramicroscopy 2014; 143:3-14. [PMID: 24637200 PMCID: PMC4045205 DOI: 10.1016/j.ultramic.2014.02.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 02/10/2014] [Accepted: 02/12/2014] [Indexed: 12/11/2022]
Abstract
Fluorescence microscopy of GFP-tagged proteins is a fundamental tool in cell biology, but without seeing the structure of the surrounding cellular space, functional information can be lost. Here we present a protocol that preserves GFP and mCherry fluorescence in mammalian cells embedded in resin with electron contrast to reveal cellular ultrastructure. Ultrathin in-resin fluorescence (IRF) sections were imaged simultaneously for fluorescence and electron signals in an integrated light and scanning electron microscope. We show, for the first time, that GFP is stable and active in resin sections in vacuo. We applied our protocol to study the subcellular localisation of diacylglycerol (DAG), a modulator of membrane morphology and membrane dynamics in nuclear envelope assembly. We show that DAG is localised to the nuclear envelope, nucleoplasmic reticulum and curved tips of the Golgi apparatus. With these developments, we demonstrate that integrated imaging is maturing into a powerful tool for accurate molecular localisation to structure.
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Affiliation(s)
- Christopher J Peddie
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
| | - Ken Blight
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
| | - Emma Wilson
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
| | - Charlotte Melia
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK; Cell Biophysics Laboratory, London Research Institute, Cancer Research UK, London WC2A 3LY, UK; Department of Molecular Cell Biology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Jo Marrison
- Department of Biology, The University of York, Heslington, York, UK
| | - Raffaella Carzaniga
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
| | - Marie-Charlotte Domart
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK; Cell Biophysics Laboratory, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
| | - Peter O'Toole
- Department of Biology, The University of York, Heslington, York, UK
| | - Banafshe Larijani
- Cell Biophysics Laboratory, London Research Institute, Cancer Research UK, London WC2A 3LY, UK; Cell Biophysics Laboratory, Unidad de Biofísica (CSIC-UPV/EHU),Sarriena s/n, 48940 Leioa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Lucy M Collinson
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, London WC2A 3LY, UK
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29
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Bhawana, Miller JL, Cahoon AB. 3D Plant cell architecture of Arabidopsis thaliana (Brassicaceae) using focused ion beam-scanning electron microscopy. APPLICATIONS IN PLANT SCIENCES 2014; 2:apps.1300090. [PMID: 25202629 PMCID: PMC4103436 DOI: 10.3732/apps.1300090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 04/25/2014] [Indexed: 09/06/2023]
Abstract
PREMISE OF THE STUDY Focused ion beam-scanning electron microscopy (FIB-SEM) combines the ability to sequentially mill the sample surface and obtain SEM images that can be used to create 3D renderings with micron-level resolution. We have applied FIB-SEM to study Arabidopsis cell architecture. The goal was to determine the efficacy of this technique in plant tissue and cellular studies and to demonstrate its usefulness in studying cell and organelle architecture and distribution. • METHODS Seed aleurone, leaf mesophyll, stem cortex, root cortex, and petal lamina from Arabidopsis were fixed and embedded for electron microscopy using protocols developed for animal tissues and modified for use with plant cells. Each sample was sectioned using the FIB and imaged with SEM. These serial images were assembled to produce 3D renderings of each cell type. • RESULTS Organelles such as nuclei and chloroplasts were easily identifiable, and other structures such as endoplasmic reticula, lipid bodies, and starch grains were distinguishable in each tissue. • DISCUSSION The application of FIB-SEM produced 3D renderings of five plant cell types and offered unique views of their shapes and internal content. These results demonstrate the usefulness of FIB-SEM for organelle distribution and cell architecture studies.
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Affiliation(s)
- Bhawana
- Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, Tennessee 37132 USA
| | - Joyce L. Miller
- MTSU Interdisciplinary Microanalysis and Imaging Center, Middle Tennessee State University, Murfreesboro, Tennessee 37132 USA
| | - A. Bruce Cahoon
- Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, Tennessee 37132 USA
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30
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Lipke E, Hörnschemeyer T, Pakzad A, Booth CR, Michalik P. Serial block-face imaging and its potential for reconstructing diminutive cell systems: a case study from arthropods. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2014; 20:946-955. [PMID: 24555994 DOI: 10.1017/s1431927614000087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Until recently, three-dimensional reconstruction on an ultrastructural level was only possible using serial section transmission electron microscopy (ssTEM). However, ssTEM is highly challenging and prone to artifacts as, e.g., section loss and image distortions. New methods, such as serial block-face scanning electron microscopy (SBFSEM) overcome these limitations and promise a high lateral resolution. However, little is known about the usability of SBFSEM in diminutive, but highly complex cellular systems. We used spider sperm (~3 µm in diameter), which fulfills these conditions, to analyze the potential of SBFSEM compared with ssTEM. Our data suggest that the resolution obtained by SBFSEM allows depicting structures on a cellular level and is sufficient to discriminate subcellular components, but is highly dependent on previous staining procedures and electron density of the target structures.
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Affiliation(s)
- Elisabeth Lipke
- 1Allgemeine und Systematische Zoologie,Zoologisches Institut und Museum,Ernst-Moritz-Arndt-Universität,J.-S.-Bach-Str. 11/12,D-17487 Greifswald,Germany
| | - Thomas Hörnschemeyer
- 2Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology,Department of Morphology,Systematics and Evolutionary Biology,Georg-August-University,Göttingen,Germany
| | | | | | - Peter Michalik
- 1Allgemeine und Systematische Zoologie,Zoologisches Institut und Museum,Ernst-Moritz-Arndt-Universität,J.-S.-Bach-Str. 11/12,D-17487 Greifswald,Germany
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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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Hughes L, Hawes C, Monteith S, Vaughan S. Serial block face scanning electron microscopy--the future of cell ultrastructure imaging. PROTOPLASMA 2014; 251:395-401. [PMID: 24240569 DOI: 10.1007/s00709-013-0580-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 10/29/2013] [Indexed: 06/02/2023]
Abstract
One of the major drawbacks in transmission electron microscopy has been the production of three-dimensional views of cells and tissues. Currently, there is no one suitable 3D microscopy technique that answers all questions and serial block face scanning electron microscopy (SEM) fills the gap between 3D imaging using high-end fluorescence microscopy and the high resolution offered by electron tomography. In this review, we discuss the potential of the serial block face SEM technique for studying the three-dimensional organisation of animal, plant and microbial cells.
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MESH Headings
- Animals
- Cells/ultrastructure
- Humans
- Image Processing, Computer-Assisted/instrumentation
- Image Processing, Computer-Assisted/methods
- Microscopy, Electron, Scanning/instrumentation
- Microscopy, Electron, Scanning/methods
- Microscopy, Electron, Transmission/instrumentation
- Microscopy, Electron, Transmission/methods
- Microscopy, Fluorescence/instrumentation
- Microscopy, Fluorescence/methods
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Affiliation(s)
- Louise Hughes
- Department of Biological & Medical Sciences, Oxford Brookes University, Headington, Oxford, OX3 0BP, UK
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Three-dimensional aspects of matrix assembly by cells in the developing cornea. Proc Natl Acad Sci U S A 2014; 111:687-92. [PMID: 24385584 DOI: 10.1073/pnas.1313561110] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cell-directed deposition of aligned collagen fibrils during corneal embryogenesis is poorly understood, despite the fact that it is the basis for the formation of a corneal stroma that must be transparent to visible light and biomechanically stable. Previous studies of the structural development of the specialized matrix in the cornea have been restricted to examinations of tissue sections by conventional light or electron microscopy. Here, we use volume scanning electron microscopy, with sequential removal of ultrathin surface tissue sections achieved either by ablation with a focused ion beam or by serial block face diamond knife microtomy, to examine the microanatomy of the cornea in three dimensions and in large tissue volumes. The results show that corneal keratocytes occupy a significantly greater tissue volume than was previously thought, and there is a clear orthogonality in cell and matrix organization, quantifiable by Fourier analysis. Three-dimensional reconstructions reveal actin-associated tubular cell protrusions, reminiscent of filopodia, but extending more than 30 µm into the extracellular space. The highly extended network of these membrane-bound structures mirrors the alignment of collagen bundles and emergent lamellae and, we propose, plays a fundamental role in dictating the orientation of collagen in the developing cornea.
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Lucas MS, Guenthert M, Gasser P, Lucas F, Wepf R. Correlative 3D imaging: CLSM and FIB-SEM tomography using high-pressure frozen, freeze-substituted biological samples. Methods Mol Biol 2014; 1117:593-616. [PMID: 24357381 DOI: 10.1007/978-1-62703-776-1_26] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Correlative light and electron microscopy aims at combining data from different imaging modalities, ideally from the same area of the one sample, in order to achieve a more holistic view of the hierarchical structural organization of cells and tissues. Modern 3D imaging techniques opened up new possibilities to expand morphological studies into the third dimension at the nanometer scale. Here we present an approach to correlate 3D light microscopy data with volume data from focused ion beam-scanning electron microscopy. An adapted sample preparation method based on high-pressure freezing for structure preservation, followed by freeze-substitution for multimodal en bloc imaging, is described. It is based on including fluorescent labeling during freeze-substitution, which enables histological context description of the structure of interest by confocal laser scanning microscopy prior to high-resolution electron microscopy. This information can be employed to relocate the respective structure in the electron microscope. This approach is most suitable for targeted small 3D volume correlation and has the potential to extract statistically relevant data of structural details for systems biology.
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Affiliation(s)
- Miriam S Lucas
- Electron Microscopy ETH Zurich (EMEZ), ETH Zurich, Zurich, Switzerland
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35
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Handschuh S, Baeumler N, Schwaha T, Ruthensteiner B. A correlative approach for combining microCT, light and transmission electron microscopy in a single 3D scenario. Front Zool 2013; 10:44. [PMID: 23915384 PMCID: PMC3750762 DOI: 10.1186/1742-9994-10-44] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/31/2013] [Indexed: 12/28/2022] Open
Abstract
Background In biomedical research, a huge variety of different techniques is currently available for the structural examination of small specimens, including conventional light microscopy (LM), transmission electron microscopy (TEM), confocal laser scanning microscopy (CLSM), microscopic X-ray computed tomography (microCT), and many others. Since every imaging method is physically limited by certain parameters, a correlative use of complementary methods often yields a significant broader range of information. Here we demonstrate the advantages of the correlative use of microCT, light microscopy, and transmission electron microscopy for the analysis of small biological samples. Results We used a small juvenile bivalve mollusc (Mytilus galloprovincialis, approximately 0.8 mm length) to demonstrate the workflow of a correlative examination by microCT, LM serial section analysis, and TEM-re-sectioning. Initially these three datasets were analyzed separately, and subsequently they were fused in one 3D scene. This workflow is very straightforward. The specimen was processed as usual for transmission electron microscopy including post-fixation in osmium tetroxide and embedding in epoxy resin. Subsequently it was imaged with microCT. Post-fixation in osmium tetroxide yielded sufficient X-ray contrast for microCT imaging, since the X-ray absorption of epoxy resin is low. Thereafter, the same specimen was serially sectioned for LM investigation. The serial section images were aligned and specific organ systems were reconstructed based on manual segmentation and surface rendering. According to the region of interest (ROI), specific LM sections were detached from the slides, re-mounted on resin blocks and re-sectioned (ultrathin) for TEM. For analysis, image data from the three different modalities was co-registered into a single 3D scene using the software AMIRA®. We were able to register both the LM section series volume and TEM slices neatly to the microCT dataset, with small geometric deviations occurring only in the peripheral areas of the specimen. Based on co-registered datasets the excretory organs, which were chosen as ROI for this study, could be investigated regarding both their ultrastructure as well as their position in the organism and their spatial relationship to adjacent tissues. We found structures typical for mollusc excretory systems, including ultrafiltration sites at the pericardial wall, and ducts leading from the pericardium towards the kidneys, which exhibit a typical basal infolding system. Conclusions The presented approach allows a comprehensive analysis and presentation of small objects regarding both the overall organization as well as cellular and subcellular details. Although our protocol involves a variety of different equipment and procedures, we maintain that it offers savings in both effort and cost. Co-registration of datasets from different imaging modalities can be accomplished with high-end desktop computers and offers new opportunities for understanding and communicating structural relationships within organisms and tissues. In general, the correlative use of different microscopic imaging techniques will continue to become more widespread in morphological and structural research in zoology. Classical TEM serial section investigations are extremely time consuming, and modern methods for 3D analysis of ultrastructure such as SBF-SEM and FIB-SEM are limited to very small volumes for examination. Thus the re-sectioning of LM sections is suitable for speeding up TEM examination substantially, while microCT could become a key-method for complementing ultrastructural examinations.
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Affiliation(s)
- Stephan Handschuh
- VetImaging, VetCore Facility for Research, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria.
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Siekmann AF, Affolter M, Belting HG. The tip cell concept 10 years after: new players tune in for a common theme. Exp Cell Res 2013; 319:1255-63. [PMID: 23419245 DOI: 10.1016/j.yexcr.2013.01.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 01/31/2013] [Indexed: 01/24/2023]
Affiliation(s)
- Arndt F Siekmann
- Max Planck Institute for Molecular Biomedicine, D-48149 Muenster, Germany.
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Takizawa T, Robinson JM. Correlative fluorescence and transmission electron microscopy in tissues. Methods Cell Biol 2012; 111:37-57. [PMID: 22857922 DOI: 10.1016/b978-0-12-416026-2.00003-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Correlative microscopy has meant different things over the years; currently, this term refers to imaging the same exact structures with two or more imaging modalities. This commonly involves combining fluorescence and electron microscopy. Much of the recent work related to correlative microscopy has been done using cell culture models. However, many biological questions cannot be addressed in these models, but require instead the 3-dimensional organization of cells found in tissues. Herein, we discuss some of the issues related to correlative microscopy of tissues including the major reporter systems presently available for correlative microscopy. We present data from our own work in which we have focused on the use of ultrathin cryosections of tissues as the substrate for immunolabeling to combine immunofluorescence and electron microscopy of the same sub-cellular structures.
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Affiliation(s)
- Toshihiro Takizawa
- Department of Molecular Anatomy, Nippon Medical School, Tokyo 113-8602, Japan
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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: 68] [Impact Index Per Article: 5.7] [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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Giuly RJ, Martone ME, Ellisman MH. Method: automatic segmentation of mitochondria utilizing patch classification, contour pair classification, and automatically seeded level sets. BMC Bioinformatics 2012; 13:29. [PMID: 22321695 PMCID: PMC3293777 DOI: 10.1186/1471-2105-13-29] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 02/09/2012] [Indexed: 11/29/2022] Open
Abstract
Background While progress has been made to develop automatic segmentation techniques for mitochondria, there remains a need for more accurate and robust techniques to delineate mitochondria in serial blockface scanning electron microscopic data. Previously developed texture based methods are limited for solving this problem because texture alone is often not sufficient to identify mitochondria. This paper presents a new three-step method, the Cytoseg process, for automated segmentation of mitochondria contained in 3D electron microscopic volumes generated through serial block face scanning electron microscopic imaging. The method consists of three steps. The first is a random forest patch classification step operating directly on 2D image patches. The second step consists of contour-pair classification. At the final step, we introduce a method to automatically seed a level set operation with output from previous steps. Results We report accuracy of the Cytoseg process on three types of tissue and compare it to a previous method based on Radon-Like Features. At step 1, we show that the patch classifier identifies mitochondria texture but creates many false positive pixels. At step 2, our contour processing step produces contours and then filters them with a second classification step, helping to improve overall accuracy. We show that our final level set operation, which is automatically seeded with output from previous steps, helps to smooth the results. Overall, our results show that use of contour pair classification and level set operations improve segmentation accuracy beyond patch classification alone. We show that the Cytoseg process performs well compared to another modern technique based on Radon-Like Features. Conclusions We demonstrated that texture based methods for mitochondria segmentation can be enhanced with multiple steps that form an image processing pipeline. While we used a random-forest based patch classifier to recognize texture, it would be possible to replace this with other texture identifiers, and we plan to explore this in future work.
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Affiliation(s)
- Richard J Giuly
- Center for Research in Biological Systems, University of California, 9500 Gilman Dr., La Jolla, CA 92093, USA.
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40
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Crumpton-Taylor M, Grandison S, Png KM, Bushby AJ, Smith AM. Control of starch granule numbers in Arabidopsis chloroplasts. PLANT PHYSIOLOGY 2012; 158:905-16. [PMID: 22135430 PMCID: PMC3271777 DOI: 10.1104/pp.111.186957] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/23/2011] [Indexed: 05/19/2023]
Abstract
The aim of this work was to investigate starch granule numbers in Arabidopsis (Arabidopsis thaliana) leaves. Lack of quantitative information on the extent of genetic, temporal, developmental, and environmental variation in granule numbers is an important limitation in understanding control of starch degradation and the mechanism of granule initiation. Two methods were developed for reliable estimation of numbers of granules per chloroplast. First, direct measurements were made on large series of consecutive sections of mesophyll tissue obtained by focused ion beam-scanning electron microscopy. Second, average numbers were calculated from the starch contents of leaves and chloroplasts and estimates of granule mass based on granule dimensions. Examination of wild-type plants and accumulation and regulation of chloroplast (arc) mutants with few, large chloroplasts provided the following new insights. There is wide variation in chloroplast volumes in cells of wild-type leaves. Granule numbers per chloroplast are correlated with chloroplast volume, i.e. large chloroplasts have more granules than small chloroplasts. Mature leaves of wild-type plants and arc mutants have approximately the same number of granules per unit volume of stroma, regardless of the size and number of chloroplasts per cell. Granule numbers per unit volume of stroma are also relatively constant in immature leaves but are greater than in mature leaves. Granule initiation occurs as chloroplasts divide in immature leaves, but relatively little initiation occurs in mature leaves. Changes in leaf starch content over the diurnal cycle are largely brought about by changes in the volume of a fixed number of granules.
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Affiliation(s)
| | | | | | | | - Alison M. Smith
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (M.C.-T., A.M.S.); School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom (S.G.); The Nanovision Centre, School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, United Kingdom (K.M.Y.P., A.J.B.)
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Lucas MS, Günthert M, Gasser P, Lucas F, Wepf R. Bridging microscopes: 3D correlative light and scanning electron microscopy of complex biological structures. Methods Cell Biol 2012; 111:325-56. [PMID: 22857936 DOI: 10.1016/b978-0-12-416026-2.00017-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The rationale of correlative light and electron microscopy (CLEM) is to collect data on different information levels--ideally from an identical area on the same sample--with the aim of combining datasets at different levels of resolution to achieve a more holistic view of the hierarchical structural organization of cells and tissues. Modern three-dimensional (3D) imaging techniques in light and electron microscopy opened up new possibilities to expand morphological studies into the third dimension at the nanometer scale and over various volume dimensions. Here, we present two alternative approaches to correlate 3D light microscopy (LM) data with scanning electron microscopy (SEM) volume data. An adapted sample preparation method based on high-pressure freezing for structure preservation, followed by freeze-substitution for multimodal en-bloc imaging or serial-section imaging is described. The advantages and potential applications are exemplarily shown on various biological samples, such as cells, individual organisms, human tissue, as well as plant tissue. The two CLEM approaches presented here are per se not mutually exclusive, but have their distinct advantages. Confocal laser scanning microscopy (CLSM) and focused ion beam-SEM (FIB-SEM) is most suitable for targeted 3D correlation of small volumes, whereas serial-section LM and SEM imaging has its strength in large-area or -volume screening and correlation. The second method can be combined with immunocytochemical methods. Both methods, however, have the potential to extract statistically relevant data of structural details for systems biology.
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Affiliation(s)
- Miriam S Lucas
- Electron Microscopy ETH Zurich – EMEZ, ETH Zurich, Switzerland
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43
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Murphy GE, Narayan K, Lowekamp BC, Hartnell LM, Heymann JAW, Fu J, Subramaniam S. Correlative 3D imaging of whole mammalian cells with light and electron microscopy. J Struct Biol 2011; 176:268-78. [PMID: 21907806 PMCID: PMC3210386 DOI: 10.1016/j.jsb.2011.08.013] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 08/22/2011] [Accepted: 08/25/2011] [Indexed: 01/19/2023]
Abstract
We report methodological advances that extend the current capabilities of ion-abrasion scanning electron microscopy (IA-SEM), also known as focused ion beam scanning electron microscopy, a newly emerging technology for high resolution imaging of large biological specimens in 3D. We establish protocols that enable the routine generation of 3D image stacks of entire plastic-embedded mammalian cells by IA-SEM at resolutions of ∼10-20nm at high contrast and with minimal artifacts from the focused ion beam. We build on these advances by describing a detailed approach for carrying out correlative live confocal microscopy and IA-SEM on the same cells. Finally, we demonstrate that by combining correlative imaging with newly developed tools for automated image processing, small 100nm-sized entities such as HIV-1 or gold beads can be localized in SEM image stacks of whole mammalian cells. We anticipate that these methods will add to the arsenal of tools available for investigating mechanisms underlying host-pathogen interactions, and more generally, the 3D subcellular architecture of mammalian cells and tissues.
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Affiliation(s)
- Gavin E. Murphy
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892 USA
| | - Kedar Narayan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892 USA
| | - Bradley C. Lowekamp
- Office of High Performance Computing and Communications, National Library of Medicine, NIH, Bethesda, MD 20814 USA
| | - Lisa M. Hartnell
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892 USA
| | - Jurgen A. W. Heymann
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892 USA
| | - Jing Fu
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892 USA
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892 USA
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Endothelial development taking shape. Curr Opin Cell Biol 2011; 23:676-85. [PMID: 22051380 DOI: 10.1016/j.ceb.2011.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 10/12/2011] [Indexed: 11/22/2022]
Abstract
Blood vessel development is a vital process during embryonic development, during tissue growth, regeneration and disease processes in the adult. In the past decade researchers have begun to unravel basic molecular mechanisms that regulate the formation of vascular lumen, sprouting angiogenesis, fusion of vessels, and pruning of the vascular plexus. The understanding of the biology of these angiogenic processes is increasingly driven through studies on vascular development at the cellular resolution. Single cell analysis in vivo, advanced genetic tools and the widespread use of powerful animal models combined with improved imaging possibilities are delivering new insights into endothelial cell form, function and behavior angiogenesis. Moreover, the combination of in silico modeling and experimentation including dynamic imaging promotes insights into higher level cooperative behavior leading to functional patterning of vascular networks. Here we summarize recent concepts and advances in the field of vascular development, focusing in detail on the endothelial cell.
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45
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Knott G, Rosset S, Cantoni M. Focussed ion beam milling and scanning electron microscopy of brain tissue. J Vis Exp 2011:e2588. [PMID: 21775953 PMCID: PMC3196160 DOI: 10.3791/2588] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
This protocol describes how biological samples, like brain tissue, can be imaged in three dimensions using the focussed ion beam/scanning electron microscope (FIB/SEM). The samples are fixed with aldehydes, heavy metal stained using osmium tetroxide and uranyl acetate. They are then dehydrated with alcohol and infiltrated with resin, which is then hardened. Using a light microscope and ultramicrotome with glass knives, a small block containing the region interest close to the surface is made. The block is then placed inside the FIB/SEM, and the ion beam used to roughly mill a vertical face along one side of the block, close to this region. Using backscattered electrons to image the underlying structures, a smaller face is then milled with a finer ion beam and the surface scrutinised more closely to determine the exact area of the face to be imaged and milled. The parameters of the microscope are then set so that the face is repeatedly milled and imaged so that serial images are collected through a volume of the block. The image stack will typically contain isotropic voxels with dimenions as small a 4 nm in each direction. This image quality in any imaging plane enables the user to analyse cell ultrastructure at any viewing angle within the image stack.
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Affiliation(s)
- Graham Knott
- Centre of interdisciplinary electron microscopy, École Polytechnique Fédérale de Lausanne.
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46
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Imaging three-dimensional tissue architectures by focused ion beam scanning electron microscopy. Nat Protoc 2011; 6:845-58. [DOI: 10.1038/nprot.2011.332] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
The zebrafish is a powerful vertebrate system with great advantages for both forward and reverse genetic screens and as a model for human disease conditions. Light microscopy has been used extensively to study zebrafish development but less frequently have these studies been combined with ultrastructural information. Zebrafish embryos are ideal for electron microscopy (EM) with a single transverse section containing many different cell types and tissues. However, conventional methods of EM do not provide optimal preservation of all tissues and are usually incompatible with immunolabelling and visualisation of expressed fluorescently tagged proteins. Here we examine methods that overcome these problems. We summarise a range of methods, applicable to the ultrastructural analysis of zebrafish embryos, including methods for fast freezing and processing of zebrafish embryos. These methods preserve antigenicity, ultrastructure and GFP fluorescence even after embedding in resin. In addition, they are compatible with electron tomography. These methods provide a new set of research tools that provide an additional level of information, complementing current methods for study of this widely used model system.
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Hanssen E, Goldie KN, Tilley L. Ultrastructure of the asexual blood stages of Plasmodium falciparum. Methods Cell Biol 2010; 96:93-116. [PMID: 20869520 DOI: 10.1016/s0091-679x(10)96005-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Plasmodium falciparum is the most deadly of the human malaria parasites. The particular virulence of this species derives from its ability to subvert the physiology of its host during the blood stages of its development. The parasite grows and divides within erythrocytes, feeding on the hemoglobin, and remodeling its host cells so they adhere to blood vessel walls. The advent of molecular transfection technology, coupled with optical microscopy of fluorescent protein reporters, has greatly improved our understanding of the ways in which the malaria parasite alters its host cell. However, a full interpretation of the information from these studies requires similar advances in our knowledge of the ultrastructure of the parasite. Here we give an overview of different electron microscopy techniques that have revealed the fine structure of the parasite at different stages of development. We present data on some of the unusual organelles of P. falciparum, in particular, the membrane structures that are elaborated in the erythrocyte cytoplasm and are thought to play an important role in trafficking of virulence proteins. We present and discuss some of the exciting whole cell imaging techniques that represent a new frontier in the studies of parasite ultrastructure.
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Affiliation(s)
- Eric Hanssen
- Electron Microscopy Unit, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
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Weston AE, Armer HEJ, Collinson LM. Towards native-state imaging in biological context in the electron microscope. J Chem Biol 2009; 3:101-12. [PMID: 19916039 DOI: 10.1007/s12154-009-0033-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 10/22/2009] [Indexed: 12/11/2022] Open
Abstract
Modern cell biology is reliant on light and fluorescence microscopy for analysis of cells, tissues and protein localisation. However, these powerful techniques are ultimately limited in resolution by the wavelength of light. Electron microscopes offer much greater resolution due to the shorter effective wavelength of electrons, allowing direct imaging of sub-cellular architecture. The harsh environment of the electron microscope chamber and the properties of the electron beam have led to complex chemical and mechanical preparation techniques, which distance biological samples from their native state and complicate data interpretation. Here we describe recent advances in sample preparation and instrumentation, which push the boundaries of high-resolution imaging. Cryopreparation, cryoelectron microscopy and environmental scanning electron microscopy strive to image samples in near native state. Advances in correlative microscopy and markers enable high-resolution localisation of proteins. Innovation in microscope design has pushed the boundaries of resolution to atomic scale, whilst automatic acquisition of high-resolution electron microscopy data through large volumes is finally able to place ultrastructure in biological context.
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Affiliation(s)
- Anne E Weston
- Electron Microscopy Unit, London Research Institute, Cancer Research UK, 44 Lincoln's Inn Fields, London, WC2A 3PX UK
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