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Kolotuev I, Williams A, Kizilyaprak C, Pellegrino S, Lewellyn L. Complementary Volume Electron Microscopy-based approaches reveal ultrastructural changes in germline intercellular bridges of D. melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.18.638836. [PMID: 40027623 PMCID: PMC11870571 DOI: 10.1101/2025.02.18.638836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Intercellular bridges are essential to connect developing germline cells. The Drosophila melanogaster egg chamber is a powerful model system to study germline intercellular bridges, or ring canals (RCs). RCs connect the developing oocyte to supporting nurse cells, and defects in their stability or growth lead to infertility. Despite their importance, it has been technically difficult to use electron microscopy-based approaches to monitor changes in RC structure during oogenesis. Here, we describe the application of a complementary set of volume EM-based approaches to visualize ultrastructural changes in the germline RCs. The combination of array tomography (AT) and focused ion beam (FIB) scanning electron microscopy (SEM) has allowed us to gain insight into previously unappreciated aspects of RC structure. We were able to quantify differences in RC size and thickness within and between germ cell clusters at different developmental stages. Within a cluster, RC size correlates with lineage; the largest RCs were formed during the first division, and the smallest RCs were formed during the fourth mitotic division. We observed the formation of membrane interdigitations in the vicinity of RCs much earlier than previously reported, and reconstruction of a RC from a mid-stage EC provided insight into the 3D orientation of these extensive cell-cell contacts. Our imaging also revealed a novel membrane structure that appeared to line the interior of the RC lumen. Although the focus was on ultrastructural changes in the germline RCs, our dataset contains valuable details of additional cell types and structures, including the fusome, the germline stem cells and their niche, and the migrating border cells. This imaging framework could be applied to other tissues or samples that face similar technical challenges, where the small structure of interest is located within a large sample volume.
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Affiliation(s)
- Irina Kolotuev
- University of Lausanne, Faculté de biologie et de médecine, Electron Microscopy Facility, CH-1015 Lausanne, Switzerland
- University of Lausanne, Faculté de biologie et de médecine, Department of Biological Sciences, CH-1005 Lausanne, Switzerland
| | - Abigayle Williams
- Butler University, Department of Biological Sciences, Indianapolis, IN, USA
| | - Caroline Kizilyaprak
- University of Lausanne, Faculté de biologie et de médecine, Electron Microscopy Facility, CH-1015 Lausanne, Switzerland
| | | | - Lindsay Lewellyn
- Butler University, Department of Biological Sciences, Indianapolis, IN, USA
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2
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Miyaki T, Homma N, Kawasaki Y, Kishi M, Yamaguchi J, Kakuta S, Shindo T, Sugiura M, Oliva Trejo JA, Kaneda H, Omotehara T, Takechi M, Negishi-Koga T, Ishijima M, Aoto K, Iseki S, Kitamura K, Muto S, Amagasa M, Hotchi S, Ogura K, Shibata S, Sakai T, Suzuki Y, Ichimura K. Ultrastructural analysis of whole glomeruli using array tomography. J Cell Sci 2024; 137:jcs262154. [PMID: 39171439 DOI: 10.1242/jcs.262154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 08/09/2024] [Indexed: 08/23/2024] Open
Abstract
The renal glomerulus produces primary urine from blood plasma by ultrafiltration. The ultrastructure of the glomerulus is closely related to filtration function and disease development. The ultrastructure of glomeruli has mainly been evaluated using transmission electron microscopy; however, the volume that can be observed using transmission electron microscopy is extremely limited relative to the total volume of the glomerulus. Consequently, observing structures that exist in only one location in each glomerulus, such as the vascular pole, and evaluating low-density or localized lesions are challenging tasks. Array tomography (AT) is a technique used to analyze the ultrastructure of tissues and cells via scanning electron microscopy of serial sections. In this study, we present an AT workflow that is optimized for observing complete serial sections of the whole glomerulus, and we share several analytical examples that use the optimized AT workflow, demonstrating the usefulness of this approach. Overall, this AT workflow can be a powerful tool for structural and pathological evaluation of the glomerulus. This workflow is also expected to provide new insights into the ultrastructure of the glomerulus and its constituent cells.
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Affiliation(s)
- Takayuki Miyaki
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Nozomi Homma
- Department of Nephrology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Yuto Kawasaki
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Mami Kishi
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Junji Yamaguchi
- Laboratory of Morphology and Image Analysis, Research Core Facilities , Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Soichiro Kakuta
- Laboratory of Morphology and Image Analysis, Research Core Facilities , Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Tomoko Shindo
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo 160-0016, Japan
| | - Makoto Sugiura
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Juan Alejandro Oliva Trejo
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Hisako Kaneda
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Takuya Omotehara
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Masaki Takechi
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Takako Negishi-Koga
- Department of Medicine for Orthopedics and Motor Organ, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
- Department of Community Medicine and Research for Bone and Joint Diseases, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Muneaki Ishijima
- Department of Medicine for Orthopedics and Motor Organ, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
- Department of Community Medicine and Research for Bone and Joint Diseases, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Kazushi Aoto
- Central Laboratory, Graduate School of Biomedical and Health Sciences , Hiroshima University, Hiroshima 734-8551, Japan
| | - Sachiko Iseki
- Department of Molecular Craniofacial Embryology and Oral Histology, Graduate School of Medical and Dental Sciences , Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kosuke Kitamura
- Department of Urology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Satoru Muto
- Department of Urology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Mao Amagasa
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Shiori Hotchi
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Kanako Ogura
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Shinsuke Shibata
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo 160-0016, Japan
- Division of Microscopic Anatomy, Graduate School of Medical and Dental Sciences , Niigata University, Niigata City 951-8510, Japan
| | - Tatsuo Sakai
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Yusuke Suzuki
- Department of Nephrology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Koichiro Ichimura
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
- Laboratory of Morphology and Image Analysis, Research Core Facilities , Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
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3
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Brunner M, Lopez-Rodriguez D, Estrada-Meza J, Dali R, Rohrbach A, Deglise T, Messina A, Thorens B, Santoni F, Langlet F. Fasting induces metabolic switches and spatial redistributions of lipid processing and neuronal interactions in tanycytes. Nat Commun 2024; 15:6604. [PMID: 39098920 PMCID: PMC11298547 DOI: 10.1038/s41467-024-50913-w] [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: 08/02/2023] [Accepted: 07/25/2024] [Indexed: 08/06/2024] Open
Abstract
The ependyma lining the third ventricle (3V) in the mediobasal hypothalamus plays a crucial role in energy balance and glucose homeostasis. It is characterized by a high functional heterogeneity and plasticity, but the underlying molecular mechanisms governing its features are not fully understood. Here, 5481 hypothalamic ependymocytes were cataloged using FACS-assisted scRNAseq from fed, 12h-fasted, and 24h-fasted adult male mice. With standard clustering analysis, typical ependymal cells and β2-tanycytes appear sharply defined, but other subpopulations, β1- and α-tanycytes, display fuzzy boundaries with few or no specific markers. Pseudospatial approaches, based on the 3V neuroanatomical distribution, enable the identification of specific versus shared tanycyte markers and subgroup-specific versus general tanycyte functions. We show that fasting dynamically shifts gene expression patterns along the 3V, leading to a spatial redistribution of cell type-specific responses. Altogether, we show that changes in energy status induce metabolic and functional switches in tanycyte subpopulations, providing insights into molecular and functional diversity and plasticity within the tanycyte population.
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Affiliation(s)
- Maxime Brunner
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - David Lopez-Rodriguez
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Judith Estrada-Meza
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Rafik Dali
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Antoine Rohrbach
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Tamara Deglise
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Andrea Messina
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Bernard Thorens
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Federico Santoni
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland.
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
- Institute for Genetic and Biomedical Research (IRGB) - CNR, Monserrato, Italy.
| | - Fanny Langlet
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
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Kolotuev I. Work smart, not hard: How array tomography can help increase the ultrastructure data output. J Microsc 2024; 295:42-60. [PMID: 37626455 DOI: 10.1111/jmi.13217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
Transmission electron microscopy has been essential for understanding cell biology for over six decades. Volume electron microscopy tools, such as serial block face and focused ion beam scanning electron microscopy acquisition, brought a new era to ultrastructure analysis. 'Array Tomography' (AT) refers to sequential image acquisition of resin-embedded sample sections on a large support (coverslip, glass slide, silicon wafers) for immunolabelling with multiple fluorescent labels, occasionally combined with ultrastructure observation. Subsequently, the term was applied to generating and imaging a series of sections to acquire a 3D representation of a structure using scanning electron microscopy (SEM). Although this is a valuable application, the potential of AT is to facilitate many tasks that are difficult or even impossible to obtain by Transmission Electron Microscopy (TEM). Due to the straightforward nature and versatility of AT sample preparation and image acquisition, the technique can be applied practically to any biological sample for selected sections or volume electron microscopy analysis. Furthermore, in addition to the benefits described here, AT is compatible with morphological analysis, multiplex immunolabelling, immune-gold labelling, and correlative light and electron microscopy workflow applicable for single cells, tissue and small organisms. This versatility makes AT attractive not only for basic research but as a diagnostic tool with a simplified routine.
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Affiliation(s)
- Irina Kolotuev
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
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5
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Son R, Yamazawa K, Oguchi A, Suga M, Tamura M, Yanagita M, Murakawa Y, Kume S. Morphomics via next-generation electron microscopy. J Mol Cell Biol 2024; 15:mjad081. [PMID: 38148118 PMCID: PMC11167312 DOI: 10.1093/jmcb/mjad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/02/2022] [Accepted: 12/23/2023] [Indexed: 12/28/2023] Open
Abstract
The living body is composed of innumerable fine and complex structures. Although these structures have been studied in the past, a vast amount of information pertaining to them still remains unknown. When attempting to observe these ultra-structures, the use of electron microscopy (EM) has become indispensable. However, conventional EM settings are limited to a narrow tissue area, which can bias observations. Recently, new trends in EM research have emerged, enabling coverage of far broader, nano-scale fields of view for two-dimensional wide areas and three-dimensional large volumes. Moreover, cutting-edge bioimage informatics conducted via deep learning has accelerated the quantification of complex morphological bioimages. Taken together, these technological and analytical advances have led to the comprehensive acquisition and quantification of cellular morphology, which now arises as a new omics science termed 'morphomics'.
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Affiliation(s)
- Raku Son
- R IKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Kenji Yamazawa
- Advanced Manufacturing Support Team, RIKEN Center for Advanced Photonics, Wako 351-0198, Japan
| | - Akiko Oguchi
- R IKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Mitsuo Suga
- Multimodal Microstructure Analysis Unit, RIKEN-JEOL Collaboration Center, Kobe 650-0047, Japan
| | - Masaru Tamura
- Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan
| | - Motoko Yanagita
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Yasuhiro Murakawa
- R IKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
- IFOM-The FIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Satoshi Kume
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
- Center for Health Science Innovation, Osaka City University, Osaka 530-0011, Japan
- Osaka Electro-Communication University, Neyagawa 572-8530, Japan
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6
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Micheva KD, Burden JJ, Schifferer M. Array tomography: trails to discovery. METHODS IN MICROSCOPY 2024; 1:9-17. [PMID: 39119254 PMCID: PMC11308915 DOI: 10.1515/mim-2024-0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/06/2024] [Indexed: 08/10/2024]
Abstract
Tissue slicing is at the core of many approaches to studying biological structures. Among the modern volume electron microscopy (vEM) methods, array tomography (AT) is based on serial ultramicrotomy, section collection onto solid support, imaging via light and/or scanning electron microscopy, and re-assembly of the serial images into a volume for analysis. While AT largely uses standard EM equipment, it provides several advantages, including long-term preservation of the sample and compatibility with multi-scale and multi-modal imaging. Furthermore, the collection of serial ultrathin sections improves axial resolution and provides access for molecular labeling, which is beneficial for light microscopy and immunolabeling, and facilitates correlation with EM. Despite these benefits, AT techniques are underrepresented in imaging facilities and labs, due to their perceived difficulty and lack of training opportunities. Here we point towards novel developments in serial sectioning and image analysis that facilitate the AT pipeline, and solutions to overcome constraints. Because no single vEM technique can serve all needs regarding field of view and resolution, we sketch a decision tree to aid researchers in navigating the plethora of options available. Lastly, we elaborate on the unexplored potential of AT approaches to add valuable insight in diverse biological fields.
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Affiliation(s)
| | | | - Martina Schifferer
- Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
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7
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Tomasch J, Kopejtka K, Bílý T, Gardiner AT, Gardian Z, Shivaramu S, Koblížek M, Kaftan D. A photoheterotrophic bacterium from Iceland has adapted its photosynthetic machinery to the long days of polar summer. mSystems 2024; 9:e0131123. [PMID: 38376261 PMCID: PMC10949492 DOI: 10.1128/msystems.01311-23] [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: 12/05/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
During their long evolution, anoxygenic phototrophic bacteria have inhabited a wide variety of natural habitats and developed specific strategies to cope with the challenges of any particular environment. Expression, assembly, and safe operation of the photosynthetic apparatus must be regulated to prevent reactive oxygen species generation under illumination in the presence of oxygen. Here, we report on the photoheterotrophic Sediminicoccus sp. strain KRV36, which was isolated from a cold stream in north-western Iceland, 30 km south of the Arctic Circle. In contrast to most aerobic anoxygenic phototrophs, which stop pigment synthesis when illuminated, strain KRV36 maintained its bacteriochlorophyll synthesis even under continuous light. Its cells also contained between 100 and 180 chromatophores, each accommodating photosynthetic complexes that exhibit an unusually large carotenoid absorption spectrum. The expression of photosynthesis genes in dark-adapted cells was transiently downregulated in the first 2 hours exposed to light but recovered to the initial level within 24 hours. An excess of membrane-bound carotenoids as well as high, constitutive expression of oxidative stress response genes provided the required potential for scavenging reactive oxygen species, safeguarding bacteriochlorophyll synthesis and photosystem assembly. The unique cellular architecture and an unusual gene expression pattern represent a specific adaptation that allows the maintenance of anoxygenic phototrophy under arctic conditions characterized by long summer days with relatively low irradiance.IMPORTANCEThe photoheterotrophic bacterium Sediminicoccus sp. KRV36 was isolated from a cold stream in Iceland. It expresses its photosynthesis genes, synthesizes bacteriochlorophyll, and assembles functional photosynthetic complexes under continuous light in the presence of oxygen. Unraveling the molecular basis of this ability, which is exceptional among aerobic anoxygenic phototrophic species, will help to understand the evolution of bacterial photosynthesis in response to changing environmental conditions. It might also open new possibilities for genetic engineering of biotechnologically relevant phototrophs, with the aim of increasing photosynthetic activity and their tolerance to reactive oxygen species.
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Affiliation(s)
- Jürgen Tomasch
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Karel Kopejtka
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Tomáš Bílý
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Alastair T. Gardiner
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Zdenko Gardian
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Sahana Shivaramu
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - David Kaftan
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department Chemistry, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
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8
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Britz S, Luccardini C, Markert SM, Merrill SA, Bessereau JL, Stigloher C. Array tomography of in vivo labeled synaptic receptors. Methods Cell Biol 2024; 187:139-174. [PMID: 38705623 DOI: 10.1016/bs.mcb.2024.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Array tomography (AT) allows one to localize sub-cellular components within the structural context of cells in 3D through the imaging of serial sections. Using this technique, the z-resolution can be improved physically by cutting ultra-thin sections. Nevertheless, conventional immunofluorescence staining of those sections is time consuming and requires relatively large amounts of costly antibody solutions. Moreover, epitopes are only readily accessible at the section's surface, leaving the volume of the serial sections unlabeled. Localization of receptors at neuronal synapses in 3D in their native cellular ultrastructural context is important for understanding signaling processes. Here, we present in vivo labeling of receptors via fluorophore-coupled tags in combination with super-resolution AT. We present two workflows where we label receptors at the plasma membrane: first, in vivo labeling via microinjection with a setup consisting of readily available components and self-manufactured microscope table equipment and second, live receptor labeling by using a cell-permeable tag. To take advantage of a near-to-native preservation of tissues for subsequent scanning electron microscopy (SEM), we also apply high-pressure freezing and freeze substitution. The advantages and disadvantages of our workflows are discussed.
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Affiliation(s)
- Sebastian Britz
- Imaging Core Facility, Theodor-Boveri-Institute, Biocenter of the Julius-Maximilians-Universität Würzburg (JMU), Würzburg, Germany.
| | - Camilla Luccardini
- Centre d'Imagerie Quantitative Lyon Est (CIQLE), SFR Santé Lyon-Est CNRS UAR3453-INSERM US7, Université Claude Bernard Lyon 1, Lyon, France
| | - Sebastian M Markert
- Imaging Core Facility, Theodor-Boveri-Institute, Biocenter of the Julius-Maximilians-Universität Würzburg (JMU), Würzburg, Germany
| | - Sean A Merrill
- Department of Biology, University of Utah, Salt Lake City, UT, United States
| | - Jean-Louis Bessereau
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR-5284, INSERM U-1314, MeLiS, Institut NeuroMyoGene, Lyon, France
| | - Christian Stigloher
- Imaging Core Facility, Theodor-Boveri-Institute, Biocenter of the Julius-Maximilians-Universität Würzburg (JMU), Würzburg, Germany.
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9
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Newman LE, Weiser Novak S, Rojas GR, Tadepalle N, Schiavon CR, Grotjahn DA, Towers CG, Tremblay MÈ, Donnelly MP, Ghosh S, Medina M, Rocha S, Rodriguez-Enriquez R, Chevez JA, Lemersal I, Manor U, Shadel GS. Mitochondrial DNA replication stress triggers a pro-inflammatory endosomal pathway of nucleoid disposal. Nat Cell Biol 2024; 26:194-206. [PMID: 38332353 PMCID: PMC11026068 DOI: 10.1038/s41556-023-01343-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/20/2023] [Indexed: 02/10/2024]
Abstract
Mitochondrial DNA (mtDNA) encodes essential subunits of the oxidative phosphorylation system, but is also a major damage-associated molecular pattern (DAMP) that engages innate immune sensors when released into the cytoplasm, outside of cells or into circulation. As a DAMP, mtDNA not only contributes to anti-viral resistance, but also causes pathogenic inflammation in many disease contexts. Cells experiencing mtDNA stress caused by depletion of the mtDNA-packaging protein, transcription factor A, mitochondrial (TFAM) or during herpes simplex virus-1 infection exhibit elongated mitochondria, enlargement of nucleoids (mtDNA-protein complexes) and activation of cGAS-STING innate immune signalling via mtDNA released into the cytoplasm. However, the relationship among aberrant mitochondria and nucleoid dynamics, mtDNA release and cGAS-STING activation remains unclear. Here we show that, under a variety of mtDNA replication stress conditions and during herpes simplex virus-1 infection, enlarged nucleoids that remain bound to TFAM exit mitochondria. Enlarged nucleoids arise from mtDNA experiencing replication stress, which causes nucleoid clustering via a block in mitochondrial fission at a stage when endoplasmic reticulum actin polymerization would normally commence, defining a fission checkpoint that ensures mtDNA has completed replication and is competent for segregation into daughter mitochondria. Chronic engagement of this checkpoint results in enlarged nucleoids trafficking into early and then late endosomes for disposal. Endosomal rupture during transit through this endosomal pathway ultimately causes mtDNA-mediated cGAS-STING activation. Thus, we propose that replication-incompetent nucleoids are selectively eliminated by an adaptive mitochondria-endosomal quality control pathway that is prone to innate immune system activation, which might represent a therapeutic target to prevent mtDNA-mediated inflammation during viral infection and other pathogenic states.
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Affiliation(s)
- Laura E Newman
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Gladys R Rojas
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | | | | | | | - Matthew P Donnelly
- Salk Institute for Biological Studies, La Jolla, CA, USA
- Medical Scientist Training Program, University of California, San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Sagnika Ghosh
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Sienna Rocha
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Joshua A Chevez
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Ian Lemersal
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Uri Manor
- Salk Institute for Biological Studies, La Jolla, CA, USA.
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
- Department of Cell & Developmental Biology, University of California, San Diego, La Jolla, CA, USA.
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10
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Iyer M, Kantarci H, Cooper MH, Ambiel N, Novak SW, Andrade LR, Lam M, Jones G, Münch AE, Yu X, Khakh BS, Manor U, Zuchero JB. Oligodendrocyte calcium signaling promotes actin-dependent myelin sheath extension. Nat Commun 2024; 15:265. [PMID: 38177161 PMCID: PMC10767123 DOI: 10.1038/s41467-023-44238-3] [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: 06/07/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
Myelin is essential for rapid nerve signaling and is increasingly found to play important roles in learning and in diverse diseases of the CNS. Morphological parameters of myelin such as sheath length are thought to precisely tune conduction velocity, but the mechanisms controlling sheath morphology are poorly understood. Local calcium signaling has been observed in nascent myelin sheaths and can be modulated by neuronal activity. However, the role of calcium signaling in sheath formation remains incompletely understood. Here, we use genetic tools to attenuate oligodendrocyte calcium signaling during myelination in the developing mouse CNS. Surprisingly, genetic calcium attenuation does not grossly affect the number of myelinated axons or myelin thickness. Instead, calcium attenuation causes myelination defects resulting in shorter, dysmorphic sheaths. Mechanistically, calcium attenuation reduces actin filaments in oligodendrocytes, and an intact actin cytoskeleton is necessary and sufficient to achieve accurate myelin morphology. Together, our work reveals a cellular mechanism required for accurate CNS myelin formation and may provide mechanistic insight into how oligodendrocytes respond to neuronal activity to sculpt and refine myelin sheaths.
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Affiliation(s)
- Manasi Iyer
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Husniye Kantarci
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Madeline H Cooper
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas Ambiel
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Sammy Weiser Novak
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Leonardo R Andrade
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mable Lam
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Graham Jones
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexandra E Münch
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Xinzhu Yu
- Department of Molecular and Integrative Physiology, Beckman Institute, University of Illinois at Urbana-, Champaign, IL, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Baljit S Khakh
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Uri Manor
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Cell and Developmental Biology, University of California, San Diego, San Diego, CA, USA
| | - J Bradley Zuchero
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA.
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11
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Galenza A, Moreno-Roman P, Su YH, Acosta-Alvarez L, Debec A, Guichet A, Knapp JM, Kizilyaprak C, Humbel BM, Kolotuev I, O'Brien LE. Basal stem cell progeny establish their apical surface in a junctional niche during turnover of an adult barrier epithelium. Nat Cell Biol 2023; 25:658-671. [PMID: 36997641 PMCID: PMC10317055 DOI: 10.1038/s41556-023-01116-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/23/2023] [Indexed: 04/01/2023]
Abstract
Barrier epithelial organs face the constant challenge of sealing the interior body from the external environment while simultaneously replacing the cells that contact this environment. New replacement cells-the progeny of basal stem cells-are born without barrier-forming structures such as a specialized apical membrane and occluding junctions. Here, we investigate how new progeny acquire barrier structures as they integrate into the intestinal epithelium of adult Drosophila. We find they gestate their future apical membrane in a sublumenal niche created by a transitional occluding junction that envelops the differentiating cell and enables it to form a deep, microvilli-lined apical pit. The transitional junction seals the pit from the intestinal lumen until differentiation-driven, basal-to-apical remodelling of the niche opens the pit and integrates the now-mature cell into the barrier. By coordinating junctional remodelling with terminal differentiation, stem cell progeny integrate into a functional, adult epithelium without jeopardizing barrier integrity.
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Affiliation(s)
- Anthony Galenza
- Department of Molecular & Cellular Physiology and Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Paola Moreno-Roman
- Department of Molecular & Cellular Physiology and Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Foldscope Instruments, Inc., Palo Alto, CA, USA
| | - Yu-Han Su
- Department of Molecular & Cellular Physiology and Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Lehi Acosta-Alvarez
- Department of Molecular & Cellular Physiology and Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Alain Debec
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
- Institute of Ecology and Environmental Sciences, iEES, Sorbonne University, UPEC, CNRS, IRD, INRA, Paris, France
| | - Antoine Guichet
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | | | - Caroline Kizilyaprak
- Université de Lausanne, Bâtiment Biophore, Quartier Sorge, Lausanne, Switzerland
| | - Bruno M Humbel
- Université de Lausanne, Bâtiment Biophore, Quartier Sorge, Lausanne, Switzerland
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Provost's Office, Okinawa Institute of Science and Technology, Tancha, Japan
| | - Irina Kolotuev
- Université de Lausanne, Bâtiment Biophore, Quartier Sorge, Lausanne, Switzerland
| | - Lucy Erin O'Brien
- Department of Molecular & Cellular Physiology and Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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12
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Liv N, Fermie J, Ten Brink CBM, de Heus C, Klumperman J. Functional characterization of endo-lysosomal compartments by correlative live-cell and volume electron microscopy. Methods Cell Biol 2023; 177:301-326. [PMID: 37451771 DOI: 10.1016/bs.mcb.2022.12.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Fluorescent biosensors are valuable tools to monitor protein activities and the functional state of organelles in live cells. However, the information provided by fluorescent microscopy (FM) is mostly limited in resolution and lacks ultrastructural context information. Protein activities are confined to organelle zones with a distinct membrane morphology, which can only be seen by electron microscopy (EM). EM, however, intrinsically lacks information on protein activities. The lack of methods to integrate these two imaging modalities has hampered understanding the functional organization of cellular organelles. Here we introduce "functional correlative microscopy" (functional CLEM) to directly infer functional information from live cells to EM with nanometer resolution. We label and visualize live cells with fluorescent biosensors after which they are processed for EM and imaged using a volume electron microscopy technique. Within a single dataset we correlate hundreds of fluorescent spots enabling quantitative analysis of the functional-ultrastructural data. We employ our method to monitor essential functional parameters of late endo-lysosomal compartments, i.e., pH, calcium, enzyme activities and cholesterol content. Our data reveal a steep functional difference in enzyme activity between late endosomes and lysosomes and unexpectedly high calcium levels in late endosomes. The presented CLEM workflow is compatible with a large repertoire of probes and paves the way for large scale functional studies of all types of cellular structures.
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Affiliation(s)
- Nalan Liv
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
| | - Job Fermie
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands; Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Corlinda B M Ten Brink
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Cecilia de Heus
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Judith Klumperman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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13
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Iyer M, Kantarci H, Ambiel N, Novak SW, Andrade LR, Lam M, Münch AE, Yu X, Khakh BS, Manor U, Zuchero JB. Oligodendrocyte calcium signaling sculpts myelin sheath morphology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536299. [PMID: 37090556 PMCID: PMC10120717 DOI: 10.1101/2023.04.11.536299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Myelin is essential for rapid nerve signaling and is increasingly found to play important roles in learning and in diverse diseases of the CNS. Morphological parameters of myelin such as sheath length and thickness are regulated by neuronal activity and can precisely tune conduction velocity, but the mechanisms controlling sheath morphology are poorly understood. Local calcium signaling has been observed in nascent myelin sheaths and can be modulated by neuronal activity. However, the role of calcium signaling in sheath formation and remodeling is unknown. Here, we used genetic tools to attenuate oligodendrocyte calcium signaling during active myelination in the developing mouse CNS. Surprisingly, we found that genetic calcium attenuation did not grossly affect the number of myelinated axons or myelin thickness. Instead, calcium attenuation caused striking myelination defects resulting in shorter, dysmorphic sheaths. Mechanistically, calcium attenuation reduced actin filaments in oligodendrocytes, and an intact actin cytoskeleton was necessary and sufficient to achieve accurate myelin morphology. Together, our work reveals a novel cellular mechanism required for accurate CNS myelin formation and provides mechanistic insight into how oligodendrocytes may respond to neuronal activity to sculpt myelin sheaths throughout the nervous system.
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14
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Fung W, Tan TM, Kolotuev I, Heiman MG. A sex-specific switch in a single glial cell patterns the apical extracellular matrix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533199. [PMID: 36993293 PMCID: PMC10055199 DOI: 10.1101/2023.03.17.533199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Apical extracellular matrix (aECM) constitutes the interface between every tissue and the outside world. It is patterned into diverse tissue-specific structures through unknown mechanisms. Here, we show that a male-specific genetic switch in a single C. elegans glial cell patterns the aECM into a ∼200 nm pore, allowing a male sensory neuron to access the environment. We find that this glial sex difference is controlled by factors shared with neurons ( mab-3, lep-2, lep-5 ) as well as previously unidentified regulators whose effects may be glia-specific ( nfya-1, bed-3, jmjd-3.1 ). The switch results in male-specific expression of a Hedgehog-related protein, GRL-18, that we discover localizes to transient nanoscale rings at sites of aECM pore formation. Blocking male-specific gene expression in glia prevents pore formation, whereas forcing male-specific expression induces an ectopic pore. Thus, a switch in gene expression in a single cell is necessary and sufficient to pattern aECM into a specific structure.
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Affiliation(s)
- Wendy Fung
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children’s Hospital, Boston, MA 02115, USA
| | - Taralyn M. Tan
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children’s Hospital, Boston, MA 02115, USA
| | - Irina Kolotuev
- Electron Microscopy Facility, University of Lausanne, 1015 Lausanne, Switzerland
| | - Maxwell G. Heiman
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children’s Hospital, Boston, MA 02115, USA
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15
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Kislinger G, Niemann C, Rodriguez L, Jiang H, Fard MK, Snaidero N, Schumacher AM, Kerschensteiner M, Misgeld T, Schifferer M. Neurons on tape: Automated Tape Collecting Ultramicrotomy-mediated volume EM for targeting neuropathology. Methods Cell Biol 2023; 177:125-170. [PMID: 37451765 DOI: 10.1016/bs.mcb.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
In this chapter, we review Automated Tape Collecting Ultramicrotomy (ATUM), which, among other array tomography methods, substantially simplified large-scale volume electron microscopy (vEM) projects. vEM reveals biological structures at nanometer resolution in three dimensions and resolves ambiguities of two-dimensional representations. However, as the structures of interest-like disease hallmarks emerging from neuropathology-are often rare but the field of view is small, this can easily turn a vEM project into a needle in a haystack problem. One solution for this is correlated light and electron microscopy (CLEM), providing tissue context, dynamic and molecular features before switching to targeted vEM to hone in on the object's ultrastructure. This requires precise coordinate transfer between the two imaging modalities (e.g., by micro computed tomography), especially for block face vEM which relies on physical destruction of sections. With array tomography methods, serial ultrathin sections are collected into a tissue library, thus allowing storage of precious samples like human biopsies and enabling repetitive imaging at different resolution levels for an SEM-based search strategy. For this, ATUM has been developed to reliably collect serial ultrathin sections via a conveyor belt onto a plastic tape that is later mounted onto silicon wafers for serial scanning EM (SEM). The ATUM-SEM procedure is highly modular and can be divided into sample preparation, serial ultramicrotomy onto tape, mounting, serial image acquisition-after which the acquired image stacks can be used for analysis. Here, we describe the steps of this workflow and how ATUM-SEM enables targeting and high resolution imaging of specific structures. ATUM-SEM is widely applicable. To illustrate this, we exemplify the approach by reconstructions of focal pathology in an Alzheimer mouse model and CLEM of a specific cortical synapse.
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Affiliation(s)
- Georg Kislinger
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Cornelia Niemann
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Lucia Rodriguez
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Hanyi Jiang
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Maryam K Fard
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Nicolas Snaidero
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany; Hertie institute for Clinical Brain Research, Tuebingen University Hospital, Tuebingen, Germany
| | - Adrian-Minh Schumacher
- Faculty of Medicine, Biomedical Center (BMC), Ludwig-Maximilians-University Munich, Munich, Germany; Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Martin Kerschensteiner
- Faculty of Medicine, Biomedical Center (BMC), Ludwig-Maximilians-University Munich, Munich, Germany; Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany; Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Thomas Misgeld
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Martina Schifferer
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Munich Cluster of Systems Neurology (SyNergy), Munich, Germany.
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16
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Ktena N, Kaplanis SI, Kolotuev I, Georgilis A, Kallergi E, Stavroulaki V, Nikoletopoulou V, Savvaki M, Karagogeos D. Autophagic degradation of CNS myelin maintains axon integrity. Cell Stress 2022; 6:93-107. [PMID: 36478958 PMCID: PMC9707329 DOI: 10.15698/cst2022.12.274] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/01/2022] [Accepted: 11/09/2022] [Indexed: 09/05/2023] Open
Abstract
(Macro)autophagy is a major lysosome-dependent degradation mechanism which engulfs, removes and recycles unwanted cytoplasmic material, including damaged organelles and toxic protein aggregates. Although a few studies implicate autophagy in CNS demyelinating pathologies, its role, particularly in mature oligodendrocytes and CNS myelin, remains poorly studied. Here, using both pharmacological and genetic inhibition of the autophagic machinery, we provide evidence that autophagy is an essential mechanism for oligodendrocyte maturation in vitro. Our study reveals that two core myelin proteins, namely proteolipid protein (PLP) and myelin basic protein (MBP) are incorporated into autophagosomes in oligodendrocytes, resulting in their degradation. Furthermore, we ablated atg5, a core gene of the autophagic machinery, specifically in myelinating glial cells in vivo by tamoxifen administration (plp-Cre ERT2 ; atg5 f/f ) and showed that myelin maintenance is perturbed, leading to PLP accumulation. Significant morphological defects in myelin membrane such as decompaction accompanied with increased axonal degeneration are observed. As a result, the mice exhibit behavioral deficits. In summary, our data highlight that the maintenance of adult myelin homeostasis in the CNS requires the involvement of a fully functional autophagic machinery.
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Affiliation(s)
- Niki Ktena
- School of Medicine, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Greece
| | - Stefanos Ioannis Kaplanis
- School of Medicine, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Greece
| | - Irina Kolotuev
- Electron Microscopy Facility (PME), University of Lausanne, Lausanne, Switzerland
| | | | - Emmanouela Kallergi
- Department of Fundamental Neurosciences (DNF), University of Lausanne, Lausanne, Switzerland
| | - Vasiliki Stavroulaki
- School of Medicine, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Greece
| | | | - Maria Savvaki
- School of Medicine, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Greece
| | - Domna Karagogeos
- School of Medicine, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Greece
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17
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Lee G, Oh Y, Nam JT, Ji S, Jang AR, Jeong DW, Kang M, Lee SS, Chae S, Cho D, Hwang JY, Lee K, Lee JO. Multifunctional-high resolution imaging plate based on hydrophilic graphene for digital pathology. NANOTECHNOLOGY 2022; 33:505101. [PMID: 36095982 DOI: 10.1088/1361-6528/ac9143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
In the present study, we showed that hydrophilic graphene can serve as an ideal imaging plate for biological specimens. Graphene being a single-atom-thick semi-metal with low secondary electron emission, array tomography analysis of serial sections of biological specimens on a graphene substrate showed excellent image quality with improvedz-axis resolution, without including any conductive surface coatings. However, the hydrophobic nature of graphene makes the placement of biological specimens difficult; graphene functionalized with polydimethylsiloxane oligomer was fabricated using a simple soft lithography technique and then processed with oxygen plasma to provide hydrophilic graphene with minimal damage to graphene. High-quality scanning electron microscopy images of biological specimens free from charging effects or distortion were obtained, and the optical transparency of graphene enabled fluorescence imaging of the specimen; high-resolution correlated electron and light microscopy analysis of the specimen became possible with the hydrophilic graphene plate.
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Affiliation(s)
- Geonhee Lee
- Advanced Materials Division, Korea Research Institute of Chemical Technology, Gajeongro 141, Daejeon, Republic of Korea
| | - Yuna Oh
- Korea Institute of Science and Technology, 5. Hwarang-ro 14-gil, Seongbuk-gu, Seoul, Republic of Korea
| | - Jung Tae Nam
- Institute of Advanced Composite Materials, Korea Institute of Science and Technology, Jeonbuk, 55324, Republic of Korea
| | - Seulgi Ji
- Advanced Materials Division, Korea Research Institute of Chemical Technology, Gajeongro 141, Daejeon, Republic of Korea
| | - A-Rang Jang
- Division of Electrical, Electronic and Control Engineering, Kongju National University, Cheonan 31080, Republic of Korea
| | - Du Won Jeong
- Advanced Materials Division, Korea Research Institute of Chemical Technology, Gajeongro 141, Daejeon, Republic of Korea
| | - MinSoung Kang
- Advanced Materials Division, Korea Research Institute of Chemical Technology, Gajeongro 141, Daejeon, Republic of Korea
| | - Sun Sook Lee
- Advanced Materials Division, Korea Research Institute of Chemical Technology, Gajeongro 141, Daejeon, Republic of Korea
| | - Soosang Chae
- Department of Nanostructured Materials, Leibniz Institute of Polymer Research Dresden, D-01069, Dresden, Germany
| | - Donghwi Cho
- Advanced Materials Division, Korea Research Institute of Chemical Technology, Gajeongro 141, Daejeon, Republic of Korea
| | - Jun Yeon Hwang
- Institute of Advanced Composite Materials, Korea Institute of Science and Technology, Jeonbuk, 55324, Republic of Korea
| | - Kyungeun Lee
- Korea Institute of Science and Technology, 5. Hwarang-ro 14-gil, Seongbuk-gu, Seoul, Republic of Korea
| | - Jeong-O Lee
- Advanced Materials Division, Korea Research Institute of Chemical Technology, Gajeongro 141, Daejeon, Republic of Korea
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18
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Peddie CJ, Genoud C, Kreshuk A, Meechan K, Micheva KD, Narayan K, Pape C, Parton RG, Schieber NL, Schwab Y, Titze B, Verkade P, Aubrey A, Collinson LM. Volume electron microscopy. NATURE REVIEWS. METHODS PRIMERS 2022; 2:51. [PMID: 37409324 PMCID: PMC7614724 DOI: 10.1038/s43586-022-00131-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 07/07/2023]
Abstract
Life exists in three dimensions, but until the turn of the century most electron microscopy methods provided only 2D image data. Recently, electron microscopy techniques capable of delving deep into the structure of cells and tissues have emerged, collectively called volume electron microscopy (vEM). Developments in vEM have been dubbed a quiet revolution as the field evolved from established transmission and scanning electron microscopy techniques, so early publications largely focused on the bioscience applications rather than the underlying technological breakthroughs. However, with an explosion in the uptake of vEM across the biosciences and fast-paced advances in volume, resolution, throughput and ease of use, it is timely to introduce the field to new audiences. In this Primer, we introduce the different vEM imaging modalities, the specialized sample processing and image analysis pipelines that accompany each modality and the types of information revealed in the data. We showcase key applications in the biosciences where vEM has helped make breakthrough discoveries and consider limitations and future directions. We aim to show new users how vEM can support discovery science in their own research fields and inspire broader uptake of the technology, finally allowing its full adoption into mainstream biological imaging.
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Affiliation(s)
- Christopher J. Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Christel Genoud
- Electron Microscopy Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Anna Kreshuk
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kimberly Meechan
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Present address: Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Kristina D. Micheva
- Department of Molecular and Cellular Physiology, Stanford University, Palo Alto, CA, USA
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Constantin Pape
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Robert G. Parton
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicole L. Schieber
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Yannick Schwab
- Cell Biology and Biophysics Unit/ Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Aubrey Aubrey
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Lucy M. Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
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19
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Heiligenstein X, Lucas MS. One for All, All for One: A Close Look at In-Resin Fluorescence Protocols for CLEM. Front Cell Dev Biol 2022; 10:866472. [PMID: 35846358 PMCID: PMC9280628 DOI: 10.3389/fcell.2022.866472] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Sample preparation is the novel bottleneck for high throughput correlative light and electron microscopy (CLEM). Protocols suitable for both imaging methods must therefore balance the requirements of each technique. For fluorescence light microscopy, a structure of interest can be targeted using: 1) staining, which is often structure or tissue specific rather than protein specific, 2) dye-coupled proteins or antibodies, or 3) genetically encoded fluorescent proteins. Each of these three methods has its own advantages. For ultrastructural investigation by electron microscopy (EM) resin embedding remains a significant sample preparation approach, as it stabilizes the sample such that it withstands the vacuum conditions of the EM, and enables long-term storage. Traditionally, samples are treated with heavy metal salts prior to resin embedding, in order to increase imaging contrast for EM. This is particularly important for volume EM (vEM) techniques. Yet, commonly used contrasting agents (e.g., osmium tetroxide, uranyl acetate) tend to impair fluorescence. The discovery that fluorescence can be preserved in resin-embedded specimens after mild heavy metal staining was a game changer for CLEM. These so-called in-resin fluorescence protocols present a significant leap forward for CLEM approaches towards high precision localization of a fluorescent signal in (volume) EM data. Integrated microscopy approaches, combining LM and EM detection into a single instrument certainly require such an “all in one” sample preparation. Preserving, or adding, dedicated fluorescence prior to resin embedding requires a compromise, which often comes at the expense of EM imaging contrast and membrane visibility. Especially vEM can be strongly hampered by a lack of heavy metal contrasting. This review critically reflects upon the fundamental aspects of resin embedding with regard to 1) specimen fixation and the physics and chemistry underlying the preservation of protein structure with respect to fluorescence and antigenicity, 2) optimization of EM contrast for transmission or scanning EM, and 3) the choice of embedding resin. On this basis, various existing workflows employing in-resin fluorescence are described, highlighting their common features, discussing advantages and disadvantages of the respective approach, and finally concluding with promising future developments for in-resin CLEM.
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Affiliation(s)
| | - Miriam S. Lucas
- Scientific Center for Light and Electron Microscopy (ScopeM), ETH Zurich, Zurich, Switzerland
- *Correspondence: Miriam S. Lucas,
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20
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Loginov SV, Fermie J, Fokkema J, Agronskaia AV, De Heus C, Blab GA, Klumperman J, Gerritsen HC, Liv N. Correlative Organelle Microscopy: Fluorescence Guided Volume Electron Microscopy of Intracellular Processes. Front Cell Dev Biol 2022; 10:829545. [PMID: 35478966 PMCID: PMC9035751 DOI: 10.3389/fcell.2022.829545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/04/2022] [Indexed: 01/19/2023] Open
Abstract
Intracellular processes depend on a strict spatial and temporal organization of proteins and organelles. Therefore, directly linking molecular to nanoscale ultrastructural information is crucial in understanding cellular physiology. Volume or three-dimensional (3D) correlative light and electron microscopy (volume-CLEM) holds unique potential to explore cellular physiology at high-resolution ultrastructural detail across cell volumes. However, the application of volume-CLEM is hampered by limitations in throughput and 3D correlation efficiency. In order to address these limitations, we describe a novel pipeline for volume-CLEM that provides high-precision (<100 nm) registration between 3D fluorescence microscopy (FM) and 3D electron microscopy (EM) datasets with significantly increased throughput. Using multi-modal fiducial nanoparticles that remain fluorescent in epoxy resins and a 3D confocal fluorescence microscope integrated into a Focused Ion Beam Scanning Electron Microscope (FIB.SEM), our approach uses FM to target extremely small volumes of even single organelles for imaging in volume EM and obviates the need for post-correlation of big 3D datasets. We extend our targeted volume-CLEM approach to include live-cell imaging, adding information on the motility of intracellular membranes selected for volume-CLEM. We demonstrate the power of our approach by targeted imaging of rare and transient contact sites between the endoplasmic reticulum (ER) and lysosomes within hours rather than days. Our data suggest that extensive ER-lysosome and mitochondria-lysosome interactions restrict lysosome motility, highlighting the unique capabilities of our integrated CLEM pipeline for linking molecular dynamic data to high-resolution ultrastructural detail in 3D.
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Affiliation(s)
- Sergey V. Loginov
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Job Fermie
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Jantina Fokkema
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Alexandra V. Agronskaia
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Cilia De Heus
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Gerhard A. Blab
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Judith Klumperman
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Hans C. Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Nalan Liv
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- *Correspondence: Nalan Liv,
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21
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Ma Z, Lytle NK, Chen B, Jyotsana N, Novak SW, Cho CJ, Caplan L, Ben-Levy O, Neininger AC, Burnette DT, Trinh VQ, Tan MCB, Patterson EA, Arrojo E Drigo R, Giraddi RR, Ramos C, Means AL, Matsumoto I, Manor U, Mills JC, Goldenring JR, Lau KS, Wahl GM, DelGiorno KE. Single-Cell Transcriptomics Reveals a Conserved Metaplasia Program in Pancreatic Injury. Gastroenterology 2022; 162:604-620.e20. [PMID: 34695382 PMCID: PMC8792222 DOI: 10.1053/j.gastro.2021.10.027] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/15/2021] [Accepted: 10/09/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Acinar to ductal metaplasia (ADM) occurs in the pancreas in response to tissue injury and is a potential precursor for adenocarcinoma. The goal of these studies was to define the populations arising from ADM, the associated transcriptional changes, and markers of disease progression. METHODS Acinar cells were lineage-traced with enhanced yellow fluorescent protein (EYFP) to follow their fate post-injury. Transcripts of more than 13,000 EYFP+ cells were determined using single-cell RNA sequencing (scRNA-seq). Developmental trajectories were generated. Data were compared with gastric metaplasia, KrasG12D-induced neoplasia, and human pancreatitis. Results were confirmed by immunostaining and electron microscopy. KrasG12D was expressed in injury-induced ADM using several inducible Cre drivers. Surgical specimens of chronic pancreatitis from 15 patients were evaluated by immunostaining. RESULTS scRNA-seq of ADM revealed emergence of a mucin/ductal population resembling gastric pyloric metaplasia. Lineage trajectories suggest that some pyloric metaplasia cells can generate tuft and enteroendocrine cells (EECs). Comparison with KrasG12D-induced ADM identifies populations associated with disease progression. Activation of KrasG12D expression in HNF1B+ or POU2F3+ ADM populations leads to neoplastic transformation and formation of MUC5AC+ gastric-pit-like cells. Human pancreatitis samples also harbor pyloric metaplasia with a similar transcriptional phenotype. CONCLUSIONS Under conditions of chronic injury, acinar cells undergo a pyloric-type metaplasia to mucinous progenitor-like populations, which seed disparate tuft cell and EEC lineages. ADM-derived EEC subtypes are diverse. KrasG12D expression is sufficient to drive neoplasia when targeted to injury-induced ADM populations and offers an alternative origin for tumorigenesis. This program is conserved in human pancreatitis, providing insight into early events in pancreas diseases.
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Affiliation(s)
- Zhibo Ma
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Nikki K Lytle
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Bob Chen
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Nidhi Jyotsana
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
| | - Sammy Weiser Novak
- Waitt Advanced Biophotonics Center, Salk Insitute for Biological Studies, La Jolla, California
| | - Charles J Cho
- Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas
| | - Leah Caplan
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
| | - Olivia Ben-Levy
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
| | - Abigail C Neininger
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
| | - Dylan T Burnette
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, Tennessee; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee; Vanderbilt Ingram Cancer Center, Nashville, Tennessee
| | - Vincent Q Trinh
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Marcus C B Tan
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee; Vanderbilt Digestive Disease Research Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Emilee A Patterson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee
| | - Rafael Arrojo E Drigo
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, Tennessee; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee
| | - Rajshekhar R Giraddi
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Cynthia Ramos
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Anna L Means
- Vanderbilt Ingram Cancer Center, Nashville, Tennessee; Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee; Vanderbilt Digestive Disease Research Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Uri Manor
- Waitt Advanced Biophotonics Center, Salk Insitute for Biological Studies, La Jolla, California
| | - Jason C Mills
- Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas
| | - James R Goldenring
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, Tennessee; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee; Vanderbilt Ingram Cancer Center, Nashville, Tennessee; Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee; Vanderbilt Digestive Disease Research Center, Vanderbilt University Medical Center, Nashville, Tennessee; Nashville VA Medical Center, Nashville, Tennessee
| | - Ken S Lau
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, Tennessee; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee; Vanderbilt Ingram Cancer Center, Nashville, Tennessee; Vanderbilt Digestive Disease Research Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Geoffrey M Wahl
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Kathleen E DelGiorno
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, Tennessee; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee; Vanderbilt Ingram Cancer Center, Nashville, Tennessee; Vanderbilt Digestive Disease Research Center, Vanderbilt University Medical Center, Nashville, Tennessee.
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22
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Lane R, Wolters AHG, Giepmans BNG, Hoogenboom JP. Integrated Array Tomography for 3D Correlative Light and Electron Microscopy. Front Mol Biosci 2022; 8:822232. [PMID: 35127826 PMCID: PMC8809480 DOI: 10.3389/fmolb.2021.822232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/15/2021] [Indexed: 12/22/2022] Open
Abstract
Volume electron microscopy (EM) of biological systems has grown exponentially in recent years due to innovative large-scale imaging approaches. As a standalone imaging method, however, large-scale EM typically has two major limitations: slow rates of acquisition and the difficulty to provide targeted biological information. We developed a 3D image acquisition and reconstruction pipeline that overcomes both of these limitations by using a widefield fluorescence microscope integrated inside of a scanning electron microscope. The workflow consists of acquiring large field of view fluorescence microscopy (FM) images, which guide to regions of interest for successive EM (integrated correlative light and electron microscopy). High precision EM-FM overlay is achieved using cathodoluminescent markers. We conduct a proof-of-concept of our integrated workflow on immunolabelled serial sections of tissues. Acquisitions are limited to regions containing biological targets, expediting total acquisition times and reducing the burden of excess data by tens or hundreds of GBs.
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Affiliation(s)
- Ryan Lane
- Imaging Physics, Delft University of Technology, Delft, Netherlands
| | - Anouk H. G. Wolters
- Department of Biomedical Sciences of Cells and Systems, University Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ben N. G. Giepmans
- Department of Biomedical Sciences of Cells and Systems, University Groningen, University Medical Center Groningen, Groningen, Netherlands
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23
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Chassefeyre R, Chaiamarit T, Verhelle A, Novak SW, Andrade LR, Leitão ADG, Manor U, Encalada SE. Endosomal sorting drives the formation of axonal prion protein endoggresomes. SCIENCE ADVANCES 2021; 7:eabg3693. [PMID: 34936461 PMCID: PMC8694590 DOI: 10.1126/sciadv.abg3693] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 11/05/2021] [Indexed: 05/15/2023]
Abstract
The pathogenic aggregation of misfolded prion protein (PrP) in axons underlies prion disease pathologies. The molecular mechanisms driving axonal misfolded PrP aggregate formation leading to neurotoxicity are unknown. We found that the small endolysosomal guanosine triphosphatase (GTPase) Arl8b recruits kinesin-1 and Vps41 (HOPS) onto endosomes carrying misfolded mutant PrP to promote their axonal entry and homotypic fusion toward aggregation inside enlarged endomembranes that we call endoggresomes. This axonal rapid endosomal sorting and transport-dependent aggregation (ARESTA) mechanism forms pathologic PrP endoggresomes that impair calcium dynamics and reduce neuronal viability. Inhibiting ARESTA diminishes endoggresome formation, rescues calcium influx, and prevents neuronal death. Our results identify ARESTA as a key pathway for the regulation of endoggresome formation and a new actionable antiaggregation target to ameliorate neuronal dysfunction in the prionopathies.
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Affiliation(s)
- Romain Chassefeyre
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
- Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tai Chaiamarit
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
- Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Adriaan Verhelle
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
- Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sammy Weiser Novak
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Leonardo R. Andrade
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - André D. G. Leitão
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
- Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Uri Manor
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Sandra E. Encalada
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
- Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
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24
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Lewczuk B, Szyryńska N. Field-Emission Scanning Electron Microscope as a Tool for Large-Area and Large-Volume Ultrastructural Studies. Animals (Basel) 2021; 11:ani11123390. [PMID: 34944167 PMCID: PMC8698110 DOI: 10.3390/ani11123390] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Ultrastructural studies of cells and tissues are usually performed using transmission electron microscopy (TEM), which enables imaging at the highest possible resolution. The weak point of TEM is the limited ability to analyze the ultrastructure of large areas and volumes of biological samples. This limitation can be overcome by using modern field-emission scanning electron microscopy (FE-SEM) with high-sensitivity detection, which enables the creation of TEM-like images from the flat surfaces of resin-embedded biological specimens. Several FE-SEM-based techniques for two- and three-dimensional ultrastructural studies of cells, tissues, organs, and organisms have been developed in the 21st century. These techniques have created a new era in structural biology and have changed the role of the scanning electron microscope (SEM) in biological and medical laboratories. Since the premiere of the first commercially available SEM in 1965, these instruments were used almost exclusively to obtain topographical information over a large range of magnifications. Currently, FE-SEM offers many attractive possibilities in the studies of cell and tissue ultrastructure, and they are presented in this review. Abstract The development of field-emission scanning electron microscopes for high-resolution imaging at very low acceleration voltages and equipped with highly sensitive detectors of backscattered electrons (BSE) has enabled transmission electron microscopy (TEM)-like imaging of the cut surfaces of tissue blocks, which are impermeable to the electron beam, or tissue sections mounted on the solid substrates. This has resulted in the development of methods that simplify and accelerate ultrastructural studies of large areas and volumes of biological samples. This article provides an overview of these methods, including their advantages and disadvantages. The imaging of large sample areas can be performed using two methods based on the detection of transmitted electrons or BSE. Effective imaging using BSE requires special fixation and en bloc contrasting of samples. BSE imaging has resulted in the development of volume imaging techniques, including array tomography (AT) and serial block-face imaging (SBF-SEM). In AT, serial ultrathin sections are collected manually on a solid substrate such as a glass and silicon wafer or automatically on a tape using a special ultramicrotome. The imaging of serial sections is used to obtain three-dimensional (3D) information. SBF-SEM is based on removing the top layer of a resin-embedded sample using an ultramicrotome inside the SEM specimen chamber and then imaging the exposed surface with a BSE detector. The steps of cutting and imaging the resin block are repeated hundreds or thousands of times to obtain a z-stack for 3D analyses.
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25
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Larsen NY, Li X, Tan X, Ji G, Lin J, Rajkowska G, Møller J, Vihrs N, Sporring J, Sun F, Nyengaard JR. Cellular 3D-reconstruction and analysis in the human cerebral cortex using automatic serial sections. Commun Biol 2021; 4:1030. [PMID: 34475516 PMCID: PMC8413324 DOI: 10.1038/s42003-021-02548-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 08/09/2021] [Indexed: 12/17/2022] Open
Abstract
Techniques involving three-dimensional (3D) tissue structure reconstruction and analysis provide a better understanding of changes in molecules and function. We have developed AutoCUTS-LM, an automated system that allows the latest advances in 3D tissue reconstruction and cellular analysis developments using light microscopy on various tissues, including archived tissue. The workflow in this paper involved advanced tissue sampling methods of the human cerebral cortex, an automated serial section collection system, digital tissue library, cell detection using convolution neural network, 3D cell reconstruction, and advanced analysis. Our results demonstrated the detailed structure of pyramidal cells (number, volume, diameter, sphericity and orientation) and their 3D spatial organization are arranged in a columnar structure. The pipeline of these combined techniques provides a detailed analysis of tissues and cells in biology and pathology. Nick Larsen et al. developed a pipeline to collect and image serial sections from fixed human cortex, then apply deep learning to detect pyramidal cells from 3D reconstructions of these sections. Their results reiterate that cortical pyramidal cells are organized in a columnar structure and highlight the potential of this method, which is universally applicable to characterize cells for various tissues.
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Affiliation(s)
- Nick Y Larsen
- Core Centre for Molecular Morphology, Section for Stereology and Microscopy, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark. .,Centre for Stochastic Geometry and Advanced Bioimaging, Aalborg University, Aarhus University and University of Copenhagen, Aalborg, Aarhus and Copenhagen, Denmark. .,Sino-Danish Center for Education and Research, Aarhus, Denmark. .,University of the Chinese Academy of Sciences, Beijing, China.
| | - Xixia Li
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xueke Tan
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Gang Ji
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jing Lin
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Grazyna Rajkowska
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jesper Møller
- Centre for Stochastic Geometry and Advanced Bioimaging, Aalborg University, Aarhus University and University of Copenhagen, Aalborg, Aarhus and Copenhagen, Denmark.,Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark
| | - Ninna Vihrs
- Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark
| | - Jon Sporring
- Centre for Stochastic Geometry and Advanced Bioimaging, Aalborg University, Aarhus University and University of Copenhagen, Aalborg, Aarhus and Copenhagen, Denmark.,Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Fei Sun
- Sino-Danish Center for Education and Research, Aarhus, Denmark.,University of the Chinese Academy of Sciences, Beijing, China.,National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jens R Nyengaard
- Core Centre for Molecular Morphology, Section for Stereology and Microscopy, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Centre for Stochastic Geometry and Advanced Bioimaging, Aalborg University, Aarhus University and University of Copenhagen, Aalborg, Aarhus and Copenhagen, Denmark.,Sino-Danish Center for Education and Research, Aarhus, Denmark.,Department of Pathology, Aarhus University, Aarhus, Denmark
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26
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Gabarre S, Vernaillen F, Baatsen P, Vints K, Cawthorne C, Boeynaems S, Michiels E, Vandael D, Gounko NV, Munck S. A workflow for streamlined acquisition and correlation of serial regions of interest in array tomography. BMC Biol 2021; 19:152. [PMID: 34330271 PMCID: PMC8323292 DOI: 10.1186/s12915-021-01072-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 06/14/2021] [Indexed: 11/20/2022] Open
Abstract
Background Array tomography (AT) is a high-resolution imaging method to resolve fine details at the organelle level and has the advantage that it can provide 3D volumes to show the tissue context. AT can be carried out in a correlative way, combing light and electron microscopy (LM, EM) techniques. However, the correlation between modalities can be a challenge and delineating specific regions of interest in consecutive sections can be time-consuming. Integrated light and electron microscopes (iLEMs) offer the possibility to provide well-correlated images and may pose an ideal solution for correlative AT. Here, we report a workflow to automate navigation between regions of interest. Results We use a targeted approach that allows imaging specific tissue features, like organelles, cell processes, and nuclei at different scales to enable fast, directly correlated in situ AT using an integrated light and electron microscope (iLEM-AT). Our workflow is based on the detection of section boundaries on an initial transmitted light acquisition that serves as a reference space to compensate for changes in shape between sections, and we apply a stepwise refinement of localizations as the magnification increases from LM to EM. With minimal user interaction, this enables autonomous and speedy acquisition of regions containing cells and cellular organelles of interest correlated across different magnifications for LM and EM modalities, providing a more efficient way to obtain 3D images. We provide a proof of concept of our approach and the developed software tools using both Golgi neuronal impregnation staining and fluorescently labeled protein condensates in cells. Conclusions Our method facilitates tracing and reconstructing cellular structures over multiple sections, is targeted at high resolution ILEMs, and can be integrated into existing devices, both commercial and custom-built systems. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01072-7.
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Affiliation(s)
- Sergio Gabarre
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,VIB-KU Leuven Center for Brain & Disease Research, Light Microscopy Expertise Unit & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Frank Vernaillen
- VIB BioInformatics Core, Technologiepark 75, 9052, Ghent, Belgium
| | - Pieter Baatsen
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | | | - Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Emiel Michiels
- VIB Center for Brain and Disease Research, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium
| | - Dorien Vandael
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Natalia V Gounko
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium. .,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.
| | - Sebastian Munck
- KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium. .,VIB-KU Leuven Center for Brain & Disease Research, Light Microscopy Expertise Unit & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.
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27
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Oorschot V, Lindsey BW, Kaslin J, Ramm G. TEM, SEM, and STEM-based immuno-CLEM workflows offer complementary advantages. Sci Rep 2021; 11:899. [PMID: 33441723 PMCID: PMC7806999 DOI: 10.1038/s41598-020-79637-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 12/08/2020] [Indexed: 11/18/2022] Open
Abstract
Identifying endogenous tissue stem cells remains a key challenge in developmental and regenerative biology. To distinguish and molecularly characterise stem cell populations in large heterogeneous tissues, the combination of cytochemical cell markers with ultrastructural morphology is highly beneficial. Here, we realise this through workflows of multi-resolution immuno-correlative light and electron microscopy (iCLEM) methodologies. Taking advantage of the antigenicity preservation of the Tokuyasu technique, we have established robust protocols and workflows and provide a side-by-side comparison of iCLEM used in combination with scanning EM (SEM), scanning TEM (STEM), or transmission EM (TEM). Evaluation of the applications and advantages of each method highlights their practicality for the identification, quantification, and characterization of heterogeneous cell populations in small organisms, organs, or tissues in healthy and diseased states. The iCLEM techniques are broadly applicable and can use either genetically encoded or cytochemical markers on plant, animal and human tissues. We demonstrate how these protocols are particularly suited for investigating neural stem and progenitor cell populations of the vertebrate nervous system.
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Affiliation(s)
- Viola Oorschot
- Ramaciotti Centre for Cryo EM, Monash University, Melbourne, VIC, 3800, Australia
- European Molecular Biology Laboratory, Electron Microscopy Core Facility, Heidelberg, Germany
| | - Benjamin W Lindsey
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, 3800, Australia
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, R3E 0J9, Canada
| | - Jan Kaslin
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, 3800, Australia.
| | - Georg Ramm
- Ramaciotti Centre for Cryo EM, Monash University, Melbourne, VIC, 3800, Australia.
- Department of Biochemistry, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.
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Kato M, Kolotuev I, Cunha A, Gharib S, Sternberg PW. Extrasynaptic acetylcholine signaling through a muscarinic receptor regulates cell migration. Proc Natl Acad Sci U S A 2021; 118:e1904338118. [PMID: 33361149 PMCID: PMC7817160 DOI: 10.1073/pnas.1904338118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acetylcholine (ACh) promotes various cell migrations in vitro, but there are few investigations into this nonsynaptic role of ACh signaling in vivo. Here we investigate the function of a muscarinic receptor on an epithelial cell migration in Caenorhabditis elegans We show that the migratory gonad leader cell, the linker cell (LC), uses an M1/M3/M5-like muscarinic ACh receptor GAR-3 to receive extrasynaptic ACh signaling from cholinergic neurons for its migration. Either the loss of the GAR-3 receptor in the LC or the inhibition of ACh release from cholinergic neurons resulted in migratory path defects. The overactivation of the GAR-3 muscarinic receptor caused the LC to reverse its orientation through its downstream effectors Gαq/egl-30, PLCβ/egl-8, and TRIO/unc-73 This reversal response only occurred in the fourth larval stage, which corresponds to the developmental time when the GAR-3::yellow fluorescent protein receptor in the membrane relocalizes from a uniform to an asymmetric distribution. These findings suggest a role for the GAR-3 muscarinic receptor in determining the direction of LC migration.
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Affiliation(s)
- Mihoko Kato
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Irina Kolotuev
- Electron Microscopy Facility, University of Lausanne, Quartier Sorge-Biophore, CH-1015 Lausanne, Switzerland
| | - Alexandre Cunha
- Center for Advanced Methods in Biological Image Analysis, California Institute of Technology, Pasadena, CA 91125
| | - Shahla Gharib
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;
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29
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Read C, Walther P, von Einem J. Quantitative Electron Microscopy to Study HCMV Morphogenesis. Methods Mol Biol 2021; 2244:265-289. [PMID: 33555592 DOI: 10.1007/978-1-0716-1111-1_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The generation and release of mature virions from human cytomegalovirus (HCMV) infected cells is a multistep process, involving a profound reorganization of cellular structures and various stages of virus particle morphogenesis in different cellular compartments. Although the general steps of HCMV morphogenesis are known, it has become clear that the detailed molecular mechanisms are complex and dependent on various viral factors and cellular pathways. The lack of a full understanding of HCMV virion morphogenesis emphasizes the need of imaging techniques to visualize the different stages of virion assembly, such as electron microscopy. Here, we describe various electron microscopy techniques and the methodology of high-pressure freezing and freeze substitution for sample preparation to visualize HCMV morphogenesis. These methods are used in our laboratory in combination with a thorough quantification to characterize phenotypic alterations and to identify the function of viral and cellular proteins for the various morphogenesis stages.
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Affiliation(s)
- Clarissa Read
- Institute of Virology, Ulm University Medical Center, Ulm, Germany.,Central Facility for Electron Microscopy, Ulm University, Ulm, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Ulm, Germany
| | - Jens von Einem
- Institute of Virology, Ulm University Medical Center, Ulm, Germany.
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30
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Homeostatic mini-intestines through scaffold-guided organoid morphogenesis. Nature 2020; 585:574-578. [PMID: 32939089 DOI: 10.1038/s41586-020-2724-8] [Citation(s) in RCA: 433] [Impact Index Per Article: 86.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 06/24/2020] [Indexed: 12/12/2022]
Abstract
Epithelial organoids, such as those derived from stem cells of the intestine, have great potential for modelling tissue and disease biology1-4. However, the approaches that are used at present to derive these organoids in three-dimensional matrices5,6 result in stochastically developing tissues with a closed, cystic architecture that restricts lifespan and size, limits experimental manipulation and prohibits homeostasis. Here, by using tissue engineering and the intrinsic self-organization properties of cells, we induce intestinal stem cells to form tube-shaped epithelia with an accessible lumen and a similar spatial arrangement of crypt- and villus-like domains to that in vivo. When connected to an external pumping system, the mini-gut tubes are perfusable; this allows the continuous removal of dead cells to prolong tissue lifespan by several weeks, and also enables the tubes to be colonized with microorganisms for modelling host-microorganism interactions. The mini-intestines include rare, specialized cell types that are seldom found in conventional organoids. They retain key physiological hallmarks of the intestine and have a notable capacity to regenerate. Our concept for extrinsically guiding the self-organization of stem cells into functional organoids-on-a-chip is broadly applicable and will enable the attainment of more physiologically relevant organoid shapes, sizes and functions.
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31
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Keevend K, Coenen T, Herrmann IK. Correlative cathodoluminescence electron microscopy bioimaging: towards single protein labelling with ultrastructural context. NANOSCALE 2020; 12:15588-15603. [PMID: 32677648 DOI: 10.1039/d0nr02563a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The understanding of living systems and their building blocks relies heavily on the assessment of structure-function relationships at the nanoscale. Ever since the development of the first optical microscope, the reliance of scientists across disciplines on microscopy has increased. The development of the first electron microscope and with it the access to information at the nanoscale has prompted numerous disruptive discoveries. While fluorescence imaging allows identification of specific entities based on the labelling with fluorophores, the unlabelled constituents of the samples remain invisible. In electron microscopy on the other hand, structures can be comprehensively visualized based on their distinct electron density and geometry. Although electron microscopy is a powerful tool, it does not implicitly provide information on the location and activity of specific organic molecules. While correlative light and electron microscopy techniques have attempted to unify the two modalities, the resolution mismatch between the two data sets poses major challenges. Recent developments in optical super resolution microscopy enable high resolution correlative light and electron microscopy, however, with considerable constraints due to sample preparation requirements. Labelling of specific structures directly for electron microscopy using small gold nanoparticles (i.e. immunogold) has been used extensively. However, identification of specific entities solely based on electron contrast, and the differentiation from endogenous dense granules, remains challenging. Recently, the use of correlative cathodoluminescence electron microscopy (CCLEM) imaging based on luminescent inorganic nanocrystals has been proposed. While nanometric resolution can be reached for both the electron and the optical signal, high energy electron beams are potentially damaging to the sample. In this review, we discuss the opportunities of (volumetric) multi-color single protein labelling based on correlative cathodoluminescence electron microscopy, and its prospective impact on biomedical research in general. We elaborate on the potential challenges of correlative cathodoluminescence electron microscopy-based bioimaging and benchmark CCLEM against alternative high-resolution correlative imaging techniques.
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Affiliation(s)
- Kerda Keevend
- Laboratory for Particles Biology Interactions, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, CH-9014, St Gallen, Switzerland.
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32
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Pasquettaz R, Kolotuev I, Rohrbach A, Gouelle C, Pellerin L, Langlet F. Peculiar protrusions along tanycyte processes face diverse neural and nonneural cell types in the hypothalamic parenchyma. J Comp Neurol 2020; 529:553-575. [PMID: 32515035 PMCID: PMC7818493 DOI: 10.1002/cne.24965] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 12/15/2022]
Abstract
Tanycytes are highly specialized ependymal cells that line the bottom and the lateral walls of the third ventricle. In contact with the cerebrospinal fluid through their cell bodies, they send processes into the arcuate nucleus, the ventromedial nucleus, and the dorsomedial nucleus of the hypothalamus. In the present work, we combined transgenic and immunohistochemical approaches to investigate the neuroanatomical associations between tanycytes and neural cells present in the hypothalamic parenchyma, in particular in the arcuate nucleus. The specific expression of tdTomato in tanycytes first allowed the observation of peculiar subcellular protrusions along tanycyte processes and at their endfeet such as spines, swelling, en passant boutons, boutons, or claws. Interestingly, these protrusions contact different neural cells in the brain parenchyma including blood vessels and neurons, and in particular NPY and POMC neurons in the arcuate nucleus. Using both fluorescent and electron microscopy, we finally observed that these tanycyte protrusions contain ribosomes, mitochondria, diverse vesicles, and transporters, suggesting dense tanycyte/neuron and tanycyte/blood vessel communications. Altogether, our results lay the neuroanatomical basis for tanycyte/neural cell interactions, which will be useful to further understand cell-to-cell communications involved in the regulation of neuroendocrine functions.
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Affiliation(s)
- Roxane Pasquettaz
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Irina Kolotuev
- Electron Microscopy Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Antoine Rohrbach
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Cathy Gouelle
- Department of Physiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Luc Pellerin
- Department of Physiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Centre de Résonance Magnétique des Systèmes Biologiques, UMR5536 CNRS, LabEx TRAIL-IBIO, Université de Bordeaux, Bordeaux Cedex, France.,Inserm U1082, Universite de Poitiers, Poitiers Cedex, France
| | - Fanny Langlet
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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Siloxane-functionalised surface patterns as templates for the ordered deposition of thin lamellar objects. Sci Rep 2019; 9:17952. [PMID: 31784635 PMCID: PMC6884528 DOI: 10.1038/s41598-019-54507-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/13/2019] [Indexed: 11/08/2022] Open
Abstract
A novel method is demonstrated for ordered deposition of thin lamellar objects from a liquid environment onto solid substrates by solid/fluid/solid-driven organisation. Surface functionalisation forms a template pattern that accumulates the lamellar objects by site-selective wetting of the target area without the need for a physical fluid containment. Contrary to conventional handling methods, no mechanical contact occurs, which facilitates the ordered deposition without wrinkles or ruptures. An additive and a subtractive process for the creation of such templates are presented. The subtractive process starts with the complete silanisation of the substrate in the vapour phase followed by site-selective oxygen plasma treatment of the siloxane film. The additive process uses microcontact printing to transfer the target pattern. Both processes are characterised by optical inspection of the wetting contours and it is found that site-selective plasma treatment shows a better pattern fidelity. The patterns obtained by site-selective plasma treatment are also subject to ToF-SIMS analysis and show good chemical contrast between hydrophilic and hydrophobic areas. The ordered deposition of lamellar objects by this new method is demonstrated for 60 nm thick ultramicrotome sections of epoxide resin on pre-patterned glass substrates.
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34
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Templier T. MagC, magnetic collection of ultrathin sections for volumetric correlative light and electron microscopy. eLife 2019; 8:e45696. [PMID: 31294691 PMCID: PMC6697447 DOI: 10.7554/elife.45696] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/02/2019] [Indexed: 01/03/2023] Open
Abstract
The non-destructive collection of ultrathin sections on silicon wafers for post-embedding staining and volumetric correlative light and electron microscopy traditionally requires exquisite manual skills and is tedious and unreliable. In MagC introduced here, sample blocks are augmented with a magnetic resin enabling the remote actuation and collection of hundreds of sections on wafer. MagC allowed the correlative visualization of neuroanatomical tracers within their ultrastructural volumetric electron microscopy context.
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Affiliation(s)
- Thomas Templier
- Institute of NeuroinformaticsUniversity of Zurich and ETH ZurichZurichSwitzerland
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35
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Booth DG, Beckett AJ, Prior IA, Meijer D. SuperCLEM: an accessible correlative light and electron microscopy approach for investigation of neurons and glia in vitro. Biol Open 2019; 8:bio.042085. [PMID: 31110056 PMCID: PMC6550067 DOI: 10.1242/bio.042085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The rapid evolution of super-resolution light microscopy has narrowed the gap between light and electron microscopy, allowing the imaging of molecules and cellular structures at high resolution within their normal cellular and tissue context. Multimodal imaging approaches such as correlative light electron microscopy (CLEM) combine these techniques to create a tool with unique imaging capacity. However, these approaches are typically reserved for specialists, and their application to the analysis of neural tissue is challenging. Here we present SuperCLEM, a relatively simple approach that combines super-resolution fluorescence light microscopy (FLM), 3D electron microscopy (3D-EM) and rendering into 3D models. We demonstrate our workflow using neuron-glia cultures from which we first acquire high-resolution fluorescent light images of myelinated axons. After resin embedding and re-identification of the region of interest, serially aligned EM sections are acquired and imaged using a serial block face scanning electron microscope (SBF-SEM). The FLM and 3D-EM datasets are then combined to render 3D models of the myelinated axons. Thus, the SuperCLEM imaging pipeline is a useful new tool for researchers pursuing similar questions in neuronal and other complex tissue culture systems. Summary: We developed an advanced, accessible and adaptable correlative light and electron microscopy pipeline for study of neuron-glia cultures and demonstrate its power by deriving accurate 3D models of myelinated axons.
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Affiliation(s)
- Daniel G Booth
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Alison J Beckett
- Biomedical Electron Microscopy Unit, Department of Molecular and Cellular Biology, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Ian A Prior
- Biomedical Electron Microscopy Unit, Department of Molecular and Cellular Biology, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Dies Meijer
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
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36
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Kizilyaprak C, Stierhof YD, Humbel BM. Volume microscopy in biology: FIB-SEM tomography. Tissue Cell 2019; 57:123-128. [DOI: 10.1016/j.tice.2018.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/30/2018] [Accepted: 09/20/2018] [Indexed: 01/10/2023]
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37
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Low IIC, Williams CR, Chong MK, McLachlan IG, Wierbowski BM, Kolotuev I, Heiman MG. Morphogenesis of neurons and glia within an epithelium. Development 2019; 146:dev171124. [PMID: 30683663 PMCID: PMC6398450 DOI: 10.1242/dev.171124] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 01/15/2019] [Indexed: 12/13/2022]
Abstract
To sense the outside world, some neurons protrude across epithelia, the cellular barriers that line every surface of our bodies. To study the morphogenesis of such neurons, we examined the C. elegans amphid, in which dendrites protrude through a glial channel at the nose. During development, amphid dendrites extend by attaching to the nose via DYF-7, a type of protein typically found in epithelial apical ECM. Here, we show that amphid neurons and glia exhibit epithelial properties, including tight junctions and apical-basal polarity, and develop in a manner resembling other epithelia. We find that DYF-7 is a fibril-forming apical ECM component that promotes formation of the tube-shaped glial channel, reminiscent of roles for apical ECM in other narrow epithelial tubes. We also identify a requirement for FRM-2, a homolog of EPBL15/moe/Yurt that promotes epithelial integrity in other systems. Finally, we show that other environmentally exposed neurons share a requirement for DYF-7. Together, our results suggest that these neurons and glia can be viewed as part of an epithelium continuous with the skin, and are shaped by mechanisms shared with other epithelia.
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Affiliation(s)
- Isabel I C Low
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Claire R Williams
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Megan K Chong
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Ian G McLachlan
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Bradley M Wierbowski
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Irina Kolotuev
- Université de Rennes 1, Plateforme microscopie électronique, 35043 Rennes, France
| | - Maxwell G Heiman
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
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38
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Mulcahy B, Witvliet D, Holmyard D, Mitchell J, Chisholm AD, Meirovitch Y, Samuel ADT, Zhen M. A Pipeline for Volume Electron Microscopy of the Caenorhabditis elegans Nervous System. Front Neural Circuits 2018; 12:94. [PMID: 30524248 PMCID: PMC6262311 DOI: 10.3389/fncir.2018.00094] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/08/2018] [Indexed: 01/01/2023] Open
Abstract
The “connectome,” a comprehensive wiring diagram of synaptic connectivity, is achieved through volume electron microscopy (vEM) analysis of an entire nervous system and all associated non-neuronal tissues. White et al. (1986) pioneered the fully manual reconstruction of a connectome using Caenorhabditis elegans. Recent advances in vEM allow mapping new C. elegans connectomes with increased throughput, and reduced subjectivity. Current vEM studies aim to not only fill the remaining gaps in the original connectome, but also address fundamental questions including how the connectome changes during development, the nature of individuality, sexual dimorphism, and how genetic and environmental factors regulate connectivity. Here we describe our current vEM pipeline and projected improvements for the study of the C. elegans nervous system and beyond.
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Affiliation(s)
- Ben Mulcahy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Daniel Witvliet
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Douglas Holmyard
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada.,Nanoscale Biomedical Imaging Facility, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
| | - James Mitchell
- Center for Brain Science, Department of Physics, Harvard University, Cambridge, MA, United States
| | - Andrew D Chisholm
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Yaron Meirovitch
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Aravinthan D T Samuel
- Center for Brain Science, Department of Physics, Harvard University, Cambridge, MA, United States
| | - Mei Zhen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Department of Physiology, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
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39
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Lee TJ, Kumar A, Balwani AH, Brittain D, Kinn S, Tovey CA, Dyer EL, da Costa NM, Reid RC, Forest CR, Bumbarger DJ. Large-scale neuroanatomy using LASSO: Loop-based Automated Serial Sectioning Operation. PLoS One 2018; 13:e0206172. [PMID: 30352088 PMCID: PMC6198950 DOI: 10.1371/journal.pone.0206172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/08/2018] [Indexed: 12/01/2022] Open
Abstract
Serial section transmission electron microscopy (ssTEM) is the most promising tool for investigating the three-dimensional anatomy of the brain with nanometer resolution. Yet as the field progresses to larger volumes of brain tissue, new methods for high-yield, low-cost, and high-throughput serial sectioning are required. Here, we introduce LASSO (Loop-based Automated Serial Sectioning Operation), in which serial sections are processed in “batches.” Batches are quantized groups of individual sections that, in LASSO, are cut with a diamond knife, picked up from an attached waterboat, and placed onto microfabricated TEM substrates using rapid, accurate, and repeatable robotic tools. Additionally, we introduce mathematical models for ssTEM with respect to yield, throughput, and cost to access ssTEM scalability. To validate the method experimentally, we processed 729 serial sections of human brain tissue (~40 nm x 1 mm x 1 mm). Section yield was 727/729 (99.7%). Sections were placed accurately and repeatably (x-direction: -20 ± 110 μm (1 s.d.), y-direction: 60 ± 150 μm (1 s.d.)) with a mean cycle time of 43 s ± 12 s (1 s.d.). High-magnification (2.5 nm/px) TEM imaging was conducted to measure the image quality. We report no significant distortion, information loss, or substrate-derived artifacts in the TEM images. Quantitatively, the edge spread function across vesicle edges and image contrast were comparable, suggesting that LASSO does not negatively affect image quality. In total, LASSO compares favorably with traditional serial sectioning methods with respect to throughput, yield, and cost for large-scale experiments, and represents a flexible, scalable, and accessible technology platform to enable the next generation of neuroanatomical studies.
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Affiliation(s)
- Timothy J. Lee
- Georgia Institute of Technology, G. W. Woodruff School of Mechanical Engineering, Atlanta, GA, United States of America
- * E-mail:
| | - Aditi Kumar
- Georgia Institute of Technology, G. W. Woodruff School of Mechanical Engineering, Atlanta, GA, United States of America
| | - Aishwarya H. Balwani
- Georgia Institute of Technology, School of Electrical and Computer Engineering, Atlanta, GA, United States of America
| | - Derrick Brittain
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Sam Kinn
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Craig A. Tovey
- Georgia Institute of Technology, H. Milton Stewart School of Industrial & Systems Engineering, Atlanta, GA, United States of America
| | - Eva L. Dyer
- Georgia Institute of Technology, School of Electrical and Computer Engineering, Atlanta, GA, United States of America
- Georgia Institute of Technology, Coulter Department of Biomedical Engineering, Atlanta, GA, United States of America
| | - Nuno M. da Costa
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - R. Clay Reid
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Craig R. Forest
- Georgia Institute of Technology, G. W. Woodruff School of Mechanical Engineering, Atlanta, GA, United States of America
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