1
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Lyu CA, Shen Y, Zhang P. Zooming in and out: Exploring RNA Viral Infections with Multiscale Microscopic Methods. Viruses 2024; 16:1504. [PMID: 39339980 PMCID: PMC11437419 DOI: 10.3390/v16091504] [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: 08/29/2024] [Revised: 09/19/2024] [Accepted: 09/22/2024] [Indexed: 09/30/2024] Open
Abstract
RNA viruses, being submicroscopic organisms, have intriguing biological makeups and substantially impact human health. Microscopic methods have been utilized for studying RNA viruses at a variety of scales. In order of observation scale from large to small, fluorescence microscopy, cryo-soft X-ray tomography (cryo-SXT), serial cryo-focused ion beam/scanning electron microscopy (cryo-FIB/SEM) volume imaging, cryo-electron tomography (cryo-ET), and cryo-electron microscopy (cryo-EM) single-particle analysis (SPA) have been employed, enabling researchers to explore the intricate world of RNA viruses, their ultrastructure, dynamics, and interactions with host cells. These methods evolve to be combined to achieve a wide resolution range from atomic to sub-nano resolutions, making correlative microscopy an emerging trend. The developments in microscopic methods provide multi-fold and spatial information, advancing our understanding of viral infections and providing critical tools for developing novel antiviral strategies and rapid responses to emerging viral threats.
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Affiliation(s)
- Cheng-An Lyu
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK;
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7BN, UK
| | - Yao Shen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK;
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK;
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7BN, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
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2
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Zhou H, Guo Y, Fu T, Peng Y, Chen Z, Cui Y, Guo M, Zhang K, Chen C, Wang Y. Three-Dimensional Label-Free Observing of the Self-Assembled Nanoparticles inside a Single Cell at Nanoscale Resolution. ACS NANO 2024. [PMID: 39001860 DOI: 10.1021/acsnano.4c06095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
Understanding the intracellular behavior of nanoparticles (NPs) plays a key role in optimizing the self-assembly performance of nanomedicine. However, conducting the 3D, label-free, quantitative observation of self-assembled NPs within intact single cells remains a substantial challenge in complicated intracellular environments. Here, we propose a deep learning combined synchrotron radiation hard X-ray nanotomography approach to visualize the self-assembled ultrasmall iron oxide (USIO) NPs in a single cell. The method allows us to explore comprehensive information on NPs, such as their distribution, morphology, location, and interaction with cell organelles, and provides quantitative analysis of the heterogeneous size and morphologies of USIO NPs under diverse conditions. This label-free, in situ method provides a tool for precise characterization of intracellular self-assembled NPs to improve the evaluation and design of a bioresponsive nanomedicine.
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Affiliation(s)
- Huige Zhou
- New Cornerstone Science Laboratory, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Research Unit of Nanoscience and Technology, Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Yuecong Guo
- New Cornerstone Science Laboratory, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianyu Fu
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Yufeng Peng
- New Cornerstone Science Laboratory, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing 100190, China
| | - Ziwei Chen
- New Cornerstone Science Laboratory, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyan Cui
- Beijing Engineering Research Center of Mixed Reality and Advanced Display, School of Optoelectronics, Beijing Institute of Technology, Beijing 100081, China
| | - Mengyu Guo
- New Cornerstone Science Laboratory, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing 100190, China
| | - Kai Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Chunying Chen
- New Cornerstone Science Laboratory, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Research Unit of Nanoscience and Technology, Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Yaling Wang
- New Cornerstone Science Laboratory, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Yoniles J, Summers JA, Zielinski KA, Antolini C, Panjalingam M, Lisova S, Moss FR, Di Perna MA, Kupitz C, Hunter MS, Pollack L, Wakatsuki S, Dahlberg PD. Time-resolved cryogenic electron tomography for the study of transient cellular processes. Mol Biol Cell 2024; 35:mr4. [PMID: 38717434 PMCID: PMC11244162 DOI: 10.1091/mbc.e24-01-0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/15/2024] [Accepted: 04/29/2024] [Indexed: 06/07/2024] Open
Abstract
Cryogenic electron tomography (cryo-ET) is the highest resolution imaging technique applicable to the life sciences, enabling subnanometer visualization of specimens preserved in their near native states. The rapid plunge freezing process used to prepare samples lends itself to time-resolved studies, which researchers have pursued for in vitro samples for decades. Here, we focus on developing a freezing apparatus for time-resolved studies in situ. The device mixes cellular samples with solution-phase stimulants before spraying them directly onto an electron microscopy grid that is transiting into cryogenic liquid ethane. By varying the flow rates of cell and stimulant solutions within the device, we can control the reaction time from tens of milliseconds to over a second before freezing. In a proof-of-principle demonstration, the freezing method is applied to a model bacterium, Caulobacter crescentus, mixed with an acidic buffer. Through cryo-ET we resolved structural changes throughout the cell, including surface-layer protein dissolution, outer membrane deformation, and cytosolic rearrangement, all within 1.5 s of reaction time. This new approach, Time-Resolved cryo-ET (TR-cryo-ET), enhances the capabilities of cryo-ET by incorporating a subsecond temporal axis and enables the visualization of induced structural changes at the molecular, organelle, or cellular level.
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Affiliation(s)
- Joseph Yoniles
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305
| | - Jacob A. Summers
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Kara A. Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Cali Antolini
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | | | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Frank R. Moss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | | | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Peter D. Dahlberg
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
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4
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Gao Z, Han K, Hua X, Liu W, Jia S. hydroSIM: super-resolution speckle illumination microscopy with a hydrogel diffuser. BIOMEDICAL OPTICS EXPRESS 2024; 15:3574-3585. [PMID: 38867780 PMCID: PMC11166422 DOI: 10.1364/boe.521521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/27/2024] [Accepted: 04/18/2024] [Indexed: 06/14/2024]
Abstract
Super-resolution microscopy has emerged as an indispensable methodology for probing the intricacies of cellular biology. Structured illumination microscopy (SIM), in particular, offers an advantageous balance of spatial and temporal resolution, allowing for visualizing cellular processes with minimal disruption to biological specimens. However, the broader adoption of SIM remains hampered by the complexity of instrumentation and alignment. Here, we introduce speckle-illumination super-resolution microscopy using hydrogel diffusers (hydroSIM). The study utilizes the high scattering and optical transmissive properties of hydrogel materials and realizes a remarkably simplified approach to plug-in super-resolution imaging via a common epi-fluorescence platform. We demonstrate the hydroSIM system using various phantom and biological samples, and the results exhibited effective 3D resolution doubling, optical sectioning, and high contrast. We foresee hydroSIM, a cost-effective, biocompatible, and user-accessible super-resolution methodology, to significantly advance a wide range of biomedical imaging and applications.
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Affiliation(s)
- Zijun Gao
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Keyi Han
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Xuanwen Hua
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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5
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Ru YX, Dong SX, Liu J, Liu JH, Zhou Y, Eyden B. Malformation of the endoplasmic reticulum system evolving into giant inclusions and Auer bodies in acute promyelocytic leukemia: an ultrastructural study of 6 cases. Ultrastruct Pathol 2024; 48:221-233. [PMID: 38619116 DOI: 10.1080/01913123.2024.2340965] [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: 02/10/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
The endoplasmic reticulum(ER)is the largest membranous network serving as a region for protein, lipid and steroid synthesis, transport and storage. Detailed information about ER-cisternae, ER-tubules and rough endoplasmic reticulum (rER) is scarce in human blood cells. This study describes a series of giant inclusions and Auer bodies in promyeloblasts in six patients with acute promyelocytic leukemia (APL), by light microscopy, transmission electron microscopy (TEM) and cytochemical stains. TEM revealed that giant inclusions and pro-Auer bodies were associated with rER and surrounded by tubular structures composed of degenerated or redundant membrane in promyeloblasts, which corresponded with elements of the ER system. This paper reveals that in the promyeloblasts of APL, ER is the source of and transforms progressively into giant inclusions and Auer bodies.
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Affiliation(s)
- Yong-Xin Ru
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of the Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Shu-Xu Dong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of the Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Jing Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of the Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Jin-Hua Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of the Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yuan Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of the Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Brian Eyden
- Department of Histopathology, Christie NHS Foundation Trust, Manchester, UK
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6
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Okolo CA, Maran JJ, Watts A, Maripillan J, Harkiolaki M, Martínez AD, Green CR, Mugisho OO. Correlative light and X-ray tomography jointly unveil the critical role of connexin43 channels on inflammation-induced cellular ultrastructural alterations. Heliyon 2024; 10:e27888. [PMID: 38560181 PMCID: PMC10979075 DOI: 10.1016/j.heliyon.2024.e27888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Non-junctional connexin43 (Cx43) plasma membrane hemichannels have been implicated in several inflammatory diseases, particularly playing a role in ATP release that triggers activation of the inflammasome. Therapies targeting the blocking of the hemichannels to prevent the pathological release or uptake of ions and signalling molecules through its pores are of therapeutic interest. To date, there is no close-to-native, high-definition documentation of the impact of Cx43 hemichannel-mediated inflammation on cellular ultrastructure, neither is there a robust account of the ultrastructural changes that occur following treatment with selective Cx43 hemichannel blockers such as Xentry-Gap19 (XG19). A combination of same-sample correlative high-resolution three-dimensional fluorescence microscopy and soft X-ray tomography at cryogenic temperatures, enabled in the identification of novel 3D molecular interactions within the cellular milieu when comparing behaviour in healthy states and during the early onset or late stages under inflammatory conditions. Notably, our findings suggest that XG19 blockage of connexin hemichannels under pro-inflammatory conditions may be crucial in preventing the direct degradation of connexosomes by lysosomes, without affecting connexin protein translation and trafficking. We also delineated fine and gross cellular phenotypes, characteristic of inflammatory insult or road-to-recovery from inflammation, where XG19 could indirectly prevent and reverse inflammatory cytokine-induced mitochondrial swelling and cellular hypertrophy through its action on Cx43 hemichannels. Our findings suggest that XG19 might have prophylactic and therapeutic effects on the inflammatory response, in line with functional studies.
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Affiliation(s)
- Chidinma Adanna Okolo
- Beamline B24, Life Sciences Division, Diamond Light Source, Didcot, Oxfordshire, United Kingdom
| | - Jack Jonathan Maran
- Buchanan Ocular Therapeutics Unit, Department of Ophthalmology, New Zealand National Eye Centre, University of Auckland, New Zealand
| | - Amy Watts
- Beamline B24, Life Sciences Division, Diamond Light Source, Didcot, Oxfordshire, United Kingdom
| | - Jaime Maripillan
- Centro Interdisciplinario de Neurociencias de Valparaíso (CINV), Universidad de Valparaíso, Valparaíso, Chile
| | - Maria Harkiolaki
- Beamline B24, Life Sciences Division, Diamond Light Source, Didcot, Oxfordshire, United Kingdom
| | - Agustín D. Martínez
- Centro Interdisciplinario de Neurociencias de Valparaíso (CINV), Universidad de Valparaíso, Valparaíso, Chile
| | - Colin R. Green
- Department of Ophthalmology, University of Auckland, New Zealand
| | - Odunayo Omolola Mugisho
- Buchanan Ocular Therapeutics Unit, Department of Ophthalmology, New Zealand National Eye Centre, University of Auckland, New Zealand
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7
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Tang Q, Yin D, Liu Y, Zhang J, Guan Y, Kong H, Wang Y, Zhang X, Li J, Wang L, Hu J, Cai X, Zhu Y. Clickable X-ray Nanoprobes for Nanoscopic Bioimaging of Cellular Structures. JACS AU 2024; 4:893-902. [PMID: 38559738 PMCID: PMC10976567 DOI: 10.1021/jacsau.4c00056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 04/04/2024]
Abstract
Synchrotron-based X-ray microscopy (XRM) has garnered widespread attention from researchers due to its high spatial resolution and excellent energy (element) resolution. Existing molecular probes suitable for XRM include immune probes and genetic labeling probes, enabling the precise imaging of various biological targets within cells. However, immune labeling techniques are prone to cross-interference between antigens and antibodies. Genetic labeling technologies have limited systems that allow express markers independently, and moreover, genetically encoded labels based on catalytic polymerization lack a fixed morphology. When applied to cell imaging, this can result in reduced localization accuracy due to the diffusion of labels within the cells. Therefore, both techniques face challenges in simultaneously labeling multiple biotargets within cells and achieving high-precision imaging. In this work, we applied the click reaction and developed a third category of imaging probes suitable for XRM, termed clickable X-ray nanoprobes (Click-XRN). Click-XRN consists of two components: an X-ray-sensitive multicolor imaging module and a particle-size-controllable morphology module. Efficient identification of intra- and extracellular biotargets is achieved through click reactions between the probe and biomolecules. Click-XRN possesses a controllable particle size, and its loading of various metal ions provides distinctive signals for imaging under XRM. Based on this, we optimized the imaging energy of Click-XRN with different particle sizes, enabling single-color and two-color imaging of the cell membrane, cell nucleus, and mitochondria with nanoscale spatial nanometers. Our work provides a potent molecular tool for investigating cellular activities through XRM.
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Affiliation(s)
- Qiaowei Tang
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, China
- Xiangfu
Laboratory, Jiashan 314102, China
| | - Dapeng Yin
- Division
of Physical Biology, CAS Key Laboratory of Interfacial Physics and
Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Yubo Liu
- Division
of Physical Biology, CAS Key Laboratory of Interfacial Physics and
Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Jichao Zhang
- Shanghai
Synchrotron Radiation Facility (SSRF), Shanghai
Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Yong Guan
- National
Synchrotron Radiation Laboratory, University
of Science and Technology of China, Hefei 230029, China
| | - Huating Kong
- Shanghai
Synchrotron Radiation Facility (SSRF), Shanghai
Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Yiliu Wang
- Division
of Physical Biology, CAS Key Laboratory of Interfacial Physics and
Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiangzhi Zhang
- Shanghai
Synchrotron Radiation Facility (SSRF), Shanghai
Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Jiang Li
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, China
- Division
of Physical Biology, CAS Key Laboratory of Interfacial Physics and
Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Lihua Wang
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, China
- Division
of Physical Biology, CAS Key Laboratory of Interfacial Physics and
Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Jun Hu
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, China
- Division
of Physical Biology, CAS Key Laboratory of Interfacial Physics and
Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiaoqing Cai
- Shanghai
Synchrotron Radiation Facility (SSRF), Shanghai
Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Ying Zhu
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, China
- Division
of Physical Biology, CAS Key Laboratory of Interfacial Physics and
Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
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8
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Fahy K, Kapishnikov S, Donnellan M, McEnroe T, O'Reilly F, Fyans W, Sheridan P. Laboratory based correlative cryo-soft X-ray tomography and cryo-fluorescence microscopy. Methods Cell Biol 2024; 187:293-320. [PMID: 38705628 DOI: 10.1016/bs.mcb.2024.02.033] [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
Cryo-soft X-ray tomography is the unique technology that can image whole intact cells in 3D under normal and pathological conditions without labelling or fixation, at high throughput and spatial resolution. The sample preparation is relatively straightforward; requiring just fast freezing of the specimen before transfer to the microscope for imaging. It is also possible to image chemically fixed samples where necessary. The technique can be correlated with cryo fluorescence microscopy to localize fluorescent proteins to organelles within the whole cell volume. Cryo-correlated light and soft X-ray tomography is particularly useful for the study of gross morphological changes brought about by disease or drugs. For example, viral fluorescent tags can be co-localized to sites of viral replication in the soft X-ray volume. In general this approach is extremely useful in the study of complex 3D organelle structure, nanoparticle uptake or in the detection of rare events in the context of whole cell structure. The main challenge of soft X-ray tomography is that the soft X-ray illumination required for imaging has heretofore only been available at a small number of synchrotron labs worldwide. Recently, a compact device with a footprint small enough to fit in a standard laboratory setting has been deployed ("the SXT-100") and is routinely imaging cryo prepared samples addressing a variety of disease and drug research applications. The SXT-100 facilitates greater access to this powerful technique and greatly increases the scope and throughput of potential research projects. Furthermore, the availability of cryo-soft X-ray tomography in the laboratory will accelerate the development of novel correlative and multimodal workflows by integration with light and electron microscope based approaches. It also allows for co-location of this powerful imaging modality at BSL3 labs or other facilities where safety or intellectual property considerations are paramount. Here we describe the compact SXT-100 microscope along with its novel integrated cryo-fluorescence imaging capability.
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Affiliation(s)
- Kenneth Fahy
- SiriusXT Ltd., Stillorgan Industrial Park, Dublin, Ireland.
| | | | | | - Tony McEnroe
- SiriusXT Ltd., Stillorgan Industrial Park, Dublin, Ireland
| | - Fergal O'Reilly
- SiriusXT Ltd., Stillorgan Industrial Park, Dublin, Ireland; University College Dublin, School of Physics, Dublin, Ireland; University College Dublin, School of Biology and Environmental Sciences, Dublin, Ireland
| | - William Fyans
- SiriusXT Ltd., Stillorgan Industrial Park, Dublin, Ireland
| | - Paul Sheridan
- SiriusXT Ltd., Stillorgan Industrial Park, Dublin, Ireland
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9
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Zanetti-Domingues LC, Hirsch M, Wang L, Eastwood TA, Baker K, Mulvihill DP, Radford S, Horne J, White P, Bateman B. Toward quantitative super-resolution methods for cryo-CLEM. Methods Cell Biol 2024; 187:249-292. [PMID: 38705627 DOI: 10.1016/bs.mcb.2024.02.028] [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
Cryogenic ultrastructural imaging techniques such as cryo-electron tomography have produced a revolution in how the structure of biological systems is investigated by enabling the determination of structures of protein complexes immersed in a complex biological matrix within vitrified cell and model organisms. However, so far, the portfolio of successes has been mostly limited to highly abundant complexes or to structures that are relatively unambiguous and easy to identify through electron microscopy. In order to realize the full potential of this revolution, researchers would have to be able to pinpoint lower abundance species and obtain functional annotations on the state of objects of interest which would then be correlated to ultrastructural information to build a complete picture of the structure-function relationships underpinning biological processes. Fluorescence imaging at cryogenic conditions has the potential to be able to meet these demands. However, wide-field images acquired at low numeric aperture (NA) using air immersion objective have a low resolving power and cannot provide accurate enough three-dimensional (3D) localization to enable the assignment of functional annotations to individual objects of interest or target sample debulking to ensure the preservation of the structures of interest. It is therefore necessary to develop super-resolved cryo-fluorescence workflows capable of fulfilling this role and enabling new biological discoveries. In this chapter, we present the current state of development of two super-resolution cryogenic fluorescence techniques, superSIL-STORM and astigmatism-based 3D STORM, show their application to a variety of biological systems and discuss their advantages and limitations. We further discuss the future applicability to cryo-CLEM workflows though examples of practical application to the study of membrane protein complexes both in mammalian cells and in Escherichia coli.
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Affiliation(s)
- Laura C Zanetti-Domingues
- CLF Octopus Facility, UKRI-Science and Technology Facilities Council, R92, Rutherford Appleton Laboratory, Didcot, United Kingdom.
| | - Michael Hirsch
- CLF Octopus Facility, UKRI-Science and Technology Facilities Council, R92, Rutherford Appleton Laboratory, Didcot, United Kingdom
| | - Lin Wang
- CLF Octopus Facility, UKRI-Science and Technology Facilities Council, R92, Rutherford Appleton Laboratory, Didcot, United Kingdom
| | - Tara A Eastwood
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Karen Baker
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | | | - Sheena Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, Leeds, United Kingdom
| | - Jim Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, Leeds, United Kingdom
| | - Paul White
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, Leeds, United Kingdom
| | - Benji Bateman
- CLF Octopus Facility, UKRI-Science and Technology Facilities Council, R92, Rutherford Appleton Laboratory, Didcot, United Kingdom
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10
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Cao M, Wang Y, Wang L, Zhang K, Guan Y, Guo Y, Chen C. In situ label-free X-ray imaging for visualizing the localization of nanomedicines and subcellular architecture in intact single cells. Nat Protoc 2024; 19:30-59. [PMID: 37957402 DOI: 10.1038/s41596-023-00902-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 08/10/2023] [Indexed: 11/15/2023]
Abstract
Understanding the intracellular behaviors of nanomedicines and morphology variation of subcellular architecture impacted by nanomaterial-biology (nano-bio) interactions could help guide the safe-by-design, manufacturing and evaluation of nanomedicines for clinical translation. The in situ and label-free analysis of nano-bio interactions in intact single cells at nanoscale remains challenging. We developed an approach based on X-ray microscopy to directly visualize the 2D or 3D intracellular distribution without labeling at nanometer resolution and analyze the chemical transformation of nanomedicines in situ. Here, we describe an optimized workflow for cell sample preparation, beamline selection, data acquisition and analysis. With several model bionanomaterials as examples, we analyze the localization of nanomedicines in various primary blood cells, macrophages, dendritic cells, monocytes and cancer cells, as well as the morphology of some organelles with soft and hard X-rays. Our protocol has been successfully implemented at three beamline facilities: 4W1A of Beijing Synchrotron Radiation Facility, BL08U1A of Shanghai Synchrotron Radiation Facility and BL07W of the National Synchrotron Radiation Laboratory. This protocol can be completed in ~2-5 d, depending on the cell types, their incubation times with nanomaterials and the selected X-ray beamline. The protocol enables the in situ analysis of the varieties of metal-containing nanomaterials, visualization of intracellular endocytosis, distribution and excretion and corresponding subcellular morphological variation influenced by nanomedicines in cell lines or primary cells by using this universal and robust platform. The results facilitate the understanding of the true principle and mechanism underlying the nano-bio interaction.
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Affiliation(s)
- Mingjing Cao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Yaling Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Liming Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Kai Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Yong Guan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
| | - Yuecong Guo
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China.
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
- GBA National Institute for Nanotechnology Innovation, Guangzhou, China.
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11
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Castro V, Pérez-Berna AJ, Calvo G, Pereiro E, Gastaminza P. Three-Dimensional Remodeling of SARS-CoV2-Infected Cells Revealed by Cryogenic Soft X-ray Tomography. ACS NANO 2023; 17:22708-22721. [PMID: 37939169 PMCID: PMC10690842 DOI: 10.1021/acsnano.3c07265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/10/2023]
Abstract
Plus-strand RNA viruses are proficient at remodeling host cell membranes for optimal viral genome replication and the production of infectious progeny. These ultrastructural alterations result in the formation of viral membranous organelles and may be observed by different imaging techniques, providing nanometric resolution. Guided by confocal and electron microscopy, this study describes the generation of wide-field volumes using cryogenic soft-X-ray tomography (cryo-SXT) on SARS-CoV-2-infected human lung adenocarcinoma cells. Confocal microscopy showed accumulation of double-stranded RNA (dsRNA) and nucleocapsid (N) protein in compact perinuclear structures, preferentially found around centrosomes at late stages of the infection. Transmission electron microscopy (TEM) showed accumulation of membranous structures in the vicinity of the infected cell nucleus, forming a viral replication organelle containing characteristic double-membrane vesicles and virus-like particles within larger vesicular structures. Cryo-SXT revealed viral replication organelles very similar to those observed by TEM but indicated that the vesicular organelle observed in TEM sections is indeed a vesiculo-tubular network that is enlarged and elongated at late stages of the infection. Overall, our data provide additional insight into the molecular architecture of the SARS-CoV-2 replication organelle.
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Affiliation(s)
- Victoria Castro
- Centro
Nacional de Biotecnología. Calle Darwin, 3, 28049 Madrid, Spain
| | | | - Gema Calvo
- Centro
Nacional de Biotecnología. Calle Darwin, 3, 28049 Madrid, Spain
| | - Eva Pereiro
- ALBA
Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Valles, Spain
| | - Pablo Gastaminza
- Centro
Nacional de Biotecnología. Calle Darwin, 3, 28049 Madrid, Spain
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12
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Golyshev SA, Kazakov EP, Kireev II, Reunov DG, Malyshev IV. Soft X-ray Microscopy in Cell Biology: Current Status, Contributions and Prospects. Acta Naturae 2023; 15:32-43. [PMID: 38234603 PMCID: PMC10790358 DOI: 10.32607/actanaturae.26551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/27/2023] [Indexed: 01/19/2024] Open
Abstract
The recent advances achieved in microscopy technology have led to a significant breakthrough in biological research. Super-resolution fluorescent microscopy now allows us to visualize subcellular structures down to the pin-pointing of the single molecules in them, while modern electron microscopy has opened new possibilities in the study of protein complexes in their native, intracellular environment at near-atomic resolution. Nonetheless, both fluorescent and electron microscopy have remained beset by their principal shortcomings: the reliance on labeling procedures and severe sample volume limitations, respectively. Soft X-ray microscopy is a candidate method that can compensate for the shortcomings of both technologies by making possible observation of the entirety of the cellular interior without chemical fixation and labeling with an isotropic resolution of 40-70 nm. This will thus bridge the resolution gap between light and electron microscopy (although this gap is being narrowed, it still exists) and resolve the issue of compatibility with the former, and possibly in the near future, the latter methods. This review aims to assess the current state of soft X-ray microscopy and its impact on our understanding of the subcellular organization. It also attempts to look into the future of X-ray microscopy, particularly as relates to its seamless integration into the cell biology toolkit.
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Affiliation(s)
- S. A. Golyshev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russian Federation
| | - E. P. Kazakov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russian Federation
| | - I. I. Kireev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russian Federation
| | - D. G. Reunov
- Institute of Physics of Microstructures RAS, Nizhny Novgorod, 603950 Russian Federation
| | - I. V. Malyshev
- Institute of Physics of Microstructures RAS, Nizhny Novgorod, 603950 Russian Federation
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13
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Li S, Jia X, Niu T, Zhang X, Qi C, Xu W, Deng H, Sun F, Ji G. HOPE-SIM, a cryo-structured illumination fluorescence microscopy system for accurately targeted cryo-electron tomography. Commun Biol 2023; 6:474. [PMID: 37120442 PMCID: PMC10148829 DOI: 10.1038/s42003-023-04850-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/18/2023] [Indexed: 05/01/2023] Open
Abstract
Cryo-focused ion beam (cryo-FIB) milling technology has been developed for the fabrication of cryo-lamella of frozen native specimens for study by in situ cryo-electron tomography (cryo-ET). However, the precision of the target of interest is still one of the major bottlenecks limiting application. Here, we have developed a cryo-correlative light and electron microscopy (cryo-CLEM) system named HOPE-SIM by incorporating a 3D structured illumination fluorescence microscopy (SIM) system and an upgraded high-vacuum stage to achieve efficiently targeted cryo-FIB. With the 3D super resolution of cryo-SIM as well as our cryo-CLEM software, 3D-View, the correlation precision of targeting region of interest can reach to 110 nm enough for the subsequent cryo-lamella fabrication. We have successfully utilized the HOPE-SIM system to prepare cryo-lamellae targeting mitochondria, centrosomes of HeLa cells and herpesvirus assembly compartment of infected BHK-21 cells, which suggests the high potency of the HOPE-SIM system for future in situ cryo-ET workflows.
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Affiliation(s)
- Shuoguo Li
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xing Jia
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Tongxin Niu
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xiaoyun Zhang
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Chen Qi
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Wei Xu
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Hongyu Deng
- University of Chinese Academy of Sciences, 100049, Beijing, China
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Fei Sun
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Gang Ji
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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14
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Lobato-Márquez D, Conesa JJ, López-Jiménez AT, Divine ME, Pruneda JN, Mostowy S. Septins and K63 ubiquitin chains are present in separate bacterial microdomains during autophagy of entrapped Shigella. J Cell Sci 2023; 136:jcs261139. [PMID: 36939083 PMCID: PMC10264824 DOI: 10.1242/jcs.261139] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/21/2023] Open
Abstract
During host cell invasion, Shigella escapes to the cytosol and polymerizes actin for cell-to-cell spread. To restrict cell-to-cell spread, host cells employ cell-autonomous immune responses including antibacterial autophagy and septin cage entrapment. How septins interact with the autophagy process to target Shigella for destruction is poorly understood. Here, we employed a correlative light and cryo-soft X-ray tomography (cryo-SXT) pipeline to study Shigella septin cage entrapment in its near-native state. Quantitative cryo-SXT showed that Shigella fragments mitochondria and enabled visualization of X-ray-dense structures (∼30 nm resolution) surrounding Shigella entrapped in septin cages. Using Airyscan confocal microscopy, we observed lysine 63 (K63)-linked ubiquitin chains decorating septin-cage-entrapped Shigella. Remarkably, septins and K63 chains are present in separate bacterial microdomains, indicating they are recruited separately during antibacterial autophagy. Cryo-SXT and live-cell imaging revealed an interaction between septins and LC3B-positive membranes during autophagy of Shigella. Together, these findings demonstrate how septin-caged Shigella are targeted for autophagy and provide fundamental insights into autophagy-cytoskeleton interactions.
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Affiliation(s)
- Damián Lobato-Márquez
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - José Javier Conesa
- MISTRAL beamline, ALBA Synchrotron Light Source, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Ana Teresa López-Jiménez
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Michael E. Divine
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Serge Mostowy
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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15
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Dumoux M, Glen T, Smith JLR, Ho EML, Perdigão LMA, Pennington A, Klumpe S, Yee NBY, Farmer DA, Lai PYA, Bowles W, Kelley R, Plitzko JM, Wu L, Basham M, Clare DK, Siebert CA, Darrow MC, Naismith JH, Grange M. Cryo-plasma FIB/SEM volume imaging of biological specimens. eLife 2023; 12:83623. [PMID: 36805107 PMCID: PMC9995114 DOI: 10.7554/elife.83623] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/20/2023] [Indexed: 02/23/2023] Open
Abstract
Serial focussed ion beam scanning electron microscopy (FIB/SEM) enables imaging and assessment of subcellular structures on the mesoscale (10 nm to 10 µm). When applied to vitrified samples, serial FIB/SEM is also a means to target specific structures in cells and tissues while maintaining constituents' hydration shells for in situ structural biology downstream. However, the application of serial FIB/SEM imaging of non-stained cryogenic biological samples is limited due to low contrast, curtaining, and charging artefacts. We address these challenges using a cryogenic plasma FIB/SEM. We evaluated the choice of plasma ion source and imaging regimes to produce high-quality SEM images of a range of different biological samples. Using an automated workflow we produced three-dimensional volumes of bacteria, human cells, and tissue, and calculated estimates for their resolution, typically achieving 20-50 nm. Additionally, a tag-free localisation tool for regions of interest is needed to drive the application of in situ structural biology towards tissue. The combination of serial FIB/SEM with plasma-based ion sources promises a framework for targeting specific features in bulk-frozen samples (>100 µm) to produce lamellae for cryogenic electron tomography.
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Affiliation(s)
- Maud Dumoux
- Structural Biology, Rosalind Franklin InstituteDidcotUnited Kingdom
| | - Thomas Glen
- Structural Biology, Rosalind Franklin InstituteDidcotUnited Kingdom
| | - Jake LR Smith
- Structural Biology, Rosalind Franklin InstituteDidcotUnited Kingdom
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Elaine ML Ho
- Artificial Intelligence and Informatics, Rosalind Franklin InstituteDidcotUnited Kingdom
| | - Luis MA Perdigão
- Artificial Intelligence and Informatics, Rosalind Franklin InstituteDidcotUnited Kingdom
| | - Avery Pennington
- Diamond Light Source, Harwell Science & Innovation CampusDidcotUnited Kingdom
| | - Sven Klumpe
- Research Group Cryo-EM Technology, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Neville BY Yee
- Artificial Intelligence and Informatics, Rosalind Franklin InstituteDidcotUnited Kingdom
| | - David Andrew Farmer
- Diamond Light Source, Harwell Science & Innovation CampusDidcotUnited Kingdom
| | - Pui YA Lai
- Diamond Light Source, Harwell Science & Innovation CampusDidcotUnited Kingdom
| | - William Bowles
- Structural Biology, Rosalind Franklin InstituteDidcotUnited Kingdom
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Diamond Light Source, Harwell Science & Innovation CampusDidcotUnited Kingdom
| | - Ron Kelley
- Materials and Structural Analysis Division, Thermo Fisher ScientificEindhovenNetherlands
| | - Jürgen M Plitzko
- Research Group Cryo-EM Technology, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Liang Wu
- Structural Biology, Rosalind Franklin InstituteDidcotUnited Kingdom
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Mark Basham
- Diamond Light Source, Harwell Science & Innovation CampusDidcotUnited Kingdom
| | - Daniel K Clare
- Diamond Light Source, Harwell Science & Innovation CampusDidcotUnited Kingdom
| | - C Alistair Siebert
- Diamond Light Source, Harwell Science & Innovation CampusDidcotUnited Kingdom
| | - Michele C Darrow
- Artificial Intelligence and Informatics, Rosalind Franklin InstituteDidcotUnited Kingdom
| | - James H Naismith
- Structural Biology, Rosalind Franklin InstituteDidcotUnited Kingdom
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Michael Grange
- Structural Biology, Rosalind Franklin InstituteDidcotUnited Kingdom
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
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16
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Zhang C, Zhang K, Cui Y, Guo Y, Wang C, Xu C, Yao Q, Zhao Y, Chen C, Wang Y. Multifunctional Nanoprobe for 3D Nanoresolution Imaging of Intact Cell HER2 Protein with Hard X-ray Tomography. Anal Chem 2023; 95:2129-2133. [PMID: 36576397 DOI: 10.1021/acs.analchem.2c03699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Three-dimensional nondestructive, nanoresolution, and in situ visualization of protein spatial localization in a large, thick single cell remains challenging. In this study, we designed a multifunctional iron oxide (Fe@BFK) nanoprobe that possesses fluorescence and hard X-ray imaging signals. This probe can specifically target the human epidermal growth factor receptor 2 (HER2) protein and help optimize the label condition and selection of suitable samples for X-ray imaging. Combining 30 nm resolution synchrotron radiation hard X-ray nanocomputed tomography and the X-ray-sensitive Fe@BFK nanoprobe, a 3D localization of HER2 on SK-BR-3 cells was obtained for the first time. HER2 was mainly localized and cluster-distributed on the cell membrane with a heterogeneous pattern. This study provides a novel method for the in situ and nondestructive synchrotron radiation imaging of the desired protein localization in large, thick cells and evaluation of the true cellular distribution of a nanoprobe with high resolution.
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Affiliation(s)
- Chunyu Zhang
- School of Pharmacy and Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Key Lab Rare & Uncommon Diseases of Shandong Province, Jinan 250117, Shandong China
| | - Kai Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyan Cui
- Beijing Engineering Research Center of Mixed Reality and Advanced Display, School of Optoelectronics, Beijing Institute of Technology, Beijing 100081, China
| | - Yuecong Guo
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology of China, Beijing 100090, China
| | - Chuan Wang
- The GBA National Institute for Nanotechnology Innovation, Guangzhou 510700, China
| | - Chao Xu
- College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, China
| | - Qingqiang Yao
- School of Pharmacy and Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Key Lab Rare & Uncommon Diseases of Shandong Province, Jinan 250117, Shandong China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology of China, Beijing 100090, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology of China, Beijing 100090, China.,The GBA National Institute for Nanotechnology Innovation, Guangzhou 510700, China
| | - Yaling Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology of China, Beijing 100090, China.,The GBA National Institute for Nanotechnology Innovation, Guangzhou 510700, China
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17
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Zhang C, Wu Z, Dang Z, Tian L, Guan Y, Liu G, Tian Y. On-Line Fluorescence Microscopy for Identification and Imaging of Apoptotic Cell with Synchrotron-Based Soft X-ray Tomography. MICROMACHINES 2023; 14:326. [PMID: 36838026 PMCID: PMC9963497 DOI: 10.3390/mi14020326] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/20/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
Synchrotron-based soft X-ray tomography (SXT), providing three-dimensional morphology and quantitative distribution of linear absorption coefficient (LAC) of the imaged objects, is widely used in many fields to obtain ultra-structure images, especially in cellular imaging. Off-line fluorescence microscopies (FMs) are combined to identify the type of organelles and status of cells. However, deformation and displacement usually occur during the transfer and loading process, which decreases the precision of two-modal images' registration. In this paper, we report on an on-line FM, at the SXT station (BL07W) of the National Synchrotron Radiation Laboratory (NSRL), which avoids deformation and displacement. Therefore, researchers can easily find the sample and take the useful data without tedious post-processing. Combining SXT with on-line FM, we achieved the identification and high-resolution imaging of an apoptotic cell. The experiments revealed that the LAC of the nucleus of the apoptotic cell was larger than that of a normal cell, which could be explained by nucleus pyknosis of the apoptotic cell.
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Affiliation(s)
| | - Zhao Wu
- Correspondence: (Z.W.); (Y.T.)
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18
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Jadhav AC, Kounatidis I. Correlative Cryo-imaging Using Soft X-Ray Tomography for the Study of Virus Biology in Cells and Tissues. Subcell Biochem 2023; 106:169-196. [PMID: 38159227 DOI: 10.1007/978-3-031-40086-5_6] [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: 01/03/2024]
Abstract
Viruses are obligate intracellular pathogens that depend on their host cell machinery and metabolism for their replicative life cycle. Virus entry, replication, and assembly are dynamic processes that lead to the reorganisation of host cell components. Therefore, a complete understanding of the viral processes requires their study in the cellular context where advanced imaging has been proven valuable in providing the necessary information. Among the available imaging techniques, soft X-ray tomography (SXT) at cryogenic temperatures can provide three-dimensional mapping to 25 nm resolution and is ideally suited to visualise the internal organisation of virus-infected cells. In this chapter, the principles and practices of synchrotron-based cryo-soft X-ray tomography (cryo-SXT) in virus research are presented. The potential of the cryo-SXT in correlative microscopy platforms is also demonstrated through working examples of reovirus and hepatitis research at Beamline B24 (Diamond Light Source Synchrotron, UK) and BL09-Mistral beamline (ALBA Synchrotron, Spain), respectively.
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Affiliation(s)
- Archana C Jadhav
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Ilias Kounatidis
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
- School of Life, Health and Chemical Sciences, The Open University, Milton Keynes, UK.
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19
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Development of Auer bodies from giant inclusions associated with rough endoplasmic reticulum in acute promyelocytic leukemia. BLOOD SCIENCE 2022; 5:111-117. [PMID: 37228776 PMCID: PMC10205345 DOI: 10.1097/bs9.0000000000000145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/29/2022] [Indexed: 02/05/2023] Open
Abstract
Giant inclusions and Auer bodies in promyeloblasts were investigated in a study which included transmission electron microscopy (TEM) for morphology and ultrastructural cytochemistry for myeloperoxidase in 10 patients with acute promyelocytic leukemia (APL). Ultrastructural cytochemistry demonstrated positive myeloperoxidase reactivity in giant inclusions, expanded rER cisternae, Auer bodies and primary granules. TEM revealed that giant inclusions were adorned by degenerated rER membrane, some of them sharing features with Auer bodies. We hypothesize a novel origin for Auer body development in promyeloblasts of APL, namely that they originate from peroxidase-positive and expanded rER cisternae, and that primary granules were directly released from these expanded rER elements, bypassing the Golgi apparatus.
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20
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Chen JH, Vanslembrouck B, Ekman A, Aho V, Larabell CA, Le Gros MA, Vihinen-Ranta M, Weinhardt V. Soft X-ray Tomography Reveals HSV-1-Induced Remodeling of Human B Cells. Viruses 2022; 14:2651. [PMID: 36560654 PMCID: PMC9781670 DOI: 10.3390/v14122651] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Upon infection, viruses hijack the cell machinery and remodel host cell structures to utilize them for viral proliferation. Since viruses are about a thousand times smaller than their host cells, imaging virus-host interactions at high spatial resolution is like looking for a needle in a haystack. Scouting gross cellular changes with fluorescent microscopy is only possible for well-established viruses, where fluorescent tagging is developed. Soft X-ray tomography (SXT) offers 3D imaging of entire cells without the need for chemical fixation or labeling. Here, we use full-rotation SXT to visualize entire human B cells infected by the herpes simplex virus 1 (HSV-1). We have mapped the temporospatial remodeling of cells during the infection and observed changes in cellular structures, such as the presence of cytoplasmic stress granules and multivesicular structures, formation of nuclear virus-induced dense bodies, and aggregates of capsids. Our results demonstrate the power of SXT imaging for scouting virus-induced changes in infected cells and understanding the orchestration of virus-host remodeling quantitatively.
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Affiliation(s)
- Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Bieke Vanslembrouck
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Axel Ekman
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vesa Aho
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
| | - Carolyn A. Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Mark A. Le Gros
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Maija Vihinen-Ranta
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
| | - Venera Weinhardt
- Centre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany
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21
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Cao M, Zhang K, Zhang S, Wang Y, Chen C. Advanced Light Source Analytical Techniques for Exploring the Biological Behavior and Fate of Nanomedicines. ACS CENTRAL SCIENCE 2022; 8:1063-1080. [PMID: 36032763 PMCID: PMC9413437 DOI: 10.1021/acscentsci.2c00680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Indexed: 05/09/2023]
Abstract
Exploration of the biological behavior and fate of nanoparticles, as affected by the nanomaterial-biology (nano-bio) interaction, has become progressively critical for guiding the rational design and optimization of nanomedicines to minimize adverse effects, support clinical translation, and aid in evaluation by regulatory agencies. Because of the complexity of the biological environment and the dynamic variations in the bioactivity of nanomedicines, in-situ, label-free analysis of the transport and transformation of nanomedicines has remained a challenge. Recent improvements in optics, detectors, and light sources have allowed the expansion of advanced light source (ALS) analytical technologies to dig into the underexplored behavior and fate of nanomedicines in vivo. It is increasingly important to further develop ALS-based analytical technologies with higher spatial and temporal resolution, multimodal data fusion, and intelligent prediction abilities to fully unlock the potential of nanomedicines. In this Outlook, we focus on several selected ALS analytical technologies, including imaging and spectroscopy, and provide an overview of the emerging opportunities for their applications in the exploration of the biological behavior and fate of nanomedicines. We also discuss the challenges and limitations faced by current approaches and tools and the expectations for the future development of advanced light sources and technologies. Improved ALS imaging and spectroscopy techniques will accelerate a profound understanding of the biological behavior of new nanomedicines. Such advancements are expected to inspire new insights into nanomedicine research and promote the development of ALS capabilities and methods more suitable for nanomedicine evaluation with the goal of clinical translation.
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Affiliation(s)
- Mingjing Cao
- CAS
Key Laboratory for Biomedical Effects of Nanomedicines and Nanosafety
& CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Kai Zhang
- Beijing
Synchrotron Radiation Facility, Institute
of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Shuhan Zhang
- CAS
Key Laboratory for Biomedical Effects of Nanomedicines and Nanosafety
& CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Yaling Wang
- CAS
Key Laboratory for Biomedical Effects of Nanomedicines and Nanosafety
& CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- The
GBA National Institute for Nanotechnology Innovation, Guangzhou 510700, China
| | - Chunying Chen
- CAS
Key Laboratory for Biomedical Effects of Nanomedicines and Nanosafety
& CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- The
GBA National Institute for Nanotechnology Innovation, Guangzhou 510700, China
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22
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Abstract
Mammalian orthoreovirus (reovirus) is a double-stranded RNA (dsRNA) virus which encapsidates its 10 genome segments within a double-layered viral particle. Reovirus infection triggers an antiviral response in host cells which serves to limit viral replication. This antiviral response is initiated by recognition of the incoming viral genome by host sensors present in the cytoplasm. However, how host sensors gain access to the reovirus genome is unclear, as this dsRNA is protected by the viral particle proteins throughout infection. To initiate infection, reovirus particles are endocytosed and the outer viral particle layer is disassembled through the action of host proteases. This disassembly event is required for viral escape into the cytoplasm to begin replication. We show that endosomal proteases are required even late in infection, when disassembly is complete, to induce an immune response to reovirus. Additionally, counter to dogma, our data demonstrate that at least some viral dsRNA genome is exposed and detectable during entry. We hypothesize that some proportion of reovirus particles remain trapped within endosomes, allowing for the breakdown of these particles and release of their genome. We show that rapidly uncoating mutants escape the endosome more rapidly and induce a diminished immune response. Further, we show that particles entering through dynamin-independent pathways evade detection by host sensors. Overall, our data provide new insight into how genomes from entering reovirus particles are detected by host cells. IMPORTANCE Viruses must infect host cells to replicate, often killing the host cell in the process. However, hosts can activate defenses to limit viral replication and protect the organism. To trigger these host defenses to viral infections, host cells must first recognize that they are infected. Mammalian orthoreovirus (reovirus) is a model system used to study host-virus interactions. This study identifies aspects of host and virus biology which determine the capacity of host cells to detect infection. Notably, entry of reovirus into host cells plays a critical role in determining the magnitude of immune response triggered during infection. Mutants of reovirus which can enter cells more rapidly are better at avoiding detection by the host. Additionally, reovirus can enter cells through multiple routes. Entry through some of these routes also helps reovirus evade detection.
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23
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Nanometer-Resolution Imaging of Living Cells Using Soft X-ray Contact Microscopy. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12147030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Soft X-ray microscopy is a powerful technique for imaging cells with nanometer resolution in their native state without chemical fixation, staining, or sectioning. The studies performed in several laboratories have demonstrated the potential of applying this technique for imaging the internal structures of intact cells. However, it is currently used mainly on synchrotrons with restricted access. Moreover, the operation of these instruments and the associated sample-preparation protocols require interdisciplinary and highly specialized personnel, limiting their wide application in practice. This is why soft X-ray microscopy is not commonly used in biological laboratories as an imaging tool. Thus, a laboratory-based and user-friendly soft X-ray contact microscope would facilitate the work of biologists. A compact, desk-top laboratory setup for soft X-ray contact microscopy (SXCM) based on a laser-plasma soft X-ray source, which can be used in any biological laboratory, together with several applications for biological imaging, are described. Moreover, the perspectives of the correlation of SXCM with other super-resolution imaging techniques based on the current literature are discussed.
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24
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Nahas KL, Connor V, Scherer KM, Kaminski CF, Harkiolaki M, Crump CM, Graham SC. Near-native state imaging by cryo-soft-X-ray tomography reveals remodelling of multiple cellular organelles during HSV-1 infection. PLoS Pathog 2022; 18:e1010629. [PMID: 35797345 PMCID: PMC9262197 DOI: 10.1371/journal.ppat.1010629] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/31/2022] [Indexed: 12/15/2022] Open
Abstract
Herpes simplex virus-1 (HSV-1) is a large, enveloped DNA virus and its assembly in the cell is a complex multi-step process during which viral particles interact with numerous cellular compartments such as the nucleus and organelles of the secretory pathway. Transmission electron microscopy and fluorescence microscopy are commonly used to study HSV-1 infection. However, 2D imaging limits our understanding of the 3D geometric changes to cellular compartments that accompany infection and sample processing can introduce morphological artefacts that complicate interpretation. In this study, we used soft X-ray tomography to observe differences in whole-cell architecture between HSV-1 infected and uninfected cells. To protect the near-native structure of cellular compartments we used a non-disruptive sample preparation technique involving rapid cryopreservation, and a fluorescent reporter virus was used to facilitate correlation of structural changes with the stage of infection in individual cells. We observed viral capsids and assembly intermediates interacting with nuclear and cytoplasmic membranes. Additionally, we observed differences in the morphology of specific organelles between uninfected and infected cells. The local concentration of cytoplasmic vesicles at the juxtanuclear compartment increased and their mean width decreased as infection proceeded, and lipid droplets transiently increased in size. Furthermore, mitochondria in infected cells were elongated and highly branched, suggesting that HSV-1 infection alters the dynamics of mitochondrial fission/fusion. Our results demonstrate that high-resolution 3D images of cellular compartments can be captured in a near-native state using soft X-ray tomography and have revealed that infection causes striking changes to the morphology of intracellular organelles.
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Affiliation(s)
- Kamal L. Nahas
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Beamline B24, Diamond Light Source, Didcot, United Kingdom
| | - Viv Connor
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Katharina M. Scherer
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | | | - Colin M. Crump
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Stephen C. Graham
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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25
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Nahas KL, Fernandes JF, Vyas N, Crump C, Graham S, Harkiolaki M. Contour, a semi-automated segmentation and quantitation tool for cryo-soft-X-ray tomography. BIOLOGICAL IMAGING 2022; 2:e3. [PMID: 35600903 PMCID: PMC7612748 DOI: 10.1017/s2633903x22000046] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cryo-soft-X-ray tomography is being increasingly used in biological research to study the morphology of cellular compartments and how they change in response to different stimuli, such as viral infections. Segmentation of these compartments is limited by time-consuming manual tools or machine learning algorithms that require extensive time and effort to train. Here we describe Contour, a new, easy-to-use, highly automated segmentation tool that enables accelerated segmentation of tomograms to delineate distinct cellular compartments. Using Contour, cellular structures can be segmented based on their projection intensity and geometrical width by applying a threshold range to the image and excluding noise smaller in width than the cellular compartments of interest. This method is less laborious and less prone to errors from human judgement than current tools that require features to be manually traced, and does not require training datasets as would machine-learning driven segmentation. We show that high-contrast compartments such as mitochondria, lipid droplets, and features at the cell surface can be easily segmented with this technique in the context of investigating herpes simplex virus 1 infection. Contour can extract geometric measurements from 3D segmented volumes, providing a new method to quantitate cryo-soft-X-ray tomography data. Contour can be freely downloaded at github.com/kamallouisnahas/Contour.
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Affiliation(s)
- Kamal L Nahas
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, United Kingdom
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - João Ferreira Fernandes
- MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Nina Vyas
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Colin Crump
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, United Kingdom
| | - Stephen Graham
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, United Kingdom
| | - Maria Harkiolaki
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
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26
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Okolo CA. A guide into the world of high-resolution 3D imaging: the case of soft X-ray tomography for the life sciences. Biochem Soc Trans 2022; 50:649-663. [PMID: 35257156 PMCID: PMC9162464 DOI: 10.1042/bst20210886] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 11/27/2022]
Abstract
In the world of bioimaging, every choice made determines the quality and content of the data collected. The choice of imaging techniques for a study could showcase or dampen expected outcomes. Synchrotron radiation is indispensable for biomedical research, driven by the need to see into biological materials and capture intricate biochemical and biophysical details at controlled environments. The same need drives correlative approaches that enable the capture of heterologous but complementary information when studying any one single target subject. Recently, the applicability of one such synchrotron technique in bioimaging, soft X-ray tomography (SXT), facilitates exploratory and basic research and is actively progressing towards filling medical and industrial needs for the rapid screening of biomaterials, reagents and processes of immediate medical significance. Soft X-ray tomography at cryogenic temperatures (cryoSXT) fills the imaging resolution gap between fluorescence microscopy (in the hundreds of nanometers but relatively accessible) and electron microscopy (few nanometers but requires extensive effort and can be difficult to access). CryoSXT currently is accessible, fully documented, can deliver 3D imaging to 25 nm resolution in a high throughput fashion, does not require laborious sample preparation procedures and can be correlated with other imaging techniques. Here, we present the current state of SXT and outline its place within the bioimaging world alongside a guided matrix that aids decision making with regards to the applicability of any given imaging technique to a particular project. Case studies where cryoSXT has facilitated a better understanding of biological processes are highlighted and future directions are discussed.
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Affiliation(s)
- Chidinma Adanna Okolo
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, U.K
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27
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Phillips MA, Susano Pinto DM, Hall N, Mateos-Langerak J, Parton RM, Titlow J, Stoychev DV, Parks T, Susano Pinto T, Sedat JW, Booth MJ, Davis I, Dobbie IM. Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.16610.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have developed “Microscope-Cockpit” (Cockpit), a highly adaptable open source user-friendly Python-based Graphical User Interface (GUI) environment for precision control of both simple and elaborate bespoke microscope systems. The user environment allows next-generation near instantaneous navigation of the entire slide landscape for efficient selection of specimens of interest and automated acquisition without the use of eyepieces. Cockpit uses “Python-Microscope” (Microscope) for high-performance coordinated control of a wide range of hardware devices using open source software. Microscope also controls complex hardware devices such as deformable mirrors for aberration correction and spatial light modulators for structured illumination via abstracted device models. We demonstrate the advantages of the Cockpit platform using several bespoke microscopes, including a simple widefield system and a complex system with adaptive optics and structured illumination. A key strength of Cockpit is its use of Python, which means that any microscope built with Cockpit is ready for future customisation by simply adding new libraries, for example machine learning algorithms to enable automated microscopy decision making while imaging.
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28
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Laporte MH, Klena N, Hamel V, Guichard P. Visualizing the native cellular organization by coupling cryofixation with expansion microscopy (Cryo-ExM). Nat Methods 2022; 19:216-222. [PMID: 35027766 PMCID: PMC8828483 DOI: 10.1038/s41592-021-01356-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/17/2021] [Indexed: 12/11/2022]
Abstract
Cryofixation has proven to be the gold standard for efficient preservation of native cell ultrastructure compared to chemical fixation, but this approach is not widely used in fluorescence microscopy owing to implementation challenges. Here, we develop Cryo-ExM, a method that preserves native cellular organization by coupling cryofixation with expansion microscopy. This method bypasses artifacts associated with chemical fixation and its simplicity will contribute to its widespread use in super-resolution microscopy.
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Affiliation(s)
- Marine H Laporte
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
| | - Nikolai Klena
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
| | - Virginie Hamel
- Department of Cell Biology, University of Geneva, Geneva, Switzerland.
| | - Paul Guichard
- Department of Cell Biology, University of Geneva, Geneva, Switzerland.
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29
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Loconte V, White KL. The use of soft X-ray tomography to explore mitochondrial structure and function. Mol Metab 2021; 57:101421. [PMID: 34942399 PMCID: PMC8829759 DOI: 10.1016/j.molmet.2021.101421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/22/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022] Open
Abstract
Background Mitochondria are cellular organelles responsible for energy production, and dysregulation of the mitochondrial network is associated with many disease states. To fully characterize the mitochondrial network's structure and function, a three-dimensional whole cell mapping technique is required. Scope of review This review highlights the use of soft X-ray tomography (SXT) as a relatively high-throughput approach to quantify mitochondrial structure and function under multiple cellular conditions. Major conclusions The use of SXT opens the door for mapping cellular rearrangements during critical processes such as insulin secretion, stem cell differentiation, or disease progression. SXT provides unique information such as biochemical compositions or molecular densities of organelles and allows for unbiased, label-free imaging of intact whole cells. Mapping mitochondria in the context of the near-native cellular environment will reveal more information regarding mitochondrial network functions within the cell. Soft X-ray tomography (SXT) generates 3D organelle maps of intact cells. 3D maps reveal the positions of mitochondria and their molecular densities. SXT can be used to quantify and compare organelle contacts between conditions. SXT is unbiased imaging that identifies the contents of subcellular neighborhoods. SXT provides an exciting path for exploring metabolic dysfunction.
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Affiliation(s)
- Valentina Loconte
- Department of Anatomy, School of Medicine, UCSF, San Francisco, California, CA 94143; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kate L White
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA.
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30
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Recent Progress in the Correlative Structured Illumination Microscopy. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9120364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The super-resolution imaging technique of structured illumination microscopy (SIM) enables the mixing of high-frequency information into the optical transmission domain via light-source modulation, thus breaking the optical diffraction limit. Correlative SIM, which combines other techniques with SIM, offers more versatility or higher imaging resolution than traditional SIM. In this review, we first briefly introduce the imaging mechanism and development trends of conventional SIM. Then, the principles and recent developments of correlative SIM techniques are reviewed. Finally, the future development directions of SIM and its correlative microscopies are presented.
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31
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Bolitho E, Sanchez-Cano C, Shi H, Quinn PD, Harkiolaki M, Imberti C, Sadler PJ. Single-Cell Chemistry of Photoactivatable Platinum Anticancer Complexes. J Am Chem Soc 2021; 143:20224-20240. [PMID: 34808054 PMCID: PMC8662725 DOI: 10.1021/jacs.1c08630] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Indexed: 02/08/2023]
Abstract
The Pt(IV) prodrug trans, trans, trans-[Pt(pyridine)2(N3)2(OH)2] (Pt1) and its coumarin derivative trans, trans, trans-[Pt(pyridine)2(N3)2(OH)(coumarin-3-carboxylate)] (Pt2) are promising agents for photoactivated chemotherapy. These complexes are inert in the dark but release Pt(II) species and radicals upon visible light irradiation, resulting in photocytotoxicity toward cancer cells. Here, we have used synchrotron techniques to investigate the in-cell behavior of these prodrugs and visualize, for the first time, changes in cellular morphology and Pt localization upon treatment with and without light irradiation. We show that photoactivation of Pt2 induces remarkable cellular damage with extreme alterations to multiple cellular components, including formation of vacuoles, while also significantly increasing the cellular accumulation of Pt species compared to dark conditions. X-ray absorption near-edge structure (XANES) measurements in cells treated with Pt2 indicate only partial reduction of the prodrug upon irradiation, highlighting that phototoxicity in cancer cells may involve not only Pt(II) photoproducts but also photoexcited Pt(IV) species.
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Affiliation(s)
- Elizabeth
M. Bolitho
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
- Diamond
Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, United
Kingdom
| | - Carlos Sanchez-Cano
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research
and Technology Alliance (BRTA), Paseo de Miramon 182, 20014 San Sebastián, Spain
| | - Huayun Shi
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Paul D. Quinn
- Diamond
Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, United
Kingdom
| | - Maria Harkiolaki
- Diamond
Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, United
Kingdom
| | - Cinzia Imberti
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Peter J. Sadler
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
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32
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Koronfel M, Kounatidis I, Mwangangi DM, Vyas N, Okolo C, Jadhav A, Fish T, Chotchuang P, Schulte A, Robinson RC, Harkiolaki M. Correlative cryo-imaging of the cellular universe with soft X-rays and laser light used to track F-actin structures in mammalian cells. Acta Crystallogr D Struct Biol 2021; 77:1479-1485. [PMID: 34866605 PMCID: PMC8647181 DOI: 10.1107/s2059798321010329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
Imaging of actin filaments is crucial due to the integral role that they play in many cellular functions such as intracellular transport, membrane remodelling and cell motility. Visualizing actin filaments has so far relied on fluorescence microscopy and electron microscopy/tomography. The former lacks the capacity to capture the overall local ultrastructure, while the latter requires rigorous sample preparation that can lead to potential artefacts, and only delivers relatively small volumes of imaging data at the thinnest areas of a cell. In this work, a correlative approach utilizing in situ super-resolution fluorescence imaging and cryo X-ray tomography was used to image bundles of actin filaments deep inside cells under near-native conditions. In this case, fluorescence 3D imaging localized the actin bundles within the intracellular space, while X-ray tomograms of the same areas provided detailed views of the local ultrastructure. Using this new approach, actin trails connecting vesicles in the perinuclear area and hotspots of actin presence within and around multivesicular bodies were observed. The characteristic prevalence of filamentous actin in cytoplasmic extensions was also documented.
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Affiliation(s)
- Mohamed Koronfel
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Ilias Kounatidis
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Dennis M. Mwangangi
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
| | - Nina Vyas
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Chidinma Okolo
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Archana Jadhav
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Tom Fish
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Phatcharin Chotchuang
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan
| | - Albert Schulte
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan
| | - Robert C. Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Maria Harkiolaki
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
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33
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Groen J, Palanca A, Aires A, Conesa JJ, Maestro D, Rehbein S, Harkiolaki M, Villar AV, Cortajarena AL, Pereiro E. Correlative 3D cryo X-ray imaging reveals intracellular location and effect of designed antifibrotic protein-nanomaterial hybrids. Chem Sci 2021; 12:15090-15103. [PMID: 34909150 PMCID: PMC8612387 DOI: 10.1039/d1sc04183e] [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: 07/30/2021] [Accepted: 10/17/2021] [Indexed: 12/20/2022] Open
Abstract
Revealing the intracellular location of novel therapeutic agents is paramount for the understanding of their effect at the cell ultrastructure level. Here, we apply a novel correlative cryo 3D imaging approach to determine the intracellular fate of a designed protein–nanomaterial hybrid with antifibrotic properties that shows great promise in mitigating myocardial fibrosis. Cryo 3D structured illumination microscopy (cryo-3D-SIM) pinpoints the location and cryo soft X-ray tomography (cryo-SXT) reveals the ultrastructural environment and subcellular localization of this nanomaterial with spatial correlation accuracy down to 70 nm in whole cells. This novel high resolution 3D cryo correlative approach unambiguously locates the nanomaterial after overnight treatment within multivesicular bodies which have been associated with endosomal trafficking events by confocal microscopy. Moreover, this approach allows assessing the cellular response towards the treatment by evaluating the morphological changes induced. This is especially relevant for the future usage of nanoformulations in clinical practices. This correlative super-resolution and X-ray imaging strategy joins high specificity, by the use of fluorescence, with high spatial resolution at 30 nm (half pitch) provided by cryo-SXT in whole cells, without the need of staining or fixation, and can be of particular benefit to locate specific molecules in the native cellular environment in bio-nanomedicine. A novel 3D cryo correlative approach locates designed therapeutic protein–nanomaterial hybrids in whole cells with high specificity and resolution. Detection of treatment-induced morphological changes, crucial for pre-clinical studies, are revealed.![]()
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Affiliation(s)
- J Groen
- MISTRAL Beamline, Experiments Division, ALBA Synchrotron Light Source Cerdanyola del Valles 08290 Barcelona Spain
| | - A Palanca
- Instituto de Biomedicina y Biotecnologia de Cantabria (IBBTEC), University of Cantabria, CSIC 39011 Santander Spain.,Department of Anatomy and Cell Biology, University of Cantabria 39011 Santander Spain
| | - A Aires
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA) Paseo de Miramón 194 20014 Donostia San Sebastian Spain
| | - J J Conesa
- MISTRAL Beamline, Experiments Division, ALBA Synchrotron Light Source Cerdanyola del Valles 08290 Barcelona Spain .,National Center for Biotechnology CSIC (CNB-CSIC), Department of Macromolecular Structures Cantoblanco 28049 Madrid Spain
| | - D Maestro
- Instituto de Biomedicina y Biotecnologia de Cantabria (IBBTEC), University of Cantabria, CSIC 39011 Santander Spain
| | - S Rehbein
- Helmholtz-Zentrum Berlin für Materialien und Energie, Bessy II D-12489 Berlin Germany
| | - M Harkiolaki
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - A V Villar
- Instituto de Biomedicina y Biotecnologia de Cantabria (IBBTEC), University of Cantabria, CSIC 39011 Santander Spain.,Department of Physiology and Pharmacology, University of Cantabria Avd. Herrera Oria s/n Santander Spain
| | - A L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA) Paseo de Miramón 194 20014 Donostia San Sebastian Spain .,Ikerbasque, Basque Foundation for Science 48009 Bilbao Spain
| | - E Pereiro
- MISTRAL Beamline, Experiments Division, ALBA Synchrotron Light Source Cerdanyola del Valles 08290 Barcelona Spain
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Loconte V, Chen JH, Cortese M, Ekman A, Le Gros MA, Larabell C, Bartenschlager R, Weinhardt V. Using soft X-ray tomography for rapid whole-cell quantitative imaging of SARS-CoV-2-infected cells. CELL REPORTS METHODS 2021; 1:100117. [PMID: 34729550 PMCID: PMC8552653 DOI: 10.1016/j.crmeth.2021.100117] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/10/2021] [Accepted: 10/22/2021] [Indexed: 02/08/2023]
Abstract
High-resolution and rapid imaging of host cell ultrastructure can generate insights toward viral disease mechanism, for example for a severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Here, we employ full-rotation soft X-ray tomography (SXT) to examine organelle remodeling induced by SARS-CoV-2 at the whole-cell level with high spatial resolution and throughput. Most of the current SXT systems suffer from a restricted field of view due to use of flat sample supports and artifacts due to missing data. In this approach using cylindrical sample holders, a full-rotation tomogram of human lung epithelial cells is performed in less than 10 min. We demonstrate the potential of SXT imaging by visualizing aggregates of SARS-CoV-2 virions and virus-induced intracellular alterations. This rapid whole-cell imaging approach allows us to visualize the spatiotemporal changes of cellular organelles upon viral infection in a quantitative manner.
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Affiliation(s)
- Valentina Loconte
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology Heidelberg University, Heidelberg, Germany
| | - Axel Ekman
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Mark A. Le Gros
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Carolyn Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology Heidelberg University, Heidelberg, Germany
- German Center for Infection Research, Heidelberg Partner Site, Heidelberg, Germany
- Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Venera Weinhardt
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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35
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Swevers L, Kontogiannatos D, Kolliopoulou A, Ren F, Feng M, Sun J. Mechanisms of Cell Entry by dsRNA Viruses: Insights for Efficient Delivery of dsRNA and Tools for Improved RNAi-Based Pest Control. Front Physiol 2021; 12:749387. [PMID: 34858204 PMCID: PMC8632066 DOI: 10.3389/fphys.2021.749387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/11/2021] [Indexed: 12/18/2022] Open
Abstract
While RNAi is often heralded as a promising new strategy for insect pest control, a major obstacle that still remains is the efficient delivery of dsRNA molecules within the cells of the targeted insects. However, it seems overlooked that dsRNA viruses already have developed efficient strategies for transport of dsRNA molecules across tissue barriers and cellular membranes. Besides protecting their dsRNA genomes in a protective shell, dsRNA viruses also display outer capsid layers that incorporate sophisticated mechanisms to disrupt the plasma membrane layer and to translocate core particles (with linear dsRNA genome fragments) within the cytoplasm. Because of the perceived efficiency of the translocation mechanism, it is well worth analyzing in detail the molecular processes that are used to achieve this feat. In this review, the mechanism of cell entry by dsRNA viruses belonging to the Reoviridae family is discussed in detail. Because of the large amount of progress in mammalian versus insect models, the mechanism of infections of reoviruses in mammals (orthoreoviruses, rotaviruses, orbiviruses) will be treated as a point of reference against which infections of reoviruses in insects (orbiviruses in midges, plant viruses in hemipterans, insect-specific cypoviruses in lepidopterans) will be compared. The goal of this discussion is to uncover the basic principles by which dsRNA viruses cross tissue barriers and translocate their cargo to the cellular cytoplasm; such knowledge subsequently can be incorporated into the design of dsRNA virus-based viral-like particles for optimal delivery of RNAi triggers in targeted insect pests.
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Affiliation(s)
- Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
| | - Dimitrios Kontogiannatos
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
| | - Anna Kolliopoulou
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
| | - Feifei Ren
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Min Feng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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36
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Garriga D, Chichón FJ, Calisto BM, Ferrero DS, Gastaminza P, Pereiro E, Pérez-Berna AJ. Imaging of Virus-Infected Cells with Soft X-ray Tomography. Viruses 2021; 13:2109. [PMID: 34834916 PMCID: PMC8618346 DOI: 10.3390/v13112109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 02/07/2023] Open
Abstract
Viruses are obligate parasites that depend on a host cell for replication and survival. Consequently, to fully understand the viral processes involved in infection and replication, it is fundamental to study them in the cellular context. Often, viral infections induce significant changes in the subcellular organization of the host cell due to the formation of viral factories, alteration of cell cytoskeleton and/or budding of newly formed particles. Accurate 3D mapping of organelle reorganization in infected cells can thus provide valuable information for both basic virus research and antiviral drug development. Among the available techniques for 3D cell imaging, cryo-soft X-ray tomography stands out for its large depth of view (allowing for 10 µm thick biological samples to be imaged without further thinning), its resolution (about 50 nm for tomographies, sufficient to detect viral particles), the minimal requirements for sample manipulation (can be used on frozen, unfixed and unstained whole cells) and the potential to be combined with other techniques (i.e., correlative fluorescence microscopy). In this review we describe the fundamentals of cryo-soft X-ray tomography, its sample requirements, its advantages and its limitations. To highlight the potential of this technique, examples of virus research performed at BL09-MISTRAL beamline in ALBA synchrotron are also presented.
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Affiliation(s)
- Damià Garriga
- ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain; (D.G.); (B.M.C.); (E.P.)
| | - Francisco Javier Chichón
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain; (F.J.C.); (P.G.)
| | - Bárbara M. Calisto
- ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain; (D.G.); (B.M.C.); (E.P.)
| | - Diego S. Ferrero
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Parc Científic de Barcelona, 08028 Barcelona, Spain;
| | - Pablo Gastaminza
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain; (F.J.C.); (P.G.)
| | - Eva Pereiro
- ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain; (D.G.); (B.M.C.); (E.P.)
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37
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Li S. Cryo-electron tomography of enveloped viruses. Trends Biochem Sci 2021; 47:173-186. [PMID: 34511334 DOI: 10.1016/j.tibs.2021.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Viruses are macromolecular machineries that hijack cellular metabolism for replication. Enveloped viruses comprise a large variety of RNA and DNA viruses, many of which are notorious human or animal pathogens. Despite their importance, the presence of lipid bilayers in their assembly has made most enveloped viruses too pleomorphic to be reconstructed as a whole by traditional structural biology methods. Furthermore, structural biology of the viral lifecycle was hindered by the sample thickness. Here, I review the recent advances in the applications of cryo-electron tomography (cryo-ET) on enveloped viral structures and intracellular viral activities.
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Affiliation(s)
- Sai Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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38
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Phillips P, Parkhurst JM, Kounatidis I, Okolo C, Fish TM, Naismith JH, Walsh MA, Harkiolaki M, Dumoux M. Single Cell Cryo-Soft X-ray Tomography Shows That Each Chlamydia Trachomatis Inclusion Is a Unique Community of Bacteria. Life (Basel) 2021; 11:life11080842. [PMID: 34440586 PMCID: PMC8399160 DOI: 10.3390/life11080842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/07/2021] [Accepted: 08/12/2021] [Indexed: 12/24/2022] Open
Abstract
Chlamydiae are strict intracellular pathogens residing within a specialised membrane-bound compartment called the inclusion. Therefore, each infected cell can, be considered as a single entity where bacteria form a community within the inclusion. It remains unclear as to how the population of bacteria within the inclusion influences individual bacterium. The life cycle of Chlamydia involves transitioning between the invasive elementary bodies (EBs) and replicative reticulate bodies (RBs). We have used cryo-soft X-ray tomography to observe individual inclusions, an approach that combines 40 nm spatial resolution and large volume imaging (up to 16 µm). Using semi-automated segmentation pipeline, we considered each inclusion as an individual bacterial niche. Within each inclusion, we identifyed and classified different forms of the bacteria and confirmed the recent finding that RBs have a variety of volumes (small, large and abnormal). We demonstrate that the proportions of these different RB forms depend on the bacterial concentration in the inclusion. We conclude that each inclusion operates as an autonomous community that influences the characteristics of individual bacteria within the inclusion.
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Affiliation(s)
- Patrick Phillips
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (P.P.); (J.M.P.); (I.K.); (C.O.); (T.M.F.); (M.A.W.); (M.H.)
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK;
- Division of Structural Biology Department, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - James M. Parkhurst
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (P.P.); (J.M.P.); (I.K.); (C.O.); (T.M.F.); (M.A.W.); (M.H.)
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Fermi Road, Didcot OX11 0FA, UK
| | - Ilias Kounatidis
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (P.P.); (J.M.P.); (I.K.); (C.O.); (T.M.F.); (M.A.W.); (M.H.)
| | - Chidinma Okolo
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (P.P.); (J.M.P.); (I.K.); (C.O.); (T.M.F.); (M.A.W.); (M.H.)
| | - Thomas M. Fish
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (P.P.); (J.M.P.); (I.K.); (C.O.); (T.M.F.); (M.A.W.); (M.H.)
| | - James H. Naismith
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK;
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Fermi Road, Didcot OX11 0FA, UK
| | - Martin A. Walsh
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (P.P.); (J.M.P.); (I.K.); (C.O.); (T.M.F.); (M.A.W.); (M.H.)
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK;
| | - Maria Harkiolaki
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (P.P.); (J.M.P.); (I.K.); (C.O.); (T.M.F.); (M.A.W.); (M.H.)
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK;
| | - Maud Dumoux
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (P.P.); (J.M.P.); (I.K.); (C.O.); (T.M.F.); (M.A.W.); (M.H.)
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK;
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Fermi Road, Didcot OX11 0FA, UK
- Correspondence:
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39
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Mendonça L, Howe A, Gilchrist JB, Sheng Y, Sun D, Knight ML, Zanetti-Domingues LC, Bateman B, Krebs AS, Chen L, Radecke J, Li VD, Ni T, Kounatidis I, Koronfel MA, Szynkiewicz M, Harkiolaki M, Martin-Fernandez ML, James W, Zhang P. Correlative multi-scale cryo-imaging unveils SARS-CoV-2 assembly and egress. Nat Commun 2021; 12:4629. [PMID: 34330917 PMCID: PMC8324836 DOI: 10.1038/s41467-021-24887-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/11/2021] [Indexed: 02/07/2023] Open
Abstract
Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified viral components and inactivated viruses. However, structural and ultrastructural evidence on how the SARS-CoV-2 infection progresses in the native cellular context is scarce, and there is a lack of comprehensive knowledge on the SARS-CoV-2 replicative cycle. To correlate cytopathic events induced by SARS-CoV-2 with virus replication processes in frozen-hydrated cells, we established a unique multi-modal, multi-scale cryo-correlative platform to image SARS-CoV-2 infection in Vero cells. This platform combines serial cryoFIB/SEM volume imaging and soft X-ray cryo-tomography with cell lamellae-based cryo-electron tomography (cryoET) and subtomogram averaging. Here we report critical SARS-CoV-2 structural events - e.g. viral RNA transport portals, virus assembly intermediates, virus egress pathway, and native virus spike structures, in the context of whole-cell volumes revealing drastic cytppathic changes. This integrated approach allows a holistic view of SARS-CoV-2 infection, from the whole cell to individual molecules.
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Affiliation(s)
- Luiza Mendonça
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Andrew Howe
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - James B. Gilchrist
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Yuewen Sheng
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Dapeng Sun
- grid.21925.3d0000 0004 1936 9000Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Michael L. Knight
- grid.4991.50000 0004 1936 8948Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Laura C. Zanetti-Domingues
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - Benji Bateman
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - Anna-Sophia Krebs
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Long Chen
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Julika Radecke
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Vivian D. Li
- grid.5335.00000000121885934Murray Edwards College, University of Cambridge, Cambridge, UK
| | - Tao Ni
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ilias Kounatidis
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Mohamed A. Koronfel
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Marta Szynkiewicz
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - Maria Harkiolaki
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Marisa L. Martin-Fernandez
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - William James
- grid.4991.50000 0004 1936 8948Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Peijun Zhang
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK ,grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK ,grid.21925.3d0000 0004 1936 9000Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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40
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Vyas N, Kunne S, Fish TM, Dobbie IM, Harkiolaki M, Paul-Gilloteaux P. Protocol for image registration of correlative soft X-ray tomography and super-resolution structured illumination microscopy images. STAR Protoc 2021; 2:100529. [PMID: 34027487 PMCID: PMC8121986 DOI: 10.1016/j.xpro.2021.100529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Correlation of 3D images acquired on different microscopes can be a daunting prospect even for experienced users. This protocol describes steps for registration of images from soft X-ray absorption contrast imaging and super-resolution fluorescence imaging of hydrated biological materials at cryogenic temperatures. Although it is developed for data generated at synchrotron beamlines that offer the above combination of microscopies, it is applicable to all analogous imaging systems where the same area of a sample is examined using successive non-destructive imaging techniques. For complete details on the use and execution of this protocol, please refer to Kounatidis et al. (2020).
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Affiliation(s)
- Nina Vyas
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Stephan Kunne
- Université de Nantes, CHU Nantes, CNRS UMR 6291, INSERM UMR 1087, L'institut du thorax, 44000 Nantes, France
| | - Thomas M. Fish
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Ian M. Dobbie
- Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Maria Harkiolaki
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Perrine Paul-Gilloteaux
- Université de Nantes, CHU Nantes, CNRS UMR 6291, INSERM UMR 1087, L'institut du thorax, 44000 Nantes, France
- Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, 44000 Nantes, France
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41
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Scher N, Rechav K, Paul-Gilloteaux P, Avinoam O. In situ fiducial markers for 3D correlative cryo-fluorescence and FIB-SEM imaging. iScience 2021; 24:102714. [PMID: 34258551 PMCID: PMC8253967 DOI: 10.1016/j.isci.2021.102714] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/12/2021] [Accepted: 06/08/2021] [Indexed: 11/26/2022] Open
Abstract
Imaging of cells and tissues has improved significantly over the last decade. Dual-beam instruments with a focused ion beam mounted on a scanning electron microscope (FIB-SEM), offering high-resolution 3D imaging of large volumes and fields-of-view are becoming widely used in the life sciences. FIB-SEM has most recently been implemented on fully hydrated, cryo-immobilized, biological samples. Correlative light and electron microscopy workflows combining fluorescence microscopy (FM) with FIB-SEM imaging exist, whereas workflows combining cryo-FM and cryo-FIB-SEM imaging are not yet commonly available. Here, we demonstrate that fluorescently labeled lipid droplets can serve as in situ fiducial markers for correlating cryo-FM and FIB-SEM datasets and that this approach can be used to target the acquisition of large FIB-SEM stacks spanning tens of microns under cryogenic conditions. We also show that cryo-FIB-SEM imaging is particularly informative for questions related to organelle structure and inter-organellar contacts, nuclear organization, and mineral deposits in cells.
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Affiliation(s)
- Nadav Scher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Katya Rechav
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Perrine Paul-Gilloteaux
- Structure Fédérative de Recherche François Bonamy, INSERM, CNRS, Université de Nantes, Nantes, France
| | - Ori Avinoam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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42
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Barrantes FJ. The Contribution of Biophysics and Structural Biology to Current Advances in COVID-19. Annu Rev Biophys 2021; 50:493-523. [PMID: 33957057 DOI: 10.1146/annurev-biophys-102620-080956] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Critical to viral infection are the multiple interactions between viral proteins and host-cell counterparts. The first such interaction is the recognition of viral envelope proteins by surface receptors that normally fulfil other physiological roles, a hijacking mechanism perfected over the course of evolution. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has successfully adopted this strategy using its spike glycoprotein to dock on the membrane-bound metalloprotease angiotensin-converting enzyme 2 (ACE2). The crystal structures of several SARS-CoV-2 proteins alone or in complex with their receptors or other ligands were recently solved at an unprecedented pace. This accomplishment is partly due to the increasing availability of data on other coronaviruses and ACE2 over the past 18 years. Likewise, other key intervening actors and mechanisms of viral infection were elucidated with the aid of biophysical approaches. An understanding of the various structurally important motifs of the interacting partners provides key mechanistic information for the development of structure-based designer drugs able to inhibit various steps of the infective cycle, including neutralizing antibodies, small organic drugs, and vaccines. This review analyzes current progress and the outlook for future structural studies.
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Affiliation(s)
- Francisco J Barrantes
- Biomedical Research Institute (BIOMED), Catholic University of Argentina (UCA)-National Scientific and Technical Research Council, Argentina (CONICET), C1107AFF Buenos Aires, Argentina;
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43
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Okolo CA, Kounatidis I, Groen J, Nahas KL, Balint S, Fish TM, Koronfel MA, Cortajarena AL, Dobbie IM, Pereiro E, Harkiolaki M. Sample preparation strategies for efficient correlation of 3D SIM and soft X-ray tomography data at cryogenic temperatures. Nat Protoc 2021; 16:2851-2885. [PMID: 33990802 DOI: 10.1038/s41596-021-00522-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 02/09/2021] [Indexed: 02/07/2023]
Abstract
3D correlative microscopy methods have revolutionized biomedical research, allowing the acquisition of multidimensional information to gain an in-depth understanding of biological systems. With the advent of relevant cryo-preservation methods, correlative imaging of cryogenically preserved samples has led to nanometer resolution imaging (2-50 nm) under harsh imaging regimes such as electron and soft X-ray tomography. These methods have now been combined with conventional and super-resolution fluorescence imaging at cryogenic temperatures to augment information content from a given sample, resulting in the immediate requirement for protocols that facilitate hassle-free, unambiguous cross-correlation between microscopes. We present here sample preparation strategies and a direct comparison of different working fiducialization regimes that facilitate 3D correlation of cryo-structured illumination microscopy and cryo-soft X-ray tomography. Our protocol has been tested at two synchrotron beamlines (B24 at Diamond Light Source in the UK and BL09 Mistral at ALBA in Spain) and has led to the development of a decision aid that facilitates experimental design with the strategic use of markers based on project requirements. This protocol takes between 1.5 h and 3.5 d to complete, depending on the cell populations used (adherent cells may require several days to grow on sample carriers).
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Affiliation(s)
- Chidinma A Okolo
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Ilias Kounatidis
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | | | - Kamal L Nahas
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.,Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Stefan Balint
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Thomas M Fish
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Mohamed A Koronfel
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Aitziber L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia San Sebastián, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Ian M Dobbie
- Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Eva Pereiro
- Beamline 09-MISTRAL, ALBA Synchrotron, Barcelona, Spain
| | - Maria Harkiolaki
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
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Phillips MA, Susano Pinto DM, Hall N, Mateos-Langerak J, Parton RM, Titlow J, Stoychev DV, Parks T, Susano Pinto T, Sedat JW, Booth MJ, Davis I, Dobbie IM. Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.16610.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have developed “Microscope-Cockpit” (Cockpit), a highly adaptable open source user-friendly Python-based Graphical User Interface (GUI) environment for precision control of both simple and elaborate bespoke microscope systems. The user environment allows next-generation near instantaneous navigation of the entire slide landscape for efficient selection of specimens of interest and automated acquisition without the use of eyepieces. Cockpit uses “Python-Microscope” (Microscope) for high-performance coordinated control of a wide range of hardware devices using open source software. Microscope also controls complex hardware devices such as deformable mirrors for aberration correction and spatial light modulators for structured illumination via abstracted device models. We demonstrate the advantages of the Cockpit platform using several bespoke microscopes, including a simple widefield system and a complex system with adaptive optics and structured illumination. A key strength of Cockpit is its use of Python, which means that any microscope built with Cockpit is ready for future customisation by simply adding new libraries, for example machine learning algorithms to enable automated microscopy decision making while imaging.
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Wang Y, Friedrich H, Voets IK, Zijlstra P, Albertazzi L. Correlative imaging for polymer science. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yuyang Wang
- Department of Applied Physics & Institute of Complex Molecular Systems (ICMS) Eindhoven University of Technology (TUE) Eindhoven The Netherlands
| | - Heiner Friedrich
- Laboratory of Physical Chemistry and Center for Multiscale Electron Microscopy, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems Eindhoven University of Technology (TUE) Eindhoven The Netherlands
| | - Ilja K. Voets
- Department of Chemical Engineering and Chemistry & Institute of Complex Molecular Systems (ICMS) Eindhoven University of Technology (TUE) Eindhoven The Netherlands
- Laboratory of Self‐Organizing Soft Matter, Department of Chemical Engineering and Chemistry & Institute of Complex Molecular Systems (ICMS) Eindhoven University of Technology (TUE) Eindhoven The Netherlands
| | - Peter Zijlstra
- Department of Applied Physics & Institute of Complex Molecular Systems (ICMS) Eindhoven University of Technology (TUE) Eindhoven The Netherlands
| | - Lorenzo Albertazzi
- Department of Biomedical Engineering, Institute of Complex Molecular Systems (ICMS) Eindhoven University of Technology (TUE) Eindhoven The Netherlands
- Institute for Bioengineering of Catalonia (IBEC) The Barcelona Institute of Science and Technology (BIST) Barcelona Spain
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Iudin A, Sarkans U, Koronfel MA, Fish T, Dobbie I, Harkiolaki M, Patwardhan A, Kleywegt GJ. Data-deposition protocols for correlative soft X-ray tomography and super-resolution structured illumination microscopy applications. STAR Protoc 2021; 2:100253. [PMID: 33490973 PMCID: PMC7811169 DOI: 10.1016/j.xpro.2020.100253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
This protocol illustrates the steps necessary to deposit correlated 3D cryo-imaging data from cryo-structured illumination microscopy and cryo-soft X-ray tomography with the BioStudies and EMPIAR deposition databases of the European Bioinformatics Institute. There is currently a real need for a robust method of data deposition to ensure unhindered access to and independent validation of correlative light and X-ray microscopy data to allow use in further comparative studies, educational activities, and data mining. For complete details on the use and execution of this protocol, please refer to Kounatidis et al. (2020).
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Affiliation(s)
- Andrii Iudin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mohamed A. Koronfel
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DW, UK
| | - Tom Fish
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DW, UK
| | - Ian Dobbie
- Micron, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Maria Harkiolaki
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DW, UK
| | - Ardan Patwardhan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gerard J. Kleywegt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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47
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Inhibition of HIF-1α accumulation in prostate cancer cells is initiated during early stages of mammalian orthoreovirus infection. Virology 2021; 558:38-48. [PMID: 33721728 DOI: 10.1016/j.virol.2021.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 02/08/2023]
Abstract
Mammalian orthoreovirus (MRV) is a safe and effective cancer killing virus that has completed Phase I-III clinical trials against numerous cancer types. While many patients experience benefit from MRV therapy, pre-defined set points necessary for FDA approval have not been reached. Therefore, additional research into MRV biology and the effect of viral therapy on different tumor genetic subtypes and microenvironments is necessary to identify tumors most amenable to MRV virotherapy. In this work we analyzed the stage of viral infection necessary to inhibit HIF-1α, an aggressive cancer activator induced by hypoxia. We demonstrated that two viral capsid proteins were not necessary and that a step parallel with virus core movement across the endosomal membrane was required for this inhibition. Altogether, this work clarifies the mechanisms of MRV-induced HIF-1α inhibition and provides biological relevance for using MRV to inhibit the devastating effects of tumor hypoxia.
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48
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Reovirus and the Host Integrated Stress Response: On the Frontlines of the Battle to Survive. Viruses 2021; 13:v13020200. [PMID: 33525628 PMCID: PMC7910986 DOI: 10.3390/v13020200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/17/2022] Open
Abstract
Cells are continually exposed to stressful events, which are overcome by the activation of a number of genetic pathways. The integrated stress response (ISR) is a large component of the overall cellular response to stress, which ultimately functions through the phosphorylation of the alpha subunit of eukaryotic initiation factor-2 (eIF2α) to inhibit the energy-taxing process of translation. This response is instrumental in the inhibition of viral infection and contributes to evolution in viruses. Mammalian orthoreovirus (MRV), an oncolytic virus that has shown promise in over 30 phase I–III clinical trials, has been shown to induce multiple arms within the ISR pathway, but it successfully evades, modulates, or subverts each cellular attempt to inhibit viral translation. MRV has not yet received Food and Drug Administration (FDA) approval for general use in the clinic; therefore, researchers continue to study virus interactions with host cells to identify circumstances where MRV effectiveness in tumor killing can be improved. In this review, we will discuss the ISR, MRV modulation of the ISR, and discuss ways in which MRV interaction with the ISR may increase the effectiveness of cancer therapeutics whose modes of action are altered by the ISR.
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Zhang P, Mendonca L, Howe A, Gilchrist J, Sun D, Knight M, Zanetti-Domingues L, Bateman B, Krebs AS, Chen L, Radecke J, Sheng Y, Li V, Ni T, Kounatidis I, Koronfel M, Szynkiewicz M, Harkiolaki M, Martin-Fernandez M, James W. Correlative Multi-scale Cryo-imaging Unveils SARS-CoV-2 Assembly and Egress. RESEARCH SQUARE 2021. [PMID: 33501431 PMCID: PMC7836121 DOI: 10.21203/rs.3.rs-134794/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified recombinant viral components and inactivated viruses. However, structural and ultrastructural evidence on how the SARS-CoV-2 infection progresses in the frozen-hydrated native cellular context is scarce, and there is a lack of comprehensive knowledge on the SARS-CoV-2 replicative cycle. To correlate the cytopathic events induced by SARS-CoV-2 with virus replication process under the frozen-hydrated condition, here we established a unique multi-modal, multi-scale cryo-correlative platform to image SARS-CoV-2 infection in Vero cells. This platform combines serial cryoFIB/SEM volume imaging and soft X-ray cryo-tomography with cell lamellae-based cryo-electron tomography (cryoET) and subtomogram averaging. The results place critical SARS-CoV-2 structural events – e.g. viral RNA transport portals on double membrane vesicles, virus assembly and budding intermediates, virus egress pathways, and native virus spike structures from intracellular assembled and extracellular released virus - in the context of whole-cell images. The latter revealed numerous heterogeneous cytoplasmic vesicles, the formation of membrane tunnels through which viruses exit, and the drastic cytoplasm invasion into the nucleus. This integrated approach allows a holistic view of SARS-CoV-2 infection, from the whole cell to individual molecules.
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50
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Walter A, Kleywegt GJ, Verkade P. Correlative multimodal imaging: Building a community. Methods Cell Biol 2021; 162:417-430. [PMID: 33707022 DOI: 10.1016/bs.mcb.2020.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Few would have thought that when Porter and colleagues used light microscopy to target their cell of interest to be analyzed in the electron microscope in the 1940s, that Correlative Imaging would develop into the thriving field it is today. Even though the first use of Correlative Light Electron Microscopy (CLEM) was established in the 1940s, it is only since the year 2000 that there has been a real surge in the application of CLEM technology. The power of CLEM is recognized in the scientific community as evidenced by the growing number of publications and dedicated sessions at scientific meetings. The field is also broadening, incorporating a multitude of other techniques including preclinical research and diagnostics, and slowly but surely the overarching field of Correlative Multimodality Imaging (CMI) is taking its place as an established technique and a research area in its own right. In this chapter, we will look at the initiatives that are being developed within the scientific world to build a coherent CMI community, with a particular emphasis on the developments in Europe. To achieve this aim, the community will need to design mechanisms for the interdisciplinary exchange of knowledge and benefits, set up training schemes, and develop standards for CMI technology and its data.
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Affiliation(s)
- Andreas Walter
- Austrian BioImaging/CMI, Vienna BioCenter Core Facilities GmbH (VBCF), Vienna, Austria
| | - Gerard J Kleywegt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, United Kingdom.
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