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Parkhurst JM, Varslot T, Dumoux M, Siebert CA, Darrow M, Basham M, Kirkland A, Grange M, Evans G, Naismith JH. Pillar data-acquisition strategies for cryo-electron tomography of beam-sensitive biological samples. Acta Crystallogr D Struct Biol 2024; 80:421-438. [PMID: 38829361 PMCID: PMC11154591 DOI: 10.1107/s2059798324004546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024] Open
Abstract
For cryo-electron tomography (cryo-ET) of beam-sensitive biological specimens, a planar sample geometry is typically used. As the sample is tilted, the effective thickness of the sample along the direction of the electron beam increases and the signal-to-noise ratio concomitantly decreases, limiting the transfer of information at high tilt angles. In addition, the tilt range where data can be collected is limited by a combination of various sample-environment constraints, including the limited space in the objective lens pole piece and the possible use of fixed conductive braids to cool the specimen. Consequently, most tilt series are limited to a maximum of ±70°, leading to the presence of a missing wedge in Fourier space. The acquisition of cryo-ET data without a missing wedge, for example using a cylindrical sample geometry, is hence attractive for volumetric analysis of low-symmetry structures such as organelles or vesicles, lysis events, pore formation or filaments for which the missing information cannot be compensated by averaging techniques. Irrespective of the geometry, electron-beam damage to the specimen is an issue and the first images acquired will transfer more high-resolution information than those acquired last. There is also an inherent trade-off between higher sampling in Fourier space and avoiding beam damage to the sample. Finally, the necessity of using a sufficient electron fluence to align the tilt images means that this fluence needs to be fractionated across a small number of images; therefore, the order of data acquisition is also a factor to consider. Here, an n-helix tilt scheme is described and simulated which uses overlapping and interleaved tilt series to maximize the use of a pillar geometry, allowing the entire pillar volume to be reconstructed as a single unit. Three related tilt schemes are also evaluated that extend the continuous and classic dose-symmetric tilt schemes for cryo-ET to pillar samples to enable the collection of isotropic information across all spatial frequencies. A fourfold dose-symmetric scheme is proposed which provides a practical compromise between uniform information transfer and complexity of data acquisition.
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Affiliation(s)
- James M. Parkhurst
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Trond Varslot
- Thermo Fisher Scientific, Vlastimila Pecha, Brno, Czechia
| | - Maud Dumoux
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - C. Alistair Siebert
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Michele Darrow
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Mark Basham
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Angus Kirkland
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
- Electron Physical Science Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, United Kingdom
| | - Michael Grange
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Gwyndaf Evans
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James H. Naismith
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
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2
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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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McCafferty CL, Klumpe S, Amaro RE, Kukulski W, Collinson L, Engel BD. Integrating cellular electron microscopy with multimodal data to explore biology across space and time. Cell 2024; 187:563-584. [PMID: 38306982 DOI: 10.1016/j.cell.2024.01.005] [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: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron microscopy (vEM) and cryo-electron tomography (cryo-ET), which together can visualize biological complexity across scales from the organization of cells in large tissues to the molecular details inside native cellular environments. In addition, we discuss emerging methodologies for integrating three-dimensional electron microscopy (3DEM) imaging with multimodal data, including fluorescence microscopy, mass spectrometry, single-particle analysis, and AI-based structure prediction. This multifaceted approach fills gaps in the biological continuum, providing functional context, spatial organization, molecular identity, and native interactions. We conclude with a perspective on incorporating diverse data into computational simulations that further bridge and extend length scales while integrating the dimension of time.
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Affiliation(s)
| | - Sven Klumpe
- Research Group CryoEM Technology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Rommie E Amaro
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Wanda Kukulski
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Benjamin D Engel
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
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4
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Mavrommatis A, Tsiplakou E, Zerva A, Pantiora PD, Georgakis ND, Tsintzou GP, Madesis P, Labrou NE. Microalgae as a Sustainable Source of Antioxidants in Animal Nutrition, Health and Livestock Development. Antioxidants (Basel) 2023; 12:1882. [PMID: 37891962 PMCID: PMC10604252 DOI: 10.3390/antiox12101882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Microalgae are a renewable and sustainable source of bioactive compounds, such as essential amino acids, polyunsaturated fatty acids, and antioxidant compounds, that have been documented to have beneficial effects on nutrition and health. Among these natural products, the demand for natural antioxidants, as an alternative to synthetic antioxidants, has increased. The antioxidant activity of microalgae significantly varies between species and depends on growth conditions. In the last decade, microalgae have been explored in livestock animals as feed additives with the aim of improving both animals' health and performance as well as product quality and the environmental impact of livestock. These findings are highly dependent on the composition of microalgae strain and their amount in the diet. The use of carbohydrate-active enzymes can increase nutrient bioavailability as a consequence of recalcitrant microalgae cell wall degradation, making it a promising strategy for monogastric nutrition for improving livestock productivity. The use of microalgae as an alternative to conventional feedstuffs is becoming increasingly important due to food-feed competition, land degradation, water deprivation, and climate change. However, the cost-effective production and use of microalgae is a major challenge in the near future, and their cultivation technology should be improved by reducing production costs, thus increasing profitability.
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Affiliation(s)
- Alexandros Mavrommatis
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 75 Iera Odos Str., GR-11855 Athens, Greece
| | - Eleni Tsiplakou
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 75 Iera Odos Str., GR-11855 Athens, Greece
| | - Anastasia Zerva
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Str., GR-11855 Athens, Greece
| | - Panagiota D Pantiora
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Str., GR-11855 Athens, Greece
| | - Nikolaos D Georgakis
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Str., GR-11855 Athens, Greece
| | - Georgia P Tsintzou
- Laboratory of Molecular Biology of Plants, School of Agricultural Sciences, University of Thessaly, GR-38221 Volos, Greece
| | - Panagiotis Madesis
- Laboratory of Molecular Biology of Plants, School of Agricultural Sciences, University of Thessaly, GR-38221 Volos, Greece
- Institute of Applied Biosciences, CERTH, 6th km Charilaou-Thermis Road, P.O. Box 361, Thermi, GR-57001 Thessaloniki, Greece
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Str., GR-11855 Athens, Greece
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Fahy K, Sheridan P, Kapishnikov S, Fyans W, O'Reilly F, McEnroe T. A Laboratory Based Soft X-ray Microscope for 3D Imaging of Whole Cells. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1151-1152. [PMID: 37613607 DOI: 10.1093/micmic/ozad067.588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
| | | | | | | | - Fergal O'Reilly
- SiriusXT Ltd., Dublin, Ireland
- University College Dublin, School of Physics, Dublin, Ireland
- University College Dublin, School of Biology and Environmental Sciences, Dublin, Ireland
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6
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Fahy K, Sheridan P, Kapishnikov S, Fyans W, O'Reilly F, McEnroe T. A Laboratory Based Soft X-ray Microscope for 3D Imaging of Whole Cells. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1171-1172. [PMID: 37613165 DOI: 10.1093/micmic/ozad067.601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
| | | | | | | | - Fergal O'Reilly
- SiriusXT Ltd., Dublin, Ireland
- University College Dublin, School of Physics, Dublin, Ireland
- University College Dublin, School of Biology and Environmental Sciences, Dublin, Ireland
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7
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Kapishnikov S, Fahy K, Fyans W, O'Reilly F, McEnroe T, Sheridan P. Integration of Laboratory Cryo Soft X-ray Tomography into CLEM Workflows for Multimodal Multiscale Imaging of Bulk Samples. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1164. [PMID: 37613245 DOI: 10.1093/micmic/ozad067.595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
| | | | | | - Fergal O'Reilly
- SiriusXT Ltd., Dublin, Ireland
- University College Dublin, School of Physics, Dublin, Ireland
- University College Dublin, School of Biology and Environmental Sciences, Dublin, Ireland
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8
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Fahy K, Kapishnikov S, Fyans W, Weinhardt V, O'Reilly F, McEnroe T, Sheridan P. Development of Full Tilt Tomography in a Laboratory based Soft X-ray Microscope. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1178. [PMID: 37613474 DOI: 10.1093/micmic/ozad067.605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
| | | | | | - Venera Weinhardt
- Heidelberg University, Centre for Organismal Studies, Heidelberg, Germany
| | - Fergal O'Reilly
- SiriusXT Ltd., Dublin, Ireland
- University College Dublin, School of Physics, Dublin, Ireland
- University College Dublin, School of Biology and Environmental Sciences, Dublin, Ireland
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9
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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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Bonany M, Pérez-Berná AJ, Dučić T, Pereiro E, Martin-Gómez H, Mas-Moruno C, van Rijt S, Zhao Z, Espanol M, Ginebra MP. Hydroxyapatite nanoparticles-cell interaction: New approaches to disclose the fate of membrane-bound and internalised nanoparticles. BIOMATERIALS ADVANCES 2022; 142:213148. [PMID: 36274359 DOI: 10.1016/j.bioadv.2022.213148] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/03/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Hydroxyapatite nanoparticles are popular tools in bone regeneration, but they have also been used for gene delivery and as anticancer drugs. Understanding their mechanism of action, particularly for the latter application, is crucial to predict their toxicity. To this end, we aimed to elucidate the importance of nanoparticle membrane interactions in the cytotoxicity of MG-63 cells using two different types of nanoparticles. In addition, conventional techniques for studying nanoparticle internalisation were evaluated and compared with newer and less exploited approaches. Hydroxyapatite and magnesium-doped hydroxyapatite nanoparticles were used as suspensions or compacted as specular discs. Comparison between cells seeded on the discs and those supplemented with the nanoparticles allowed direct interaction of the cell membrane with the material to be ruled out as the main mechanism of toxicity. In addition, standard techniques such as flow cytometry were inconclusive when used to assess nanoparticles toxicity. Interestingly, the use of intracellular calcium fluorescent probes revealed the presence of a high number of calcium-rich vesicles after nanoparticle supplementation in cell culture. These structures could not be detected by transmission electron microscopy due to their liquid content. However, by using cryo-soft X-ray imaging, which was used to visualise the cellular ultrastructure without further treatment other than vitrification and to quantify the linear absorption coefficient of each organelle, it was possible to identify them as multivesicular bodies, potentially acting as calcium stores. In the study, an advanced state of degradation of the hydroxyapatite and magnesium-doped hydroxyapatite nanoparticles within MG-63 cells was observed. Overall, we demonstrate that the combination of fluorescent calcium probes together with cryo-SXT is an excellent approach to investigate intracellular calcium, especially when found in its soluble form.
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Affiliation(s)
- Mar Bonany
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; Barcelona Research Centre in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain; Biomedical Engineering Research Center (CREB), UPC, 08028 Barcelona, Spain
| | | | - Tanja Dučić
- MISTRAL Beamline Experiments Division, ALBA Synchrotron Light Source, 08290 Barcelona, Spain
| | - Eva Pereiro
- MISTRAL Beamline Experiments Division, ALBA Synchrotron Light Source, 08290 Barcelona, Spain
| | - Helena Martin-Gómez
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; Barcelona Research Centre in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain
| | - Carlos Mas-Moruno
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; Barcelona Research Centre in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain; Biomedical Engineering Research Center (CREB), UPC, 08028 Barcelona, Spain
| | - Sabine van Rijt
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6200, MD, Maastricht, the Netherlands
| | - Zhitong Zhao
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Montserrat Espanol
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; Barcelona Research Centre in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain; Biomedical Engineering Research Center (CREB), UPC, 08028 Barcelona, Spain.
| | - Maria-Pau Ginebra
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; Barcelona Research Centre in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain; Biomedical Engineering Research Center (CREB), UPC, 08028 Barcelona, Spain; Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
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Vanslembrouck B, Chen JH, Larabell C, van Hengel J. Microscopic Visualization of Cell-Cell Adhesion Complexes at Micro and Nanoscale. Front Cell Dev Biol 2022; 10:819534. [PMID: 35517500 PMCID: PMC9065677 DOI: 10.3389/fcell.2022.819534] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 03/21/2022] [Indexed: 12/25/2022] Open
Abstract
Considerable progress has been made in our knowledge of the morphological and functional varieties of anchoring junctions. Cell-cell adhesion contacts consist of discrete junctional structures responsible for the mechanical coupling of cytoskeletons and allow the transmission of mechanical signals across the cell collective. The three main adhesion complexes are adherens junctions, tight junctions, and desmosomes. Microscopy has played a fundamental role in understanding these adhesion complexes on different levels in both physiological and pathological conditions. In this review, we discuss the main light and electron microscopy techniques used to unravel the structure and composition of the three cell-cell contacts in epithelial and endothelial cells. It functions as a guide to pick the appropriate imaging technique(s) for the adhesion complexes of interest. We also point out the latest techniques that have emerged. At the end, we discuss the problems investigators encounter during their cell-cell adhesion research using microscopic techniques.
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Affiliation(s)
- Bieke Vanslembrouck
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Anatomy, University of San Francisco, San Francisco, CA, United States
- *Correspondence: Bieke Vanslembrouck, ; Jolanda van Hengel,
| | - Jian-hua Chen
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Anatomy, University of San Francisco, San Francisco, CA, United States
| | - Carolyn Larabell
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Anatomy, University of San Francisco, San Francisco, CA, United States
| | - Jolanda van Hengel
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- *Correspondence: Bieke Vanslembrouck, ; Jolanda van Hengel,
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12
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Chen JH, Vanslembrouck B, Loconte V, Ekman A, Cortese M, Bartenschlager R, McDermott G, Larabell CA, Le Gros MA, Weinhardt V. A protocol for full-rotation soft X-ray tomography of single cells. STAR Protoc 2022; 3:101176. [PMID: 35199039 PMCID: PMC8844304 DOI: 10.1016/j.xpro.2022.101176] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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
The protocol describes step-by-step sample preparation, data acquisition, and segmentation of cellular organelles with soft X-ray tomography. It is designed for microscopes built to perform full-rotation data acquisition on specimens in cylindrical sample holders, such as the XM-2 microscope at the Advanced Light Source, LBNL; however, it might be generalized for similar sample holder designs for both synchrotron and table-top microscopes. For complete details on the use and execution of this profile, please refer to Loconte et al. (2021).
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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
| | - Valentina Loconte
- 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
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology Heidelberg University, Heidelberg 69120, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology Heidelberg University, Heidelberg 69120, Germany
- German Center for Infection Research, Heidelberg Partner Site, Heidelberg 69120, Germany
- Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Gerry McDermott
- 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
| | - 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
| | - Venera Weinhardt
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
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Salsman J, Dellaire G. Super-Resolution Radial Fluctuations (SRRF) Microscopy. Methods Mol Biol 2022; 2440:225-251. [PMID: 35218543 DOI: 10.1007/978-1-0716-2051-9_14] [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: 06/14/2023]
Abstract
Super-resolution Radial Fluctuations (SRRF) imaging is a computational approach to fixed and live-cell super-resolution microscopy that is highly accessible to life science researchers since it uses common microscopes and open-source software plugins for ImageJ. This allows users to generate super-resolution images using the same equipment, fluorophores, fluorescent proteins and methods they routinely employ for their studies without specialized sample preparations or reagents. Here, we discuss a step-by-step workflow for acquiring and analyzing images using the NanoJ-SRRF software developed by the Ricardo Henriques group, with a focus on imaging chromatin. Increased accessibility of affordable super-resolution imaging techniques is an important step in extending the reach of this revolution in cellular imaging to a greater number of laboratories.
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Affiliation(s)
- Jayme Salsman
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, NS, Canada.
- Department of Biochemistry, Dalhousie University, Halifax, NS, Canada.
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14
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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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15
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Panneels V, Diaz A, Imsand C, Guizar-Sicairos M, Müller E, Bittermann AG, Ishikawa T, Menzel A, Kaech A, Holler M, Grimm C, Schertler G. Imaging of retina cellular and subcellular structures using ptychographic hard X-ray tomography. J Cell Sci 2021; 134:272479. [PMID: 34494099 DOI: 10.1242/jcs.258561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 09/01/2021] [Indexed: 11/20/2022] Open
Abstract
Ptychographic hard X-ray computed tomography (PXCT) is a recent method allowing imaging with quantitative electron-density contrast. Here, we imaged, at cryogenic temperature and without sectioning, cellular and subcellular structures of a chemically fixed and stained wild-type mouse retina, including axons and synapses, with complete isotropic 3D information over tens of microns. Comparison with tomograms of degenerative retina from a mouse model of retinitis pigmentosa illustrates the potential of this method for analyzing disease processes like neurodegeneration at sub-200 nm resolution. As a non-destructive imaging method, PXCT is very suitable for correlative imaging. Within the outer plexiform layer containing the photoreceptor synapses, we identified somatic synapses. We used a small region inside the X-ray-imaged sample for further high-resolution focused ion beam/scanning electron microscope tomography. The subcellular structures of synapses obtained with the X-ray technique matched the electron microscopy data, demonstrating that PXCT is a powerful scanning method for tissue volumes of more than 60 cells and sensitive enough for identification of regions as small as 200 nm, which remain available for further structural and biochemical investigations.
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Affiliation(s)
- Valerie Panneels
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Ana Diaz
- Division of Photon Science, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Cornelia Imsand
- Laboratory for Retinal Cell Biology, Department of Ophthalmology, University Hospital Zurich, University of Zurich, 8952 Schlieren, Switzerland
| | - Manuel Guizar-Sicairos
- Division of Photon Science, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Elisabeth Müller
- Division of Biology and Chemistry, Laboratory for Nanoscale Biology, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Anne Greet Bittermann
- ScopeM, Scientific Center for Optical and Electron Microscopy, ETH Zurich, 8093 Zurich, Switzerland
| | - Takashi Ishikawa
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, 5232 Villigen, Switzerland.,Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Andreas Menzel
- Division of Photon Science, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zurich, 8006 Zurich, Switzerland
| | - Mirko Holler
- Division of Photon Science, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Christian Grimm
- Laboratory for Retinal Cell Biology, Department of Ophthalmology, University Hospital Zurich, University of Zurich, 8952 Schlieren, Switzerland
| | - Gebhard Schertler
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, 5232 Villigen, Switzerland.,Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
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16
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Costa IM, Cheng J, Osytek KM, Imberti C, Terry SYA. Methods and techniques for in vitro subcellular localization of radiopharmaceuticals and radionuclides. Nucl Med Biol 2021; 98-99:18-29. [PMID: 33964707 PMCID: PMC7610823 DOI: 10.1016/j.nucmedbio.2021.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/18/2021] [Accepted: 03/30/2021] [Indexed: 12/28/2022]
Abstract
In oncology, the holy grail of radiotherapy is specific radiation dose deposition in tumours with minimal healthy tissue toxicity. If used appropriately, injectable, systemic radionuclide therapies could meet these criteria, even for treatment of micrometastases and single circulating tumour cells. The clinical use of α and β- particle-emitting molecular radionuclide therapies is rising, however clinical translation of Auger electron-emitting radionuclides is hampered by uncertainty around their exact subcellular localisation, which in turn affects the accuracy of dosimetry. This review aims to discuss and compare the advantages and disadvantages of various subcellular localisation methods available to localise radiopharmaceuticals and radionuclides for in vitro investigations.
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Affiliation(s)
- Ines M Costa
- Department of Imaging Chemistry and Biology, School of Biomedical Engineering and Imaging Sciences, King's College London, London SE1 7EH, United Kingdom
| | - Jordan Cheng
- Department of Imaging Chemistry and Biology, School of Biomedical Engineering and Imaging Sciences, King's College London, London SE1 7EH, United Kingdom
| | - Katarzyna M Osytek
- Department of Imaging Chemistry and Biology, School of Biomedical Engineering and Imaging Sciences, King's College London, London SE1 7EH, United Kingdom
| | - Cinzia Imberti
- Department of Imaging Chemistry and Biology, School of Biomedical Engineering and Imaging Sciences, King's College London, London SE1 7EH, United Kingdom; Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Samantha Y A Terry
- Department of Imaging Chemistry and Biology, School of Biomedical Engineering and Imaging Sciences, King's College London, London SE1 7EH, United Kingdom.
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17
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Table-Top Water-Window Microscope Using a Capillary Discharge Plasma Source with Spatial Resolution 75 nm. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10186373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We present a design of a compact transmission water-window microscope based on the Z-pinching capillary discharge nitrogen plasma source. The microscope operates at wavelength of 2.88 nm (430 eV), and with its table-top dimensions provides an alternative to large-scale soft X-ray (SXR) microscope systems based on synchrotrons and free-electron lasers. The emitted soft X-ray radiation is filtered by a titanium foil and focused by an ellipsoidal condenser mirror into the sample plane. A Fresnel zone plate was used to create a transmission image of the sample onto a charge-coupled device (CCD) camera. To assess the resolution of the microscope, we imaged a standard sample-copper mesh. The spatial resolution of the microscope is 75 nm at half-pitch, calculated via a 10–90% intensity knife-edge test. The applicability of the microscope is demonstrated by the imaging of green algae-Desmodesmus communis. This paper describes the principle of capillary discharge source, design of the microscope, and experimental imaging results of Cu mesh and biological sample.
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18
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Weinhardt V, Chen JH, Ekman AA, Guo J, Remesh SG, Hammel M, McDermott G, Chao W, Oh S, Le Gros MA, Larabell CA. Switchable resolution in soft x-ray tomography of single cells. PLoS One 2020; 15:e0227601. [PMID: 31978064 PMCID: PMC6980406 DOI: 10.1371/journal.pone.0227601] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/24/2019] [Indexed: 11/18/2022] Open
Abstract
The diversity of living cells, in both size and internal complexity, calls for imaging methods with adaptable spatial resolution. Soft x-ray tomography (SXT) is a three-dimensional imaging technique ideally suited to visualizing and quantifying the internal organization of single cells of varying sizes in a near-native state. The achievable resolution of the soft x-ray microscope is largely determined by the objective lens, but switching between objectives is extremely time-consuming and typically undertaken only during microscope maintenance procedures. Since the resolution of the optic is inversely proportional to the depth of focus, an optic capable of imaging the thickest cells is routinely selected. This unnecessarily limits the achievable resolution in smaller cells and eliminates the ability to obtain high-resolution images of regions of interest in larger cells. Here, we describe developments to overcome this shortfall and allow selection of microscope optics best suited to the specimen characteristics and data requirements. We demonstrate that switchable objective capability advances the flexibility of SXT to enable imaging cells ranging in size from bacteria to yeast and mammalian cells without physically modifying the microscope, and we demonstrate the use of this technology to image the same specimen with both optics.
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Affiliation(s)
- Venera Weinhardt
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Axel A. Ekman
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Jessica Guo
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Soumya G. Remesh
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Gerry McDermott
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Weilun Chao
- Center for X-ray Optics, Material Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Sharon Oh
- Center for X-ray Optics, Material Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Mark A. Le Gros
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Carolyn A. Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
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