1
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Cacho-Navas C, López-Pujante C, Reglero-Real N, Colás-Algora N, Cuervo A, Conesa JJ, Barroso S, de Rivas G, Ciordia S, Paradela A, D'Agostino G, Manzo C, Feito J, Andrés G, Molina-Jiménez F, Majano P, Correas I, Carazo JM, Nourshargh S, Huch M, Millán J. ICAM-1 nanoclusters regulate hepatic epithelial cell polarity by leukocyte adhesion-independent control of apical actomyosin. eLife 2024; 12:RP89261. [PMID: 38597186 PMCID: PMC11006420 DOI: 10.7554/elife.89261] [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] [Indexed: 04/11/2024] Open
Abstract
Epithelial intercellular adhesion molecule (ICAM)-1 is apically polarized, interacts with, and guides leukocytes across epithelial barriers. Polarized hepatic epithelia organize their apical membrane domain into bile canaliculi and ducts, which are not accessible to circulating immune cells but that nevertheless confine most of ICAM-1. Here, by analyzing ICAM-1_KO human hepatic cells, liver organoids from ICAM-1_KO mice and rescue-of-function experiments, we show that ICAM-1 regulates epithelial apicobasal polarity in a leukocyte adhesion-independent manner. ICAM-1 signals to an actomyosin network at the base of canalicular microvilli, thereby controlling the dynamics and size of bile canalicular-like structures. We identified the scaffolding protein EBP50/NHERF1/SLC9A3R1, which connects membrane proteins with the underlying actin cytoskeleton, in the proximity interactome of ICAM-1. EBP50 and ICAM-1 form nano-scale domains that overlap in microvilli, from which ICAM-1 regulates EBP50 nano-organization. Indeed, EBP50 expression is required for ICAM-1-mediated control of BC morphogenesis and actomyosin. Our findings indicate that ICAM-1 regulates the dynamics of epithelial apical membrane domains beyond its role as a heterotypic cell-cell adhesion molecule and reveal potential therapeutic strategies for preserving epithelial architecture during inflammatory stress.
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Affiliation(s)
| | | | - Natalia Reglero-Real
- William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of LondonLondonUnited Kingdom
| | | | - Ana Cuervo
- Centro Nacional de Biotecnologia (CSIC)MadridSpain
| | | | - Susana Barroso
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAMMadridSpain
| | - Gema de Rivas
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAMMadridSpain
| | | | | | | | - Carlo Manzo
- Facultat de Ciències, Tecnologia i Enginyeries, Universitat de Vic – Universitat Central de Catalunya (UVic-UCC)VicSpain
| | - Jorge Feito
- Servicio de Anatomía Patológica, Hospital Universitario de SalamancaSalamancaSpain
| | - Germán Andrés
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAMMadridSpain
| | - Francisca Molina-Jiménez
- Molecular Biology Unit, Hospital Universitario de la PrincesaMadridSpain
- Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa)MadridSpain
| | - Pedro Majano
- Molecular Biology Unit, Hospital Universitario de la PrincesaMadridSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)MadridSpain
- Department of Cellular Biology, Universidad Complutense de MadridMadridSpain
| | - Isabel Correas
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAMMadridSpain
| | | | - Sussan Nourshargh
- William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of LondonLondonUnited Kingdom
| | - Meritxell Huch
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Jaime Millán
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAMMadridSpain
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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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3
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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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4
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Ohsuna T, Oh-Ishi K. Model-based deconvolution for particle analysis applied to a through-focus series of HAADF-STEM images. Microscopy (Oxf) 2023; 72:368-380. [PMID: 36537122 DOI: 10.1093/jmicro/dfac070] [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: 06/01/2022] [Revised: 11/06/2022] [Accepted: 12/19/2022] [Indexed: 08/05/2023] Open
Abstract
This paper presents an approach for determining the sizes and three-dimensional (3D) positions of nanoparticles from a through-focus series of high-angle annular dark-field scanning transmission electron microscopy images. By assuming spherical particles with uniform density, the sizes and 3D positions can be derived via Wiener deconvolution using a series of kernels prepared by the convolution of the 3D point spread function of the electron beam and the 3D density distribution of spheres with different radii. This process is referred to as a model-based deconvolution. Four 3D datasets with a volume size of 148 × 148 × 560 nm3 were obtained from the four sets of 256 high-angle annular dark-field scanning transmission electron microscopy images of 256 × 256 pixels taken from the same field of view under the through-focus condition. The 3D positions and radii of 14 particles in each 3D dataset were derived using the model-based deconvolution for ∼8 min. The observation errors of the 3D position were estimated as σx ≅ σy ≅ 0.3 nm and σz < 1.6 nm.
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Affiliation(s)
- Tetsu Ohsuna
- Materials Analysis & Evaluation Research-Domain, Toyota Central R&D Labs., Co. Ltd, 41-1, Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Keiichiro Oh-Ishi
- Materials Analysis & Evaluation Research-Domain, Toyota Central R&D Labs., Co. Ltd, 41-1, Yokomichi, Nagakute, Aichi 480-1192, Japan
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5
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Rojas‐Gómez A, Dosil SG, Chichón FJ, Fernández‐Gallego N, Ferrarini A, Calvo E, Calzada‐Fraile D, Requena S, Otón J, Serrano A, Tarifa R, Arroyo M, Sorrentino A, Pereiro E, Vázquez J, Valpuesta JM, Sánchez‐Madrid F, Martín‐Cófreces NB. Chaperonin CCT controls extracellular vesicle production and cell metabolism through kinesin dynamics. J Extracell Vesicles 2023; 12:e12333. [PMID: 37328936 PMCID: PMC10276179 DOI: 10.1002/jev2.12333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 05/02/2023] [Indexed: 06/18/2023] Open
Abstract
Cell proteostasis includes gene transcription, protein translation, folding of de novo proteins, post-translational modifications, secretion, degradation and recycling. By profiling the proteome of extracellular vesicles (EVs) from T cells, we have found the chaperonin complex CCT, involved in the correct folding of particular proteins. By limiting CCT cell-content by siRNA, cells undergo altered lipid composition and metabolic rewiring towards a lipid-dependent metabolism, with increased activity of peroxisomes and mitochondria. This is due to dysregulation of the dynamics of interorganelle contacts between lipid droplets, mitochondria, peroxisomes and the endolysosomal system. This process accelerates the biogenesis of multivesicular bodies leading to higher EV production through the dynamic regulation of microtubule-based kinesin motors. These findings connect proteostasis with lipid metabolism through an unexpected role of CCT.
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Affiliation(s)
- Amelia Rojas‐Gómez
- Immunology ServiceHospital Universitario de la Princesa, UAM, IIS‐IPMadridSpain
- Area of Vascular Pathophysiology, Laboratory of Intercellular CommunicationFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Sara G. Dosil
- Immunology ServiceHospital Universitario de la Princesa, UAM, IIS‐IPMadridSpain
- Area of Vascular Pathophysiology, Laboratory of Intercellular CommunicationFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Francisco J. Chichón
- Cryoelectron Microscopy UnitCentro Nacional de Biotecnología (CNB‐CSIC)MadridSpain
- Department of Macromolecular StructureCentro Nacional de Biotecnología (CNB‐CSIC)MadridSpain
| | - Nieves Fernández‐Gallego
- Immunology ServiceHospital Universitario de la Princesa, UAM, IIS‐IPMadridSpain
- Area of Vascular Pathophysiology, Laboratory of Intercellular CommunicationFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Alessia Ferrarini
- Laboratory of Cardiovascular ProteomicsFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Enrique Calvo
- Laboratory of Cardiovascular ProteomicsFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Diego Calzada‐Fraile
- Area of Vascular Pathophysiology, Laboratory of Intercellular CommunicationFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Silvia Requena
- Immunology ServiceHospital Universitario de la Princesa, UAM, IIS‐IPMadridSpain
- CIBER de Enfermedades Cardiovasculares (CIBERCV)MadridSpain
| | - Joaquin Otón
- Structural Studies DivisionMRC Laboratory of Molecular BiologyCambridgeUK
- ALBA Synchrotron Light SourceBarcelonaSpain
| | - Alvaro Serrano
- Area of Vascular Pathophysiology, Laboratory of Intercellular CommunicationFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Rocio Tarifa
- Laboratory of Cardiovascular ProteomicsFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Montserrat Arroyo
- Immunology ServiceHospital Universitario de la Princesa, UAM, IIS‐IPMadridSpain
| | | | | | - Jesus Vázquez
- Laboratory of Cardiovascular ProteomicsFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
- CIBER de Enfermedades Cardiovasculares (CIBERCV)MadridSpain
| | - José M. Valpuesta
- Department of Macromolecular StructureCentro Nacional de Biotecnología (CNB‐CSIC)MadridSpain
| | - Francisco Sánchez‐Madrid
- Immunology ServiceHospital Universitario de la Princesa, UAM, IIS‐IPMadridSpain
- Area of Vascular Pathophysiology, Laboratory of Intercellular CommunicationFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
- CIBER de Enfermedades Cardiovasculares (CIBERCV)MadridSpain
| | - Noa B. Martín‐Cófreces
- Immunology ServiceHospital Universitario de la Princesa, UAM, IIS‐IPMadridSpain
- Area of Vascular Pathophysiology, Laboratory of Intercellular CommunicationFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
- CIBER de Enfermedades Cardiovasculares (CIBERCV)MadridSpain
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6
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Chevrier DM, Juhin A, Menguy N, Bolzoni R, Soto-Rodriguez PED, Kojadinovic-Sirinelli M, Paterson GA, Belkhou R, Williams W, Skouri-Panet F, Kosta A, Le Guenno H, Pereiro E, Faivre D, Benzerara K, Monteil CL, Lefevre CT. Collective magnetotaxis of microbial holobionts is optimized by the three-dimensional organization and magnetic properties of ectosymbionts. Proc Natl Acad Sci U S A 2023; 120:e2216975120. [PMID: 36848579 PMCID: PMC10013862 DOI: 10.1073/pnas.2216975120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/17/2023] [Indexed: 03/01/2023] Open
Abstract
Over the last few decades, symbiosis and the concept of holobiont-a host entity with a population of symbionts-have gained a central role in our understanding of life functioning and diversification. Regardless of the type of partner interactions, understanding how the biophysical properties of each individual symbiont and their assembly may generate collective behaviors at the holobiont scale remains a fundamental challenge. This is particularly intriguing in the case of the newly discovered magnetotactic holobionts (MHB) whose motility relies on a collective magnetotaxis (i.e., a magnetic field-assisted motility guided by a chemoaerotaxis system). This complex behavior raises many questions regarding how magnetic properties of symbionts determine holobiont magnetism and motility. Here, a suite of light-, electron- and X-ray-based microscopy techniques [including X-ray magnetic circular dichroism (XMCD)] reveals that symbionts optimize the motility, the ultrastructure, and the magnetic properties of MHBs from the microscale to the nanoscale. In the case of these magnetic symbionts, the magnetic moment transferred to the host cell is in excess (102 to 103 times stronger than free-living magnetotactic bacteria), well above the threshold for the host cell to gain a magnetotactic advantage. The surface organization of symbionts is explicitly presented herein, depicting bacterial membrane structures that ensure longitudinal alignment of cells. Magnetic dipole and nanocrystalline orientations of magnetosomes were also shown to be consistently oriented in the longitudinal direction, maximizing the magnetic moment of each symbiont. With an excessive magnetic moment given to the host cell, the benefit provided by magnetosome biomineralization beyond magnetotaxis can be questioned.
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Affiliation(s)
- Daniel M. Chevrier
- Aix-Marseille Université, Centre national de la recherche scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UMR7265, Bioscience and biotechnology institute of Aix-Marseille (BIAM), Saint-Paul-lez-Durance13108, France
| | - Amélie Juhin
- Sorbonne Université, UMR CNRS 7590, Muséum national d'Histoire naturelle (MNHN), Institut de recherche pour le développement (IRD), Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 75005Paris, France
| | - Nicolas Menguy
- Sorbonne Université, UMR CNRS 7590, Muséum national d'Histoire naturelle (MNHN), Institut de recherche pour le développement (IRD), Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 75005Paris, France
| | - Romain Bolzoni
- Aix-Marseille Université, Centre national de la recherche scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UMR7265, Bioscience and biotechnology institute of Aix-Marseille (BIAM), Saint-Paul-lez-Durance13108, France
| | - Paul E. D. Soto-Rodriguez
- Aix-Marseille Université, Centre national de la recherche scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UMR7265, Bioscience and biotechnology institute of Aix-Marseille (BIAM), Saint-Paul-lez-Durance13108, France
| | - Mila Kojadinovic-Sirinelli
- Aix-Marseille Université, Centre national de la recherche scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UMR7265, Bioscience and biotechnology institute of Aix-Marseille (BIAM), Saint-Paul-lez-Durance13108, France
| | - Greig A. Paterson
- Department of Earth, Ocean and Ecological Sciences, University of Liverpool, L69 7ZELiverpool, UK
| | - Rachid Belkhou
- Synchrotron Soleil, L'Orme des Merisiers, 91192Gif-sur-Yvette Cedex, France
| | - Wyn Williams
- School of GeoSciences, Grant Institute, University of Edinburgh, EdinburghEH9 3JW, UK
| | - Fériel Skouri-Panet
- Sorbonne Université, UMR CNRS 7590, Muséum national d'Histoire naturelle (MNHN), Institut de recherche pour le développement (IRD), Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 75005Paris, France
| | - Artemis Kosta
- Plateforme de Microscopie de l'Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, FR3479, Campus CNRS, 13402Marseille cedex 20, France
| | - Hugo Le Guenno
- Plateforme de Microscopie de l'Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, FR3479, Campus CNRS, 13402Marseille cedex 20, France
| | - Eva Pereiro
- ALBA Synchrotron Light Source, Cerdanyola del Vallés, Barcelona08290, Spain
| | - Damien Faivre
- Aix-Marseille Université, Centre national de la recherche scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UMR7265, Bioscience and biotechnology institute of Aix-Marseille (BIAM), Saint-Paul-lez-Durance13108, France
| | - Karim Benzerara
- Sorbonne Université, UMR CNRS 7590, Muséum national d'Histoire naturelle (MNHN), Institut de recherche pour le développement (IRD), Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 75005Paris, France
| | - Caroline L. Monteil
- Aix-Marseille Université, Centre national de la recherche scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UMR7265, Bioscience and biotechnology institute of Aix-Marseille (BIAM), Saint-Paul-lez-Durance13108, France
| | - Christopher T. Lefevre
- Aix-Marseille Université, Centre national de la recherche scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UMR7265, Bioscience and biotechnology institute of Aix-Marseille (BIAM), Saint-Paul-lez-Durance13108, France
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7
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Cossa A, Trépout S, Wien F, Groen J, Le Brun E, Turbant F, Besse L, Pereiro E, Arluison V. Cryo soft X-ray tomography to explore Escherichia coli nucleoid remodeling by Hfq master regulator. J Struct Biol 2022; 214:107912. [PMID: 36283630 DOI: 10.1016/j.jsb.2022.107912] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/28/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022]
Abstract
The bacterial chromosomic DNA is packed within a membrane-less structure, the nucleoid, due to the association of DNA with proteins called Nucleoid Associated Proteins (NAPs). Among these NAPs, Hfq is one of the most intriguing as it plays both direct and indirect roles on DNA structure. Indeed, Hfq is best known to mediate post-transcriptional regulation by using small noncoding RNA (sRNA). Although Hfq presence in the nucleoid has been demonstrated for years, its precise role is still unclear. Recently, it has been shown in vitro that Hfq forms amyloid-like structures through its C-terminal region, hence belonging to the bridging family of NAPs. Here, using cryo soft X-ray tomography imaging of native unlabeled cells and using a semi-automatic analysis and segmentation procedure, we show that Hfq significantly remodels the Escherichia coli nucleoid. More specifically, Hfq influences nucleoid density especially during the stationary growth phase when it is more abundant. Our results indicate that Hfq could regulate nucleoid compaction directly via its interaction with DNA, but also at the post-transcriptional level via its interaction with RNAs. Taken together, our findings reveal a new role for this protein in nucleoid remodeling in vivo, that may serve in response to stress conditions and in adapting to changing environments.
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Affiliation(s)
- Antoine Cossa
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France; Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Sylvain Trépout
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France; Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria 3800, Australia.
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
| | - Johannes Groen
- Mistral Beamline, Alba Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain
| | - Etienne Le Brun
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Laetitia Besse
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France
| | - Eva Pereiro
- Mistral Beamline, Alba Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; Université Paris Cité, UFR Sciences du vivant, 75006 Paris cedex, France.
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8
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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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9
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Sun R, Wang Y, Zhang J, Deng T, Yi Q, Yu B, Huang M, Li G, Jiang X. Synchrotron radiation X-ray imaging with large field of view and high resolution using micro-scanning method. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:1241-1250. [PMID: 36073883 PMCID: PMC9455207 DOI: 10.1107/s1600577522007652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
In synchrotron radiation X-ray imaging, the imaging field of view and spatial resolution are mutually restricted, which makes it impossible to have both a large field of view and high resolution when carrying out experiments. Constructing an oversampled image through the micro-scanning method and using the deconvolution algorithm to eliminate the point spread function introduced by pixel overlap can increase the resolution under a fixed imaging field of view, thereby improving the ratio of the field of view to the spatial resolution. In this paper, numerical simulation and synchrotron radiation experiments are carried out with a different number of micro-scanning steps. In numerical simulation experiments only affected by the image pixel size, as the number of micro-scanning steps increases, the ability of the oversampled image with deconvolution to improve the resolution is stronger. The achievable resolution of the oversampled image with deconvolution is basically the same as that of the sample image. In the synchrotron radiation experiments, the resolution of the oversampled image with deconvolution in the 2 × 2 mode is significantly improved. However, as the number of micro-scanning steps increases, the resolution improvement is limited, or even no longer improved. Finally, by analyzing the results of numerical simulation and synchrotron radiation experiments, three factors (four other factors affecting the resolution besides the camera resolution, translational accuracy of micro-scanning, and the signal-to-noise ratio of projections) affecting the micro-scanning method are proposed and verified by experiments.
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Affiliation(s)
- Rui Sun
- Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
| | - Yanping Wang
- Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
| | - Jie Zhang
- Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
| | - Tijian Deng
- Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
| | - Qiru Yi
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
| | - Bei Yu
- Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
| | - Mei Huang
- Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
| | - Gang Li
- Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
| | - Xiaoming Jiang
- Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
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10
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Linklater DP, Le Guével X, Bryant G, Baulin VA, Pereiro E, Perera PGT, Wandiyanto JV, Juodkazis S, Ivanova EP. Lethal Interactions of Atomically Precise Gold Nanoclusters and Pseudomonas aeruginosa and Staphylococcus aureus Bacterial Cells. ACS APPLIED MATERIALS & INTERFACES 2022; 14:32634-32645. [PMID: 35758190 DOI: 10.1021/acsami.2c04410] [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] [Indexed: 06/15/2023]
Abstract
Ultrasmall metal nanoclusters (NCs) are employed in an array of diagnostic and therapeutic applications due to their tunable photoluminescence, high biocompatibility, polyvalent effect, ease of modification, and photothermal stability. However, gold nanoclusters' (AuNCs') intrinsically antimicrobial properties remain poorly explored and are not well understood. Here, we share an insight into the antimicrobial action of atomically precise AuNCs based on their ability to passively translocate across the bacterial membrane. Functionalized by a hydrophilic modified-bidentate sulfobetaine zwitterionic molecule (AuNC-ZwBuEt) or a more hydrophobic monodentate-thiolate, mercaptohexanoic acid (AuNC-MHA) molecule, 2 nm AuNCs were lethal to both Gram-negative Pseudomonas aeruginosa and Gram-positive Staphylococcus aureus bacteria. The bactericidal efficiency was found to be bacterial strain-, time-, and concentration-dependent. The direct visualizations of the translocation of AuNCs and AuNC-cell and subcellular interactions were investigated using cryo-soft X-ray nano-tomography, transmission electron microscopy (TEM), and scanning TEM energy-dispersive spectroscopy analyses. AuNC-MHA were identified in the bacterial cytoplasm within 30 min, without evidence of the loss of membrane integrity. It is proposed that the bactericidal effect of AuNCs is attributed to their size, which allows for efficient energy-independent translocation across the cell membrane. The internalization of both AuNCs caused massive internal damage to the cells, including collapsed subcellular structures and altered cell morphology, leading to the eventual loss of cellular integrity.
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Affiliation(s)
- Denver P Linklater
- STEM College, School of Science, RMIT University, Melbourne, Victoria 3001, Australia
| | - Xavier Le Guével
- Cancer Targets and Experimental Therapeutics, Institute for Advanced Biosciences, University of Grenoble Alpes, Site Santé─Allée des Alpes, La Tronche 38700, France
| | - Gary Bryant
- STEM College, School of Science, RMIT University, Melbourne, Victoria 3001, Australia
| | - Vladimir A Baulin
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, C/ Marcel.lí Domingo s/n, Tarragona 43007, Spain
| | - Eva Pereiro
- MISTRAL Beamline-Experiments Division, ALBA Synchrotron Light Source, Cerdanyola del Vallès 08290, Barcelona, Spain
| | | | - Jason V Wandiyanto
- Optical Sciences Centre, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
| | - Saulius Juodkazis
- Optical Sciences Centre, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
| | - Elena P Ivanova
- STEM College, School of Science, RMIT University, Melbourne, Victoria 3001, Australia
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11
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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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12
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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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13
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Perez-Berna AJ, Benseny-Cases N, Rodríguez MJ, Valcarcel R, Carrascosa JL, Gastaminza P, Pereiro E. Monitoring reversion of hepatitis C virus-induced cellular alterations by direct-acting antivirals using cryo soft X-ray tomography and infrared microscopy. Acta Crystallogr D Struct Biol 2021; 77:1365-1377. [PMID: 34726165 PMCID: PMC8561738 DOI: 10.1107/s2059798321009955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/24/2021] [Indexed: 01/01/2023] Open
Abstract
Hepatitis C virus (HCV) is an enveloped RNA virus. One of the hallmarks of HCV infection is a rearrangement of the host cell membranes, known as the `membranous web'. Full-field cryo soft X-ray tomography (cryo-SXT) in the water-window energy range (284-543 eV) was performed on the MISTRAL beamline to investigate, in whole unstained cells, the morphology of the membranous rearrangements induced in HCV replicon-harbouring cells in conditions close to the living physiological state. All morphological alterations could be reverted by a combination of sofosbuvir/daclatasvir, which are clinically approved antivirals (direct-acting antivirals; DAAs) for HCV infection. Correlatively combining cryo-SXT and 2D synchrotron-based infrared microscopy provides critical information on the chemical nature of specific infection-related structures, which allows specific patterns of the infection process or the DAA-mediated healing process to be distinguished.
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Affiliation(s)
- Ana J. Perez-Berna
- ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Valles, Spain
| | - Nuria Benseny-Cases
- ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Valles, Spain
| | - María José Rodríguez
- Centro Nacional de Biotecnología, Campus de Cantoblanco, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ricardo Valcarcel
- ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Valles, Spain
| | - José L. Carrascosa
- Centro Nacional de Biotecnología, Campus de Cantoblanco, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo Gastaminza
- Centro Nacional de Biotecnología, Campus de Cantoblanco, Universidad Autónoma de Madrid, Madrid, Spain
| | - Eva Pereiro
- ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Valles, Spain
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14
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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:v13112109. [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.)
| | - Ana Joaquina Pérez-Berna
- ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain; (D.G.); (B.M.C.); (E.P.)
- Correspondence: ; Tel.: +34-93-592-4371
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15
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Sorrentino A, Malucelli E, Rossi F, Cappadone C, Farruggia G, Moscheni C, Perez-Berna AJ, Conesa JJ, Colletti C, Roveri N, Pereiro E, Iotti S. Calcite as a Precursor of Hydroxyapatite in the Early Biomineralization of Differentiating Human Bone-Marrow Mesenchymal Stem Cells. Int J Mol Sci 2021; 22:ijms22094939. [PMID: 34066542 PMCID: PMC8125725 DOI: 10.3390/ijms22094939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 02/03/2023] Open
Abstract
Biomineralization is the process by which living organisms generate organized mineral crystals. In human cells, this phenomenon culminates with the formation of hydroxyapatite, which is a naturally occurring mineral form of calcium apatite. The mechanism that explains the genesis within the cell and the propagation of the mineral in the extracellular matrix still remains largely unexplained, and its characterization is highly controversial, especially in humans. In fact, up to now, biomineralization core knowledge has been provided by investigations on the advanced phases of this process. In this study, we characterize the contents of calcium depositions in human bone mesenchymal stem cells exposed to an osteogenic cocktail for 4 and 10 days using synchrotron-based cryo-soft-X-ray tomography and cryo-XANES microscopy. The reported results suggest crystalline calcite as a precursor of hydroxyapatite depositions within the cells in the biomineralization process. In particular, both calcite and hydroxyapatite were detected within the cell during the early phase of osteogenic differentiation. This striking finding may redefine most of the biomineralization models published so far, taking into account that they have been formulated using murine samples while studies in human cell lines are still scarce.
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Affiliation(s)
- Andrea Sorrentino
- Mistral Beamline, ALBA Synchrotron Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain; (A.S.); (A.J.P.-B.); (J.J.C.); (E.P.)
| | - Emil Malucelli
- Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy; (F.R.); (C.C.); (G.F.); (S.I.)
- Correspondence:
| | - Francesca Rossi
- Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy; (F.R.); (C.C.); (G.F.); (S.I.)
| | - Concettina Cappadone
- Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy; (F.R.); (C.C.); (G.F.); (S.I.)
| | - Giovanna Farruggia
- Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy; (F.R.); (C.C.); (G.F.); (S.I.)
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
| | - Claudia Moscheni
- Department of Biomedical and Clinical Sciences “Luigi Sacco”, Università degli Studi di Milano, 20157 Milan, Italy;
| | - Ana J. Perez-Berna
- Mistral Beamline, ALBA Synchrotron Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain; (A.S.); (A.J.P.-B.); (J.J.C.); (E.P.)
| | - Jose Javier Conesa
- Mistral Beamline, ALBA Synchrotron Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain; (A.S.); (A.J.P.-B.); (J.J.C.); (E.P.)
| | - Chiara Colletti
- Chemical Center S.r.l, Granarolo dell’ Emilia, 40057 Bologna, Italy; (C.C.); (N.R.)
| | - Norberto Roveri
- Chemical Center S.r.l, Granarolo dell’ Emilia, 40057 Bologna, Italy; (C.C.); (N.R.)
| | - Eva Pereiro
- Mistral Beamline, ALBA Synchrotron Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain; (A.S.); (A.J.P.-B.); (J.J.C.); (E.P.)
| | - Stefano Iotti
- Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy; (F.R.); (C.C.); (G.F.); (S.I.)
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
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16
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Martin-Cofreces NB, Chichon FJ, Calvo E, Torralba D, Bustos-Moran E, Dosil SG, Rojas-Gomez A, Bonzon-Kulichenko E, Lopez JA, Otón J, Sorrentino A, Zabala JC, Vernos I, Vazquez J, Valpuesta JM, Sanchez-Madrid F. The chaperonin CCT controls T cell receptor-driven 3D configuration of centrioles. SCIENCE ADVANCES 2020; 6:eabb7242. [PMID: 33268369 PMCID: PMC7821906 DOI: 10.1126/sciadv.abb7242] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 10/19/2020] [Indexed: 05/17/2023]
Abstract
T lymphocyte activation requires the formation of immune synapses (IS) with antigen-presenting cells. The dynamics of membrane receptors, signaling scaffolds, microfilaments, and microtubules at the IS determine the potency of T cell activation and subsequent immune response. Here, we show that the cytosolic chaperonin CCT (chaperonin-containing TCP1) controls the changes in reciprocal orientation of the centrioles and polarization of the tubulin dynamics induced by T cell receptor in T lymphocytes forming an IS. CCT also controls the mitochondrial ultrastructure and the metabolic status of T cells, regulating the de novo synthesis of tubulin as well as posttranslational modifications (poly-glutamylation, acetylation, Δ1 and Δ2) of αβ-tubulin heterodimers, fine-tuning tubulin dynamics. These changes ultimately determine the function and organization of the centrioles, as shown by three-dimensional reconstruction of resting and stimulated primary T cells using cryo-soft x-ray tomography. Through this mechanism, CCT governs T cell activation and polarity.
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Affiliation(s)
- N B Martin-Cofreces
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain.
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Spain
| | - F J Chichon
- Department of Macromolecular Structure, Computational Systems Biology Group, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| | - E Calvo
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Spain
- Laboratory of Cardiovascular Proteomics. Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - D Torralba
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - E Bustos-Moran
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - S G Dosil
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - A Rojas-Gomez
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - E Bonzon-Kulichenko
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Spain
- Laboratory of Cardiovascular Proteomics. Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - J A Lopez
- Laboratory of Cardiovascular Proteomics. Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - J Otón
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - A Sorrentino
- ALBA Synchrotron Light Source, Cerdanyola del Vallès, Barcelona 08290, Spain
| | - J C Zabala
- Departament of Molecular Biology, Facultad de Medicina, Universidad de Cantabria, Santander, 39005 Spain
| | - I Vernos
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona 08003, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - J Vazquez
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Spain
- Laboratory of Cardiovascular Proteomics. Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
| | - J M Valpuesta
- Department of Macromolecular Structure, Computational Systems Biology Group, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain.
| | - F Sanchez-Madrid
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006 Spain.
- Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029 Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Spain
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17
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Four-Dimensional Characterization of the Babesia divergens Asexual Life Cycle, from the Trophozoite to the Multiparasite Stage. mSphere 2020; 5:5/5/e00928-20. [PMID: 33055261 PMCID: PMC7565898 DOI: 10.1128/msphere.00928-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Babesiosis is a disease caused by intraerythrocytic Babesia parasites, which possess many clinical features that are similar to those of malaria. This worldwide disease is increasing in frequency and geographical range and has a significant impact on human and animal health. Babesia divergens is one of the species responsible for human and cattle babesiosis causing death unless treated promptly. When B. divergens infects its vertebrate hosts, it reproduces asexually within red blood cells. During its asexual life cycle, B. divergens builds a population of numerous intraerythrocytic (IE) parasites of difficult interpretation. This complex population is largely unexplored, and we have therefore combined three- and four-dimensional imaging techniques to elucidate the origin, architecture, and kinetics of IE parasites. Unveiling the nature of these parasites has provided a vision of the B. divergens asexual cycle in unprecedented detail and is a key step to develop control strategies against babesiosis. Babesia is an apicomplexan parasite of significance that causes the disease known as babesiosis in domestic and wild animals and in humans worldwide. Babesia infects vertebrate hosts and reproduces asexually by a form of binary fission within erythrocytes/red blood cells (RBCs), yielding a complex pleomorphic population of intraerythrocytic parasites. Seven of them, clearly visible in human RBCs infected with Babesia divergens, are considered the main forms and named single, double, and quadruple trophozoites, paired and double paired pyriforms, tetrad or Maltese Cross, and multiparasite stage. However, these main intraerythrocytic forms coexist with RBCs infected with transient parasite combinations of unclear origin and development. In fact, little is understood about how Babesia builds this complex population during its asexual life cycle. By combining cryo-soft X-ray tomography and video microscopy, main and transitory parasites were characterized in a native whole cellular context and at nanometric resolution. The architecture and kinetics of the parasite population was observed in detail and provide additional data to the previous B. divergens asexual life cycle model that was built on light microscopy. Importantly, the process of multiplication by binary fission, involving budding, was visualized in live parasites for the first time, revealing that fundamental changes in cell shape and continuous rounds of multiplication occur as the parasites go through their asexual multiplication cycle. A four-dimensional asexual life cycle model was built highlighting the origin of several transient morphological forms that, surprisingly, intersperse in a chronological order between one main stage and the next in the cycle. IMPORTANCE Babesiosis is a disease caused by intraerythrocytic Babesia parasites, which possess many clinical features that are similar to those of malaria. This worldwide disease is increasing in frequency and geographical range and has a significant impact on human and animal health. Babesia divergens is one of the species responsible for human and cattle babesiosis causing death unless treated promptly. When B. divergens infects its vertebrate hosts, it reproduces asexually within red blood cells. During its asexual life cycle, B. divergens builds a population of numerous intraerythrocytic (IE) parasites of difficult interpretation. This complex population is largely unexplored, and we have therefore combined three- and four-dimensional imaging techniques to elucidate the origin, architecture, and kinetics of IE parasites. Unveiling the nature of these parasites has provided a vision of the B. divergens asexual cycle in unprecedented detail and is a key step to develop control strategies against babesiosis.
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18
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Reineck P, Abraham AN, Poddar A, Shukla R, Abe H, Ohshima T, Gibson BC, Dekiwadia C, Conesa JJ, Pereiro E, Gelmi A, Bryant G. Multimodal Imaging and Soft X-Ray Tomography of Fluorescent Nanodiamonds in Cancer Cells. Biotechnol J 2020; 16:e2000289. [PMID: 32975037 DOI: 10.1002/biot.202000289] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/09/2020] [Indexed: 12/11/2022]
Abstract
Multimodal imaging promises to revolutionize the understanding of biological processes across scales in space and time by combining the strengths of multiple imaging techniques. Fluorescent nanodiamonds (FNDs) are biocompatible, chemically inert, provide high contrast in light- and electron-based microscopy, and are versatile optical quantum sensors. Here it is demonstrated that FNDs also provide high absorption contrast in nanoscale 3D soft X-ray tomograms with a resolution of 28 nm in all dimensions. Confocal fluorescence, atomic force, and scanning electron microscopy images of FNDs inside and on the surface of PC3 cancer cells with sub-micrometer precision are correlated. FNDs are found inside ≈1 µm sized vesicles present in the cytoplasm, providing direct evidence of the active uptake of bare FNDs by cancer cells. Imaging artefacts are quantified and separated from changes in cell morphology caused by sample preparation. These results demonstrate the utility of FNDs in multimodal imaging, contribute to the understanding of the fate of FNDs in cells, and open up new possibilities for biological imaging and sensing across the nano- and microscale.
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Affiliation(s)
- Philipp Reineck
- ARC Centre of Excellence for Nanoscale BioPhotonics, School of Science, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Amanda N Abraham
- ARC Centre of Excellence for Nanoscale BioPhotonics, School of Science, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Arpita Poddar
- Ian Potter NanoBiosensing Facility, NanoBiotechnology Research Laboratory (NBRL), School of Science, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Ravi Shukla
- Ian Potter NanoBiosensing Facility, NanoBiotechnology Research Laboratory (NBRL), School of Science, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Hiroshi Abe
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology, Takasaki, Gunma, 370-1292, Japan
| | - Takeshi Ohshima
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology, Takasaki, Gunma, 370-1292, Japan
| | - Brant C Gibson
- ARC Centre of Excellence for Nanoscale BioPhotonics, School of Science, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Chaitali Dekiwadia
- RMIT Microscopy and Microanalysis Facility (RMMF), RMIT University, Melbourne, Victoria, 3001, Australia
| | - José J Conesa
- ALBA Synchrotron Light Source, MISTRAL Beamline-Experiments division, Cerdanyola del Vallès, Barcelona, 08290, Spain
| | - Eva Pereiro
- ALBA Synchrotron Light Source, MISTRAL Beamline-Experiments division, Cerdanyola del Vallès, Barcelona, 08290, Spain
| | - Amy Gelmi
- Applied Chemistry and Environmental Science, School of Science, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Gary Bryant
- School of Science, RMIT University, Melbourne, Victoria, 3001, Australia
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19
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Hempel C, Kapishnikov S, Perez-Berna AJ, Werner S, Guttmann P, Pereiro E, Qvortrup K, Andresen TL. The need to freeze-Dehydration during specimen preparation for electron microscopy collapses the endothelial glycocalyx regardless of fixation method. Microcirculation 2020; 27:e12643. [PMID: 32542908 DOI: 10.1111/micc.12643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/25/2020] [Accepted: 06/06/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVE The endothelial glycocalyx covers the luminal surface of the endothelium and plays key roles in vascular function. Despite its biological importance, ideal visualization techniques are lacking. The current study aimed to improve the preservation and subsequent imaging quality of the endothelial glycocalyx. METHODS In mice, the endothelial glycocalyx was contrasted with a mixture of lanthanum and dysprosium (LaDy). Standard chemical fixation was compared with high-pressure frozen specimens processed with freeze substitution. Also, isolated brain microvessels and cultured endothelial cells were high-pressure frozen and by transmission soft x-rays, imaged under cryogenic conditions. RESULTS The endothelial glycocalyx was in some tissues significantly more voluminous from chemically fixed specimens compared with high-pressure frozen specimens. LaDy labeling introduced excessive absorption contrast, which impeded glycocalyx measurements in isolated brain microvessels when using transmission soft x-rays. In non-contrasted vessels, the glycocalyx was not resolved. LaDy-contrasted, cultured brain endothelial cells allowed to assess glycocalyx volume in vitro. CONCLUSIONS Both chemical and cryogenic fixation followed by dehydration lead to substantial collapse of the glycocalyx. Cryogenic fixation without freeze substitution could be a way forward although transmission soft x-ray tomography based solely on amplitude contrast seems unsuitable.
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Affiliation(s)
- Casper Hempel
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.,Centre for Medical Parasitology, Department for Clinical Microbiology, Copenhagen University Hospital, Copenhagen, Denmark.,Department for Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Kapishnikov
- Department X-Ray microscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany.,Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Stephan Werner
- Department X-Ray microscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
| | - Peter Guttmann
- Department X-Ray microscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
| | - Eva Pereiro
- MISTRAL Beamline-Experiments Division, ALBA Synchrotron Light Source, Barcelona, Spain
| | - Klaus Qvortrup
- Core Facility for Integrated Microscopy (CFIM), University of Copenhagen, Copenhagen, Denmark
| | - Thomas Lars Andresen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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20
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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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21
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Pereiro E. Correlative cryo-soft X-ray tomography of cells. Biophys Rev 2019; 11:529-530. [PMID: 31286400 PMCID: PMC6682186 DOI: 10.1007/s12551-019-00560-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 06/15/2019] [Indexed: 01/05/2023] Open
Affiliation(s)
- Eva Pereiro
- ALBA Synchhrotron, Carrer de la Llum 2-26, Cerdanyola del Vallès, 08290, Barcelona, Spain.
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22
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Groen J, Conesa JJ, Valcárcel R, Pereiro E. The cellular landscape by cryo soft X-ray tomography. Biophys Rev 2019; 11:611-619. [PMID: 31273607 PMCID: PMC6682196 DOI: 10.1007/s12551-019-00567-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 06/20/2019] [Indexed: 01/02/2023] Open
Abstract
Imaging techniques in structural cell biology are indispensable to understand cell organization and machinery. In this frame, cryo soft X-ray tomography (cryo-SXT), a synchrotron-based imaging technique, is used to analyze the ultrastructure of intact, cryo-preserved cells at nanometric spatial resolution bridging electron microscopy and visible light fluorescence. With their unique interaction with matter and high penetration depth, X-rays are a very useful and complementary source to obtain both high-resolution and quantitative information. In this review, we are elaborating a typical cryo correlative workflow at the Mistral Beamline at the Alba Synchrotron (Spain) with the goal of providing a cartographic description of the cell by cryo-SXT that illustrates the possibilities this technique brings for specific localization of cellular features, organelle organization, and particular events in specific structural cell biology research.
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Affiliation(s)
- J. Groen
- Mistral Beamline, Alba Light Source (Cells), Cerdanyola del Valles, 08290 Barcelona, Spain
| | - J. J. Conesa
- Mistral Beamline, Alba Light Source (Cells), Cerdanyola del Valles, 08290 Barcelona, Spain
- Department of Macromolecular Structures, Cantoblanco, 28049 Madrid, Spain
| | - R. Valcárcel
- Mistral Beamline, Alba Light Source (Cells), Cerdanyola del Valles, 08290 Barcelona, Spain
| | - E. Pereiro
- Mistral Beamline, Alba Light Source (Cells), Cerdanyola del Valles, 08290 Barcelona, Spain
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23
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Varsano N, Beghi F, Dadosh T, Elad N, Pereiro E, Haran G, Leiserowitz L, Addadi L. The Effect of the Phospholipid Bilayer Environment on Cholesterol Crystal Polymorphism. Chempluschem 2019; 84:338-344. [DOI: 10.1002/cplu.201800632] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 01/10/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Neta Varsano
- Department of Structural BiologyWeizmann Institute of Science 234 Herzl Street Rehovot Israel
| | - Fabio Beghi
- Department of ChemistryUniversità Degli Studi di Milano Italy
| | - Tali Dadosh
- Department of Chemical Research SupportWeizmann Institute of Science
| | - Nadav Elad
- Department of Chemical Research SupportWeizmann Institute of Science
| | - Eva Pereiro
- MISTRAL Beamline-Experiments DivisionALBA Synchrotron Light Source Cerdanyola del Valles 08290 Barcelona Spain
| | - Gilad Haran
- Department of Chemical & Biological PhysicsWeizmann Institute of Science
| | | | - Lia Addadi
- Department of Structural BiologyWeizmann Institute of Science 234 Herzl Street Rehovot Israel
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24
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Ekman A, Weinhardt V, Chen JH, McDermott G, Le Gros MA, Larabell C. PSF correction in soft X-ray tomography. J Struct Biol 2018; 204:9-18. [PMID: 29908247 DOI: 10.1016/j.jsb.2018.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/05/2018] [Accepted: 06/07/2018] [Indexed: 11/29/2022]
Abstract
In this article, we introduce a linear approximation of the forward model of soft X-ray tomography, such that the reconstruction is solvable by standard iterative schemes. This linear model takes into account the three-dimensional point spread function (PSF) of the optical system, which consequently enhances the reconstruction of data. The feasibility of the model is demonstrated on both simulated and experimental data, based on theoretically estimated and experimentally measured PSFs.
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Affiliation(s)
- Axel Ekman
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Venera Weinhardt
- Department of Anatomy, University of California, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jian-Hua Chen
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Gerry McDermott
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Mark A Le Gros
- Department of Anatomy, University of California, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Carolyn Larabell
- Department of Anatomy, University of California, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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25
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Cryo-soft X-ray tomography: using soft X-rays to explore the ultrastructure of whole cells. Emerg Top Life Sci 2018; 2:81-92. [PMID: 33525785 PMCID: PMC7289011 DOI: 10.1042/etls20170086] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 12/31/2022]
Abstract
Cryo-soft X-ray tomography is an imaging technique that addresses the need for mesoscale imaging of cellular ultrastructure of relatively thick samples without the need for staining or chemical modification. It allows the imaging of cellular ultrastructure to a resolution of 25–40 nm and can be used in correlation with other imaging modalities, such as electron tomography and fluorescence microscopy, to further enhance the information content derived from biological samples. An overview of the technique, discussion of sample suitability and information about sample preparation, data collection and data analysis is presented here. Recent developments and future outlook are also discussed.
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26
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Biochemistry of malaria parasite infected red blood cells by X-ray microscopy. Sci Rep 2017; 7:802. [PMID: 28400621 PMCID: PMC5429762 DOI: 10.1038/s41598-017-00921-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/16/2017] [Indexed: 01/17/2023] Open
Abstract
Red blood cells infected by the malaria parasite Plasmodium falciparum are correlatively imaged by tomography using soft X-rays as well as by scanning hard nano-X-ray beam to obtain fluorescence maps of various elements such as S and Fe. In this way one can deduce the amount of Fe bound either in hemoglobin or in hemozoin crystals in the digestive vacuole of the malaria parasite as well as determine the hemoglobin concentrations in the cytosols of the red blood cell and of the parasite. Fluorescence map of K shows that in the parasite’s schizont stage the K concentration in the red blood cell cytosol is diminished by a factor of seven relative to a pristine red blood cell but the total amount of K in the infected red blood cell is the same as in the pristine red blood cell.
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27
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Otón J, Pereiro E, Conesa JJ, Chichón FJ, Luque D, Rodríguez JM, Pérez-Berná AJ, Sorzano COS, Klukowska J, Herman GT, Vargas J, Marabini R, Carrascosa JL, Carazo JM. XTEND: Extending the depth of field in cryo soft X-ray tomography. Sci Rep 2017; 7:45808. [PMID: 28374769 PMCID: PMC5379191 DOI: 10.1038/srep45808] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 03/06/2017] [Indexed: 12/21/2022] Open
Abstract
We have developed a new data collection method and processing framework in full field cryo soft X-ray tomography to computationally extend the depth of field (DOF) of a Fresnel zone plate lens. Structural features of 3D-reconstructed eukaryotic cells that are affected by DOF artifacts in standard reconstruction are now recovered. This approach, based on focal series projections, is easily applicable with closed expressions to select specific data acquisition parameters.
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Affiliation(s)
- Joaquín Otón
- Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, Madrid, 28049, Spain
| | - Eva Pereiro
- ALBA Synchrotron Light Source, Cerdanyola del Vallès, Barcelona, 08290, Spain
| | - José J Conesa
- Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, Madrid, 28049, Spain
| | - Francisco J Chichón
- Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, Madrid, 28049, Spain
| | - Daniel Luque
- Centro Nacional de Microbiología, ISCIII, Majadahonda, Madrid, 28220, Spain
| | - Javier M Rodríguez
- Centro Nacional de Microbiología, ISCIII, Majadahonda, Madrid, 28220, Spain
| | - Ana J Pérez-Berná
- ALBA Synchrotron Light Source, Cerdanyola del Vallès, Barcelona, 08290, Spain
| | | | - Joanna Klukowska
- Department of Computer Science, The Graduate Center, City University of New York, NY 10016, USA
| | - Gabor T Herman
- Department of Computer Science, The Graduate Center, City University of New York, NY 10016, USA
| | - Javier Vargas
- Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, Madrid, 28049, Spain
| | - Roberto Marabini
- Escuela Politécnica Superior, Univ. Autónoma de Madrid, Cantoblanco, Madrid, 28049, Spain
| | - José L Carrascosa
- Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, Madrid, 28049, Spain.,Unidad Asociada CNB-Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia),Cantoblanco, Madrid, 28049, Spain
| | - José M Carazo
- Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, Madrid, 28049, Spain
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