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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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2
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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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3
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Scrimieri R, Locatelli L, Cazzaniga A, Cazzola R, Malucelli E, Sorrentino A, Iotti S, Maier JA. Ultrastructural features mirror metabolic derangement in human endothelial cells exposed to high glucose. Sci Rep 2023; 13:15133. [PMID: 37704683 PMCID: PMC10499809 DOI: 10.1038/s41598-023-42333-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023] Open
Abstract
High glucose-induced endothelial dysfunction is the early event that initiates diabetes-induced vascular disease. Here we employed Cryo Soft X-ray Tomography to obtain three-dimensional maps of high D-glucose-treated endothelial cells and their controls at nanometric spatial resolution. We then correlated ultrastructural differences with metabolic rewiring. While the total mitochondrial mass does not change, high D-glucose promotes mitochondrial fragmentation, as confirmed by the modulation of fission-fusion markers, and dysfunction, as demonstrated by the drop of membrane potential, the decreased oxygen consumption and the increased production of reactive oxygen species. The 3D ultrastructural analysis also indicates the accumulation of lipid droplets in cells cultured in high D-glucose. Indeed, because of the decrease of fatty acid β-oxidation induced by high D-glucose concentration, triglycerides are esterified into fatty acids and then stored into lipid droplets. We propose that the increase of lipid droplets represents an adaptive mechanism to cope with the overload of glucose and associated oxidative stress and metabolic dysregulation.
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Affiliation(s)
- Roberta Scrimieri
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20157, Milan, Italy.
| | - Laura Locatelli
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20157, Milan, Italy
| | - Alessandra Cazzaniga
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20157, Milan, Italy
| | - Roberta Cazzola
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20157, Milan, Italy
| | - Emil Malucelli
- Department of Pharmacy and Biotechnology, Università di Bologna, 40127, Bologna, Italy
| | - Andrea Sorrentino
- Mistral Beamline, ALBA Synchrotron Light Source, Cerdanyola del Valles, 08290, Barcelona, Spain
| | - Stefano Iotti
- Department of Pharmacy and Biotechnology, Università di Bologna, 40127, Bologna, Italy
- National Institute of Biostructures and Biosystems, Viale Delle Medaglie d'Oro 305, 00136, Rome, Italy
| | - Jeanette A Maier
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20157, Milan, Italy.
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Vijayakrishnan S. In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview. Subcell Biochem 2023; 106:3-36. [PMID: 38159222 DOI: 10.1007/978-3-031-40086-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Cryo-electron tomography (cryo-ET) has emerged as a powerful tool in structural biology to study viruses and is undergoing a resolution revolution. Enveloped viruses comprise several RNA and DNA pleomorphic viruses that are pathogens of clinical importance to humans and animals. Considerable efforts in cryogenic correlative light and electron microscopy (cryo-CLEM), cryogenic focused ion beam milling (cryo-FIB), and integrative structural techniques are helping to identify virus structures within cells leading to a rise of in situ discoveries shedding light on how viruses interact with their hosts during different stages of infection. This chapter reviews recent advances in the application of cryo-ET in imaging enveloped viruses and the structural and mechanistic insights revealed studying the viral infection cycle within their eukaryotic cellular hosts, with particular attention to viral entry, replication, assembly, and egress during infection.
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Affiliation(s)
- Swetha Vijayakrishnan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, Glasgow, Scotland, UK.
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5
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Duponchel S, Monnier L, Molle J, Bendridi N, Alam MR, Gaballah A, Grigorov B, Ivanov A, Schmiel M, Odenthal M, Ovize M, Rieusset J, Zoulim F, Bartosch B. Hepatitis C virus replication requires integrity of mitochondria-associated ER membranes. JHEP REPORTS : INNOVATION IN HEPATOLOGY 2022; 5:100647. [PMID: 36718430 PMCID: PMC9883273 DOI: 10.1016/j.jhepr.2022.100647] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022]
Abstract
Background & Aims Chronic HCV infection causes cellular stress, fibrosis and predisposes to hepatocarcinogenesis. Mitochondria play key roles in orchestrating stress responses by regulating bioenergetics, inflammation and apoptosis. To better understand the role of mitochondria in the viral life cycle and disease progression of chronic hepatitis C, we studied morphological and functional mitochondrial alterations induced by HCV using productively infected hepatoma cells and patient livers. Methods Biochemical and imaging assays were used to assess localization of cellular and viral proteins and mitochondrial functions in cell cultures and liver biopsies. Cyclophilin D (CypD) knockout was performed using CRISPR/Cas9 technology. Viral replication was quantified by quantitative reverse-transcription PCR and western blotting. Results Several HCV proteins were found to associate with mitochondria-associated endoplasmic reticulum (ER) membranes (MAMs), the points of contact between the ER and mitochondria. Downregulation of CypD, which is known to disrupt MAM integrity, reduced viral replication, suggesting that MAMs play an important role in the viral life cycle. This process was rescued by ectopic CypD expression. Furthermore, HCV proteins were found to associate with voltage dependent anion channel 1 (VDAC1) at MAMs and to reduce VDAC1 protein levels at MAMs in vitro and in patient biopsies. This association did not affect MAM-associated functions in glucose homeostasis and Ca2+ signaling. Conclusions HCV proteins associate specifically with MAMs and MAMs play an important role in viral replication. The association between viral proteins and MAMs did not impact Ca2+ signaling between the ER and mitochondria or glucose homeostasis. Whether additional functions of MAMs and/or VDAC are impacted by HCV and contribute to the associated pathology remains to be assessed. Impact and implications Hepatitis C virus infects the liver, where it causes inflammation, cell damage and increases the long-term risk of liver cancer. We show that several HCV proteins interact with mitochondria in liver cells and alter the composition of mitochondrial subdomains. Importantly, HCV requires the architecture of these mitochondrial subdomains to remain intact for efficient viral replication.
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Key Words
- CypD, cyclophilin D
- DMVs, double membrane vesicles
- EM, electron microscopy
- ER, endoplasmic reticulum
- Grp75, glucose-regulated protein 75
- HCC, hepatocellular carcinoma
- HCVcc, cell culture-derived HCV
- IP, immunoprecipitation
- IP3R1, inositol trisphosphate receptor 1
- KO, knockout
- MAMs, mitochondria-associated ER membranes
- MOI, multiplicity of infection
- OMM, outer mitochondrial membrane
- PLA, proximity ligation assay
- S1R, sigma 1 receptor
- VDAC, voltage-dependent anion channel
- dpi, days post infection
- fibrosis
- hepatitis C virus
- mitochondria-associated ER membranes
- voltage-dependent anion channel 1
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Affiliation(s)
- Sarah Duponchel
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69434, France
| | - Lea Monnier
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69434, France
| | - Jennifer Molle
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69434, France
| | - Nadia Bendridi
- Laboratoire CarMeN, INSERM U-1060, INRA U-1397, Université Lyon, Université Claude Bernard Lyon 1, Pierre Bénite, 69495, France
| | - Muhammad Rizwan Alam
- CarMeN Laboratory, Hôpital Louis Pradel, Hospices Civils de Lyon, Université de Lyon and Explorations Fonctionnelles Cardiovasculaires, INSERM U1060, Lyon, France
| | - Ahmed Gaballah
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69434, France,Microbiology Department, Medical Research Institute, Alexandria University, Egypt
| | - Boyan Grigorov
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69434, France
| | - Alexander Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Marcel Schmiel
- Institute of Pathology, University Hospital of Cologne and Center for Molecular Medicine (CMMC), University of Cologne, Germany
| | - Margarete Odenthal
- Institute of Pathology, University Hospital of Cologne and Center for Molecular Medicine (CMMC), University of Cologne, Germany
| | - Michel Ovize
- CarMeN Laboratory, Hôpital Louis Pradel, Hospices Civils de Lyon, Université de Lyon and Explorations Fonctionnelles Cardiovasculaires, INSERM U1060, Lyon, France
| | - Jennifer Rieusset
- Laboratoire CarMeN, INSERM U-1060, INRA U-1397, Université Lyon, Université Claude Bernard Lyon 1, Pierre Bénite, 69495, France
| | - Fabien Zoulim
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69434, France,Hospices Civils de Lyon, France
| | - Birke Bartosch
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, 69434, France,Corresponding author. Address: Cancer Research Center Lyon, 151 cours Albert Thomas, 69434 Lyon, France; Tel.: 0033472681975, fax: 0033472681971
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6
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Cao M, Zhang K, Zhang S, Wang Y, Chen C. Advanced Light Source Analytical Techniques for Exploring the Biological Behavior and Fate of Nanomedicines. ACS CENTRAL SCIENCE 2022; 8:1063-1080. [PMID: 36032763 PMCID: PMC9413437 DOI: 10.1021/acscentsci.2c00680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Indexed: 05/09/2023]
Abstract
Exploration of the biological behavior and fate of nanoparticles, as affected by the nanomaterial-biology (nano-bio) interaction, has become progressively critical for guiding the rational design and optimization of nanomedicines to minimize adverse effects, support clinical translation, and aid in evaluation by regulatory agencies. Because of the complexity of the biological environment and the dynamic variations in the bioactivity of nanomedicines, in-situ, label-free analysis of the transport and transformation of nanomedicines has remained a challenge. Recent improvements in optics, detectors, and light sources have allowed the expansion of advanced light source (ALS) analytical technologies to dig into the underexplored behavior and fate of nanomedicines in vivo. It is increasingly important to further develop ALS-based analytical technologies with higher spatial and temporal resolution, multimodal data fusion, and intelligent prediction abilities to fully unlock the potential of nanomedicines. In this Outlook, we focus on several selected ALS analytical technologies, including imaging and spectroscopy, and provide an overview of the emerging opportunities for their applications in the exploration of the biological behavior and fate of nanomedicines. We also discuss the challenges and limitations faced by current approaches and tools and the expectations for the future development of advanced light sources and technologies. Improved ALS imaging and spectroscopy techniques will accelerate a profound understanding of the biological behavior of new nanomedicines. Such advancements are expected to inspire new insights into nanomedicine research and promote the development of ALS capabilities and methods more suitable for nanomedicine evaluation with the goal of clinical translation.
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Affiliation(s)
- Mingjing Cao
- CAS
Key Laboratory for Biomedical Effects of Nanomedicines and Nanosafety
& CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Kai Zhang
- Beijing
Synchrotron Radiation Facility, Institute
of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Shuhan Zhang
- CAS
Key Laboratory for Biomedical Effects of Nanomedicines and Nanosafety
& CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Yaling Wang
- CAS
Key Laboratory for Biomedical Effects of Nanomedicines and Nanosafety
& CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- The
GBA National Institute for Nanotechnology Innovation, Guangzhou 510700, China
| | - Chunying Chen
- CAS
Key Laboratory for Biomedical Effects of Nanomedicines and Nanosafety
& CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- The
GBA National Institute for Nanotechnology Innovation, Guangzhou 510700, China
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7
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Castroflorio E, Pérez Berná AJ, López-Márquez A, Badosa C, Loza-Alvarez P, Roldán M, Jiménez-Mallebrera C. The Capillary Morphogenesis Gene 2 Triggers the Intracellular Hallmarks of Collagen VI-Related Muscular Dystrophy. Int J Mol Sci 2022; 23:ijms23147651. [PMID: 35886995 PMCID: PMC9322809 DOI: 10.3390/ijms23147651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022] Open
Abstract
Collagen VI-related disorders (COL6-RD) represent a severe form of congenital disease for which there is no treatment. Dominant-negative pathogenic variants in the genes encoding α chains of collagen VI are the main cause of COL6-RD. Here we report that patient-derived fibroblasts carrying a common single nucleotide variant mutation are unable to build the extracellular collagen VI network. This correlates with the intracellular accumulation of endosomes and lysosomes triggered by the increased phosphorylation of the collagen VI receptor CMG2. Notably, using a CRISPR-Cas9 gene-editing tool to silence the dominant-negative mutation in patients’ cells, we rescued the normal extracellular collagen VI network, CMG2 phosphorylation levels, and the accumulation of endosomes and lysosomes. Our findings reveal an unanticipated role of CMG2 in regulating endosomal and lysosomal homeostasis and suggest that mutated collagen VI dysregulates the intracellular environment in fibroblasts in collagen VI-related muscular dystrophy.
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Affiliation(s)
- Enrico Castroflorio
- ICFO-The Institute of Photonic Sciences, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Spain;
- Correspondence: (E.C.); (C.J.-M.)
| | | | - Arístides López-Márquez
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain; (A.L.-M.); (C.B.)
- Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain;
- Centro de Investigaciones Biomédicas en Red de Enfermedades Rara (CIBERER), 28029 Madrid, Spain
| | - Carmen Badosa
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain; (A.L.-M.); (C.B.)
- Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain;
| | - Pablo Loza-Alvarez
- ICFO-The Institute of Photonic Sciences, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Spain;
| | - Mónica Roldán
- Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain;
- Unitat de Microscòpia Confocal i Imatge Cellular, Servei de Medicina Genètica i Molecular, Institut Pediàtric de Malaties Rares (IPER), Hospital Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain
| | - Cecilia Jiménez-Mallebrera
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain; (A.L.-M.); (C.B.)
- Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain;
- Centro de Investigaciones Biomédicas en Red de Enfermedades Rara (CIBERER), 28029 Madrid, Spain
- Department of Genetics, University of Barcelona, 08028 Barcelona, Spain
- Correspondence: (E.C.); (C.J.-M.)
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Abstract
Nup98, an essential component of the nuclear pore that also participates in annulate lamella pore structures localized in the cytosol, is involved in hepatitis C virus (HCV) assembly. Here, we combined confocal microscopy and biochemical assays to study the interplay between Nup98, core (i.e., the HCV capsid protein), and viral genomes. Our results show that in HCV-infected cells, core protein is necessary and sufficient to induce relocalization of Nup98 from annulate lamellae to lipid droplet-apposed areas in which core/NS5A and HCV genomic RNA [(+)RNA] are clustered to promote viral assembly. Furthermore, we found that Nup98 interacts with HCV RNA and that upon Nup98 downregulation, the viral (+)RNA genome was specifically excluded from areas that contain active translating ribosomes and the core and NS5A proteins. Altogether, these results indicate that Nup98 is recruited by HCV core from annulate lamellae to viral assembly sites to locally increase the concentration of (+)RNA genome, which may favor its encapsidation into nascent virions.
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9
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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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10
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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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11
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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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12
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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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13
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Okolo CA, Kounatidis I, Groen J, Nahas KL, Balint S, Fish TM, Koronfel MA, Cortajarena AL, Dobbie IM, Pereiro E, Harkiolaki M. Sample preparation strategies for efficient correlation of 3D SIM and soft X-ray tomography data at cryogenic temperatures. Nat Protoc 2021; 16:2851-2885. [PMID: 33990802 DOI: 10.1038/s41596-021-00522-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 02/09/2021] [Indexed: 02/07/2023]
Abstract
3D correlative microscopy methods have revolutionized biomedical research, allowing the acquisition of multidimensional information to gain an in-depth understanding of biological systems. With the advent of relevant cryo-preservation methods, correlative imaging of cryogenically preserved samples has led to nanometer resolution imaging (2-50 nm) under harsh imaging regimes such as electron and soft X-ray tomography. These methods have now been combined with conventional and super-resolution fluorescence imaging at cryogenic temperatures to augment information content from a given sample, resulting in the immediate requirement for protocols that facilitate hassle-free, unambiguous cross-correlation between microscopes. We present here sample preparation strategies and a direct comparison of different working fiducialization regimes that facilitate 3D correlation of cryo-structured illumination microscopy and cryo-soft X-ray tomography. Our protocol has been tested at two synchrotron beamlines (B24 at Diamond Light Source in the UK and BL09 Mistral at ALBA in Spain) and has led to the development of a decision aid that facilitates experimental design with the strategic use of markers based on project requirements. This protocol takes between 1.5 h and 3.5 d to complete, depending on the cell populations used (adherent cells may require several days to grow on sample carriers).
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Affiliation(s)
- Chidinma A Okolo
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Ilias Kounatidis
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | | | - Kamal L Nahas
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.,Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Stefan Balint
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Thomas M Fish
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Mohamed A Koronfel
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Aitziber L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia San Sebastián, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Ian M Dobbie
- Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Eva Pereiro
- Beamline 09-MISTRAL, ALBA Synchrotron, Barcelona, Spain
| | - Maria Harkiolaki
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
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14
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Quantitative conversion of biomass in giant DNA virus infection. Sci Rep 2021; 11:5025. [PMID: 33658544 PMCID: PMC7930090 DOI: 10.1038/s41598-021-83547-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 02/03/2021] [Indexed: 01/08/2023] Open
Abstract
Bioconversion of organic materials is the foundation of many applications in chemical engineering, microbiology and biochemistry. Herein, we introduce a new methodology to quantitatively determine conversion of biomass in viral infections while simultaneously imaging morphological changes of the host cell. As proof of concept, the viral replication of an unidentified giant DNA virus and the cellular response of an amoebal host are studied using soft X-ray microscopy, titration dilution measurements and thermal gravimetric analysis. We find that virions produced inside the cell are visible from 18 h post infection and their numbers increase gradually to a burst size of 280–660 virions. Due to the large size of the virion and its strong X-ray absorption contrast, we estimate that the burst size corresponds to a conversion of 6–12% of carbonaceous biomass from amoebal host to virus. The occurrence of virion production correlates with the appearance of a possible viral factory and morphological changes in the phagosomes and contractile vacuole complex of the amoeba, whereas the nucleus and nucleolus appear unaffected throughout most of the replication cycle.
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15
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Bruno SR, Anathy V. Lung epithelial endoplasmic reticulum and mitochondrial 3D ultrastructure: a new frontier in lung diseases. Histochem Cell Biol 2021; 155:291-300. [PMID: 33598824 PMCID: PMC7889473 DOI: 10.1007/s00418-020-01950-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2020] [Indexed: 12/15/2022]
Abstract
It has long been appreciated that the endoplasmic reticulum (ER) and mitochondria, organelles important for regular cell function and survival, also play key roles in pathogenesis of various lung diseases, including asthma, fibrosis, and infections. Alterations in processes regulated within these organelles, including but not limited to protein folding in the ER and oxidative phosphorylation in the mitochondria, are important in disease pathogenesis. In recent years it has also become increasingly apparent that organelle structure dictates function. It is now clear that organelles must maintain precise organization and localization for proper function. Newer microscopy capabilities have allowed the scientific community to reveal, via 3D imaging, that the structure of these organelles and their interactions with each other are a main component of regulating function and, therefore, effects on the disease state. In this review, we will examine how 3D imaging through techniques could allow advancements in knowledge of how the ER and mitochondria function and the roles they may play in lung epithelia in progression of lung disease.
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Affiliation(s)
- Sierra R Bruno
- Department of Pathology and Laboratory Medicine, University of Vermont, Larner College of Medicine, 149 Beaumont Ave, Burlington, VT, 05405, USA
| | - Vikas Anathy
- Department of Pathology and Laboratory Medicine, University of Vermont, Larner College of Medicine, 149 Beaumont Ave, Burlington, VT, 05405, USA.
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16
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Zhang C, Yao S, Xu C, Chang Y, Zong Y, Zhang K, Zhang X, Zhang L, Chen C, Zhao Y, Jiang H, Gao X, Wang Y. 3D Imaging and Quantification of the Integrin at a Single-Cell Base on a Multisignal Nanoprobe and Synchrotron Radiation Soft X-ray Tomography Microscopy. Anal Chem 2020; 93:1237-1241. [DOI: 10.1021/acs.analchem.0c04662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Chunyu Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100090, China
- Department of Chemistry and Chemical Engineering, Beijing University of Technology, Beijing 100124, China
| | - Shengkun Yao
- School of Physical Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Shandong Provincial Engineering and Technical Center of Light Manipulations & Shandong Provincial Key Laboratory of Optics and Photonic Device, School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Chao Xu
- College of Chemistry and Material Science, Shandong Agricultural University, Tai’an 271018, China
| | - Yanan Chang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Yunbing Zong
- School of Physical Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Kai Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangzhi Zhang
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lijuan Zhang
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100090, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100090, China
| | - Huaidong Jiang
- School of Physical Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Xueyun Gao
- Department of Chemistry and Chemical Engineering, Beijing University of Technology, Beijing 100124, China
| | - Yaling Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100090, China
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17
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Tran HT, Tsai EHR, Lewis AJ, Moors T, Bol JGJM, Rostami I, Diaz A, Jonker AJ, Guizar-Sicairos M, Raabe J, Stahlberg H, van de Berg WDJ, Holler M, Shahmoradian SH. Alterations in Sub-Axonal Architecture Between Normal Aging and Parkinson's Diseased Human Brains Using Label-Free Cryogenic X-ray Nanotomography. Front Neurosci 2020; 14:570019. [PMID: 33324142 PMCID: PMC7724048 DOI: 10.3389/fnins.2020.570019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/14/2020] [Indexed: 01/25/2023] Open
Abstract
Gaining insight to pathologically relevant processes in continuous volumes of unstained brain tissue is important for a better understanding of neurological diseases. Many pathological processes in neurodegenerative disorders affect myelinated axons, which are a critical part of the neuronal circuitry. Cryo ptychographic X-ray computed tomography in the multi-keV energy range is an emerging technology providing phase contrast at high sensitivity, allowing label-free and non-destructive three dimensional imaging of large continuous volumes of tissue, currently spanning up to 400,000 μm3. This aspect makes the technique especially attractive for imaging complex biological material, especially neuronal tissues, in combination with downstream optical or electron microscopy techniques. A further advantage is that dehydration, additional contrast staining, and destructive sectioning/milling are not required for imaging. We have developed a pipeline for cryo ptychographic X-ray tomography of relatively large, hydrated and unstained biological tissue volumes beyond what is typical for the X-ray imaging, using human brain tissue and combining the technique with complementary methods. We present four imaged volumes of a Parkinson's diseased human brain and five volumes from a non-diseased control human brain using cryo ptychographic X-ray tomography. In both cases, we distinguish neuromelanin-containing neurons, lipid and melanic pigment, blood vessels and red blood cells, and nuclei of other brain cells. In the diseased sample, we observed several swellings containing dense granular material resembling clustered vesicles between the myelin sheaths arising from the cytoplasm of the parent oligodendrocyte, rather than the axoplasm. We further investigated the pathological relevance of such swollen axons in adjacent tissue sections by immunofluorescence microscopy for phosphorylated alpha-synuclein combined with multispectral imaging. Since cryo ptychographic X-ray tomography is non-destructive, the large dataset volumes were used to guide further investigation of such swollen axons by correlative electron microscopy and immunogold labeling post X-ray imaging, a possibility demonstrated for the first time. Interestingly, we find that protein antigenicity and ultrastructure of the tissue are preserved after the X-ray measurement. As many pathological processes in neurodegeneration affect myelinated axons, our work sets an unprecedented foundation for studies addressing axonal integrity and disease-related changes in unstained brain tissues.
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Affiliation(s)
| | | | - Amanda J. Lewis
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Tim Moors
- Department of Anatomy and Neurosciences, Section Clinical Neuroanatomy, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - J. G. J. M. Bol
- Department of Anatomy and Neurosciences, Section Clinical Neuroanatomy, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | - Ana Diaz
- Paul Scherrer Institut, Villigen, Switzerland
| | - Allert J. Jonker
- Department of Anatomy and Neurosciences, Section Clinical Neuroanatomy, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | - Joerg Raabe
- Paul Scherrer Institut, Villigen, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Wilma D. J. van de Berg
- Department of Anatomy and Neurosciences, Section Clinical Neuroanatomy, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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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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19
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Jamme F, Cinquin B, Gohon Y, Pereiro E, Réfrégiers M, Froissard M. Synchrotron multimodal imaging in a whole cell reveals lipid droplet core organization. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:772-778. [PMID: 32381780 PMCID: PMC7206545 DOI: 10.1107/s1600577520003847] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
A lipid droplet (LD) core of a cell consists mainly of neutral lipids, triacylglycerols and/or steryl esters (SEs). The structuration of these lipids inside the core is still under debate. Lipid segregation inside LDs has been observed but is sometimes suggested to be an artefact of LD isolation and chemical fixation. LD imaging in their native state and in unaltered cellular environments appears essential to overcome these possible technical pitfalls. Here, imaging techniques for ultrastructural study of native LDs in cellulo are provided and it is shown that LDs are organized structures. Cryo soft X-ray tomography and deep-ultraviolet (DUV) transmittance imaging are showing a partitioning of SEs at the periphery of the LD core. Furthermore, DUV transmittance and tryptophan/tyrosine auto-fluorescence imaging on living cells are combined to obtain complementary information on cell chemical contents. This multimodal approach paves the way for a new label-free organelle imaging technique in living cells.
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Affiliation(s)
- Frédéric Jamme
- DISCO Beamline, Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Bertrand Cinquin
- DISCO Beamline, Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Yann Gohon
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
| | - Eva Pereiro
- MISTRAL Beamline, ALBA Synchrotron, Cerdanyola del Vallès, Barcelona 08290, Spain
| | | | - Marine Froissard
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
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20
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Peng MW, Guan Y, Liu JH, Chen L, Wang H, Xie ZZ, Li HY, Chen YP, Liu P, Yan P, Guo JS, Liu G, Shen Y, Fang F. Quantitative three-dimensional nondestructive imaging of whole anaerobic ammonium-oxidizing bacteria. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:753-761. [PMID: 32381778 PMCID: PMC7285686 DOI: 10.1107/s1600577520002349] [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: 08/21/2019] [Accepted: 02/19/2020] [Indexed: 06/11/2023]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria play a key role in the global nitrogen cycle and in nitrogenous wastewater treatment. The anammox bacteria ultrastructure is unique and distinctly different from that of other prokaryotic cells. The morphological structure of an organism is related to its function; however, research on the ultrastructure of intact anammox bacteria is lacking. In this study, in situ three-dimensional nondestructive ultrastructure imaging of a whole anammox cell was performed using synchrotron soft X-ray tomography (SXT) and the total variation-based simultaneous algebraic reconstruction technique (TV-SART). Statistical and quantitative analyses of the intact anammox bacteria were performed. High soft X-ray absorption composition inside anammoxosome was detected and verified to be relevant to iron-binding protein. On this basis, the shape adaptation of the anammox bacteria response to iron was explored.
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Affiliation(s)
- Meng-Wen Peng
- Key Laboratory of the Three Gorges Reservoir Region’s Eco-Environments of MOE, Chongqing University, Chongqing 400045, People’s Republic of China
| | - Yong Guan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230026, People’s Republic of China
| | - Jian-Hong Liu
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230026, People’s Republic of China
| | - Liang Chen
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230026, People’s Republic of China
| | - Han Wang
- Key Laboratory of the Three Gorges Reservoir Region’s Eco-Environments of MOE, Chongqing University, Chongqing 400045, People’s Republic of China
| | - Zheng-Zhe Xie
- i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, People’s Republic of China
| | - Hai-Yan Li
- Key Laboratory of the Three Gorges Reservoir Region’s Eco-Environments of MOE, Chongqing University, Chongqing 400045, People’s Republic of China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region’s Eco-Environments of MOE, Chongqing University, Chongqing 400045, People’s Republic of China
| | - Peng Liu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, People’s Republic of China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region’s Eco-Environments of MOE, Chongqing University, Chongqing 400045, People’s Republic of China
| | - Jin-Song Guo
- Key Laboratory of the Three Gorges Reservoir Region’s Eco-Environments of MOE, Chongqing University, Chongqing 400045, People’s Republic of China
| | - Gang Liu
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230026, People’s Republic of China
| | - Yu Shen
- National Base of International Science and Technology Cooperation for Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, People’s Republic of China
| | - Fang Fang
- Key Laboratory of the Three Gorges Reservoir Region’s Eco-Environments of MOE, Chongqing University, Chongqing 400045, People’s Republic of China
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21
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Gil S, Solano E, Martínez-Trucharte F, Martínez-Esaín J, Pérez-Berná AJ, Conesa JJ, Kamma-Lorger C, Alsina M, Sabés M. Multiparametric analysis of the effectiveness of cisplatin on cutaneous squamous carcinoma cells using two different types of adjuvants. PLoS One 2020; 15:e0230022. [PMID: 32143211 PMCID: PMC7060073 DOI: 10.1371/journal.pone.0230022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/19/2020] [Indexed: 12/25/2022] Open
Abstract
The objective of this study was to regulate the cytotoxicity of cisplatin (cisPt) minimizing its adverse effects. For this purpose, the lowest cisPt concentration needed to obtain a significant positive response in cutaneous squamous cell carcinoma (cSCC) was explored. Two adjuvant agents as gold nanoparticles (AuNP) and chelating tricine were tested as enhancers in cisPt treatment. Effectiveness of all treatments was assessed by means of biochemical techniques, which offer quantitative data, as well as two microscopy–based techniques that provided qualitative cell imaging. The present work confirms the effectiveness of free cisplatin at very low concentrations. In order to enhance its effectiveness while the side effects were probably diminished, cisPt 3.5 μM was administered with AuNP 2.5 mM, showing an effectiveness practically equal to that observed with free cisPt. However, the second treatment investigated, based on cisPt 3.5 μM combined with tricine 50 mM, enhanced drug effectiveness, increasing the percentage of cells dying by apoptosis. This treatment was even better in terms of cell damage than free cisPt at 15 μM. Images obtained by TEM and cryo-SXT confirmed these results, since a notable number of apoptotic bodies were detected when cisPt was combined with tricine. Thus, tricine was clearly a better adjuvant for cisPt treatments.
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Affiliation(s)
- Silvia Gil
- Hospital Clínic de Barcelona, Barcelona, Spain
- Hospital Parc Taulí, Sabadell, Barcelona, Spain
- * E-mail:
| | | | | | | | | | | | - Christina Kamma-Lorger
- Australian Synchrotron–Australian Nuclear Science and Technology Organisation, Clayton, Victoria, Australia
| | | | - Manel Sabés
- ALBA Synchrotron Light Source, Barcelona, Spain
- Unitat de Biofísica, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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22
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Kepsutlu B, Wycisk V, Achazi K, Kapishnikov S, Pérez-Berná AJ, Guttmann P, Cossmer A, Pereiro E, Ewers H, Ballauff M, Schneider G, McNally JG. Cells Undergo Major Changes in the Quantity of Cytoplasmic Organelles after Uptake of Gold Nanoparticles with Biologically Relevant Surface Coatings. ACS NANO 2020; 14:2248-2264. [PMID: 31951375 DOI: 10.1021/acsnano.9b09264] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Here, we use cryo soft X-ray tomography (cryo-SXT), which delivers 3D ultrastructural volumes of intact cells without chemical fixation or staining, to gain insight about nanoparticle uptake for nanomedicine. We initially used dendritic polyglycerol sulfate (dPGS) with potential diagnostic and therapeutic applications in inflammation. Although dPGS-coated gold nanoparticle (dPGS-AuNP) uptake followed a conventional endocytic/degradative pathway in human lung epithelial cell lines (A549), with cryo-SXT, we detected ∼5% of dPGS-AuNPs in the cytoplasm, a level undetectable by confocal light microscopy. We also observed ∼5% of dPGS-AuNPs in a rarely identified subcellular site, namely, lipid droplets, which are important for cellular energy metabolism. Finally, we also found substantial changes in the quantity of cytoplasmic organelles upon dPGS-AuNP uptake over the 1-6 h incubation period; the number of small vesicles and mitochondria significantly increased, and the number of multivesicular bodies and the number and volume of lipid droplets significantly decreased. Although nearly all organelle numbers at 6 h were still significantly different from controls, most appeared to be returning to normal levels. To test for generality, we also examined cells after uptake of gold nanoparticles coated with a different agent, polyethylenimine (PEI), used for nucleic acid delivery. PEI nanoparticles did not enter lipid droplets, but they induced similar, albeit less pronounced, changes in the quantity of cytoplasmic organelles. We confirmed these changes in organelle quantities for both nanoparticle coatings by confocal fluorescence microscopy. We suggest this cytoplasmic remodeling could reflect a more common cellular response to coated gold nanoparticle uptake.
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Affiliation(s)
- Burcu Kepsutlu
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
| | - Virginia Wycisk
- Organische Chemie, Institut für Chemie und Biochemie , Freie Universität Berlin , Takustrasse 3 , D-14195 Berlin , Germany
| | - Katharina Achazi
- Organische Chemie, Institut für Chemie und Biochemie , Freie Universität Berlin , Takustrasse 3 , D-14195 Berlin , Germany
| | - Sergey Kapishnikov
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
| | - Ana Joaquina Pérez-Berná
- ALBA Synchrotron Light Source , MISTRAL Beamline Experiments Division , Cerdanyola del Vallès , 08290 Barcelona , Spain
| | - Peter Guttmann
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
| | - Antje Cossmer
- Division 1.1 - Inorganic Trace Analysis , Federal Institute for Materials Research and Testing (BAM) , Richard-Willstätter-Str. 11 , 12489 Berlin , Germany
| | - Eva Pereiro
- ALBA Synchrotron Light Source , MISTRAL Beamline Experiments Division , Cerdanyola del Vallès , 08290 Barcelona , Spain
| | - Helge Ewers
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
- Institute of Chemistry and Biochemisty, Department of Biology, Chemistry and Pharmacy , Freie Universität Berlin , Thielallee 63 , 14195 Berlin , Germany
| | - Matthias Ballauff
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
- Institute of Physics , Humboldt Universität zu Berlin , Newtonstraße 15 , 12489 Berlin , Germany
| | - Gerd Schneider
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
- Institute of Physics , Humboldt Universität zu Berlin , Newtonstraße 15 , 12489 Berlin , Germany
| | - James G McNally
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
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23
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Poddar A, Conesa JJ, Liang K, Dhakal S, Reineck P, Bryant G, Pereiro E, Ricco R, Amenitsch H, Doonan C, Mulet X, Doherty CM, Falcaro P, Shukla R. Encapsulation, Visualization and Expression of Genes with Biomimetically Mineralized Zeolitic Imidazolate Framework-8 (ZIF-8). SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1902268. [PMID: 31259481 DOI: 10.1002/smll.201902268] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/07/2019] [Indexed: 06/09/2023]
Abstract
Recent work in biomolecule-metal-organic framework (MOF) composites has proven to be an effective strategy for the protection of proteins. However, for other biomacromolecules such as nucleic acids, the encapsulation into nano MOFs and the related characterizations are in their infancy. Herein, encapsulation of a complete gene-set in zeolitic imidazolate framework-8 (ZIF-8) MOFs and cellular expression of the gene delivered by the nano MOF composites are reported. Using a green fluorescent protein (GFP) plasmid (plGFP) as a proof-of-concept genetic macromolecule, successful transfection of mammalian cancer cells with plGFP for up to 4 days is shown. Cell transfection assays and soft X-ray cryo-tomography (cryo-SXT) demonstrate the feasibility of DNA@MOF biocomposites as intracellular gene delivery vehicles. Expression occurs over relatively prolonged time points where the cargo nucleic acid is released gradually in order to maintain sustained expression.
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Affiliation(s)
- Arpita Poddar
- Ian Potter NanoBiosensing Facility, NanoBiotechnology Research Laboratory (NBRL), School of Science, RMIT University, Melbourne, Victoria, 3001, Australia
- CSIRO Manufacturing, Clayton, Victoria, 3168, Australia
| | - José J Conesa
- ALBA Synchrotron Light Source, MISTRAL Beamline - Experiments division. Cerdanyola del Vallès, Barcelona, 08290, Spain
| | - Kang Liang
- School of Chemical Engineering and Graduate School of Biomedical Engineering, University of New South Wales, Library Road, Kensington, Sydney, NSW, 2052, Australia
| | - Sudip Dhakal
- Ian Potter NanoBiosensing Facility, NanoBiotechnology Research Laboratory (NBRL), School of Science, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Philipp Reineck
- ARC Centre of Excellence for Nanoscale BioPhotonics, School of Science, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Gary Bryant
- Centre for Molecular and Nanoscale Physics, School of Science, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Eva Pereiro
- ALBA Synchrotron Light Source, MISTRAL Beamline - Experiments division. Cerdanyola del Vallès, Barcelona, 08290, Spain
| | - Raffaele Ricco
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, 8010, Graz, Austria
| | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, 8010, Graz, Austria
| | - Christian Doonan
- Department of Chemistry and the Centre for Advanced Nanomaterials, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Xavier Mulet
- CSIRO Manufacturing, Clayton, Victoria, 3168, Australia
| | | | - Paolo Falcaro
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, 8010, Graz, Austria
| | - Ravi Shukla
- Ian Potter NanoBiosensing Facility, NanoBiotechnology Research Laboratory (NBRL), School of Science, RMIT University, Melbourne, Victoria, 3001, Australia
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24
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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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25
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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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26
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Weinhardt V, Chen JH, Ekman A, McDermott G, Le Gros MA, Larabell C. Imaging cell morphology and physiology using X-rays. Biochem Soc Trans 2019; 47:489-508. [PMID: 30952801 PMCID: PMC6716605 DOI: 10.1042/bst20180036] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 01/02/2019] [Accepted: 01/09/2019] [Indexed: 02/07/2023]
Abstract
Morphometric measurements, such as quantifying cell shape, characterizing sub-cellular organization, and probing cell-cell interactions, are fundamental in cell biology and clinical medicine. Until quite recently, the main source of morphometric data on cells has been light- and electron-based microscope images. However, many technological advances have propelled X-ray microscopy into becoming another source of high-quality morphometric information. Here, we review the status of X-ray microscopy as a quantitative biological imaging modality. We also describe the combination of X-ray microscopy data with information from other modalities to generate polychromatic views of biological systems. For example, the amalgamation of molecular localization data, from fluorescence microscopy or spectromicroscopy, with structural information from X-ray tomography. This combination of data from the same specimen generates a more complete picture of the system than that can be obtained by a single microscopy method. Such multimodal combinations greatly enhance our understanding of biology by combining physiological and morphological data to create models that more accurately reflect the complexities of life.
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Affiliation(s)
- Venera Weinhardt
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Anatomy, University of California San Francisco, San Francisco, California, U.S.A
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Axel Ekman
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Gerry McDermott
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Mark A Le Gros
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Anatomy, University of California San Francisco, San Francisco, California, U.S.A
| | - Carolyn Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A.
- Department of Anatomy, University of California San Francisco, San Francisco, California, U.S.A
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27
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Mingorance L, Castro V, Ávila-Pérez G, Calvo G, Rodriguez MJ, Carrascosa JL, Pérez-del-Pulgar S, Forns X, Gastaminza P. Host phosphatidic acid phosphatase lipin1 is rate limiting for functional hepatitis C virus replicase complex formation. PLoS Pathog 2018; 14:e1007284. [PMID: 30226904 PMCID: PMC6161900 DOI: 10.1371/journal.ppat.1007284] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 09/28/2018] [Accepted: 08/14/2018] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) infection constitutes a significant health burden worldwide, because it is a major etiologic agent of chronic liver disease, cirrhosis and hepatocellular carcinoma. HCV replication cycle is closely tied to lipid metabolism and infection by this virus causes profound changes in host lipid homeostasis. We focused our attention on a phosphatidate phosphate (PAP) enzyme family (the lipin family), which mediate the conversion of phosphatidate to diacylglycerol in the cytoplasm, playing a key role in triglyceride biosynthesis and in phospholipid homeostasis. Lipins may also translocate to the nucleus to act as transcriptional regulators of genes involved in lipid metabolism. The best-characterized member of this family is lipin1, which cooperates with lipin2 to maintain glycerophospholipid homeostasis in the liver. Lipin1-deficient cell lines were generated by RNAi to study the role of this protein in different steps of HCV replication cycle. Using surrogate models that recapitulate different aspects of HCV infection, we concluded that lipin1 is rate limiting for the generation of functional replicase complexes, in a step downstream primary translation that leads to early HCV RNA replication. Infection studies in lipin1-deficient cells overexpressing wild type or phosphatase-defective lipin1 proteins suggest that lipin1 phosphatase activity is required to support HCV infection. Finally, ultrastructural and biochemical analyses in replication-independent models suggest that lipin1 may facilitate the generation of the membranous compartment that contains functional HCV replicase complexes. Hepatitis C virus (HCV) infection is an important biomedical problem worldwide because it causes severe liver disease and cancer. Although immunological events are major players in HCV pathogenesis, interference with host cell metabolism contribute to HCV-associated pathologies. HCV utilizes resources of the cellular lipid metabolism to strongly modify subcellular compartments, using them as platforms for replication and infectious particle assembly. In particular, HCV induces the formation of a “membranous web” that hosts the viral machinery dedicated to the production of new copies of the viral genome. This lipid-rich structure provides an optimized platform for viral genome replication and hides new viral genomes from host´s antiviral surveillance. In this study, we have identified a cellular protein, lipin1, involved in the production of a subset of cellular lipids, as a rate-limiting factor for HCV infection. Our results indicate that the enzymatic activity of lipin1 is required to build the membranous compartment dedicated to viral genome replication. Lipin1 is probably contributing to the formation of the viral replication machinery by locally providing certain lipids required for an optimal membranous environment. Based on these results, interfering with lipin1 capacity to modify lipids may therefore constitute a potential strategy to limit HCV infection.
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Affiliation(s)
- Lidia Mingorance
- Department of Cellular and Molecular Biology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid (Spain)
| | - Victoria Castro
- Department of Cellular and Molecular Biology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid (Spain)
| | - Ginés Ávila-Pérez
- Department of Cellular and Molecular Biology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid (Spain)
| | - Gema Calvo
- Department of Cellular and Molecular Biology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid (Spain)
| | - María Josefa Rodriguez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid (Spain)
| | - José L. Carrascosa
- Department of Macromolecular Structures, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid (Spain)
| | - Sofía Pérez-del-Pulgar
- Liver Unit, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Consorcio Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universitat de Barcelona, Barcelona (Spain)
| | - Xavier Forns
- Liver Unit, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Consorcio Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universitat de Barcelona, Barcelona (Spain)
| | - Pablo Gastaminza
- Department of Cellular and Molecular Biology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid (Spain)
- Liver Unit, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Consorcio Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universitat de Barcelona, Barcelona (Spain)
- * E-mail:
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28
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Visualisation and analysis of hepatitis C virus non-structural proteins using super-resolution microscopy. Sci Rep 2018; 8:13604. [PMID: 30206266 PMCID: PMC6134135 DOI: 10.1038/s41598-018-31861-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 08/29/2018] [Indexed: 01/17/2023] Open
Abstract
Hepatitis C virus (HCV) RNA replication occurs in the cytosol of infected cells within a specialised membranous compartment. How the viral non-structural (NS) proteins are associated and organised within these structures remains poorly defined. We employed a super-resolution microscopy approach to visualise NS3 and NS5A in HCV infected cells. Using single molecule localisation microscopy, both NS proteins were resolved as clusters of localisations smaller than the diffraction-limited volume observed by wide-field. Analysis of the protein clusters identified a significant difference in size between the NS proteins. We also observed a reduction in NS5A cluster size following inhibition of RNA replication using daclatasvir, a phenotype which was maintained in the presence of the Y93H resistance associated substitution and not observed for NS3 clusters. These results provide insight into the NS protein organisation within hepatitis C virus RNA replication complexes and the mode of action of NS5A inhibitors.
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29
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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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30
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Yao S, Fan J, Chen Z, Zong Y, Zhang J, Sun Z, Zhang L, Tai R, Liu Z, Chen C, Jiang H. Three-dimensional ultrastructural imaging reveals the nanoscale architecture of mammalian cells. IUCRJ 2018; 5:141-149. [PMID: 29765603 PMCID: PMC5947718 DOI: 10.1107/s2052252517017912] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/15/2017] [Indexed: 05/20/2023]
Abstract
Knowledge of the interactions between nanomaterials and large-size mammalian cells, including cellular uptake, intracellular localization and translocation, has greatly advanced nanomedicine and nanotoxicology. Imaging techniques that can locate nanomaterials within the structures of intact large-size cells at nanoscale resolution play crucial roles in acquiring this knowledge. Here, the quantitative imaging of intracellular nanomaterials in three dimensions was performed by combining dual-energy contrast X-ray microscopy and an iterative tomographic algorithm termed equally sloped tomography (EST). Macrophages with a size of ∼20 µm that had been exposed to the potential antitumour agent [Gd@C82(OH)22] n were investigated. Large numbers of nanoparticles (NPs) aggregated within the cell and were mainly located in phagosomes. No NPs were observed in the nucleus. Imaging of the nanomedicine within whole cells advanced the understanding of the high-efficiency antitumour activity and the low toxicity of this agent. This imaging technique can be used to probe nanomaterials within intact large-size cells at nanometre resolution uniformly in three dimensions and may greatly benefit the fields of nanomedicine and nanotoxicology.
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Affiliation(s)
- Shengkun Yao
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, People’s Republic of China
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, People’s Republic of China
| | - Jiadong Fan
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, People’s Republic of China
| | - Zhiyun Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, No. 11 ZhongGuanCun BeiYiTiao, Beijing 100190, People’s Republic of China
| | - Yunbing Zong
- State Key Laboratory of Crystal Materials, Shandong University, 27 Shanda Nanlu, Jinan, Shandong 250100, People’s Republic of China
| | - Jianhua Zhang
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, People’s Republic of China
- State Key Laboratory of Crystal Materials, Shandong University, 27 Shanda Nanlu, Jinan, Shandong 250100, People’s Republic of China
| | - Zhibin Sun
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, People’s Republic of China
- State Key Laboratory of Crystal Materials, Shandong University, 27 Shanda Nanlu, Jinan, Shandong 250100, People’s Republic of China
| | - Lijuan Zhang
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Science, 239 Zhangheng Road, Pudong New District, Shanghai 201204, People’s Republic of China
| | - Renzhong Tai
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Science, 239 Zhangheng Road, Pudong New District, Shanghai 201204, People’s Republic of China
| | - Zhi Liu
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, People’s Republic of China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, No. 11 ZhongGuanCun BeiYiTiao, Beijing 100190, People’s Republic of China
| | - Huaidong Jiang
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, People’s Republic of China
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, People’s Republic of China
- State Key Laboratory of Crystal Materials, Shandong University, 27 Shanda Nanlu, Jinan, Shandong 250100, People’s Republic of China
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31
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Du M, Jacobsen C. Relative merits and limiting factors for x-ray and electron microscopy of thick, hydrated organic materials. Ultramicroscopy 2018; 184:293-309. [PMID: 29073575 PMCID: PMC5696083 DOI: 10.1016/j.ultramic.2017.10.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/05/2017] [Indexed: 12/01/2022]
Abstract
Electron and x-ray microscopes allow one to image the entire, unlabeled structure of hydrated materials at a resolution well beyond what visible light microscopes can achieve. However, both approaches involve ionizing radiation, so that radiation damage must be considered as one of the limits to imaging. Drawing upon earlier work, we describe here a unified approach to estimating the image contrast (and thus the required exposure and corresponding radiation dose) in both x-ray and electron microscopy. This approach accounts for factors such as plural and inelastic scattering, and (in electron microscopy) the use of energy filters to obtain so-called "zero loss" images. As expected, it shows that electron microscopy offers lower dose for specimens thinner than about 1 µm (such as for studies of macromolecules, viruses, bacteria and archaebacteria, and thin sectioned material), while x-ray microscopy offers superior characteristics for imaging thicker specimen such as whole eukaryotic cells, thick-sectioned tissues, and organs. The required radiation dose scales strongly as a function of the desired spatial resolution, allowing one to understand the limits of live and frozen hydrated specimen imaging. Finally, we consider the factors limiting x-ray microscopy of thicker materials, suggesting that specimens as thick as a whole mouse brain can be imaged with x-ray microscopes without significant image degradation should appropriate image reconstruction methods be identified.
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Affiliation(s)
- Ming Du
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston IL 60208, USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne IL 60439, USA; Department of Physics & Astronomy, Northwestern University, 2145 Sheridan Road, Evanston IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston IL 60208, USA.
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32
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Wallander H, Wallentin J. Simulated sample heating from a nanofocused X-ray beam. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:925-933. [PMID: 28862614 PMCID: PMC5580787 DOI: 10.1107/s1600577517008712] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/12/2017] [Indexed: 05/25/2023]
Abstract
Recent developments in synchrotron brilliance and X-ray optics are pushing the flux density in nanofocusing experiments to unprecedented levels, which increases the risk of different types of radiation damage. The effect of X-ray induced sample heating has been investigated using time-resolved and steady-state three-dimensional finite-element modelling of representative nanostructures. Simulations of a semiconductor nanowire indicate that the heat generated by X-ray absorption is efficiently transported within the nanowire, and that the temperature becomes homogeneous after about 5 ns. The most important channel for heat loss is conduction to the substrate, where the heat transfer coefficient and the interfacial area are limiting the heat transport. While convective heat transfer to air is significant, the thermal radiation is negligible. The steady-state average temperature in the nanowire is 8 K above room temperature at the reference parameters. In the absence of heat transfer to the substrate, the temperature increase at the same flux reaches 55 K in air and far beyond the melting temperature in vacuum. Reducing the size of the X-ray focus at constant flux only increases the maximum temperature marginally. These results suggest that the key strategy for reducing the X-ray induced heating is to improve the heat transfer to the surrounding.
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Affiliation(s)
- Harald Wallander
- Synchrotron Radiation Research, Lund University, Box 118, Lund 22100, Sweden
| | - Jesper Wallentin
- Synchrotron Radiation Research, Lund University, Box 118, Lund 22100, Sweden
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Carrascosa JL, Leake MC. Imaging the cell. Biophys Rev 2017; 9:295-296. [PMID: 28776256 DOI: 10.1007/s12551-017-0280-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 07/12/2017] [Indexed: 11/24/2022] Open
Affiliation(s)
- José L Carrascosa
- Centro Nacional de Biotecnologia (CNB-CSIC) and Unidad de Nanobiotecnología and IMDEA Nanociencia-CNB-CSIC, Madrid, Spain
| | - Mark C Leake
- Biological Physical Sciences Institute (BPSI), Departments of Physics and Biology, University of York, York, UK.
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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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35
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Cunha ES, Sfriso P, Rojas AL, Roversi P, Hospital A, Orozco M, Abrescia NG. Mechanism of Structural Tuning of the Hepatitis C Virus Human Cellular Receptor CD81 Large Extracellular Loop. Structure 2017; 25:53-65. [DOI: 10.1016/j.str.2016.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 09/21/2016] [Accepted: 10/27/2016] [Indexed: 12/12/2022]
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36
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Otón J, Pereiro E, Pérez-Berná AJ, Millach L, Sorzano COS, Marabini R, Carazo JM. Characterization of transfer function, resolution and depth of field of a soft X-ray microscope applied to tomography enhancement by Wiener deconvolution. BIOMEDICAL OPTICS EXPRESS 2016; 7:5092-5103. [PMID: 28018727 PMCID: PMC5175554 DOI: 10.1364/boe.7.005092] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/18/2016] [Accepted: 10/22/2016] [Indexed: 05/05/2023]
Abstract
Full field soft X-ray microscopy is becoming a powerful imaging technique to analyze whole cells preserved under cryo conditions. Images obtained in these X-ray microscopes can be combined by tomographic reconstruction to quantitatively estimate the three-dimensional (3D) distribution of absorption coefficients inside the cell. The impulse response of an imaging system is one of the factors that limits the quality of the X-ray microscope reconstructions. The main goal of this work is to experimentally measure the 3D impulse response and to assess the optical resolution and depth of field of the Mistral microscope at ALBA synchrotron (Barcelona, Spain). To this end we measure the microscope apparent transfer function (ATF) and we use it to design a deblurring Wiener filter, obtaining an increase in the image quality when applied to experimental datasets collected at ALBA.
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Affiliation(s)
- Joaquín Otón
- Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, 28049, Madrid,
Spain
| | - Eva Pereiro
- ALBA Synchrotron Light Source, Cerdanyola del Vallès, 08290, Barcelona,
Spain
| | - Ana J. Pérez-Berná
- ALBA Synchrotron Light Source, Cerdanyola del Vallès, 08290, Barcelona,
Spain
| | - Laia Millach
- Facultat de Biociències. Departament de Genètica i Microbiologia. UAB. Cerdanyola del Vallès, 08193, Barcelona,
Spain
| | | | - Roberto Marabini
- Escuela Politecnica Superior, Univ. Autonoma de Madrid, Cantoblanco, 28049, Madrid,
Spain
| | - José M. Carazo
- Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, 28049, Madrid,
Spain
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37
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Varsano N, Dadosh T, Kapishnikov S, Pereiro E, Shimoni E, Jin X, Kruth HS, Leiserowitz L, Addadi L. Development of Correlative Cryo-soft X-ray Tomography and Stochastic Reconstruction Microscopy. A Study of Cholesterol Crystal Early Formation in Cells. J Am Chem Soc 2016; 138:14931-14940. [PMID: 27934213 DOI: 10.1021/jacs.6b07584] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We have developed a high resolution correlative method involving cryo-soft X-ray tomography (cryo-SXT) and stochastic optical reconstruction microscopy (STORM), which provides information in three dimensions on large cellular volumes at 70 nm resolution. Cryo-SXT morphologically identified and localized aggregations of carbon-rich materials. STORM identified specific markers on the desired epitopes, enabling colocalization between the identified objects, in this case cholesterol crystals, and the cellular environment. The samples were studied under ambient and cryogenic conditions without dehydration or heavy metal staining. The early events of cholesterol crystal development were investigated in relation to atherosclerosis, using as model macrophage cell cultures enriched with LDL particles. Atherosclerotic plaques build up in arteries in a slow process involving cholesterol crystal accumulation. Cholesterol crystal deposition is a crucial stage in the pathological cascade. Our results show that cholesterol crystals can be identified and imaged at a very early stage on the cell plasma membrane and in intracellular locations. This technique can in principle be applied to other biological samples where specific molecular identification is required in conjunction with high resolution 3D-imaging.
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Affiliation(s)
| | | | - Sergey Kapishnikov
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin , Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Eva Pereiro
- ALBA Synchrotron Light Source, MISTRAL Beamline-Experiments Division, 08290 Cerdanyola del Valles, Barcelona, Spain
| | | | - Xueting Jin
- Experimental Atherosclerosis Section, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892-1422, United States
| | - Howard S Kruth
- Experimental Atherosclerosis Section, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892-1422, United States
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Darrow MC, Zhang Y, Cinquin BP, Smith EA, Boudreau R, Rochat RH, Schmid MF, Xia Y, Larabell CA, Chiu W. Visualizing red blood cell sickling and the effects of inhibition of sphingosine kinase 1 using soft X-ray tomography. J Cell Sci 2016; 129:3511-7. [PMID: 27505892 DOI: 10.1242/jcs.189225] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 08/01/2016] [Indexed: 01/17/2023] Open
Abstract
Sickle cell disease is a destructive genetic disorder characterized by the formation of fibrils of deoxygenated hemoglobin, leading to the red blood cell (RBC) morphology changes that underlie the clinical manifestations of this disease. Using cryogenic soft X-ray tomography (SXT), we characterized the morphology of sickled RBCs in terms of volume and the number of protrusions per cell. We were able to identify statistically a relationship between the number of protrusions and the volume of the cell, which is known to correlate to the severity of sickling. This structural polymorphism allows for the classification of the stages of the sickling process. Recent studies have shown that elevated sphingosine kinase 1 (Sphk1)-mediated sphingosine 1-phosphate production contributes to sickling. Here, we further demonstrate that compound 5C, an inhibitor of Sphk1, has anti-sickling properties. Additionally, the variation in cellular morphology upon treatment suggests that this drug acts to delay the sickling process. SXT is an effective tool that can be used to identify the morphology of the sickling process and assess the effectiveness of potential therapeutics.
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Affiliation(s)
- Michele C Darrow
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yujin Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Bertrand P Cinquin
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elizabeth A Smith
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rosanne Boudreau
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ryan H Rochat
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael F Schmid
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yang Xia
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA University of Texas at Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA Department of Nephrology, The First Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Carolyn A Larabell
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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