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Erozan A, Lösel PD, Heuveline V, Weinhardt V. Automated 3D cytoplasm segmentation in soft X-ray tomography. iScience 2024; 27:109856. [PMID: 38784019 PMCID: PMC11112332 DOI: 10.1016/j.isci.2024.109856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/22/2024] [Accepted: 04/27/2024] [Indexed: 05/25/2024] Open
Abstract
Cells' structure is key to understanding cellular function, diagnostics, and therapy development. Soft X-ray tomography (SXT) is a unique tool to image cellular structure without fixation or labeling at high spatial resolution and throughput. Fast acquisition times increase demand for accelerated image analysis, like segmentation. Currently, segmenting cellular structures is done manually and is a major bottleneck in the SXT data analysis. This paper introduces ACSeg, an automated 3D cytoplasm segmentation model. ACSeg is generated using semi-automated labels and 3D U-Net and is trained on 43 SXT tomograms of immune T cells, rapidly converging to high-accuracy segmentation, therefore reducing time and labor. Furthermore, adding only 6 SXT tomograms of other cell types diversifies the model, showing potential for optimal experimental design. ACSeg successfully segmented unseen tomograms and is published on Biomedisa, enabling high-throughput analysis of cell volume and structure of cytoplasm in diverse cell types.
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Affiliation(s)
- Ayse Erozan
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
- Engineering Mathematics and Computing Lab, Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
- Data Mining and Uncertainty Quantification, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Philipp D. Lösel
- Engineering Mathematics and Computing Lab, Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
- Data Mining and Uncertainty Quantification, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Department of Materials Physics Research School of Physics, The Australian National University, Acton ACT, Australia
| | - Vincent Heuveline
- Engineering Mathematics and Computing Lab, Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
- Data Mining and Uncertainty Quantification, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Venera Weinhardt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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2
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Hoffmann C, Milovanovic D. Dipping contacts - a novel type of contact site at the interface between membraneless organelles and membranes. J Cell Sci 2023; 136:jcs261413. [PMID: 38149872 PMCID: PMC10785658 DOI: 10.1242/jcs.261413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
Liquid-liquid phase separation is a major mechanism for organizing macromolecules, particularly proteins with intrinsically disordered regions, in compartments not limited by a membrane or a scaffold. The cell can therefore be perceived as a complex emulsion containing many of these membraneless organelles, also referred to as biomolecular condensates, together with numerous membrane-bound organelles. It is currently unclear how such a complex concoction operates to allow for intracellular trafficking, signaling and metabolic processes to occur with high spatiotemporal precision. Based on experimental observations of synaptic vesicle condensates - a membraneless organelle that is in fact packed with membranes - we present here the framework of dipping contacts: a novel type of contact site between membraneless organelles and membranes. In this Hypothesis, we propose that our framework of dipping contacts can serve as a foundation to investigate the interface that couples the diffusion and material properties of condensates to biochemical processes occurring in membranes. The identity and regulation of this interface is especially critical in the case of neurodegenerative diseases, where aberrant inclusions of misfolded proteins and damaged organelles underlie cellular pathology.
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Affiliation(s)
- Christian Hoffmann
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Dragomir Milovanovic
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- National Center for X-ray Tomography, Advanced Light Source, Berkeley, CA 94720, USA
- Einstein Center for Neuroscience, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Berlin and Berlin Institute of Health, 10117 Berlin, Germany
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3
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Li T, Dresselhaus JL, Ivanov N, Prasciolu M, Fleckenstein H, Yefanov O, Zhang W, Pennicard D, Dippel AC, Gutowski O, Villanueva-Perez P, Chapman HN, Bajt S. Dose-efficient scanning Compton X-ray microscopy. LIGHT, SCIENCE & APPLICATIONS 2023; 12:130. [PMID: 37248250 DOI: 10.1038/s41377-023-01176-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/31/2023]
Abstract
The highest resolution of images of soft matter and biological materials is ultimately limited by modification of the structure, induced by the necessarily high energy of short-wavelength radiation. Imaging the inelastically scattered X-rays at a photon energy of 60 keV (0.02 nm wavelength) offers greater signal per energy transferred to the sample than coherent-scattering techniques such as phase-contrast microscopy and projection holography. We present images of dried, unstained, and unfixed biological objects obtained by scanning Compton X-ray microscopy, at a resolution of about 70 nm. This microscope was realised using novel wedged multilayer Laue lenses that were fabricated to sub-ångström precision, a new wavefront measurement scheme for hard X rays, and efficient pixel-array detectors. The doses required to form these images were as little as 0.02% of the tolerable dose and 0.05% of that needed for phase-contrast imaging at similar resolution using 17 keV photon energy. The images obtained provide a quantitative map of the projected mass density in the sample, as confirmed by imaging a silicon wedge. Based on these results, we find that it should be possible to obtain radiation damage-free images of biological samples at a resolution below 10 nm.
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Affiliation(s)
- Tang Li
- The Hamburg Centre for Ultrafast Imaging, 22761, Hamburg, Germany
| | | | - Nikolay Ivanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Mauro Prasciolu
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Wenhui Zhang
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - David Pennicard
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | | | - Olof Gutowski
- Deutsches Elektronen Synchrotron DESY, 22607, Hamburg, Germany
| | | | - Henry N Chapman
- The Hamburg Centre for Ultrafast Imaging, 22761, Hamburg, Germany.
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany.
- Department of Physics, Universität Hamburg, 22761, Hamburg, Germany.
| | - Saša Bajt
- The Hamburg Centre for Ultrafast Imaging, 22761, Hamburg, Germany.
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany.
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4
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Merolle L, Pascolo L, Zupin L, Parisse P, Bonanni V, Gariani G, Kenig S, Bedolla DE, Crovella S, Ricci G, Iotti S, Malucelli E, Kourousias G, Gianoncelli A. Impact of Sample Preparation Methods on Single-Cell X-ray Microscopy and Light Elemental Analysis Evaluated by Combined Low Energy X-ray Fluorescence, STXM and AFM. Molecules 2023; 28:molecules28041992. [PMID: 36838979 PMCID: PMC9962160 DOI: 10.3390/molecules28041992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/08/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Although X-ray fluorescence microscopy is becoming a widely used technique for single-cell analysis, sample preparation for this microscopy remains one of the main challenges in obtaining optimal conditions for the measurements in the X-ray regime. The information available to researchers on sample treatment is inadequate and unclear, sometimes leading to wasted time and jeopardizing the experiment's success. Many cell fixation methods have been described, but none of them have been systematically tested and declared the most suitable for synchrotron X-ray microscopy. METHODS The HEC-1-A endometrial cells, human spermatozoa, and human embryonic kidney (HEK-293) cells were fixed with organic solvents and cross-linking methods: 70% ethanol, 3.7%, and 2% paraformaldehyde; in addition, HEK-293 cells were subjected to methanol/ C3H6O treatment and cryofixation. Fixation methods were compared by coupling low-energy X-ray fluorescence with scanning transmission X-ray microscopy and atomic force microscopy. RESULTS Organic solvents lead to greater dehydration of cells, which has the most significant effect on the distribution and depletion of diffusion elements. Paraformaldehyde provides robust and reproducible data. Finally, the cryofixed cells provide the best morphology and element content results. CONCLUSION Although cryofixation seems to be the most appropriate method as it allows for keeping cells closer to physiological conditions, it has some technical limitations. Paraformaldehyde, when used at the average concentration of 3.7%, is also an excellent alternative for X-ray microscopy.
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Affiliation(s)
- Lucia Merolle
- AUSL-IRCCS di Reggio Emilia, Transfusion Medicine Unit, 42123 Reggio Emilia, Italy
| | - Lorella Pascolo
- IRCCS Burlo Garofolo, Institute for Maternal and Child Health, 34137 Trieste, Italy
| | - Luisa Zupin
- IRCCS Burlo Garofolo, Institute for Maternal and Child Health, 34137 Trieste, Italy
| | - Pietro Parisse
- Consiglio Nazionale delle Ricerche, Istituto Officina dei Materiali, 34149 Trieste, Italy
- Elettra—Sincrotrone Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
| | - Valentina Bonanni
- Elettra—Sincrotrone Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
| | - Gianluca Gariani
- Elettra—Sincrotrone Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
| | - Sasa Kenig
- Faculty of Health Sciences, University of Primorska, Polje 42, 6310 Izola, Slovenia
| | - Diana E. Bedolla
- Elettra—Sincrotrone Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
- Area Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Sergio Crovella
- Biological Science Program, Department of Biological and Environmental Science, College of Arts and Sciences, Qatar University, Doha 2713, Qatar
| | - Giuseppe Ricci
- IRCCS Burlo Garofolo, Institute for Maternal and Child Health, 34137 Trieste, Italy
- Department of Medical, Surgical, and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Stefano Iotti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
| | - Emil Malucelli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - George Kourousias
- Elettra—Sincrotrone Trieste S.C.p.A., Basovizza, 34149 Trieste, Italy
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5
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Loconte V, Chen J, Vanslembrouck B, Ekman AA, McDermott G, Le Gros MA, Larabell CA. Soft X-ray tomograms provide a structural basis for whole-cell modeling. FASEB J 2023; 37:e22681. [PMID: 36519968 PMCID: PMC10107707 DOI: 10.1096/fj.202200253r] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 11/13/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022]
Abstract
Developing in silico models that accurately reflect a whole, functional cell is an ongoing challenge in biology. Current efforts bring together mathematical models, probabilistic models, visual representations, and data to create a multi-scale description of cellular processes. A realistic whole-cell model requires imaging data since it provides spatial constraints and other critical cellular characteristics that are still impossible to obtain by calculation alone. This review introduces Soft X-ray Tomography (SXT) as a powerful imaging technique to visualize and quantify the mesoscopic (~25 nm spatial scale) organelle landscape in whole cells. SXT generates three-dimensional reconstructions of cellular ultrastructure and provides a measured structural framework for whole-cell modeling. Combining SXT with data from disparate technologies at varying spatial resolutions provides further biochemical details and constraints for modeling cellular mechanisms. We conclude, based on the results discussed here, that SXT provides a foundational dataset for a broad spectrum of whole-cell modeling experiments.
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Affiliation(s)
- Valentina Loconte
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Jian‐Hua Chen
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Bieke Vanslembrouck
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Axel A. Ekman
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Gerry McDermott
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Mark A. Le Gros
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Carolyn A. Larabell
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
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6
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Nanometer-Resolution Imaging of Living Cells Using Soft X-ray Contact Microscopy. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12147030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Soft X-ray microscopy is a powerful technique for imaging cells with nanometer resolution in their native state without chemical fixation, staining, or sectioning. The studies performed in several laboratories have demonstrated the potential of applying this technique for imaging the internal structures of intact cells. However, it is currently used mainly on synchrotrons with restricted access. Moreover, the operation of these instruments and the associated sample-preparation protocols require interdisciplinary and highly specialized personnel, limiting their wide application in practice. This is why soft X-ray microscopy is not commonly used in biological laboratories as an imaging tool. Thus, a laboratory-based and user-friendly soft X-ray contact microscope would facilitate the work of biologists. A compact, desk-top laboratory setup for soft X-ray contact microscopy (SXCM) based on a laser-plasma soft X-ray source, which can be used in any biological laboratory, together with several applications for biological imaging, are described. Moreover, the perspectives of the correlation of SXCM with other super-resolution imaging techniques based on the current literature are discussed.
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7
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Vanslembrouck B, Chen JH, Larabell C, van Hengel J. Microscopic Visualization of Cell-Cell Adhesion Complexes at Micro and Nanoscale. Front Cell Dev Biol 2022; 10:819534. [PMID: 35517500 PMCID: PMC9065677 DOI: 10.3389/fcell.2022.819534] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 03/21/2022] [Indexed: 12/25/2022] Open
Abstract
Considerable progress has been made in our knowledge of the morphological and functional varieties of anchoring junctions. Cell-cell adhesion contacts consist of discrete junctional structures responsible for the mechanical coupling of cytoskeletons and allow the transmission of mechanical signals across the cell collective. The three main adhesion complexes are adherens junctions, tight junctions, and desmosomes. Microscopy has played a fundamental role in understanding these adhesion complexes on different levels in both physiological and pathological conditions. In this review, we discuss the main light and electron microscopy techniques used to unravel the structure and composition of the three cell-cell contacts in epithelial and endothelial cells. It functions as a guide to pick the appropriate imaging technique(s) for the adhesion complexes of interest. We also point out the latest techniques that have emerged. At the end, we discuss the problems investigators encounter during their cell-cell adhesion research using microscopic techniques.
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Affiliation(s)
- Bieke Vanslembrouck
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Anatomy, University of San Francisco, San Francisco, CA, United States
- *Correspondence: Bieke Vanslembrouck, ; Jolanda van Hengel,
| | - Jian-hua Chen
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Anatomy, University of San Francisco, San Francisco, CA, United States
| | - Carolyn Larabell
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Anatomy, University of San Francisco, San Francisco, CA, United States
| | - Jolanda van Hengel
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- *Correspondence: Bieke Vanslembrouck, ; Jolanda van Hengel,
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8
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Li A, Zhang X, Singla J, White K, Loconte V, Hu C, Zhang C, Li S, Li W, Francis JP, Wang C, Sali A, Sun L, He X, Stevens RC. Auto-segmentation and time-dependent systematic analysis of mesoscale cellular structure in β-cells during insulin secretion. PLoS One 2022; 17:e0265567. [PMID: 35324950 PMCID: PMC8947144 DOI: 10.1371/journal.pone.0265567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/03/2022] [Indexed: 02/07/2023] Open
Abstract
The mesoscale description of the subcellular organization informs about cellular mechanisms in disease state. However, applications of soft X-ray tomography (SXT), an important approach for characterizing organelle organization, are limited by labor-intensive manual segmentation. Here we report a pipeline for automated segmentation and systematic analysis of SXT tomograms. Our approach combines semantic and first-applied instance segmentation to produce separate organelle masks with high Dice and Recall indexes, followed by analysis of organelle localization based on the radial distribution function. We demonstrated this technique by investigating the organization of INS-1E pancreatic β-cell organization under different treatments at multiple time points. Consistent with a previous analysis of a similar dataset, our results revealed the impact of glucose stimulation on the localization and molecular density of insulin vesicles and mitochondria. This pipeline can be extended to SXT tomograms of any cell type to shed light on the subcellular rearrangements under different drug treatments.
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Affiliation(s)
- Angdi Li
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangyi Zhang
- School of Information Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jitin Singla
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA, United States of America
| | - Kate White
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA, United States of America
| | - Valentina Loconte
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Chuanyang Hu
- School of Information Science and Technology, ShanghaiTech University, Shanghai, China
| | - Chuyu Zhang
- School of Information Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shuailin Li
- School of Information Science and Technology, ShanghaiTech University, Shanghai, China
| | - Weimin Li
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - John Paul Francis
- Department of Computer Science, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, United States of America
| | - Chenxi Wang
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Andrej Sali
- California Institute for Quantitative Biosciences, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America
| | - Liping Sun
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- * E-mail: (LS); (XH); (RCS)
| | - Xuming He
- School of Information Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Engineering Research Center of Intelligent Vision and Imaging, Shanghai, China
- * E-mail: (LS); (XH); (RCS)
| | - Raymond C. Stevens
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA, United States of America
- * E-mail: (LS); (XH); (RCS)
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9
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Ou X, Chen X, Xu X, Xie L, Chen X, Hong Z, Bai H, Liu X, Chen Q, Li L, Yang H. Recent Development in X-Ray Imaging Technology: Future and Challenges. RESEARCH (WASHINGTON, D.C.) 2021; 2021:9892152. [PMID: 35028585 PMCID: PMC8724686 DOI: 10.34133/2021/9892152] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 11/23/2021] [Indexed: 11/18/2022]
Abstract
X-ray imaging is a low-cost, powerful technology that has been extensively used in medical diagnosis and industrial nondestructive inspection. The ability of X-rays to penetrate through the body presents great advances for noninvasive imaging of its internal structure. In particular, the technological importance of X-ray imaging has led to the rapid development of high-performance X-ray detectors and the associated imaging applications. Here, we present an overview of the recent development of X-ray imaging-related technologies since the discovery of X-rays in the 1890s and discuss the fundamental mechanism of diverse X-ray imaging instruments, as well as their advantages and disadvantages on X-ray imaging performance. We also highlight various applications of advanced X-ray imaging in a diversity of fields. We further discuss future research directions and challenges in developing advanced next-generation materials that are crucial to the fabrication of flexible, low-dose, high-resolution X-ray imaging detectors.
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Affiliation(s)
- Xiangyu Ou
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Xue Chen
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Xianning Xu
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Lili Xie
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Xiaofeng Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Zhongzhu Hong
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Hua Bai
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Xiaowang Liu
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Qiushui Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou 350108, China
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou 350108, China
| | - Lin Li
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou 350108, China
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou 350108, China
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10
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Osuchowska PN, Wachulak P, Kasprzycka W, Nowak-Stępniowska A, Wakuła M, Bartnik A, Fiedorowicz H, Trafny EA. Adhesion of Triple-Negative Breast Cancer Cells under Fluorescent and Soft X-ray Contact Microscopy. Int J Mol Sci 2021; 22:ijms22147279. [PMID: 34298899 PMCID: PMC8306697 DOI: 10.3390/ijms22147279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/24/2021] [Accepted: 07/02/2021] [Indexed: 12/20/2022] Open
Abstract
Understanding cancer cell adhesion could help to diminish tumor progression and metastasis. Adhesion mechanisms are currently the main therapeutic target of TNBC-resistant cells. This work shows the distribution and size of adhesive complexes determined with a common fluorescence microscopy technique and soft X-ray contact microscopy (SXCM). The results presented here demonstrate the potential of applying SXCM for imaging cell protrusions with high resolution when the cells are still alive in a physiological buffer. The possibility to observe the internal components of cells at a pristine and hydrated state with nanometer resolution distinguishes SXCM from the other more commonly used techniques for cell imaging. Thus, SXCM can be a promising technique for investigating the adhesion and organization of the actin cytoskeleton in cancer cells.
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Affiliation(s)
- Paulina Natalia Osuchowska
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, Kaliskiego 2, 00-908 Warsaw, Poland; (P.N.O.); (W.K.); (A.N.-S.)
| | - Przemysław Wachulak
- Laser Technology Division, Institute of Optoelectronics, Military University of Technology, Kaliskiego 2, 00-908 Warsaw, Poland; (P.W.); (A.B.)
| | - Wiktoria Kasprzycka
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, Kaliskiego 2, 00-908 Warsaw, Poland; (P.N.O.); (W.K.); (A.N.-S.)
| | - Agata Nowak-Stępniowska
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, Kaliskiego 2, 00-908 Warsaw, Poland; (P.N.O.); (W.K.); (A.N.-S.)
| | - Maciej Wakuła
- Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781 Warsaw, Poland; (M.W.); (H.F.)
| | - Andrzej Bartnik
- Laser Technology Division, Institute of Optoelectronics, Military University of Technology, Kaliskiego 2, 00-908 Warsaw, Poland; (P.W.); (A.B.)
| | - Henryk Fiedorowicz
- Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781 Warsaw, Poland; (M.W.); (H.F.)
| | - Elżbieta Anna Trafny
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, Kaliskiego 2, 00-908 Warsaw, Poland; (P.N.O.); (W.K.); (A.N.-S.)
- Correspondence: ; Tel.: +48-261-839-544
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11
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Sanchez-Cano C, Alvarez-Puebla RA, Abendroth JM, Beck T, Blick R, Cao Y, Caruso F, Chakraborty I, Chapman HN, Chen C, Cohen BE, Conceição ALC, Cormode DP, Cui D, Dawson KA, Falkenberg G, Fan C, Feliu N, Gao M, Gargioni E, Glüer CC, Grüner F, Hassan M, Hu Y, Huang Y, Huber S, Huse N, Kang Y, Khademhosseini A, Keller TF, Körnig C, Kotov NA, Koziej D, Liang XJ, Liu B, Liu S, Liu Y, Liu Z, Liz-Marzán LM, Ma X, Machicote A, Maison W, Mancuso AP, Megahed S, Nickel B, Otto F, Palencia C, Pascarelli S, Pearson A, Peñate-Medina O, Qi B, Rädler J, Richardson JJ, Rosenhahn A, Rothkamm K, Rübhausen M, Sanyal MK, Schaak RE, Schlemmer HP, Schmidt M, Schmutzler O, Schotten T, Schulz F, Sood AK, Spiers KM, Staufer T, Stemer DM, Stierle A, Sun X, Tsakanova G, Weiss PS, Weller H, Westermeier F, Xu M, Yan H, Zeng Y, Zhao Y, Zhao Y, Zhu D, Zhu Y, Parak WJ. X-ray-Based Techniques to Study the Nano-Bio Interface. ACS NANO 2021; 15:3754-3807. [PMID: 33650433 PMCID: PMC7992135 DOI: 10.1021/acsnano.0c09563] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/25/2021] [Indexed: 05/03/2023]
Abstract
X-ray-based analytics are routinely applied in many fields, including physics, chemistry, materials science, and engineering. The full potential of such techniques in the life sciences and medicine, however, has not yet been fully exploited. We highlight current and upcoming advances in this direction. We describe different X-ray-based methodologies (including those performed at synchrotron light sources and X-ray free-electron lasers) and their potentials for application to investigate the nano-bio interface. The discussion is predominantly guided by asking how such methods could better help to understand and to improve nanoparticle-based drug delivery, though the concepts also apply to nano-bio interactions in general. We discuss current limitations and how they might be overcome, particularly for future use in vivo.
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Affiliation(s)
- Carlos Sanchez-Cano
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014 Donostia San Sebastián, Spain
| | - Ramon A. Alvarez-Puebla
- Universitat
Rovira i Virgili, 43007 Tarragona, Spain
- ICREA, Passeig Lluís
Companys 23, 08010 Barcelona, Spain
| | - John M. Abendroth
- Department
of Materials Science and Engineering, Stanford
University, Stanford, California 94305, United States
| | - Tobias Beck
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Robert Blick
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Yuan Cao
- Department
of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces
Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Frank Caruso
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology
and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Indranath Chakraborty
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Henry N. Chapman
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Centre
for Ultrafast Imaging, Universität
Hamburg, 22761 Hamburg, Germany
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Chunying Chen
- National
Center for Nanoscience and Technology (NCNST), 100190 Beijing China
| | - Bruce E. Cohen
- The
Molecular Foundry and Division of Molecular Biophysics and Integrated
Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | - David P. Cormode
- Radiology
Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Daxiang Cui
- School
of Chemistry and Chemical Engineering, Frontiers Science Center for
Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | | | - Gerald Falkenberg
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Chunhai Fan
- School
of Chemistry and Chemical Engineering, Frontiers Science Center for
Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Neus Feliu
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- CAN, Fraunhofer Institut, 20146 Hamburg, Germany
| | - Mingyuan Gao
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Elisabetta Gargioni
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Claus-C. Glüer
- Section
Biomedical Imaging, Department of Radiology and Neuroradiology, University Medical Clinic Schleswig-Holstein and Christian-Albrechts-University
Kiel, 24105 Kiel, Germany
| | - Florian Grüner
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Universität
Hamburg and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Moustapha Hassan
- Karolinska University Hospital, Huddinge, and Karolinska
Institutet, 17177 Stockholm, Sweden
| | - Yong Hu
- College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
| | - Yalan Huang
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Samuel Huber
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Nils Huse
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Yanan Kang
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Ali Khademhosseini
- Terasaki Institute for Biomedical Innovation, Los Angeles, California 90049, United States
| | - Thomas F. Keller
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Christian Körnig
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Universität
Hamburg and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Nicholas A. Kotov
- Department
of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces
Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Michigan
Institute for Translational Nanotechnology (MITRAN), Ypsilanti, Michigan 48198, United States
| | - Dorota Koziej
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Xing-Jie Liang
- National
Center for Nanoscience and Technology (NCNST), 100190 Beijing China
| | - Beibei Liu
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology,
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 China
| | - Yang Liu
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Ziyao Liu
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Luis M. Liz-Marzán
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014 Donostia San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Centro de Investigación Biomédica
en Red de Bioingeniería,
Biomateriales y Nanomedicina (CIBER-BBN), Paseo de Miramon 182, 20014 Donostia-San Sebastián, Spain
| | - Xiaowei Ma
- National
Center for Nanoscience and Technology (NCNST), 100190 Beijing China
| | - Andres Machicote
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Wolfgang Maison
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Adrian P. Mancuso
- European XFEL, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La
Trobe Institute for Molecular
Science, La Trobe University, Melbourne 3086, Victoria, Australia
| | - Saad Megahed
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Bert Nickel
- Sektion Physik, Ludwig Maximilians Universität
München, 80539 München, Germany
| | - Ferdinand Otto
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Cristina Palencia
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | | | - Arwen Pearson
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Oula Peñate-Medina
- Section
Biomedical Imaging, Department of Radiology and Neuroradiology, University Medical Clinic Schleswig-Holstein and Christian-Albrechts-University
Kiel, 24105 Kiel, Germany
| | - Bing Qi
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Joachim Rädler
- Sektion Physik, Ludwig Maximilians Universität
München, 80539 München, Germany
| | - Joseph J. Richardson
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology
and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Axel Rosenhahn
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Kai Rothkamm
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Michael Rübhausen
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | | | - Raymond E. Schaak
- Department of Chemistry, Department of Chemical Engineering,
and
Materials Research Institute, The Pennsylvania
State University, University Park, Pensylvania 16802, United States
| | - Heinz-Peter Schlemmer
- Department of Radiology, German Cancer
Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marius Schmidt
- Department of Physics, University
of Wisconsin-Milwaukee, 3135 N. Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Oliver Schmutzler
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Universität
Hamburg and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | | | - Florian Schulz
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - A. K. Sood
- Department of Physics, Indian Institute
of Science, Bangalore 560012, India
| | - Kathryn M. Spiers
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Theresa Staufer
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Universität
Hamburg and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Dominik M. Stemer
- California NanoSystems Institute, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Andreas Stierle
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Xing Sun
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Molecular Science and Biomedicine Laboratory (MBL) State
Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry
and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Gohar Tsakanova
- Institute of Molecular Biology of National
Academy of Sciences of
Republic of Armenia, 7 Hasratyan str., 0014 Yerevan, Armenia
- CANDLE Synchrotron Research Institute, 31 Acharyan str., 0040 Yerevan, Armenia
| | - Paul S. Weiss
- California NanoSystems Institute, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Bioengineering, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Horst Weller
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- CAN, Fraunhofer Institut, 20146 Hamburg, Germany
| | - Fabian Westermeier
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Ming Xu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology,
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 China
| | - Huijie Yan
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Yuan Zeng
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Ying Zhao
- Karolinska University Hospital, Huddinge, and Karolinska
Institutet, 17177 Stockholm, Sweden
| | - Yuliang Zhao
- National
Center for Nanoscience and Technology (NCNST), 100190 Beijing China
| | - Dingcheng Zhu
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Ying Zhu
- Bioimaging Center, Shanghai Synchrotron Radiation Facility,
Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Division of Physical Biology, CAS Key Laboratory
of Interfacial
Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Wolfgang J. Parak
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014 Donostia San Sebastián, Spain
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- School
of Chemistry and Chemical Engineering, Frontiers Science Center for
Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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12
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Rodrigues PV, Tostes K, Bosque BP, de Godoy JVP, Amorim Neto DP, Dias CSB, Fonseca MDC. Illuminating the Brain With X-Rays: Contributions and Future Perspectives of High-Resolution Microtomography to Neuroscience. Front Neurosci 2021; 15:627994. [PMID: 33815039 PMCID: PMC8010130 DOI: 10.3389/fnins.2021.627994] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/26/2021] [Indexed: 12/27/2022] Open
Abstract
The assessment of three-dimensional (3D) brain cytoarchitecture at a cellular resolution remains a great challenge in the field of neuroscience and constant development of imaging techniques has become crucial, particularly when it comes to offering direct and clear obtention of data from macro to nano scales. Magnetic resonance imaging (MRI) and electron or optical microscopy, although valuable, still face some issues such as the lack of contrast and extensive sample preparation protocols. In this context, x-ray microtomography (μCT) has become a promising non-destructive tool for imaging a broad range of samples, from dense materials to soft biological specimens. It is a new supplemental method to be explored for deciphering the cytoarchitecture and connectivity of the brain. This review aims to bring together published works using x-ray μCT in neurobiology in order to discuss the achievements made so far and the future of this technique for neuroscience.
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Affiliation(s)
- Paulla Vieira Rodrigues
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Katiane Tostes
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Beatriz Pelegrini Bosque
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - João Vitor Pereira de Godoy
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Dionisio Pedro Amorim Neto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Carlos Sato Baraldi Dias
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Matheus de Castro Fonseca
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
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13
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Separovic F, Keizer DW, Sani MA. In-cell Solid-State NMR Studies of Antimicrobial Peptides. FRONTIERS IN MEDICAL TECHNOLOGY 2020; 2:610203. [PMID: 35047891 PMCID: PMC8757805 DOI: 10.3389/fmedt.2020.610203] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/30/2020] [Indexed: 12/23/2022] Open
Abstract
Antimicrobial peptides (AMPs) have attracted attention as alternatives to classic antibiotics due to their expected limited pressure on bacterial resistance mechanisms. Yet, their modes of action, in particular in vivo, remain to be elucidated. In situ atomistic-scale details of complex biomolecular assemblies is a challenging requirement for deciphering the complex modes of action of AMPs. The large diversity of molecules that modulate complex interactions limits the resolution achievable using imaging methodology. Herein, the latest advances in in-cell solid-state NMR (ssNMR) are discussed, which demonstrate the power of this non-invasive technique to provide atomic details of molecular structure and dynamics. Practical requirements for investigations of intact bacteria are discussed. An overview of recent in situ NMR investigations of the architecture and metabolism of bacteria and the effect of AMPs on various bacterial structures is presented. In-cell ssNMR revealed that the studied AMPs have a disruptive action on the molecular packing of bacterial membranes and DNA. Despite the limited number of studies, in-cell ssNMR is emerging as a powerful technique to monitor in situ the interplay between bacteria and AMPs.
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Affiliation(s)
- Frances Separovic
- School of Chemistry, University of Melbourne, Melbourne, VIC, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia
| | - David W. Keizer
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Marc-Antoine Sani
- School of Chemistry, University of Melbourne, Melbourne, VIC, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia
- *Correspondence: Marc-Antoine Sani
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14
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Imaging of Cell Structures Using Optimized Soft X-ray Contact Microscopy. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10196895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This work is to study the relationship between the exposure conditions and the quality of cell imaging with soft X-ray contact microscopy (SXCM). It is a crucial step in the efficient visualization of cell structures. Three different human cell lines: DU145 prostate carcinoma cells, HCC38 breast cancer cells, and Poietics mesenchymal stem cells were used to establish the optimal exposure conditions in SXCM. The image quality depended on the soft X-ray (SXR) absorbed energy and photoresist development conditions. At lower SXR energy (200 or 400 SXR pulses), sharp cell edges, membrane projections, and cell–cell connections were visible. In contrast, higher energy (600 or 800 SXR pulses) allowed observation of the cytoskeleton and the nucleus in a cell type-dependent manner (the influence of cell thickness and internal complexity was noted).
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15
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Weinhardt V, Chen JH, Ekman AA, Guo J, Remesh SG, Hammel M, McDermott G, Chao W, Oh S, Le Gros MA, Larabell CA. Switchable resolution in soft x-ray tomography of single cells. PLoS One 2020; 15:e0227601. [PMID: 31978064 PMCID: PMC6980406 DOI: 10.1371/journal.pone.0227601] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/24/2019] [Indexed: 11/18/2022] Open
Abstract
The diversity of living cells, in both size and internal complexity, calls for imaging methods with adaptable spatial resolution. Soft x-ray tomography (SXT) is a three-dimensional imaging technique ideally suited to visualizing and quantifying the internal organization of single cells of varying sizes in a near-native state. The achievable resolution of the soft x-ray microscope is largely determined by the objective lens, but switching between objectives is extremely time-consuming and typically undertaken only during microscope maintenance procedures. Since the resolution of the optic is inversely proportional to the depth of focus, an optic capable of imaging the thickest cells is routinely selected. This unnecessarily limits the achievable resolution in smaller cells and eliminates the ability to obtain high-resolution images of regions of interest in larger cells. Here, we describe developments to overcome this shortfall and allow selection of microscope optics best suited to the specimen characteristics and data requirements. We demonstrate that switchable objective capability advances the flexibility of SXT to enable imaging cells ranging in size from bacteria to yeast and mammalian cells without physically modifying the microscope, and we demonstrate the use of this technology to image the same specimen with both optics.
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Affiliation(s)
- Venera Weinhardt
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Axel A. Ekman
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Jessica Guo
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Soumya G. Remesh
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Gerry McDermott
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Weilun Chao
- Center for X-ray Optics, Material Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Sharon Oh
- Center for X-ray Optics, Material Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Mark A. Le Gros
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Carolyn A. Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
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16
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Smith JW, Chen Q. Liquid-phase electron microscopy imaging of cellular and biomolecular systems. J Mater Chem B 2020; 8:8490-8506. [DOI: 10.1039/d0tb01300e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liquid-phase electron microscopy, a new method for real-time nanoscopic imaging in liquid, makes it possible to study cells or biomolecules with a singular combination of spatial and temporal resolution. We review the state of the art in biological research in this growing and promising field.
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Affiliation(s)
- John W. Smith
- Department of Materials Science and Engineering, University of Illinois at Urbana–Champaign
- Urbana
- USA
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana–Champaign
- Urbana
- USA
- Department of Chemistry
- University of Illinois at Urbana–Champaign
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17
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Guo J, Larabell CA. Soft X-ray tomography: virtual sculptures from cell cultures. Curr Opin Struct Biol 2019; 58:324-332. [PMID: 31495562 PMCID: PMC6791522 DOI: 10.1016/j.sbi.2019.06.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/24/2019] [Accepted: 06/27/2019] [Indexed: 12/20/2022]
Abstract
Cellular complexity is represented best in high-spatial resolution, three-dimensional (3D) reconstructions. Soft X-ray tomography (SXT) generates detailed volumetric reconstructions of cells preserved in a near-to-native, frozen-hydrated state. SXT is broadly applicable and can image specimens ranging from bacteria to large mammalian cells. As a reference, we summarize light and electron microscopic methods. We then present an overview of SXT and discuss its role in cellular imaging. We detail the methods used to image biological specimens and present recent highlights that illustrate the capabilities of the technique. We conclude by discussing correlative imaging, specifically the combination of SXT and fluorescence microscopy performed on the same specimen. This correlated approach combines the structural morphology of a cell with its physiological characteristics to build a deeply informative composite view.
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Affiliation(s)
- Jessica Guo
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Carolyn A Larabell
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
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