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Golyshev SA, Kazakov EP, Kireev II, Reunov DG, Malyshev IV. Soft X-ray Microscopy in Cell Biology: Current Status, Contributions and Prospects. Acta Naturae 2023; 15:32-43. [PMID: 38234603 PMCID: PMC10790358 DOI: 10.32607/actanaturae.26551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/27/2023] [Indexed: 01/19/2024] Open
Abstract
The recent advances achieved in microscopy technology have led to a significant breakthrough in biological research. Super-resolution fluorescent microscopy now allows us to visualize subcellular structures down to the pin-pointing of the single molecules in them, while modern electron microscopy has opened new possibilities in the study of protein complexes in their native, intracellular environment at near-atomic resolution. Nonetheless, both fluorescent and electron microscopy have remained beset by their principal shortcomings: the reliance on labeling procedures and severe sample volume limitations, respectively. Soft X-ray microscopy is a candidate method that can compensate for the shortcomings of both technologies by making possible observation of the entirety of the cellular interior without chemical fixation and labeling with an isotropic resolution of 40-70 nm. This will thus bridge the resolution gap between light and electron microscopy (although this gap is being narrowed, it still exists) and resolve the issue of compatibility with the former, and possibly in the near future, the latter methods. This review aims to assess the current state of soft X-ray microscopy and its impact on our understanding of the subcellular organization. It also attempts to look into the future of X-ray microscopy, particularly as relates to its seamless integration into the cell biology toolkit.
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Affiliation(s)
- S. A. Golyshev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russian Federation
| | - E. P. Kazakov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russian Federation
| | - I. I. Kireev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russian Federation
| | - D. G. Reunov
- Institute of Physics of Microstructures RAS, Nizhny Novgorod, 603950 Russian Federation
| | - I. V. Malyshev
- Institute of Physics of Microstructures RAS, Nizhny Novgorod, 603950 Russian Federation
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2
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Victor-Lovelace TW, Miller LM. The development and use of metal-based probes for X-ray fluorescence microscopy. METALLOMICS : INTEGRATED BIOMETAL SCIENCE 2022; 14:6852953. [PMID: 36537552 DOI: 10.1093/mtomcs/mfac093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
Abstract
X-ray fluorescence microscopy (XFM) has become a widely used technique for imaging the concentration and distribution of metal ions in cells and tissues. Recent advances in synchrotron sources, optics, and detectors have improved the spatial resolution of the technique to <10 nm with attogram detection sensitivity. However, to make XFM most beneficial for bioimaging-especially at the nanoscale-the metal ion distribution must be visualized within the subcellular context of the cell. Over the years, a number of approaches have been taken to develop X-ray-sensitive tags that permit the visualization of specific organelles or proteins using XFM. In this review, we examine the types of X-ray fluorophore used, including nanomaterials and metal ions, and the approaches used to incorporate the metal into their target binding site via antibodies, genetically encoded metal-binding peptides, affinity labeling, or cell-specific peptides. We evaluate their advantages and disadvantages, review the scientific findings, and discuss the needs for future development.
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Affiliation(s)
| | - Lisa M Miller
- N ational Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973,USA.,Department of Chemistry, Stony Brook University, Stony Brook, NY 11794,USA
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3
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Bonany M, Pérez-Berná AJ, Dučić T, Pereiro E, Martin-Gómez H, Mas-Moruno C, van Rijt S, Zhao Z, Espanol M, Ginebra MP. Hydroxyapatite nanoparticles-cell interaction: New approaches to disclose the fate of membrane-bound and internalised nanoparticles. BIOMATERIALS ADVANCES 2022; 142:213148. [PMID: 36274359 DOI: 10.1016/j.bioadv.2022.213148] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/03/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Hydroxyapatite nanoparticles are popular tools in bone regeneration, but they have also been used for gene delivery and as anticancer drugs. Understanding their mechanism of action, particularly for the latter application, is crucial to predict their toxicity. To this end, we aimed to elucidate the importance of nanoparticle membrane interactions in the cytotoxicity of MG-63 cells using two different types of nanoparticles. In addition, conventional techniques for studying nanoparticle internalisation were evaluated and compared with newer and less exploited approaches. Hydroxyapatite and magnesium-doped hydroxyapatite nanoparticles were used as suspensions or compacted as specular discs. Comparison between cells seeded on the discs and those supplemented with the nanoparticles allowed direct interaction of the cell membrane with the material to be ruled out as the main mechanism of toxicity. In addition, standard techniques such as flow cytometry were inconclusive when used to assess nanoparticles toxicity. Interestingly, the use of intracellular calcium fluorescent probes revealed the presence of a high number of calcium-rich vesicles after nanoparticle supplementation in cell culture. These structures could not be detected by transmission electron microscopy due to their liquid content. However, by using cryo-soft X-ray imaging, which was used to visualise the cellular ultrastructure without further treatment other than vitrification and to quantify the linear absorption coefficient of each organelle, it was possible to identify them as multivesicular bodies, potentially acting as calcium stores. In the study, an advanced state of degradation of the hydroxyapatite and magnesium-doped hydroxyapatite nanoparticles within MG-63 cells was observed. Overall, we demonstrate that the combination of fluorescent calcium probes together with cryo-SXT is an excellent approach to investigate intracellular calcium, especially when found in its soluble form.
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Affiliation(s)
- Mar Bonany
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; Barcelona Research Centre in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain; Biomedical Engineering Research Center (CREB), UPC, 08028 Barcelona, Spain
| | | | - Tanja Dučić
- MISTRAL Beamline Experiments Division, ALBA Synchrotron Light Source, 08290 Barcelona, Spain
| | - Eva Pereiro
- MISTRAL Beamline Experiments Division, ALBA Synchrotron Light Source, 08290 Barcelona, Spain
| | - Helena Martin-Gómez
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; Barcelona Research Centre in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain
| | - Carlos Mas-Moruno
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; Barcelona Research Centre in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain; Biomedical Engineering Research Center (CREB), UPC, 08028 Barcelona, Spain
| | - Sabine van Rijt
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6200, MD, Maastricht, the Netherlands
| | - Zhitong Zhao
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Montserrat Espanol
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; Barcelona Research Centre in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain; Biomedical Engineering Research Center (CREB), UPC, 08028 Barcelona, Spain.
| | - Maria-Pau Ginebra
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; Barcelona Research Centre in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain; Biomedical Engineering Research Center (CREB), UPC, 08028 Barcelona, Spain; Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
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4
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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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5
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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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6
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Kong H, Zhang J, Li J, Wang J, Shin HJ, Tai R, Yan Q, Xia K, Hu J, Wang L, Zhu Y, Fan C. Genetically encoded X-ray cellular imaging for nanoscale protein localization. Natl Sci Rev 2020; 7:1218-1227. [PMID: 34692146 PMCID: PMC8288996 DOI: 10.1093/nsr/nwaa055] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/07/2020] [Accepted: 04/02/2020] [Indexed: 12/20/2022] Open
Abstract
Spatial resolution defines the physical limit of microscopes for probing biomolecular localization and interactions in cells. Whereas synchrotron-based X-ray microscopy (XRM) represents a unique approach for imaging a whole cell with nanoscale resolution due to its intrinsic nanoscale resolution and great penetration ability, existing approaches to label biomolecules rely on the use of exogenous tags that are multi-step and error-prone. Here, we repurpose engineered peroxidases as genetically encoded X-ray-sensitive tags (GXET) for site-specific labeling of protein-of-interest in mammalian cells. We find that 3,3′-diaminobenzidine (DAB) polymers that are in-situ catalytically formed by fusion-expressed peroxidases are visible under XRM. Using this new tag, we imaged the protein location associated with the alteration of a DNA-methylation pathway with an ultra-high resolution of 30 nanometers. Importantly, the excellent energy resolution of XRM enables multicolor imaging using different peroxidase tags. The development of GXET enlightens the way to nanoscopic imaging for biological studies.
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Affiliation(s)
- Huating Kong
- 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
| | - Jichao Zhang
- 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
| | - Jiang Li
- 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
| | - Jian Wang
- Canadian Light Source Inc., University of Saskatchewan, Saskatoon, SK S7N 2V3, Canada
| | - Hyun-Joon Shin
- Pohang Accelerator Laboratory, POSTECH, Pohang 37673, Korea
| | - Renzhong Tai
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Qinglong Yan
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Kai Xia
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jun Hu
- 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
| | - Lihua Wang
- 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
| | - 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
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, and Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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7
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Abramczyk H, Brozek-Pluska B, Jarota A, Surmacki J, Imiela A, Kopec M. A look into the use of Raman spectroscopy for brain and breast cancer diagnostics: linear and non-linear optics in cancer research as a gateway to tumor cell identity. Expert Rev Mol Diagn 2020; 20:99-115. [PMID: 32013616 DOI: 10.1080/14737159.2020.1724092] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Introduction: Currently, intensely developing of linear and non-linear optical methods for cancer detection provides a valuable tool to improve sensitivity and specificity. One of the main reasons for insufficient progress in cancer diagnostics is related to the fact that most cancer types are not only heterogeneous in their genetic composition but also reside in varying microenvironments and interact with different cell types. Until now, no technology has been fully proven for effective detecting of invasive cancer, which infiltrating the extracellular matrix.Areas covered: This review investigates the current status of Raman spectroscopy and Raman imaging for brain and breast cancer diagnostics. Moreover, the review provides a comprehensive overview of the applicability of atomic force microscopy (AFM), linear and non-linear optics in cancer research as a gateway to tumor cell identity.Expert commentary: A combination of linear and non-linear optics, particularly Raman-driven methods, has many additional advantages to identify alterations in cancer cells that are crucial for their proliferation and that distinguish them from normal cells.
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Affiliation(s)
- Halina Abramczyk
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| | - Beata Brozek-Pluska
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| | - Arkadiusz Jarota
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| | - Jakub Surmacki
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| | - Anna Imiela
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| | - Monika Kopec
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
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Sahoo L, Sahoo S, Mohanty M, Sankar M, Dixit S, Das P, Rasal KD, Rather MA, Sundaray JK. Molecular characterization, computational analysis and expression profiling of Dmrt1 gene in Indian major carp, Labeo rohita (Hamilton 1822). Anim Biotechnol 2019; 32:413-426. [PMID: 31880491 DOI: 10.1080/10495398.2019.1707683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Sexual dimorphism of fish morphology, physiology and behavior is diverse and complex in nature. Doublesex and mab-3 related transcription factor (Dmrt) is a large protein family whose function is sexual development and differentiation in vertebrates. Here, we report a full-length cDNA sequence of Labeo rohita (rohu) Dmrt1 of 907 bp length having 798 bp of open reading frame encoding 265 amino acids. The molecular weight of rohu DMRT1 protein was found to be 28.74 KDa and isoelectric point was 7.53. DMRT1 protein contains 23 positively and 24 negatively charged amino acids with a GRAVY score of -0.618. A characteristic DM domain was found in DMRT1 protein, which is a novel DNA-binding domain. Phylogenetic analysis showed maximum similarity with Cyprinus carpio when compared with DMRT1 of other vertebrates. Molecular docking study identified active sites to be targeted for drug designing. Rohu DMRT1 was observed to interact with other proteins such as FOXL2, CYP19a1a, AMH and SOX9a. Differential expression study revealed higher expression in testis tissue implying its role in male sex differentiation and testicular development. The information generated in the present work could facilitate further research to resolve the issues related to gonadal maturation and reproduction of commercially important aquaculture species.
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Affiliation(s)
- L Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - S Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - M Mohanty
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - M Sankar
- ICAR-Central Marine Research Institute, Mandapam Regional Centre, Tamil Nadu, India
| | - S Dixit
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - P Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - K D Rasal
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - M A Rather
- Division of Fish genetics and Biotechnology, Faculty of Fisheries, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - J K Sundaray
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
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9
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Ma L, Zhang X, Xu Z, Späth A, Xing Z, Sun T, Tai R. Three-dimensional focal stack imaging in scanning transmission X-ray microscopy with an improved reconstruction algorithm. OPTICS EXPRESS 2019; 27:7787-7802. [PMID: 30876336 DOI: 10.1364/oe.27.007787] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 01/25/2019] [Indexed: 06/09/2023]
Abstract
Focal stack (FS) is an effective technique for fast 3D imaging in high-resolution scanning transmission X-ray microscopy. Its crucial issue is to assign each object within the sample to the correct position along the optical axis according to a proper focus measure. There is probably information loss with previous algorithms for FS reconstruction because the old algorithms can only detect one focused object along each optical-axial pixel line (OAPL). In this study, we present an improved FS algorithm, which utilizes an elaborately calculated threshold for normalized local variances to extract multiple focused objects in each OAPL. Simulation and experimental results show its feasibility and high efficiency for 3D imaging of high contrast, sparse samples. It is expected that our advanced approach has potential applications in 3D X-ray microscopy for more complex samples.
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10
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Khimchenko A, Bikis C, Pacureanu A, Hieber SE, Thalmann P, Deyhle H, Schweighauser G, Hench J, Frank S, Müller‐Gerbl M, Schulz G, Cloetens P, Müller B. Hard X-Ray Nanoholotomography: Large-Scale, Label-Free, 3D Neuroimaging beyond Optical Limit. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018; 5:1700694. [PMID: 29938163 PMCID: PMC6010902 DOI: 10.1002/advs.201700694] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 02/17/2018] [Indexed: 05/22/2023]
Abstract
There have been great efforts on the nanoscale 3D probing of brain tissues to image subcellular morphologies. However, limitations in terms of tissue coverage, anisotropic resolution, stain dependence, and complex sample preparation all hinder achieving a better understanding of the human brain functioning in the subcellular context. Herein, X-ray nanoholotomography is introduced as an emerging synchrotron radiation-based technology for large-scale, label-free, direct imaging with isotropic voxel sizes down to 25 nm, exhibiting a spatial resolution down to 88 nm. The procedure is nondestructive as it does not require physical slicing. Hence, it allows subsequent imaging by complementary techniques, including histology. The feasibility of this 3D imaging approach is demonstrated on human cerebellum and neocortex specimens derived from paraffin-embedded tissue blocks. The obtained results are compared to hematoxylin and eosin stained histological sections and showcase the ability for rapid hierarchical neuroimaging and automatic rebuilding of the neuronal architecture at the level of a single cell nucleolus. The findings indicate that nanoholotomography can complement microscopy not only by large isotropic volumetric data but also by morphological details on the sub-100 nm level, addressing many of the present challenges in brain tissue characterization and probably becoming an important tool in nanoanatomy.
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Affiliation(s)
- Anna Khimchenko
- Biomaterials Science Center (BMC)Department of Biomedical EngineeringUniversity of Basel4123AllschwilSwitzerland
| | - Christos Bikis
- Biomaterials Science Center (BMC)Department of Biomedical EngineeringUniversity of Basel4123AllschwilSwitzerland
| | - Alexandra Pacureanu
- ID16A‐NI Nano‐Imaging BeamlineEuropean Synchrotron Radiation Facility (ESRF)38043GrenobleFrance
| | - Simone E. Hieber
- Biomaterials Science Center (BMC)Department of Biomedical EngineeringUniversity of Basel4123AllschwilSwitzerland
| | - Peter Thalmann
- Biomaterials Science Center (BMC)Department of Biomedical EngineeringUniversity of Basel4123AllschwilSwitzerland
| | - Hans Deyhle
- Biomaterials Science Center (BMC)Department of Biomedical EngineeringUniversity of Basel4123AllschwilSwitzerland
| | - Gabriel Schweighauser
- Institute of PathologyDepartment of NeuropathologyBasel University Hospital4056BaselSwitzerland
| | - Jürgen Hench
- Institute of PathologyDepartment of NeuropathologyBasel University Hospital4056BaselSwitzerland
| | - Stephan Frank
- Institute of PathologyDepartment of NeuropathologyBasel University Hospital4056BaselSwitzerland
| | - Magdalena Müller‐Gerbl
- Musculoskeletal Research GroupDepartment of BiomedicineUniversity of Basel4056BaselSwitzerland
| | - Georg Schulz
- Biomaterials Science Center (BMC)Department of Biomedical EngineeringUniversity of Basel4123AllschwilSwitzerland
| | - Peter Cloetens
- ID16A‐NI Nano‐Imaging BeamlineEuropean Synchrotron Radiation Facility (ESRF)38043GrenobleFrance
| | - Bert Müller
- Biomaterials Science Center (BMC)Department of Biomedical EngineeringUniversity of Basel4123AllschwilSwitzerland
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11
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Yao S, Zong Y, Huang X, Liu Y, Gong N, Zhang J, Li Z, Cao F, Wang X, Liang XJ, Jiang H. Periodic microstructures of blood capillaries revealed by synchrotron X-ray multi-resolution microscopic analysis. BIOMEDICAL OPTICS EXPRESS 2017; 8:5825-5833. [PMID: 29296507 PMCID: PMC5745122 DOI: 10.1364/boe.8.005825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 06/07/2023]
Abstract
Cardiovascular diseases are closely related to structural blood capillaries lesions. Herein, microscopic investigations of mouse blood capillaries were performed at multiple spatial resolution by using synchrotron X-ray in-line phase contrast tomography and scanning transmission X-ray microscopy (STXM). The chemically fixed blood capillaries without any contrast agents were selected. For the first time, a periodic bamboo-shaped structure was observed at nanoscale resolution by STXM, and the three-dimensional tomographic slices at sub-micrometer resolution further confirmed the periodic wave profile of the blood capillaries. Then, a periodic microstructural model was suggested based on the microscopic images. By using high-performance imaging techniques, this work provides a better understanding of the relationship between the structure and function of blood capillaries, will be helpful in elucidating the causes of cardiovascular system diseases.
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Affiliation(s)
- Shengkun Yao
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- These authors contributed equally to this paper
| | - Yunbing Zong
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
- Department of Data and Business Analysis Product, Inspur International Ltd., Jinan 250101, China
- These authors contributed equally to this paper
| | - Xu Huang
- Department of Cardiology, Chinese PLA General Hospital, Beijing 100853, China
| | - Yang Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Ningqiang Gong
- Laboratory of Controllable Nanopharmaceuticals, Chinese Academy of Sciences (CAS) Center for Excellence in Nanoscience; and CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, No. 11, First North Road Zhongguangcun, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhua Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Ziqing Li
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Feng Cao
- Department of Cardiology, Chinese PLA General Hospital, Beijing 100853, China
| | - Xiangcheng Wang
- Department of Data and Business Analysis Product, Inspur International Ltd., Jinan 250101, China
| | - Xing-Jie Liang
- Laboratory of Controllable Nanopharmaceuticals, Chinese Academy of Sciences (CAS) Center for Excellence in Nanoscience; and CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, No. 11, First North Road Zhongguangcun, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huaidong Jiang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
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12
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Hémonnot CYJ, Köster S. Imaging of Biological Materials and Cells by X-ray Scattering and Diffraction. ACS NANO 2017; 11:8542-8559. [PMID: 28787573 DOI: 10.1021/acsnano.7b03447] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Cells and biological materials are large objects in comparison to the size of internal components such as organelles and proteins. An understanding of the functions of these nanoscale elements is key to elucidating cellular function. In this review, we describe the advances in X-ray scattering and diffraction techniques for imaging biological systems at the nanoscale. We present a number of principal technological advances in X-ray optics and development of sample environments. We identify radiation damage as one of the most severe challenges in the field, thus rendering the dose an important parameter when putting different X-ray methods in perspective. Furthermore, we describe different successful approaches, including scanning and full-field techniques, along with prominent examples. Finally, we present a few recent studies that combined several techniques in one experiment in order to collect highly complementary data for a multidimensional sample characterization.
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Affiliation(s)
- Clément Y J Hémonnot
- Institute for X-Ray Physics, University of Goettingen , Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Northwestern Argonne Institute of Science and Engineering, Northwestern University , 9700 South Cass Avenue, Argonne, Illinois 60439, United States
- Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Sarah Köster
- Institute for X-Ray Physics, University of Goettingen , Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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13
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Abstract
Volume is an essential characteristic of a cell, and this review describes the main methods of its measurement that have been used in the past several decades. The discussed methods include various implementations of light scattering, estimates based on one or two cell dimensions, surface scanning, fluorescence confocal and transmission slice-by-slice imaging, intracellular volume markers, displacement of extracellular solution, quantitative phase imaging, radioactive methods, and some others. Suitability of these methods to some typical samples and applications is discussed. © 2017 International Society for Advancement of Cytometry.
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Affiliation(s)
- Michael A Model
- Department of Biological Sciences, Kent State University, Kent, Ohio
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14
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Zhu Y, Zhang J, Li A, Zhang Y, Fan C. Synchrotron-based X-ray microscopy for sub-100nm resolution cell imaging. Curr Opin Chem Biol 2017; 39:11-16. [PMID: 28521258 DOI: 10.1016/j.cbpa.2017.04.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 04/23/2017] [Indexed: 12/27/2022]
Abstract
Microscopic imaging provides a straightforward approach to deepen our understanding of cellular events. While the resolution of optical microscopes is generally limited to 200-300nm due to the diffraction limit, there has been ever growing interest in studying cells at the sub-100nm regime. By exploiting the short wavelength, long penetration depth and elemental specificity of X-rays, synchrotron-based X-ray microscopy (XRM) has demonstrated its power in exploring the structure and function of cells at the nanometer resolution. Here we summarize recent advances in using XRM for imaging ultrastructure of organelles and specific biomolecular locations in cells, and provide a perspective on potentials and applications of XRM.
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Affiliation(s)
- Ying Zhu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jichao Zhang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Aiguo Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yuanqing Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 201200, China.
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