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McKenzie AT, Zeleznikow-Johnston A, Sparks JS, Nnadi O, Smart J, Wiley K, Cerullo MA, de Wolf A, Minerva F, Risco R, Church GM, de Magalhães JP, Kendziorra EF. Structural brain preservation: a potential bridge to future medical technologies. FRONTIERS IN MEDICAL TECHNOLOGY 2024; 6:1400615. [PMID: 39315362 PMCID: PMC11416988 DOI: 10.3389/fmedt.2024.1400615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 08/21/2024] [Indexed: 09/25/2024] Open
Abstract
When faced with the prospect of death, some people would prefer a form of long-term preservation that may allow them to be restored to healthy life in the future, if technology ever develops to the point that this is feasible and humane. Some believe that we may have the capacity to perform this type of experimental preservation today-although it has never been proven-using contemporary methods to preserve the structure of the brain. The idea is that the morphomolecular organization of the brain encodes the information required for psychological properties such as personality and long-term memories. If these structures in the brain can be maintained intact over time, this could theoretically provide a bridge to access restorative technologies in the future. To consider this hypothesis, we first describe possible metrics that can be used to assess structural brain preservation quality. We next explore several possible methods to preserve structural information in the brain, including the traditional cryonics method of cryopreservation, as well as aldehyde-stabilized cryopreservation and fluid preservation. We focus in-depth on fluid preservation, which relies on aldehyde fixation to induce chemical gel formation in a wide set of biomolecules and appears to be a cost-effective method. We describe two theoretical recovery technologies, alongside several of the ethical and legal complexities of brain preservation, all of which will require a prudent approach. We believe contemporary structural brain preservation methods have a non-negligible chance of allowing successful restoration in the future and that this deserves serious research efforts by the scientific community.
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Affiliation(s)
| | - Ariel Zeleznikow-Johnston
- School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
- Turner Institute for Brain and Mental Health, Monash University, Melbourne, VIC, Australia
| | | | - Oge Nnadi
- Brain Preservation Foundation, Ashburn, VA, United States
| | - John Smart
- Brain Preservation Foundation, Ashburn, VA, United States
| | - Keith Wiley
- Brain Preservation Foundation, Ashburn, VA, United States
| | | | | | | | - Ramón Risco
- Escuela Superior de Ingeniería, Universidad de Sevilla & National Accelerators Center, CNA-CSIC, Seville, Spain
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
| | - João Pedro de Magalhães
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- Oxford Uehiro Centre for Practical Ethics, University of Oxford, Oxford, United Kingdom
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2
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Schwenzer N, Teiwes NK, Kohl T, Pohl C, Giller MJ, Lehnart SE, Steinem C. Ca V1.3 channel clusters characterized by live-cell and isolated plasma membrane nanoscopy. Commun Biol 2024; 7:620. [PMID: 38783117 PMCID: PMC11116533 DOI: 10.1038/s42003-024-06313-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
A key player of excitable cells in the heart and brain is the L-type calcium channel CaV1.3. In the heart, it is required for voltage-dependent Ca2+-signaling, i.e., for controlling and modulating atrial cardiomyocyte excitation-contraction coupling. The clustering of CaV1.3 in functionally relevant channel multimers has not been addressed due to a lack of stoichiometric labeling combined with high-resolution imaging. Here, we developed a HaloTag-labeling strategy to visualize and quantify CaV1.3 clusters using STED nanoscopy to address the questions of cluster size and intra-cluster channel density. Channel clusters were identified in the plasma membrane of transfected live HEK293 cells as well as in giant plasma membrane vesicles derived from these cells that were spread on modified glass support to obtain supported plasma membrane bilayers (SPMBs). A small fraction of the channel clusters was colocalized with early and recycling endosomes at the membranes. STED nanoscopy in conjunction with live-cell and SPMB imaging enabled us to quantify CaV1.3 cluster sizes and their molecular density revealing significantly lower channel densities than expected for dense channel packing. CaV1.3 channel cluster size and molecular density were increased in SPMBs after treatment of the cells with the sympathomimetic compound isoprenaline, suggesting a regulated channel cluster condensation mechanism.
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Affiliation(s)
- Niko Schwenzer
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Robert‑Koch‑Str. 42a, 37075, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37073, Göttingen, Germany
| | - Nikolas K Teiwes
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37073, Göttingen, Germany
- Georg-August Universität, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077, Göttingen, Germany
| | - Tobias Kohl
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Robert‑Koch‑Str. 42a, 37075, Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Celine Pohl
- Georg-August Universität, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077, Göttingen, Germany
| | - Michelle J Giller
- Georg-August Universität, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077, Göttingen, Germany
| | - Stephan E Lehnart
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Robert‑Koch‑Str. 42a, 37075, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37073, Göttingen, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
- Collaborative Research Center SFB 1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
| | - Claudia Steinem
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37073, Göttingen, Germany.
- Georg-August Universität, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077, Göttingen, Germany.
- Max-Planck-Institut für Dynamik und Selbstorganisation, Am Fassberg 17, 37077, Göttingen, Germany.
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3
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Chen J, Stephan T, Gaedke F, Liu T, Li Y, Schauss A, Chen P, Wulff V, Jakobs S, Jüngst C, Chen Z. An aldehyde-crosslinking mitochondrial probe for STED imaging in fixed cells. Proc Natl Acad Sci U S A 2024; 121:e2317703121. [PMID: 38687792 PMCID: PMC11087744 DOI: 10.1073/pnas.2317703121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/22/2024] [Indexed: 05/02/2024] Open
Abstract
Fluorescence labeling of chemically fixed specimens, especially immunolabeling, plays a vital role in super-resolution imaging as it offers a convenient way to visualize cellular structures like mitochondria or the distribution of biomolecules with high detail. Despite the development of various distinct probes that enable super-resolved stimulated emission depletion (STED) imaging of mitochondria in live cells, most of these membrane-potential-dependent fluorophores cannot be retained well in mitochondria after chemical fixation. This lack of suitable mitochondrial probes has limited STED imaging of mitochondria to live cell samples. In this study, we introduce a mitochondria-specific probe, PK Mito Orange FX (PKMO FX), which features a fixation-driven cross-linking motif and accumulates in the mitochondrial inner membrane. It exhibits high fluorescence retention after chemical fixation and efficient depletion at 775 nm, enabling nanoscopic imaging both before and after aldehyde fixation. We demonstrate the compatibility of this probe with conventional immunolabeling and other strategies commonly used for fluorescence labeling of fixed samples. Moreover, we show that PKMO FX facilitates correlative super-resolution light and electron microscopy, enabling the correlation of multicolor fluorescence images and transmission EM images via the characteristic mitochondrial pattern. Our probe further expands the mitochondrial toolkit for multimodal microscopy at nanometer resolutions.
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Affiliation(s)
- Jingting Chen
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing100871, China
| | - Till Stephan
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen37077, Germany
- Clinic of Neurology, University Medical Center Göttingen, Göttingen37075, Germany
| | - Felix Gaedke
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Tianyan Liu
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Yiyan Li
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Astrid Schauss
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Peng Chen
- Peking University-Nanjing Institute of Translational Medicine, Nanjing211800, China
- Genvivo Biotech (PuHaiJingShan), Nanjing211800, China
| | - Veronika Wulff
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen37077, Germany
- Clinic of Neurology, University Medical Center Göttingen, Göttingen37075, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology Translational, Neuroinflammation and Automated Microscopy, Göttingen37075, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells”, University of Göttingen, Göttingen37099, Germany
| | - Christian Jüngst
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Zhixing Chen
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
- Peking University-Nanjing Institute of Translational Medicine, Nanjing211800, China
- Genvivo Biotech (PuHaiJingShan), Nanjing211800, China
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4
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Lin Z, Zhang X, Nandi P, Lin Y, Wang L, Chu YS, Paape T, Yang Y, Xiao X, Liu Q. Correlative single-cell hard X-ray computed tomography and X-ray fluorescence imaging. Commun Biol 2024; 7:280. [PMID: 38448784 PMCID: PMC10917812 DOI: 10.1038/s42003-024-05950-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 02/21/2024] [Indexed: 03/08/2024] Open
Abstract
X-ray computed tomography (XCT) and X-ray fluorescence (XRF) imaging are two non-invasive imaging techniques to study cellular structures and chemical element distributions, respectively. However, correlative X-ray computed tomography and fluorescence imaging for the same cell have yet to be routinely realized due to challenges in sample preparation and X-ray radiation damage. Here we report an integrated experimental and computational workflow for achieving correlative multi-modality X-ray imaging of a single cell. The method consists of the preparation of radiation-resistant single-cell samples using live-cell imaging-assisted chemical fixation and freeze-drying procedures, targeting and labeling cells for correlative XCT and XRF measurement, and computational reconstruction of the correlative and multi-modality images. With XCT, cellular structures including the overall structure and intracellular organelles are visualized, while XRF imaging reveals the distribution of multiple chemical elements within the same cell. Our correlative method demonstrates the feasibility and broad applicability of using X-rays to understand cellular structures and the roles of chemical elements and related proteins in signaling and other biological processes.
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Affiliation(s)
- Zihan Lin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Xiao Zhang
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Purbasha Nandi
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Yuewei Lin
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Liguo Wang
- Laboratory for BioMolecular Structure, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Yong S Chu
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Timothy Paape
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
- U.S. Department of Agriculture's Agricultural Research Service at Children's Nutrition Research Center, Houston, TX, 77030, USA
| | - Yang Yang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA.
| | - Xianghui Xiao
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA.
| | - Qun Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA.
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA.
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5
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Nalezinková M, Loskot J, Myslivcová Fučíková A. The use of scanning electron microscopy and fixation methods to evaluate the interaction of blood with the surfaces of medical devices. Sci Rep 2024; 14:4622. [PMID: 38409219 PMCID: PMC10897226 DOI: 10.1038/s41598-024-55136-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/20/2024] [Indexed: 02/28/2024] Open
Abstract
Testing the hemocompatibility of medical devices after their interaction with blood entails the need to evaluate the activation of blood elements and the degree of their coagulation and adhesion to the device surface. One possible way to achieve this is to use scanning electron microscopy (SEM). The aim was to develop a novel SEM-based method to assess the thrombogenic potential of medical devices and their adhesiveness to blood cells. As a part of this task, also find a convenient procedure of efficient and non-destructive sample fixation for SEM while reducing the use of highly toxic substances and shortening the fixation time. A polymeric surgical mesh was exposed to blood so that blood elements adhered to its surface. Such prepared samples were then chemically fixed for a subsequent SEM measurement; a number of fixation procedures were tested to find the optimal one. The fixation results were evaluated from SEM images, and the degree of blood elements' adhesion was determined from the images using ImageJ software. The best fixation was achieved with the May-Grünwald solution, which is less toxic than chemicals traditionally used. Moreover, manipulation with highly toxic osmium tetroxide can be avoided in the proposed procedure. A convenient methodology for SEM image analysis has been developed too, enabling to quantitatively evaluate the interaction of blood with the surfaces of various medical devices. Our method replaces the subjective assessment of surface coverage with a better-defined procedure, thus offering more precise and reliable results.
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Affiliation(s)
- Martina Nalezinková
- Department of Biology, Faculty of Science, University of Hradec Králové, Rokitanského 62, Hradec Králové, 500 03, Czech Republic.
| | - Jan Loskot
- Department of Physics, Faculty of Science, University of Hradec Králové, Rokitanského 62, Hradec Králové, 500 03, Czech Republic
| | - Alena Myslivcová Fučíková
- Department of Biology, Faculty of Science, University of Hradec Králové, Rokitanského 62, Hradec Králové, 500 03, Czech Republic
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6
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Kim JY, Yang JE, Mitchell JW, English LA, Yang SZ, Tenpas T, Dent EW, Wildonger J, Wright ER. Handling Difficult Cryo-ET Samples: A Study with Primary Neurons from Drosophila melanogaster. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:2127-2148. [PMID: 37966978 PMCID: PMC11168236 DOI: 10.1093/micmic/ozad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/01/2023] [Accepted: 10/18/2023] [Indexed: 11/17/2023]
Abstract
Cellular neurobiology has benefited from recent advances in the field of cryo-electron tomography (cryo-ET). Numerous structural and ultrastructural insights have been obtained from plunge-frozen primary neurons cultured on electron microscopy grids. With most primary neurons having been derived from rodent sources, we sought to expand the breadth of sample availability by using primary neurons derived from 3rd instar Drosophila melanogaster larval brains. Ultrastructural abnormalities were encountered while establishing this model system for cryo-ET, which were exemplified by excessive membrane blebbing and cellular fragmentation. To optimize neuronal samples, we integrated substrate selection, micropatterning, montage data collection, and chemical fixation. Efforts to address difficulties in establishing Drosophila neurons for future cryo-ET studies in cellular neurobiology also provided insights that future practitioners can use when attempting to establish other cell-based model systems.
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Affiliation(s)
- Joseph Y. Kim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jie E. Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Josephine W. Mitchell
- Department of Chemistry and Biochemistry, Kalamazoo College, Kalamazoo, MI 49006, USA
| | - Lauren A. English
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sihui Z. Yang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Tanner Tenpas
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Erik W. Dent
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jill Wildonger
- Departments of Pediatrics and Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53715, USA
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7
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Yadav A, Kumar A. Artificial intelligence in rectal cancer: What is the future? Artif Intell Cancer 2023; 4:11-22. [DOI: 10.35713/aic.v4.i2.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/18/2023] [Accepted: 09/25/2023] [Indexed: 12/07/2023] Open
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer in both men and women, and it is the second leading cause of cancer-related deaths globally. Around 60%-70% of CRC patients are diagnosed at advanced stages, with nearly 20% having liver metastases. It is noteworthy that the 5-year survival rates decline significantly from 80%-90% for localized disease to a mere 10%-15% for patients with metastasis at the time of diagnosis. Early diagnosis, appropriate therapeutic strategy, accurate assessment of treatment response, and prognostication is essential for better outcome. There has been significant technological development in the last couple of decades to improve the outcome of rectal cancer including Artificial intelligence (AI). AI is a broad term used to describe the study of machines that mimic human intelligence, such as perceiving the environment, drawing logical conclusions from observations, and performing complex tasks. At present AI has demonstrated a promising role in early diagnosis, prognosis, and treatment outcomes for patients with rectal cancer, a limited role in surgical decision making, and had a bright future.
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Affiliation(s)
- Alka Yadav
- Department of Surgical Gastroenterology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow 226014, UP, India
| | - Ashok Kumar
- Department of Surgical Gastroenterology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow 226014, UP, India
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Lyndby NH, Murthy S, Bessette S, Jakobsen SL, Meibom A, Kühl M. Non-invasive investigation of the morphology and optical properties of the upside-down jellyfish Cassiopea with optical coherence tomography. Proc Biol Sci 2023; 290:20230127. [PMID: 37752841 PMCID: PMC10523073 DOI: 10.1098/rspb.2023.0127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023] Open
Abstract
The jellyfish Cassiopea largely cover their carbon demand via photosynthates produced by microalgal endosymbionts, but how holobiont morphology and tissue optical properties affect the light microclimate and symbiont photosynthesis in Cassiopea remain unexplored. Here, we use optical coherence tomography (OCT) to study the morphology of Cassiopea medusae at high spatial resolution. We include detailed 3D reconstructions of external micromorphology, and show the spatial distribution of endosymbionts and white granules in the bell tissue. Furthermore, we use OCT data to extract inherent optical properties from light-scattering white granules in Cassiopea, and show that granules enhance local light-availability for symbionts in close proximity. Individual granules had a scattering coefficient of µs = 200-300 cm-1, and scattering anisotropy factor of g = 0.7, while large tissue-regions filled with white granules had a lower µs = 40-100 cm-1, and g = 0.8-0.9. We combined OCT information with isotopic labelling experiments to investigate the effect of enhanced light-availability in whitish tissue regions. Endosymbionts located in whitish tissue exhibited significantly higher carbon fixation compared to symbionts in anastomosing tissue (i.e. tissue without light-scattering white granules). Our findings support previous suggestions that white granules in Cassiopea play an important role in the host modulation of the light-microenvironment.
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Affiliation(s)
- Niclas Heidelberg Lyndby
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Swathi Murthy
- Marine Biological Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark
| | - Sandrine Bessette
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Laboratoire MAPIEM, Université de Toulon, 4323 Toulon, France
| | - Sofie Lindegaard Jakobsen
- Marine Biological Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Center for Advanced Surface Analysis, Institute of Earth Science, University of Lausanne, 1015 Lausanne, Switzerland
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark
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9
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Lu X, Han X, Meirovitch Y, Sjöstedt E, Schalek RL, Lichtman JW. Preserving extracellular space for high-quality optical and ultrastructural studies of whole mammalian brains. CELL REPORTS METHODS 2023; 3:100520. [PMID: 37533653 PMCID: PMC10391564 DOI: 10.1016/j.crmeth.2023.100520] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/08/2023] [Accepted: 06/07/2023] [Indexed: 08/04/2023]
Abstract
Analysis of brain structure, connectivity, and molecular diversity relies on effective tissue fixation. Conventional tissue fixation causes extracellular space (ECS) loss, complicating the segmentation of cellular objects from electron microscopy datasets. Previous techniques for preserving ECS in mammalian brains utilizing high-pressure perfusion can give inconsistent results owing to variations in the hydrostatic pressure within the vasculature. A more reliable fixation protocol that uniformly preserves the ECS throughout whole brains would greatly benefit a wide range of neuroscience studies. Here, we report a straightforward transcardial perfusion strategy that preserves ECS throughout the whole rodent brain. No special setup is needed besides sequential solution changes, and the protocol offers excellent reproducibility. In addition to better capturing tissue ultrastructure, preservation of ECS has many downstream advantages such as accelerating heavy-metal staining for electron microscopy, improving detergent-free immunohistochemistry for correlated light and electron microscopy, and facilitating lipid removal for tissue clearing.
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Affiliation(s)
- Xiaotang Lu
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Xiaomeng Han
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Yaron Meirovitch
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Evelina Sjöstedt
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Richard L. Schalek
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Jeff W. Lichtman
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
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10
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Kim JY, Yang JE, Mitchell JW, English LA, Yang SZ, Tenpas T, Dent EW, Wildonger J, Wright ER. Handling difficult cryo-ET samples: A study with primary neurons from Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548468. [PMID: 37502991 PMCID: PMC10369871 DOI: 10.1101/2023.07.10.548468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Cellular neurobiology has benefited from recent advances in the field of cryo-electron tomography (cryo-ET). Numerous structural and ultrastructural insights have been obtained from plunge-frozen primary neurons cultured on electron microscopy grids. With most primary neurons been derived from rodent sources, we sought to expand the breadth of sample availability by using primary neurons derived from 3rd instar Drosophila melanogaster larval brains. Ultrastructural abnormalities were encountered while establishing this model system for cryo-ET, which were exemplified by excessive membrane blebbing and cellular fragmentation. To optimize neuronal samples, we integrated substrate selection, micropatterning, montage data collection, and chemical fixation. Efforts to address difficulties in establishing Drosophila neurons for future cryo-ET studies in cellular neurobiology also provided insights that future practitioners can use when attempting to establish other cell-based model systems.
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Affiliation(s)
- Joseph Y. Kim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jie E. Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Josephine W. Mitchell
- Department of Chemistry and Biochemistry, Kalamazoo College, Kalamazoo, MI, 49006, USA
| | - Lauren A. English
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Sihui Z. Yang
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Tanner Tenpas
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Erik W. Dent
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Jill Wildonger
- Departments of Pediatrics and Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53715, USA
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11
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Yoshida SR, Maity BK, Chong S. Visualizing Protein Localizations in Fixed Cells: Caveats and the Underlying Mechanisms. J Phys Chem B 2023; 127:4165-4173. [PMID: 37161904 DOI: 10.1021/acs.jpcb.3c01658] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Fluorescence microscopy techniques have been widely adopted in biology for their ability to visualize the structure and dynamics of a wide range of cellular and subcellular processes. The specificity and sensitivity that these techniques afford have made them primary tools in the characterization of protein localizations within cells. Many of the fluorescence microscopy techniques require cells to be fixed via chemical or alternative methods before being imaged. However, some fixation methods have been found to induce the redistribution of particular proteins in the cell, resulting in artifacts in the characterization of protein localizations and functions under physiological conditions. Here, we review the ability of commonly used cell fixation methods to faithfully preserve the localizations of proteins that bind to chromatin, undergo liquid-liquid phase separation (LLPS), and are involved in the formation of various membrane-bound organelles. We also review the mechanisms underlying various fixation artifacts and discuss potential alternative fixation methods to minimize the artifacts while investigating different proteins and cellular structures. Overall, fixed-cell fluorescence microscopy is a very powerful tool in biomedical research; however, each experiment demands the careful selection of an appropriate fixation method to avoid potential artifacts and may benefit from live-cell imaging validation.
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Affiliation(s)
- Shawn R Yoshida
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Barun K Maity
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Shasha Chong
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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12
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Edabashi H, Elghadafi R, Rajkanth N, Mody JS, Ma W, Dibart S, Tang X. A hybrid technique for measurement of intra/extracellular proteins. PLoS One 2023; 18:e0282948. [PMID: 37141290 PMCID: PMC10159171 DOI: 10.1371/journal.pone.0282948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/27/2023] [Indexed: 05/05/2023] Open
Abstract
ELISA or Western blot is known as a basic technique to be used for measurement of intracellular proteins, but in some cases, they cannot overcome problems such as normalization between samples or extraneous costs for required commercial kits. In order to address this problem, we developed a rapid and effective method (a hybrid of Western blot and ELISA). We use this new hybrid method to detect and normalize trace protein changes in gene expression intracellularly at a lower cost.
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Affiliation(s)
- Haiam Edabashi
- Department of Periodontology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, MA, United States of America
| | - Radwa Elghadafi
- Department of Periodontology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, MA, United States of America
| | - Nischwethaa Rajkanth
- Department of Periodontology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, MA, United States of America
| | - Janvi Saurabh Mody
- Department of Periodontology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, MA, United States of America
| | - Weiyuan Ma
- Department of Periodontology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, MA, United States of America
| | - Serge Dibart
- Department of Periodontology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, MA, United States of America
| | - Xiaoren Tang
- Department of Periodontology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, MA, United States of America
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13
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HS1 deficiency protects against sepsis by attenuating neutrophil-inflicted lung damage. Eur J Cell Biol 2022; 101:151214. [PMID: 35286924 PMCID: PMC10170315 DOI: 10.1016/j.ejcb.2022.151214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 12/20/2022] Open
Abstract
Sepsis remains an important health problem worldwide due to inefficient treatments often resulting in multi-organ failure. Neutrophil recruitment is critical during sepsis. While neutrophils are required to combat invading bacteria, excessive neutrophil recruitment contributes to tissue damage due to their arsenal of molecular weapons that do not distinguish between host and pathogen. Thus, neutrophil recruitment needs to be fine-tuned to ensure bacterial killing, while avoiding neutrophil-inflicted tissue damage. We recently showed that the actin-binding protein HS1 promotes neutrophil extravasation; and hypothesized that HS1 is also a critical regulator of sepsis progression. We evaluated the role of HS1 in a model of lethal sepsis induced by cecal-ligation and puncture. We found that septic HS1-deficient mice had a better survival rate compared to WT mice due to absence of lung damage. Lungs of septic HS1-deficient mice showed less inflammation, fibrosis, and vascular congestion. Importantly, systemic CLP-induced neutrophil recruitment was attenuated in the lungs, the peritoneum and the cremaster in the absence of HS1. Lungs of HS1-deficient mice produced significantly more interleukin-10. Compared to WT neutrophils, those HS1-deficient neutrophils that reached the lungs had increased surface levels of Gr-1, ICAM-1, and L-selectin. Interestingly, HS1-deficient neutrophils had similar F-actin content and phagocytic activity, but they failed to polymerize actin and deform in response to CXCL-1 likely explaining the reduced systemic neutrophil recruitment in HS1-deficient mice. Our data show that HS1 deficiency protects against sepsis by attenuating neutrophil recruitment to amounts sufficient to combat bacterial infection, but insufficient to induce tissue damage.
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14
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Huebinger J, Grecco H, Masip ME, Christmann J, Fuhr GR, Bastiaens PIH. Ultrarapid cryo-arrest of living cells on a microscope enables multiscale imaging of out-of-equilibrium molecular patterns. SCIENCE ADVANCES 2021; 7:eabk0882. [PMID: 34890224 PMCID: PMC8664253 DOI: 10.1126/sciadv.abk0882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
Imaging molecular patterns in cells by fluorescence micro- or nanoscopy has the potential to relate collective molecular behavior to cellular function. However, spatial and spectroscopic resolution is fundamentally limited by motional blur caused by finite photon fluxes and photobleaching. At physiological temperatures, photochemical reactivity does not only limit imaging at multiple scales but is also toxic to biochemical reactions that maintain cellular organization. Here, we present cryoprotectant-free ultrarapid cryo-arrest directly on a multimodal fluorescence microscope that preserves the out-of-equilibrium molecular organization of living cells. This allows the imaging of dynamic processes before cryo-arrest in combination with precise molecular pattern determination at multiple scales within the same cells under cryo-arrest. We both experimentally and theoretically show that ultrarapid cryo-arrest overcomes the fundamental resolution barrier imposed by motional blur and photochemical reactivity, enabling observation of native molecular distributions and reaction patterns that are not resolvable at physiological temperatures.
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Affiliation(s)
- Jan Huebinger
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany
| | - Hernan Grecco
- Department of Physics, FCEN, University of Buenos Aires and IFIBA, CONICET, Buenos Aires, Argentina
| | - Martín E. Masip
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany
| | - Jens Christmann
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany
| | - Günter R. Fuhr
- Fraunhofer Institute for Biomedical Engineering, Joseph-von-Fraunhofer-Weg 1, 66280 Sulzbach, Germany
| | - Philippe I. H. Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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15
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Valli J, Sanderson J. Super-Resolution Fluorescence Microscopy Methods for Assessing Mouse Biology. Curr Protoc 2021; 1:e224. [PMID: 34436832 DOI: 10.1002/cpz1.224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Super-resolution (diffraction unlimited) microscopy was developed 15 years ago; the developers were awarded the Nobel Prize in Chemistry in recognition of their work in 2014. Super-resolution microscopy is increasingly being applied to diverse scientific fields, from single molecules to cell organelles, viruses, bacteria, plants, and animals, especially the mammalian model organism Mus musculus. In this review, we explain how super-resolution microscopy, along with fluorescence microscopy from which it grew, has aided the renaissance of the light microscope. We cover experiment planning and specimen preparation and explain structured illumination microscopy, super-resolution radial fluctuations, stimulated emission depletion microscopy, single-molecule localization microscopy, and super-resolution imaging by pixel reassignment. The final section of this review discusses the strengths and weaknesses of each super-resolution technique and how to choose the best approach for your research. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Jessica Valli
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
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16
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Zarębski M, Bosire R, Wesołowska J, Szelest O, Eatmann A, Jasińska-Konior K, Kepp O, Kroemer G, Szabo G, Dobrucki JW. Translocation of chromatin proteins to nucleoli-The influence of protein dynamics on post-fixation localization. Cytometry A 2021; 99:1230-1239. [PMID: 34110091 PMCID: PMC9543561 DOI: 10.1002/cyto.a.24464] [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: 02/18/2021] [Revised: 05/16/2021] [Accepted: 05/19/2021] [Indexed: 11/23/2022]
Abstract
It is expected that the subnuclear localization of a protein in a fixed cell, detected by microscopy, reflects its position in the living cell. We demonstrate, however, that some dynamic nuclear proteins can change their localization upon fixation by either crosslinking or non‐crosslinking methods. We examined the subnuclear localization of the chromatin architectural protein HMGB1, linker histone H1, and core histone H2B in cells fixed by formaldehyde, glutaraldehyde, glyoxal, ethanol, or zinc salts. We demonstrate that some dynamic, weakly binding nuclear proteins, like HMGB1 and H1, may not only be unexpectedly lost from their original binding sites during the fixation process, but they can also diffuse through the nucleus and eventually bind in nucleoli. Such translocation to nucleoli does not occur in the case of core histone H2B, which is more stably bound to DNA and other histones. We suggest that the diminished binding of some dynamic proteins to DNA during fixation, and their subsequent translocation to nucleoli, is induced by changes of DNA structure, arising from interaction with a fixative. Detachment of dynamic proteins from chromatin can also be induced in cells already fixed by non‐crosslinking methods when DNA structure is distorted by intercalating molecules. The proteins translocated during fixation from chromatin to nucleoli bind there to RNA‐containing structures.
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Affiliation(s)
- Mirosław Zarębski
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Poland
| | - Rosevalentine Bosire
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Julita Wesołowska
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Poland
| | - Oskar Szelest
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Poland
| | - Ahmed Eatmann
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Poland
| | - Katarzyna Jasińska-Konior
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Poland
| | - Oliver Kepp
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Paris, France.,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Paris, France.,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, Paris, AP-HP, France.,Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China.,Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden
| | - Gabor Szabo
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Jurek W Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Poland
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17
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Pegg TJ, Gladish DK, Baker RL. Algae to angiosperms: Autofluorescence for rapid visualization of plant anatomy among diverse taxa. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11437. [PMID: 34268017 PMCID: PMC8272585 DOI: 10.1002/aps3.11437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/19/2021] [Indexed: 05/22/2023]
Abstract
PREMISE Fluorescence microscopy is an effective tool for viewing plant internal anatomy. However, using fluorescent antibodies or labels hinders throughput. We present a minimal protocol that takes advantage of inherent autofluorescence and aldehyde-induced fluorescence in plant cellular and subcellular structures to markedly increase throughput in cellular and ultrastructural visualization. METHODS AND RESULTS Twelve species distributed across the plant phylogeny were each subjected to five fixative treatments: 1% paraformaldehyde and 2% glutaraldehyde, 2% paraformaldehyde, 2% glutaraldehyde, formalin-acid-alcohol (FAA), and 70% ethanol. Samples were prepared by embedding and mechanically sectioning or via whole mount. A confocal laser scanning system was used to collect micrographs. We evaluated and compared fixative influence on sample structural preservation and tissue autofluorescence. CONCLUSIONS Formaldehyde fixation of Viridiplantae taxa samples generates useful structural data while requiring no additional histological staining or clearing. In addition, a fluorescence-capable microscope is the only specialized equipment required for image acquisition. The minimal protocol developed in this experiment enables high-throughput sample processing by eliminating the need for multi-day preparations.
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Affiliation(s)
- Timothy J. Pegg
- Department of BiologyMiami UniversityOxfordOhio45056USA
- Graduate Program in BotanyMiami UniversityOxfordOhio45056USA
| | - Daniel K. Gladish
- Department of BiologyMiami UniversityOxfordOhio45056USA
- Graduate Program in BotanyMiami UniversityOxfordOhio45056USA
| | - Robert L. Baker
- Department of BiologyMiami UniversityOxfordOhio45056USA
- Graduate Program in BotanyMiami UniversityOxfordOhio45056USA
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18
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Yao RW, Luan PF, Chen LL. An optimized fixation method containing glyoxal and paraformaldehyde for imaging nuclear bodies. RNA (NEW YORK, N.Y.) 2021; 27:725-733. [PMID: 33846273 PMCID: PMC8127994 DOI: 10.1261/rna.078671.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/08/2021] [Indexed: 05/26/2023]
Abstract
The mammalian cell nucleus contains different types of membrane-less nuclear bodies (NBs) consisting of proteins and RNAs. Microscopic imaging has been widely applied to study the organization and structure of NBs. However, current fixation methods are not optimized for such imaging: When a fixation method is chosen to maximize the quality of the RNA fluorescence in situ hybridization (FISH), it often limits the labeling efficiency of proteins or affects the ultrastructure of NBs. Here, we report that addition of glyoxal (GO) into the classical paraformaldehyde (PFA) fixation step not only improves FISH signals for RNAs in NBs via augmented permeability of the fixed nucleus and enhanced accessibility of probes, but also largely preserves protein fluorescent signals during fixation and immunostaining. We also show that GO/PFA fixation enables the covisualization of different types of nuclear bodies with minimal impact on their ultrastructures under super-resolution microscopy.
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Affiliation(s)
- Run-Wen Yao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Peng-Fei Luan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 330106, China
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19
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Qin Y, Jiang W, Li A, Gao M, Liu H, Gao Y, Tian X, Gong G. The Combination of Paraformaldehyde and Glutaraldehyde Is a Potential Fixative for Mitochondria. Biomolecules 2021; 11:711. [PMID: 34068806 PMCID: PMC8151741 DOI: 10.3390/biom11050711] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/30/2021] [Accepted: 05/07/2021] [Indexed: 01/31/2023] Open
Abstract
Mitochondria are highly dynamic organelles, constantly undergoing shape changes, which are controlled by mitochondrial movement, fusion, and fission. Mitochondria play a pivotal role in various cellular processes under physiological and pathological conditions, including metabolism, superoxide generation, calcium homeostasis, and apoptosis. Abnormal mitochondrial morphology and mitochondrial protein expression are always closely related to the health status of cells. Analysis of mitochondrial morphology and mitochondrial protein expression in situ is widely used to reflect the abnormality of cell function in the chemical fixed sample. Paraformaldehyde (PFA), the most commonly used fixative in cellular immunostaining, still has disadvantages, including loss of antigenicity and disruption of morphology during fixation. We tested the effect of ethanol (ETHO), PFA, and glutaraldehyde (GA) fixation on cellular mitochondria. The results showed that 3% PFA and 1.5% GA (PFA-GA) combination reserved mitochondrial morphology better than them alone in situ in cells. Mitochondrial network and protein antigenicity were well maintained, indicated by preserved MitoTracker and mitochondrial immunostaining after PFA-GA fixation. Our results suggest that the PFA-GA combination is a valuable fixative for the study of mitochondria in situ.
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Affiliation(s)
- Yuan Qin
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (Y.Q.); (W.J.); (A.L.); (M.G.); (H.L.); (Y.G.)
- Department of Pharmacy, Shanghai East Hospital, Tongji University, Shanghai 200120, China
| | - Wenting Jiang
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (Y.Q.); (W.J.); (A.L.); (M.G.); (H.L.); (Y.G.)
| | - Anqi Li
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (Y.Q.); (W.J.); (A.L.); (M.G.); (H.L.); (Y.G.)
| | - Meng Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (Y.Q.); (W.J.); (A.L.); (M.G.); (H.L.); (Y.G.)
| | - Hanyu Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (Y.Q.); (W.J.); (A.L.); (M.G.); (H.L.); (Y.G.)
| | - Yufei Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (Y.Q.); (W.J.); (A.L.); (M.G.); (H.L.); (Y.G.)
| | - Xiangang Tian
- Department of Cardiovascular Surgery, Daping Hospital, Army Medical Center of PLA, Chongqing 400037, China;
| | - Guohua Gong
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (Y.Q.); (W.J.); (A.L.); (M.G.); (H.L.); (Y.G.)
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20
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Kramer M, Rodriguez-Heredia M, Saccon F, Mosebach L, Twachtmann M, Krieger-Liszkay A, Duffy C, Knell RJ, Finazzi G, Hanke GT. Regulation of photosynthetic electron flow on dark to light transition by ferredoxin:NADP(H) oxidoreductase interactions. eLife 2021; 10:56088. [PMID: 33685582 PMCID: PMC7984839 DOI: 10.7554/elife.56088] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 02/25/2021] [Indexed: 01/12/2023] Open
Abstract
During photosynthesis, electron transport is necessary for carbon assimilation and must be regulated to minimize free radical damage. There is a longstanding controversy over the role of a critical enzyme in this process (ferredoxin:NADP(H) oxidoreductase, or FNR), and in particular its location within chloroplasts. Here we use immunogold labelling to prove that FNR previously assigned as soluble is in fact membrane associated. We combined this technique with a genetic approach in the model plant Arabidopsis to show that the distribution of this enzyme between different membrane regions depends on its interaction with specific tether proteins. We further demonstrate a correlation between the interaction of FNR with different proteins and the activity of alternative photosynthetic electron transport pathways. This supports a role for FNR location in regulating photosynthetic electron flow during the transition from dark to light.
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Affiliation(s)
- Manuela Kramer
- School of Biochemistry and Chemistry, Queen Mary University of London, London, United Kingdom.,Department of Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, Osnabrück, Germany
| | | | - Francesco Saccon
- School of Biochemistry and Chemistry, Queen Mary University of London, London, United Kingdom
| | - Laura Mosebach
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Manuel Twachtmann
- Department of Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Anja Krieger-Liszkay
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Paris, France
| | - Chris Duffy
- School of Biochemistry and Chemistry, Queen Mary University of London, London, United Kingdom
| | - Robert J Knell
- School of Biochemistry and Chemistry, Queen Mary University of London, London, United Kingdom
| | - Giovanni Finazzi
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS), Commissariat a` l'Energie Atomique et aux Energies Alternatives (CEA), Université Grenoble Alpes, Institut National Recherche Agronomique (INRA), Institut de Recherche en Sciences et Technologies pour le Vivant (iRTSV), CEA Grenoble, Grenoble, France
| | - Guy Thomas Hanke
- School of Biochemistry and Chemistry, Queen Mary University of London, London, United Kingdom.,Department of Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, Osnabrück, Germany
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21
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Supra-Molecular Assemblies of ORAI1 at Rest Precede Local Accumulation into Puncta after Activation. Int J Mol Sci 2021; 22:ijms22020799. [PMID: 33466866 PMCID: PMC7831003 DOI: 10.3390/ijms22020799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/04/2021] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
The Ca2+ selective channel ORAI1 and endoplasmic reticulum (ER)-resident STIM proteins form the core of the channel complex mediating store operated Ca2+ entry (SOCE). Using liquid phase electron microscopy (LPEM), the distribution of ORAI1 proteins was examined at rest and after SOCE-activation at nanoscale resolution. The analysis of over seven hundred thousand ORAI1 positions revealed a number of ORAI1 channels had formed STIM-independent distinct supra-molecular clusters. Upon SOCE activation and in the presence of STIM proteins, a fraction of ORAI1 assembled in micron-sized two-dimensional structures, such as the known puncta at the ER plasma membrane contact zones, but also in divergent structures such as strands, and ring-like shapes. Our results thus question the hypothesis that stochastically migrating single ORAI1 channels are trapped at regions containing activated STIM, and we propose instead that supra-molecular ORAI1 clusters fulfill an amplifying function for creating dense ORAI1 accumulations upon SOCE-activation.
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22
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Cambier CJ, Banik SM, Buonomo JA, Bertozzi CR. Spreading of a mycobacterial cell-surface lipid into host epithelial membranes promotes infectivity. eLife 2020; 9:60648. [PMID: 33226343 PMCID: PMC7735756 DOI: 10.7554/elife.60648] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/23/2020] [Indexed: 12/31/2022] Open
Abstract
Several virulence lipids populate the outer cell wall of pathogenic mycobacteria. Phthiocerol dimycocerosate (PDIM), one of the most abundant outer membrane lipids, plays important roles in both defending against host antimicrobial programs and in evading these programs altogether. Immediately following infection, mycobacteria rely on PDIM to evade Myd88-dependent recruitment of microbicidal monocytes which can clear infection. To circumvent the limitations in using genetics to understand virulence lipids, we developed a chemical approach to track PDIM during Mycobacterium marinum infection of zebrafish. We found that PDIM's methyl-branched lipid tails enabled it to spread into host epithelial membranes to prevent immune activation. Additionally, PDIM’s affinity for cholesterol promoted this phenotype; treatment of zebrafish with statins, cholesterol synthesis inhibitors, decreased spreading and provided protection from infection. This work establishes that interactions between host and pathogen lipids influence mycobacterial infectivity and suggests the use of statins as tuberculosis preventive therapy by inhibiting PDIM spread.
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Affiliation(s)
- C J Cambier
- Department of Chemistry, Stanford University, Stanford, United States
| | - Steven M Banik
- Department of Chemistry, Stanford University, Stanford, United States
| | - Joseph A Buonomo
- Department of Chemistry, Stanford University, Stanford, United States
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
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23
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Miyoshi H, Shimizu Y, Yasui Y, Sugiyama S. Expansion of mouse primitive hematopoietic cells in three-dimensional cultures on chemically fixed stromal cell layers. Cytotechnology 2020; 72:741-750. [PMID: 32897481 DOI: 10.1007/s10616-020-00417-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/29/2020] [Indexed: 11/27/2022] Open
Abstract
To establish a practical and convenient method to expand hematopoietic cells (HCs), we applied chemically-fixed stromal cell layers formed within three-dimensional (3D) scaffolds to feeder of HC cultures. The HCs were expanded using two successive cultures. First, stromal cells were cultured within porous polymer scaffolds and formed tissue-engineered constructs (TECs); the scaffolds containing stromal cells, were fixed using aldehyde (formaldehyde or glutaraldehyde) or organic solvents (acetone, methanol or ethanol). Second, mouse fetal liver cells (FLCs), as a source of HCs, were cultured on the TECs for 2 weeks, and the effects of fixative solutions on expansion of primitive HCs (c-kit+ and CD34+ cells) were examined. In the cultures on aldehyde-fixed TECs, primitive HCs were expanded 2.5- to 5.1-fold in the cultures on TECs fixed with glutaraldehyde, whereas no expansions were detected in those fixed with formaldehyde. However, we achieved expansion of primitive HCs > fivefold in the cultures using TECs fixed with organic solvents. Among these solvents, the highest expansions-of roughly tenfold-were obtained using acetone fixation. Ethanol-fixed TECs also supported the expansion of the primitive HCs well (6.6- to 8.0-fold). In addition to these sufficient expansions, the procedure and storage of fixed TECs is fairly easy. Thus, HC expansion on chemically-fixed TECs may be a practical method for expanding primitive HCs.
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Affiliation(s)
- Hirotoshi Miyoshi
- Department of Biomedical Engineering, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
| | - Yuichiro Shimizu
- Department of Biomedical Engineering, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Yutaka Yasui
- Department of Biomedical Engineering, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Satoshi Sugiyama
- Department of Biomedical Engineering, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
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24
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Hobson BD, Kong L, Hartwick EW, Gonzalez RL, Sims PA. Elongation inhibitors do not prevent the release of puromycylated nascent polypeptide chains from ribosomes. eLife 2020; 9:60048. [PMID: 32844746 PMCID: PMC7490010 DOI: 10.7554/elife.60048] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/04/2020] [Indexed: 12/21/2022] Open
Abstract
Puromycin is an amino-acyl transfer RNA analog widely employed in studies of protein synthesis. Since puromycin is covalently incorporated into nascent polypeptide chains, anti-puromycin immunofluorescence enables visualization of nascent protein synthesis. A common assumption in studies of local messenger RNA translation is that the anti-puromycin staining of puromycylated nascent polypeptides in fixed cells accurately reports on their original site of translation, particularly when ribosomes are stalled with elongation inhibitors prior to puromycin treatment. However, when we attempted to implement a proximity ligation assay to detect ribosome-puromycin complexes, we found no evidence to support this assumption. We further demonstrated, using biochemical assays and live cell imaging of nascent polypeptides in mammalian cells, that puromycylated nascent polypeptides rapidly dissociate from ribosomes even in the presence of elongation inhibitors. Our results suggest that attempts to define precise subcellular translation sites using anti-puromycin immunostaining may be confounded by release of puromycylated nascent polypeptide chains prior to fixation.
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Affiliation(s)
- Benjamin D Hobson
- Department of Systems Biology, Columbia University Irving Medical Center, New York, United States.,Medical Scientist Training Program, Columbia University Irving Medical Center, New York, United States
| | - Linghao Kong
- Department of Systems Biology, Columbia University Irving Medical Center, New York, United States
| | - Erik W Hartwick
- Department of Chemistry, Columbia University, New York, United States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, United States
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, United States.,Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, United States.,Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, United States
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25
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Loussert-Fonta C, Toullec G, Paraecattil AA, Jeangros Q, Krueger T, Escrig S, Meibom A. Correlation of fluorescence microscopy, electron microscopy, and NanoSIMS stable isotope imaging on a single tissue section. Commun Biol 2020; 3:362. [PMID: 32647198 PMCID: PMC7347930 DOI: 10.1038/s42003-020-1095-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/19/2020] [Indexed: 12/28/2022] Open
Abstract
Correlative light and electron microscopy allows localization of specific molecules at the ultrastructural level in biological tissue but does not provide information about metabolic turnover or the distribution of labile molecules, such as micronutrients. We present a method to directly correlate (immuno)fluorescent microscopy, (immuno)TEM imaging and NanoSIMS isotopic mapping of the same tissue section, with nanometer-scale spatial precision. The process involves chemical fixation of the tissue, cryo sectioning, thawing, and air-drying under a thin film of polyvinyl alcohol. It permits to effectively retain labile compounds and strongly increases NanoSIMS sensitivity for 13C-enrichment. The method is illustrated here with correlated distribution maps of a carbonic anhydrase enzyme isotype, β-tubulin proteins, and 13C- and 15N-labeled labile micronutrients (and their anabolic derivates) within the tissue of a reef-building symbiotic coral. This broadly applicable workflow expands the wealth of information that can be obtained from multi-modal, sub-cellular observation of biological tissue.
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Affiliation(s)
- Céline Loussert-Fonta
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
| | - Gaëlle Toullec
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | | | - Quentin Jeangros
- Photovoltaics and Thin-Film Electronics Laboratory, Institute of Microengineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-2002, Neuchâtel, Switzerland
| | - Thomas Krueger
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Stephane Escrig
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, CH-1015, Lausanne, Switzerland
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26
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Abstract
Desmosomes are cell-cell junctions responsible for mechanically integrating adjacent cells. Due to the small size of the junctions, their protein architecture cannot be elucidated using conventional fluorescence microscopy. Super-resolution microscopy techniques, including dSTORM, deliver higher-resolution images which can reveal the localization or arrangement of proteins within individual desmosomes. Herein we describe an imaging and analysis method to determine the nanoscale architecture of desmosomes using super-resolution dSTORM.
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Affiliation(s)
- Reena R Beggs
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - William F Dean
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alexa L Mattheyses
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
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27
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Jaiswal A, Hoerth CH, Zúñiga Pereira AM, Lorenz H. Improved spatial resolution by induced live cell and organelle swelling in hypotonic solutions. Sci Rep 2019; 9:12911. [PMID: 31501484 PMCID: PMC6733880 DOI: 10.1038/s41598-019-49408-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/23/2019] [Indexed: 12/21/2022] Open
Abstract
Induced morphology changes of cells and organelles are by far the easiest way to determine precise protein sub-locations and organelle quantities in light microscopy. By using hypotonic solutions to swell mammalian cell organelles we demonstrate that precise membrane, lumen or matrix protein locations within the endoplasmic reticulum, Golgi and mitochondria can reliably be established. We also show the benefit of this approach for organelle quantifications, especially for clumped or intertwined organelles like peroxisomes and mitochondria. Since cell and organelle swelling is reversible, it can be applied to live cells for successive high-resolution analyses. Our approach outperforms many existing imaging modalities with respect to resolution, ease-of-use and cost-effectiveness without excluding any co-utilization with existing optical (super)resolution techniques.
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Affiliation(s)
- Astha Jaiswal
- Center of Molecular Biology, University of Heidelberg (ZMBH), Heidelberg, Germany
| | - Christian H Hoerth
- Center of Molecular Biology, University of Heidelberg (ZMBH), Heidelberg, Germany
| | - Ana M Zúñiga Pereira
- Center of Molecular Biology, University of Heidelberg (ZMBH), Heidelberg, Germany.,Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Holger Lorenz
- Center of Molecular Biology, University of Heidelberg (ZMBH), Heidelberg, Germany.
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