1
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Chen S, Wang J, Guan D, Tan B, Zhai T, Yang L, Han Y, Liu Y, Liu Q, Zhang Y. Near-Infrared Spontaneously Blinking Fluorophores for Live Cell Super-Resolution Imaging with Minimized Phototoxicity. Anal Chem 2024; 96:10860-10869. [PMID: 38889184 DOI: 10.1021/acs.analchem.4c02445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Single-molecule localization microscopy (SMLM) requires high-intensity laser irradiation, typically exceeding kW/cm2, to yield a sufficient photon count. However, this intense visible light exposure incurs substantial cellular toxicity, hindering its use in living cells. Here, we developed a class of near-infrared (NIR) spontaneously blinking fluorophores for SMLM. These NIR fluorophores are a combination of rhodamine spirolactams and merocyanine derivatives, where the rhodamine spirolactam component converts between a bright and dark state based on pH-dependent spirocyclization and merocyanine derivatives shift the excitation wavelength into the infrared. Single-molecule characterizations demonstrated their potential for SMLM. At a moderate power density of 3.93 kW/cm2, these probes exhibit duty cycle as low as 0.18% and an emission rate as high as 26,700 photons/s. Phototoxicity assessment under single-molecule imaging conditions reveals that NIR illumination (721 nm) minimizes harm to living cells. Employing these NIR fluorophores, we successfully captured time-lapse super-resolution tracking of mitochondria at a Fourier ring correlation (FRC) resolution of 69.4 nm and reconstructed the ultrastructures of endoplasmic reticulum (ER) in living cells.
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Affiliation(s)
- Song Chen
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Jing Wang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Daoming Guan
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Baojin Tan
- School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Tianli Zhai
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Lu Yang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Yuheng Han
- School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Yi Liu
- School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Qian Liu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Yunxiang Zhang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
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2
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Saunders N, Monel B, Cayet N, Archetti L, Moreno H, Jeanne A, Marguier A, Buchrieser J, Wai T, Schwartz O, Fréchin M. Dynamic label-free analysis of SARS-CoV-2 infection reveals virus-induced subcellular remodeling. Nat Commun 2024; 15:4996. [PMID: 38862527 PMCID: PMC11166935 DOI: 10.1038/s41467-024-49260-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 05/30/2024] [Indexed: 06/13/2024] Open
Abstract
Assessing the impact of SARS-CoV-2 on organelle dynamics allows a better understanding of the mechanisms of viral replication. We combine label-free holotomographic microscopy with Artificial Intelligence to visualize and quantify the subcellular changes triggered by SARS-CoV-2 infection. We study the dynamics of shape, position and dry mass of nucleoli, nuclei, lipid droplets and mitochondria within hundreds of single cells from early infection to syncytia formation and death. SARS-CoV-2 infection enlarges nucleoli, perturbs lipid droplets, changes mitochondrial shape and dry mass, and separates lipid droplets from mitochondria. We then used Bayesian network modeling on organelle dry mass states to define organelle cross-regulation networks and report modifications of organelle cross-regulation that are triggered by infection and syncytia formation. Our work highlights the subcellular remodeling induced by SARS-CoV-2 infection and provides an Artificial Intelligence-enhanced, label-free methodology to study in real-time the dynamics of cell populations and their content.
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Affiliation(s)
- Nell Saunders
- Virus & Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 3569, Paris, France
| | - Blandine Monel
- Virus & Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 3569, Paris, France
| | - Nadège Cayet
- Institut Pasteur, Université Paris Cité, Ultrastructural Bioimaging Unit, 75015, Paris, France
| | - Lorenzo Archetti
- Deep Quantitative Biology Department, Nanolive SA, Tolochenaz, Switzerland
| | - Hugo Moreno
- Deep Quantitative Biology Department, Nanolive SA, Tolochenaz, Switzerland
| | - Alexandre Jeanne
- Deep Quantitative Biology Department, Nanolive SA, Tolochenaz, Switzerland
| | - Agathe Marguier
- Deep Quantitative Biology Department, Nanolive SA, Tolochenaz, Switzerland
| | - Julian Buchrieser
- Virus & Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 3569, Paris, France
| | - Timothy Wai
- Mitochondrial Biology Group, Institut Pasteur, Université Paris Cité, CNRS, UMR 3691, Paris, France
| | - Olivier Schwartz
- Virus & Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 3569, Paris, France.
- Vaccine Research Institute, Creteil, France.
| | - Mathieu Fréchin
- Deep Quantitative Biology Department, Nanolive SA, Tolochenaz, Switzerland.
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3
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Gómez-de-Mariscal E, Del Rosario M, Pylvänäinen JW, Jacquemet G, Henriques R. Harnessing artificial intelligence to reduce phototoxicity in live imaging. J Cell Sci 2024; 137:jcs261545. [PMID: 38324353 PMCID: PMC10912813 DOI: 10.1242/jcs.261545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024] Open
Abstract
Fluorescence microscopy is essential for studying living cells, tissues and organisms. However, the fluorescent light that switches on fluorescent molecules also harms the samples, jeopardizing the validity of results - particularly in techniques such as super-resolution microscopy, which demands extended illumination. Artificial intelligence (AI)-enabled software capable of denoising, image restoration, temporal interpolation or cross-modal style transfer has great potential to rescue live imaging data and limit photodamage. Yet we believe the focus should be on maintaining light-induced damage at levels that preserve natural cell behaviour. In this Opinion piece, we argue that a shift in role for AIs is needed - AI should be used to extract rich insights from gentle imaging rather than recover compromised data from harsh illumination. Although AI can enhance imaging, our ultimate goal should be to uncover biological truths, not just retrieve data. It is essential to prioritize minimizing photodamage over merely pushing technical limits. Our approach is aimed towards gentle acquisition and observation of undisturbed living systems, aligning with the essence of live-cell fluorescence microscopy.
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Affiliation(s)
| | | | - Joanna W. Pylvänäinen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku 20500, Finland
| | - Guillaume Jacquemet
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku 20500, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, Åbo Akademi University, Turku 20100, Finland
| | - Ricardo Henriques
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
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4
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Breton V, Nazac P, Boulet D, Danglot L. Molecular mapping of neuronal architecture using STORM microscopy and new fluorescent probes for SMLM imaging. NEUROPHOTONICS 2024; 11:014414. [PMID: 38464866 PMCID: PMC10923464 DOI: 10.1117/1.nph.11.1.014414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/27/2024] [Accepted: 01/31/2024] [Indexed: 03/12/2024]
Abstract
Imaging neuronal architecture has been a recurrent challenge over the years, and the localization of synaptic proteins is a frequent challenge in neuroscience. To quantitatively detect and analyze the structure of synapses, we recently developed free SODA software to detect the association of pre and postsynaptic proteins. To fully take advantage of spatial distribution analysis in complex cells, such as neurons, we also selected some new dyes for plasma membrane labeling. Using Icy SODA plugin, we could detect and analyze synaptic association in both conventional and single molecule localization microscopy, giving access to a molecular map at the nanoscale level. To replace those molecular distributions within the neuronal three-dimensional (3D) shape, we used MemBright probes and 3D STORM analysis to decipher the entire 3D shape of various dendritic spine types at the single-molecule resolution level. We report here the example of synaptic proteins within neuronal mask, but these tools have a broader spectrum of interest since they can be used whatever the proteins or the cellular type. Altogether with SODA plugin, MemBright probes thus provide the perfect toolkit to decipher a nanometric molecular map of proteins within a 3D cellular context.
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Affiliation(s)
- Victor Breton
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy and Diseased Brain, Paris, France
| | - Paul Nazac
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy and Diseased Brain, Paris, France
| | - David Boulet
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy and Diseased Brain, Paris, France
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, NeurImag Core Facility, Paris, France
| | - Lydia Danglot
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy and Diseased Brain, Paris, France
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, NeurImag Core Facility, Paris, France
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5
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Shen YJ, Liao EY, Tai TM, Liao YH, Sun CK, Lee CK, See S, Chen HW. Deep learning-based photodamage reduction on harmonic generation microscope at low-level optical power. JOURNAL OF BIOPHOTONICS 2024; 17:e202300285. [PMID: 37738103 DOI: 10.1002/jbio.202300285] [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: 07/23/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
The trade-off between high-quality images and cellular health in optical bioimaging is a crucial problem. We demonstrated a deep-learning-based power-enhancement (PE) model in a harmonic generation microscope (HGM), including second harmonic generation (SHG) and third harmonic generation (THG). Our model can predict high-power HGM images from low-power images, greatly reducing the risk of phototoxicity and photodamage. Furthermore, the PE model trained only on normal skin data can also be used to predict abnormal skin data, enabling the dermatopathologist to successfully identify and label cancer cells. The PE model shows potential for in-vivo and ex-vivo HGM imaging.
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Affiliation(s)
- Yi-Jiun Shen
- International Intercollegiate Ph.D. Program, National Tsing Hua University, Hsinchu, Taiwan
| | - En-Yu Liao
- Department of Electrical Engineering and Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei, Taiwan
| | | | - Yi-Hua Liao
- Department of Dermatology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chi-Kuang Sun
- Department of Electrical Engineering and Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei, Taiwan
| | | | - Simon See
- NVIDIA AI Technology Center, NVIDIA, Taipei, Taiwan
| | - Hung-Wen Chen
- International Intercollegiate Ph.D. Program, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Photonics Technologies, National Tsing Hua University, Hsinchu, Taiwan
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6
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Harada T, Hata S, Takagi R, Komori T, Fukuyama M, Chinen T, Kitagawa D. An antioxidant screen identifies ascorbic acid for prevention of light-induced mitotic prolongation in live cell imaging. Commun Biol 2023; 6:1107. [PMID: 37914777 PMCID: PMC10620154 DOI: 10.1038/s42003-023-05479-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/18/2023] [Indexed: 11/03/2023] Open
Abstract
Phototoxicity is an important issue in fluorescence live imaging of light-sensitive cellular processes such as mitosis. Among several approaches to reduce phototoxicity, the addition of antioxidants to the media has been used as a simple method. Here, we analyzed the impact of phototoxicity on the mitotic progression in fluorescence live imaging of human cells and performed a screen to identify the most efficient antioxidative agents that reduce it. Quantitative analysis shows that high amounts of light illumination cause various mitotic defects such as prolonged mitosis and delays of chromosome alignment and centrosome separation. Among several antioxidants, our screen reveals that ascorbic acid significantly alleviates these phototoxic effects in mitosis. Furthermore, we demonstrate that adding ascorbic acid to the media enables fluorescence imaging of mitotic events at very high temporal resolution without obvious photodamage. Thus, this study provides an optimal method to effectively reduce the phototoxic effects in fluorescence live cell imaging.
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Affiliation(s)
- Tomoki Harada
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shoji Hata
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan.
- Precursory Research for Embryonic Science and Technology (PRESTO) Program, Japan Science and Technology Agency, Honcho Kawaguchi, Saitama, Japan.
| | - Rioka Takagi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Takuma Komori
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Masamitsu Fukuyama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Takumi Chinen
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Daiju Kitagawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan.
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7
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Balasubramanian H, Hobson CM, Chew TL, Aaron JS. Imagining the future of optical microscopy: everything, everywhere, all at once. Commun Biol 2023; 6:1096. [PMID: 37898673 PMCID: PMC10613274 DOI: 10.1038/s42003-023-05468-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
The optical microscope has revolutionized biology since at least the 17th Century. Since then, it has progressed from a largely observational tool to a powerful bioanalytical platform. However, realizing its full potential to study live specimens is hindered by a daunting array of technical challenges. Here, we delve into the current state of live imaging to explore the barriers that must be overcome and the possibilities that lie ahead. We venture to envision a future where we can visualize and study everything, everywhere, all at once - from the intricate inner workings of a single cell to the dynamic interplay across entire organisms, and a world where scientists could access the necessary microscopy technologies anywhere.
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Affiliation(s)
| | - Chad M Hobson
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Teng-Leong Chew
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Jesse S Aaron
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA.
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8
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Wang Y, Hartung JE, Goad A, Preisegger MA, Chacon B, Gold MS, Gogotsi Y, Cohen-Karni T. Photothermal Excitation of Neurons Using MXene: Cellular Stress and Phototoxicity Evaluation. Adv Healthc Mater 2023:e2302330. [PMID: 37755313 PMCID: PMC10963341 DOI: 10.1002/adhm.202302330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/17/2023] [Indexed: 09/28/2023]
Abstract
Understanding the communication of individual neurons necessitates precise control of neural activity. Photothermal modulation is a remote and non-genetic technique to control neural activity with high spatiotemporal resolution. The local heat release by photothermally active nanomaterial will change the membrane properties of the interfaced neurons during light illumination. Recently, it is demonstrated that the two-dimensional Ti3 C2 Tx MXene is an outstanding candidate to photothermally excite neurons with low incident energy. However, the safety of using Ti3 C2 Tx for neural modulation is unknown. Here, the biosafety of Ti3 C2 Tx -based photothermal modulation is thoroughly investigated, including assessments of plasma membrane integrity, mitochondrial stress, and oxidative stress. It is demonstrated that culturing neurons on 25 µg cm-2 Ti3 C2 Tx films and illuminating them with laser pulses (635 nm) with different incident energies (2-10 µJ per pulse) and different pulse frequencies (1 pulse, 1 Hz, and 10 Hz) neither damage the cell membrane, induce cellular stress, nor generate oxidative stress. The threshold energy to cause damage (i.e., 14 µJ per pulse) exceeded the incident energy for neural excitation (<10 µJ per pulse). This multi-assay safety evaluation provides crucial insights for guiding the establishment of light conditions and protocols in the clinical translation of photothermal modulation.
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Affiliation(s)
- Yingqiao Wang
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213
| | - Jane E. Hartung
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, 15260
| | - Adam Goad
- A.J. Drexel Nanomaterials Institute and Department of Materials Science and Engineering, Drexel University, Philadelphia, PA, 19104
| | | | - Benjamin Chacon
- A.J. Drexel Nanomaterials Institute and Department of Materials Science and Engineering, Drexel University, Philadelphia, PA, 19104
| | - Michael S. Gold
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, 15260
| | - Yury Gogotsi
- A.J. Drexel Nanomaterials Institute and Department of Materials Science and Engineering, Drexel University, Philadelphia, PA, 19104
| | - Tzahi Cohen-Karni
- Department of Materials Science and Engineering and Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213
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9
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Senft RA, Diaz-Rohrer B, Colarusso P, Swift L, Jamali N, Jambor H, Pengo T, Brideau C, Llopis PM, Uhlmann V, Kirk J, Gonzales KA, Bankhead P, Evans EL, Eliceiri KW, Cimini BA. A biologist's guide to planning and performing quantitative bioimaging experiments. PLoS Biol 2023; 21:e3002167. [PMID: 37368874 PMCID: PMC10298797 DOI: 10.1371/journal.pbio.3002167] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023] Open
Abstract
Technological advancements in biology and microscopy have empowered a transition from bioimaging as an observational method to a quantitative one. However, as biologists are adopting quantitative bioimaging and these experiments become more complex, researchers need additional expertise to carry out this work in a rigorous and reproducible manner. This Essay provides a navigational guide for experimental biologists to aid understanding of quantitative bioimaging from sample preparation through to image acquisition, image analysis, and data interpretation. We discuss the interconnectedness of these steps, and for each, we provide general recommendations, key questions to consider, and links to high-quality open-access resources for further learning. This synthesis of information will empower biologists to plan and execute rigorous quantitative bioimaging experiments efficiently.
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Affiliation(s)
- Rebecca A. Senft
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Barbara Diaz-Rohrer
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Pina Colarusso
- Live Cell Imaging Laboratory, University of Calgary, Calgary, Alberta, Canada
| | - Lucy Swift
- Live Cell Imaging Laboratory, University of Calgary, Calgary, Alberta, Canada
| | - Nasim Jamali
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Helena Jambor
- National Center for Tumor Diseases, University Cancer Center, NCT-UCC, Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden, Dresden, Germany
| | - Thomas Pengo
- Informatics Institute, University of Minnesota Twin Cities, Minneapolis, Minnesota, United States of America
| | - Craig Brideau
- Live Cell Imaging Laboratory, University of Calgary, Calgary, Alberta, Canada
| | - Paula Montero Llopis
- MicRoN Core, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Virginie Uhlmann
- European Bioinformatic Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Jason Kirk
- Optical Imaging & Vital Microscopy Core, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kevin Andrew Gonzales
- Mammalian Cell Biology and Development, Rockefeller University, New York, New York, United States of America
| | - Peter Bankhead
- Edinburgh Pathology, Centre for Genomic and Experimental Medicine, and CRUK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Edward L. Evans
- Morgridge Institute and University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kevin W. Eliceiri
- Morgridge Institute and University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Beth A. Cimini
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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10
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Pasternak T, Kircher S, Pérez-Pérez JM, Palme K. A simple pipeline for cell cycle kinetic studies in the root apical meristem. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4683-4695. [PMID: 35312781 DOI: 10.1093/jxb/erac123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Root system architecture ultimately depends on precise signaling between different cells and tissues in the root apical meristem (RAM) and integration with environmental cues. This study describes a simple pipeline to simultaneously determine cellular parameters, nucleus geometry, and cell cycle kinetics in the RAM. The method uses marker-free techniques for nucleus and cell boundary detection, and 5-ethynyl-2'-deoxyuridine (EdU) staining for DNA replication quantification. Based on this approach, we characterized differences in cell volume, nucleus volume, and nucleus shape across different domains of the Arabidopsis RAM. We found that DNA replication patterns were cell layer and region dependent. G2 phase duration, which varied from 3.5 h in the pericycle to more than 4.5 h in the epidermis, was found to be associated with some features of nucleus geometry. Endocycle duration was determined as the time required to achieve 100% EdU-positive cells in the elongation zone and, as such, it was estimated to be in the region of 5 h for the epidermis and cortex. This experimental pipeline could be used to precisely map cell cycle duration in the RAM of mutants and in response to environmental stress in several plant species without the need for introgressing molecular cell cycle markers.
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Affiliation(s)
- Taras Pasternak
- Faculty for Biology, Institute of Biology II/Molecular Plant Physiology, Germany
- Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - Stefan Kircher
- Faculty for Biology, Institute of Biology II/Molecular Plant Physiology, Germany
| | | | - Klaus Palme
- Faculty for Biology, Institute of Biology II/Molecular Plant Physiology, Germany
- Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, China
- ScreenSYS GmbH, Engesserstr. 4, 79108 Freiburg, Germany
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11
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Lu K, Wazawa T, Sakamoto J, Vu CQ, Nakano M, Kamei Y, Nagai T. Intracellular Heat Transfer and Thermal Property Revealed by Kilohertz Temperature Imaging with a Genetically Encoded Nanothermometer. NANO LETTERS 2022; 22:5698-5707. [PMID: 35792763 PMCID: PMC9335883 DOI: 10.1021/acs.nanolett.2c00608] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Despite improved sensitivity of nanothermometers, direct observation of heat transport inside single cells has remained challenging for the lack of high-speed temperature imaging techniques. Here, we identified insufficient temperature resolution under short signal integration time and slow sensor kinetics as two major bottlenecks. To overcome the limitations, we developed B-gTEMP, a nanothermometer based on the tandem fusion of mNeonGreen and tdTomato fluorescent proteins. We visualized the propagation of heat inside intracellular space by tracking the temporal variation of local temperature at a time resolution of 155 μs and a temperature resolution 0.042 °C. By comparing the fast in situ temperature dynamics with computer-simulated heat diffusion, we estimated the thermal diffusivity of live HeLa cells. The present thermal diffusivity in cells was about 1/5.3 of that of water and much smaller than the values reported for bulk tissues, which may account for observations of heterogeneous intracellular temperature distributions.
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Affiliation(s)
- Kai Lu
- SANKEN
(The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuichi Wazawa
- SANKEN
(The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Joe Sakamoto
- National
Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Cong Quang Vu
- SANKEN
(The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate
School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masahiro Nakano
- SANKEN
(The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yasuhiro Kamei
- National
Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Takeharu Nagai
- SANKEN
(The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate
School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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12
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Kähärä I, Durandin N, Ilina P, Efimov A, Laaksonen T, Vuorimaa-Laukkanen E, Lisitsyna E. Phototoxicity of BODIPY in long-term imaging can be reduced by intramolecular motion. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES : OFFICIAL JOURNAL OF THE EUROPEAN PHOTOCHEMISTRY ASSOCIATION AND THE EUROPEAN SOCIETY FOR PHOTOBIOLOGY 2022; 21:1677-1687. [PMID: 35796875 DOI: 10.1007/s43630-022-00250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/23/2022] [Indexed: 11/24/2022]
Abstract
For long-term live-cell fluorescence imaging and biosensing, it is crucial to work with a dye that has high fluorescence quantum yield and photostability without being detrimental to the cells. In this paper, we demonstrate that neutral boron-dipyrromethene (BODIPY)-based molecular rotors have great properties for high-light-dosage demanding live-cell fluorescence imaging applications that require repetitive illuminations. In molecular rotors, an intramolecular rotation (IMR) allows an alternative route for the decay of the singlet excited state (S1) via the formation of an intramolecular charge transfer state (CT). The occurrence of IMR reduces the probability of the formation of a triplet state (T1) which could further react with molecular oxygen (3O2) to form cytotoxic reactive oxygen species, e.g., singlet oxygen (1O2). We demonstrate that the oxygen-related nature of the phototoxicity for BODIPY derivatives can be significantly reduced if a neutral molecular rotor is used as a probe. The studied neutral molecular rotor probe shows remarkably lower phototoxicity when compared with both the non-rotating BODIPY derivative and the cationic BODIPY-based molecular rotor in different light dosages and dye concentrations. It is also evident that the charge and localization of the fluorescent probe are as significant as the IMR in terms of the phototoxicity in a long-term live-cell imaging.
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Affiliation(s)
- Iida Kähärä
- Chemistry and Advanced Materials, Unit of Materials Science and Environmental Engineering, Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, 33014, Tampere, Finland.
| | - Nikita Durandin
- Chemistry and Advanced Materials, Unit of Materials Science and Environmental Engineering, Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, 33014, Tampere, Finland
| | - Polina Ilina
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Alexander Efimov
- Chemistry and Advanced Materials, Unit of Materials Science and Environmental Engineering, Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, 33014, Tampere, Finland
| | - Timo Laaksonen
- Chemistry and Advanced Materials, Unit of Materials Science and Environmental Engineering, Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, 33014, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Elina Vuorimaa-Laukkanen
- Chemistry and Advanced Materials, Unit of Materials Science and Environmental Engineering, Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, 33014, Tampere, Finland
| | - Ekaterina Lisitsyna
- Chemistry and Advanced Materials, Unit of Materials Science and Environmental Engineering, Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, 33014, Tampere, Finland.
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13
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A proposed unified interphase nucleus chromosome structure: Preliminary preponderance of evidence. Proc Natl Acad Sci U S A 2022; 119:e2119101119. [PMID: 35749363 PMCID: PMC9245672 DOI: 10.1073/pnas.2119101119] [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] [Indexed: 11/18/2022] Open
Abstract
Cryopreservation of the nuclear interior allows a large-scale interphase chromosome structure—present throughout the nucleus—to be seen in its native state by electron tomography. This structure appears as a coiled chain of nucleosomes, wrapped like a Slinky toy. This coiled structure can be further used to explain the enigmatic architectures of polytene and lampbrush chromosomes. In addition, this new structure can further be organized as chromosome territories: for example, all 46 human interphase chromosomes easily fit into a 10-μm-diameter nucleus. Thus, interphase chromosomes can be unified into a flexibly defined structure. Cryoelectron tomography of the cell nucleus using scanning transmission electron microscopy and deconvolution processing technology has highlighted a large-scale, 100- to 300-nm interphase chromosome structure, which is present throughout the nucleus. This study further documents and analyzes these chromosome structures. The paper is divided into four parts: 1) evidence (preliminary) for a unified interphase chromosome structure; 2) a proposed unified interphase chromosome architecture; 3) organization as chromosome territories (e.g., fitting the 46 human chromosomes into a 10-μm-diameter nucleus); and 4) structure unification into a polytene chromosome architecture and lampbrush chromosomes. Finally, the paper concludes with a living light microscopy cell study showing that the G1 nucleus contains very similar structures throughout. The main finding is that this chromosome structure appears to coil the 11-nm nucleosome fiber into a defined hollow structure, analogous to a Slinky helical spring [https://en.wikipedia.org/wiki/Slinky; motif used in Bowerman et al., eLife 10, e65587 (2021)]. This Slinky architecture can be used to build chromosome territories, extended to the polytene chromosome structure, as well as to the structure of lampbrush chromosomes.
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14
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Chiu YF, Huang YW, Chen CY, Chen YC, Gong YN, Kuo RL, Huang CG, Shih SR. Visualizing Influenza A Virus vRNA Replication. Front Microbiol 2022; 13:812711. [PMID: 35733972 PMCID: PMC9207383 DOI: 10.3389/fmicb.2022.812711] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Influenza A virus (IAV) has caused recurrent epidemics and severe pandemics. In this study, we adapted an MS2-MCP live-cell imaging system to visualize IAV replication. A reporter plasmid, pHH-PB2-vMSL, was constructed by replacing a part of the PB2-coding sequence in pHH-PB2 with a sequence encoding 24 copies of a stem-loop structure from bacteriophage MS2 (MSL). Binding of MS2 coat protein (MCP) fused to green fluorescent protein (GFP) to MSL enabled the detection of vRNA as fluorescent punctate signals in live-cell imaging. The introduction of pHH-PB2-vMSL into A549 cells transduced to express an MCP-GFP fusion protein lacking the nuclear localization signal (MCP-GFPdN), subsequently allowed tracking of the distribution and replication of PB2-vMSL vRNA after IAV PR8 infection. Spatial and temporal measurements revealed exponential increases in vRNA punctate signal intensity, which was only observed after membrane blebbing in apoptotic cells. Similar signal intensity increases in apoptotic cells were also observed after MDCK cells, transduced to express MCP-GFPdN, were infected with IAV carrying PB2-vMSL vRNA. Notably, PB2-vMSL vRNA replication was observed to occur only in apoptotic cells, at a consistent time after apoptosis initiation. There was a lack of observable PB2-vMSL vRNA replication in non-apoptotic cells, and vRNA replication was suppressed in the presence of apoptosis inhibitors. These findings point to an important role for apoptosis in IAV vRNA replication. The utility of the MS2-imaging system for visualizing time-sensitive processes such as viral replication in live host cells is also demonstrated in this study.
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Affiliation(s)
- Ya-Fang Chiu
- Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan.,Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan.,Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yi-Wen Huang
- Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan
| | - Chi-Yuan Chen
- Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Chia Chen
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Nong Gong
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan.,Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Rei-Lin Kuo
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
| | - Chung-Guei Huang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
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15
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Pócsi I, Szigeti ZM, Emri T, Boczonádi I, Vereb G, Szöllősi J. Use of red, far-red, and near-infrared light in imaging of yeasts and filamentous fungi. Appl Microbiol Biotechnol 2022; 106:3895-3912. [PMID: 35599256 PMCID: PMC9200671 DOI: 10.1007/s00253-022-11967-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/02/2022] [Accepted: 05/07/2022] [Indexed: 11/30/2022]
Abstract
Abstract While phototoxicity can be a useful therapeutic modality not only for eliminating malignant cells but also in treating fungal infections, mycologists aiming to observe morphological changes or molecular events in fungi, especially when long observation periods or high light fluxes are warranted, encounter problems owed to altered regulatory pathways or even cell death caused by various photosensing mechanisms. Consequently, the ever expanding repertoire of visible fluorescent protein toolboxes and high-resolution microscopy methods designed to investigate fungi in vitro and in vivo need to comply with an additional requirement: to decrease the unwanted side effects of illumination. In addition to optimizing exposure, an obvious solution is red-shifted illumination, which, however, does not come without compromises. This review summarizes the interactions of fungi with light and the various molecular biology and technology approaches developed for exploring their functions on the molecular, cellular, and in vivo microscopic levels, and outlines the progress towards reducing phototoxicity through applying far-red and near-infrared light. Key points • Fungal biological processes alter upon illumination, also under the microscope • Red shifted fluorescent protein toolboxes decrease interference by illumination • Innovations like two-photon, lightsheet, and near IR microscopy reduce phototoxicity
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Affiliation(s)
- István Pócsi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.
| | - Zsuzsa M Szigeti
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Tamás Emri
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Imre Boczonádi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - György Vereb
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,Faculty of Pharmacy, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - János Szöllősi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
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16
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Vanslembrouck B, Chen JH, Larabell C, van Hengel J. Microscopic Visualization of Cell-Cell Adhesion Complexes at Micro and Nanoscale. Front Cell Dev Biol 2022; 10:819534. [PMID: 35517500 PMCID: PMC9065677 DOI: 10.3389/fcell.2022.819534] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 03/21/2022] [Indexed: 12/25/2022] Open
Abstract
Considerable progress has been made in our knowledge of the morphological and functional varieties of anchoring junctions. Cell-cell adhesion contacts consist of discrete junctional structures responsible for the mechanical coupling of cytoskeletons and allow the transmission of mechanical signals across the cell collective. The three main adhesion complexes are adherens junctions, tight junctions, and desmosomes. Microscopy has played a fundamental role in understanding these adhesion complexes on different levels in both physiological and pathological conditions. In this review, we discuss the main light and electron microscopy techniques used to unravel the structure and composition of the three cell-cell contacts in epithelial and endothelial cells. It functions as a guide to pick the appropriate imaging technique(s) for the adhesion complexes of interest. We also point out the latest techniques that have emerged. At the end, we discuss the problems investigators encounter during their cell-cell adhesion research using microscopic techniques.
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Affiliation(s)
- Bieke Vanslembrouck
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Anatomy, University of San Francisco, San Francisco, CA, United States
- *Correspondence: Bieke Vanslembrouck, ; Jolanda van Hengel,
| | - Jian-hua Chen
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Anatomy, University of San Francisco, San Francisco, CA, United States
| | - Carolyn Larabell
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Anatomy, University of San Francisco, San Francisco, CA, United States
| | - Jolanda van Hengel
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- *Correspondence: Bieke Vanslembrouck, ; Jolanda van Hengel,
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17
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Three-dimensional structured illumination microscopy data of mitochondria and lysosomes in cardiomyoblasts under normal and galactose-adapted conditions. Sci Data 2022; 9:98. [PMID: 35322035 PMCID: PMC8943179 DOI: 10.1038/s41597-022-01207-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/11/2022] [Indexed: 11/23/2022] Open
Abstract
This three-dimensional structured illumination microscopy (3DSIM) dataset was generated to highlight the suitability of 3DSIM to investigate mitochondria-derived vesicles (MDVs) in H9c2 cardiomyoblasts in living or fixed cells. MDVs act as a mitochondria quality control mechanism. The cells were stably expressing the tandem-tag eGFP-mCherry-OMP25-TM (outer mitochondrial membrane) which can be used as a sensor for acidity. A part of the dataset is showing correlative imaging of lysosomes labeled using LysoTracker in fixed and living cells. The cells were cultivated in either normal or glucose-deprived medium containing galactose. The resulting 3DSIM data were of high quality and can be used to undertake a variety of studies. Interestingly, many dynamic tubules derived from mitochondria are visible in the 3DSIM videos under both glucose and galactose-adapted growth conditions. As the raw 3DSIM data, optical parameters, and reconstructed 3DSIM images are provided, the data is especially suitable for use in the development of SIM reconstruction algorithms, bioimage analysis methods, and for biological studies of mitochondria. Measurement(s) | fluorescence microscopy images of mitochondria | Technology Type(s) | three dimensional structured illumination microscopy | Sample Characteristic - Organism | Rattus norvegicus • H9c2 cardiomyoblast cell-line |
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18
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Reiche MA, Aaron JS, Boehm U, DeSantis MC, Hobson CM, Khuon S, Lee RM, Chew TL. When light meets biology - how the specimen affects quantitative microscopy. J Cell Sci 2022; 135:274812. [PMID: 35319069 DOI: 10.1242/jcs.259656] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Fluorescence microscopy images should not be treated as perfect representations of biology. Many factors within the biospecimen itself can drastically affect quantitative microscopy data. Whereas some sample-specific considerations, such as photobleaching and autofluorescence, are more commonly discussed, a holistic discussion of sample-related issues (which includes less-routine topics such as quenching, scattering and biological anisotropy) is required to appropriately guide life scientists through the subtleties inherent to bioimaging. Here, we consider how the interplay between light and a sample can cause common experimental pitfalls and unanticipated errors when drawing biological conclusions. Although some of these discrepancies can be minimized or controlled for, others require more pragmatic considerations when interpreting image data. Ultimately, the power lies in the hands of the experimenter. The goal of this Review is therefore to survey how biological samples can skew quantification and interpretation of microscopy data. Furthermore, we offer a perspective on how to manage many of these potential pitfalls.
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Affiliation(s)
- Michael A Reiche
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Jesse S Aaron
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Ulrike Boehm
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Michael C DeSantis
- Light Microscopy Facility, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147,USA
| | - Chad M Hobson
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Satya Khuon
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA.,Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Rachel M Lee
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA.,Light Microscopy Facility, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147,USA
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19
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Teranikar T, Lim J, Ijaseun T, Lee J. Development of Planar Illumination Strategies for Solving Mysteries in the Sub-Cellular Realm. Int J Mol Sci 2022; 23:1643. [PMID: 35163562 PMCID: PMC8835835 DOI: 10.3390/ijms23031643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 02/04/2023] Open
Abstract
Optical microscopy has vastly expanded the frontiers of structural and functional biology, due to the non-invasive probing of dynamic volumes in vivo. However, traditional widefield microscopy illuminating the entire field of view (FOV) is adversely affected by out-of-focus light scatter. Consequently, standard upright or inverted microscopes are inept in sampling diffraction-limited volumes smaller than the optical system's point spread function (PSF). Over the last few decades, several planar and structured (sinusoidal) illumination modalities have offered unprecedented access to sub-cellular organelles and 4D (3D + time) image acquisition. Furthermore, these optical sectioning systems remain unaffected by the size of biological samples, providing high signal-to-noise (SNR) ratios for objective lenses (OLs) with long working distances (WDs). This review aims to guide biologists regarding planar illumination strategies, capable of harnessing sub-micron spatial resolution with a millimeter depth of penetration.
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Affiliation(s)
| | | | | | - Juhyun Lee
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX 75022, USA; (T.T.); (J.L.); (T.I.)
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20
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Barrantes FJ. Fluorescence sensors for imaging membrane lipid domains and cholesterol. CURRENT TOPICS IN MEMBRANES 2021; 88:257-314. [PMID: 34862029 DOI: 10.1016/bs.ctm.2021.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Lipid membrane domains are supramolecular lateral heterogeneities of biological membranes. Of nanoscopic dimensions, they constitute specialized hubs used by the cell as transient signaling platforms for a great variety of biologically important mechanisms. Their property to form and dissolve in the bulk lipid bilayer endow them with the ability to engage in highly dynamic processes, and temporarily recruit subpopulations of membrane proteins in reduced nanometric compartments that can coalesce to form larger mesoscale assemblies. Cholesterol is an essential component of these lipid domains; its unique molecular structure is suitable for interacting intricately with crevices and cavities of transmembrane protein surfaces through its rough β face while "talking" to fatty acid acyl chains of glycerophospholipids and sphingolipids via its smooth α face. Progress in the field of membrane domains has been closely associated with innovative improvements in fluorescence microscopy and new fluorescence sensors. These advances enabled the exploration of the biophysical properties of lipids and their supramolecular platforms. Here I review the rationale behind the use of biosensors over the last few decades and their contributions towards elucidation of the in-plane and transbilayer topography of cholesterol-enriched lipid domains and their molecular constituents. The challenges introduced by super-resolution optical microscopy are discussed, as well as possible scenarios for future developments in the field, including virtual ("no staining") staining.
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Affiliation(s)
- Francisco J Barrantes
- Biomedical Research Institute (BIOMED), Catholic University of Argentina (UCA)-National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina.
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21
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Hobson CM, Aaron JS, Heddleston JM, Chew TL. Visualizing the Invisible: Advanced Optical Microscopy as a Tool to Measure Biomechanical Forces. Front Cell Dev Biol 2021; 9:706126. [PMID: 34552926 PMCID: PMC8450411 DOI: 10.3389/fcell.2021.706126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/09/2021] [Indexed: 01/28/2023] Open
Abstract
The importance of mechanical force in biology is evident across diverse length scales, ranging from tissue morphogenesis during embryo development to mechanotransduction across single adhesion proteins at the cell surface. Consequently, many force measurement techniques rely on optical microscopy to measure forces being applied by cells on their environment, to visualize specimen deformations due to external forces, or even to directly apply a physical perturbation to the sample via photoablation or optogenetic tools. Recent developments in advanced microscopy offer improved approaches to enhance spatiotemporal resolution, imaging depth, and sample viability. These advances can be coupled with already existing force measurement methods to improve sensitivity, duration and speed, amongst other parameters. However, gaining access to advanced microscopy instrumentation and the expertise necessary to extract meaningful insights from these techniques is an unavoidable hurdle. In this Live Cell Imaging special issue Review, we survey common microscopy-based force measurement techniques and examine how they can be bolstered by emerging microscopy methods. We further explore challenges related to the accompanying data analysis in biomechanical studies and discuss the various resources available to tackle the global issue of technology dissemination, an important avenue for biologists to gain access to pre-commercial instruments that can be leveraged for biomechanical studies.
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Affiliation(s)
- Chad M. Hobson
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, United States
| | - Jesse S. Aaron
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, United States
| | - John M. Heddleston
- Cleveland Clinic Florida Research and Innovation Center, Port St. Lucie, FL, United States
| | - Teng-Leong Chew
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, United States
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22
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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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23
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Larsen JB, Taebnia N, Dolatshahi-Pirouz A, Eriksen AZ, Hjørringgaard C, Kristensen K, Larsen NW, Larsen NB, Marie R, Mündler AK, Parhamifar L, Urquhart AJ, Weller A, Mortensen KI, Flyvbjerg H, Andresen TL. Imaging therapeutic peptide transport across intestinal barriers. RSC Chem Biol 2021; 2:1115-1143. [PMID: 34458827 PMCID: PMC8341777 DOI: 10.1039/d1cb00024a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
Oral delivery is a highly preferred method for drug administration due to high patient compliance. However, oral administration is intrinsically challenging for pharmacologically interesting drug classes, in particular pharmaceutical peptides, due to the biological barriers associated with the gastrointestinal tract. In this review, we start by summarizing the pharmacological performance of several clinically relevant orally administrated therapeutic peptides, highlighting their low bioavailabilities. Thus, there is a strong need to increase the transport of peptide drugs across the intestinal barrier to realize future treatment needs and further development in the field. Currently, progress is hampered by a lack of understanding of transport mechanisms that govern intestinal absorption and transport of peptide drugs, including the effects of the permeability enhancers commonly used to mediate uptake. We describe how, for the past decades, mechanistic insights have predominantly been gained using functional assays with end-point read-out capabilities, which only allow indirect study of peptide transport mechanisms. We then focus on fluorescence imaging that, on the other hand, provides opportunities to directly visualize and thus follow peptide transport at high spatiotemporal resolution. Consequently, it may provide new and detailed mechanistic understanding of the interplay between the physicochemical properties of peptides and cellular processes; an interplay that determines the efficiency of transport. We review current methodology and state of the art in the field of fluorescence imaging to study intestinal barrier transport of peptides, and provide a comprehensive overview of the imaging-compatible in vitro, ex vivo, and in vivo platforms that currently are being developed to accelerate this emerging field of research.
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Affiliation(s)
- Jannik Bruun Larsen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Nayere Taebnia
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Alireza Dolatshahi-Pirouz
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Anne Zebitz Eriksen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Claudia Hjørringgaard
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Kasper Kristensen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Nanna Wichmann Larsen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Niels Bent Larsen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Rodolphe Marie
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Ann-Kathrin Mündler
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Ladan Parhamifar
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Andrew James Urquhart
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Arjen Weller
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Kim I Mortensen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Henrik Flyvbjerg
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
| | - Thomas Lars Andresen
- Center for Intestinal Absorption and Transport of Biopharmaceuticals, Department of Health Technology, Technical University of Denmark DK-2800, Kgs. Lyngby Denmark
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24
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Algar WR, Massey M, Rees K, Higgins R, Krause KD, Darwish GH, Peveler WJ, Xiao Z, Tsai HY, Gupta R, Lix K, Tran MV, Kim H. Photoluminescent Nanoparticles for Chemical and Biological Analysis and Imaging. Chem Rev 2021; 121:9243-9358. [PMID: 34282906 DOI: 10.1021/acs.chemrev.0c01176] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Research related to the development and application of luminescent nanoparticles (LNPs) for chemical and biological analysis and imaging is flourishing. Novel materials and new applications continue to be reported after two decades of research. This review provides a comprehensive and heuristic overview of this field. It is targeted to both newcomers and experts who are interested in a critical assessment of LNP materials, their properties, strengths and weaknesses, and prospective applications. Numerous LNP materials are cataloged by fundamental descriptions of their chemical identities and physical morphology, quantitative photoluminescence (PL) properties, PL mechanisms, and surface chemistry. These materials include various semiconductor quantum dots, carbon nanotubes, graphene derivatives, carbon dots, nanodiamonds, luminescent metal nanoclusters, lanthanide-doped upconversion nanoparticles and downshifting nanoparticles, triplet-triplet annihilation nanoparticles, persistent-luminescence nanoparticles, conjugated polymer nanoparticles and semiconducting polymer dots, multi-nanoparticle assemblies, and doped and labeled nanoparticles, including but not limited to those based on polymers and silica. As an exercise in the critical assessment of LNP properties, these materials are ranked by several application-related functional criteria. Additional sections highlight recent examples of advances in chemical and biological analysis, point-of-care diagnostics, and cellular, tissue, and in vivo imaging and theranostics. These examples are drawn from the recent literature and organized by both LNP material and the particular properties that are leveraged to an advantage. Finally, a perspective on what comes next for the field is offered.
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Affiliation(s)
- W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Melissa Massey
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Kelly Rees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Rehan Higgins
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Katherine D Krause
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Ghinwa H Darwish
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - William J Peveler
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Zhujun Xiao
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Hsin-Yun Tsai
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Rupsa Gupta
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Kelsi Lix
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Michael V Tran
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Hyungki Kim
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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25
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Nguyen DP, Nguyen HTH, Do LH. Tools and Methods for Investigating Synthetic Metal-Catalyzed Reactions in Living Cells. ACS Catal 2021; 11:5148-5165. [PMID: 34824879 PMCID: PMC8612649 DOI: 10.1021/acscatal.1c00438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Although abiotic catalysts are capable of promoting numerous new-to-nature reactions, only a small subset has so far been successfully integrated into living systems. Research in intracellular catalysis requires an interdisciplinary approach that takes advantage of both chemical and biological tools as well as state-of-the-art instrumentations. In this perspective, we will focus on the techniques that have made studying metal-catalyzed reactions in cells possible using representative examples from the literature. Although the lack of quantitative data in vitro and in vivo has somewhat limited progress in the catalyst development process, recent advances in characterization methods should help overcome some of these deficiencies. Given its tremendous potential, we believe that intracellular catalysis will play a more prominent role in the development of future biotechnologies and therapeutics.
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Affiliation(s)
- Dat P. Nguyen
- Department of Chemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas 77004, United States
| | - Huong T. H. Nguyen
- Department of Chemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas 77004, United States
| | - Loi H. Do
- Department of Chemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas 77004, United States
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26
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von Chamier L, Laine RF, Jukkala J, Spahn C, Krentzel D, Nehme E, Lerche M, Hernández-Pérez S, Mattila PK, Karinou E, Holden S, Solak AC, Krull A, Buchholz TO, Jones ML, Royer LA, Leterrier C, Shechtman Y, Jug F, Heilemann M, Jacquemet G, Henriques R. Democratising deep learning for microscopy with ZeroCostDL4Mic. Nat Commun 2021; 12:2276. [PMID: 33859193 PMCID: PMC8050272 DOI: 10.1038/s41467-021-22518-0] [Citation(s) in RCA: 194] [Impact Index Per Article: 64.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 03/10/2021] [Indexed: 02/02/2023] Open
Abstract
Deep Learning (DL) methods are powerful analytical tools for microscopy and can outperform conventional image processing pipelines. Despite the enthusiasm and innovations fuelled by DL technology, the need to access powerful and compatible resources to train DL networks leads to an accessibility barrier that novice users often find difficult to overcome. Here, we present ZeroCostDL4Mic, an entry-level platform simplifying DL access by leveraging the free, cloud-based computational resources of Google Colab. ZeroCostDL4Mic allows researchers with no coding expertise to train and apply key DL networks to perform tasks including segmentation (using U-Net and StarDist), object detection (using YOLOv2), denoising (using CARE and Noise2Void), super-resolution microscopy (using Deep-STORM), and image-to-image translation (using Label-free prediction - fnet, pix2pix and CycleGAN). Importantly, we provide suitable quantitative tools for each network to evaluate model performance, allowing model optimisation. We demonstrate the application of the platform to study multiple biological processes.
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Affiliation(s)
- Lucas von Chamier
- MRC-Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Romain F Laine
- MRC-Laboratory for Molecular Cell Biology, University College London, London, UK
- The Francis Crick Institute, London, UK
| | - Johanna Jukkala
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Christoph Spahn
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Daniel Krentzel
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - Elias Nehme
- Department of Electrical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Martina Lerche
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Sara Hernández-Pérez
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Turku, Finland
| | - Pieta K Mattila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Turku, Finland
| | - Eleni Karinou
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Séamus Holden
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | | | - Alexander Krull
- Center for Systems Biology Dresden (CSBD), Dresden, Germany
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for Physics of Complex Systems, Dresden, Germany
| | - Tim-Oliver Buchholz
- Center for Systems Biology Dresden (CSBD), Dresden, Germany
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Martin L Jones
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | | | | | - Yoav Shechtman
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Florian Jug
- Center for Systems Biology Dresden (CSBD), Dresden, Germany
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
- Fondatione Human Technopole, Milano, Italy
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland.
| | - Ricardo Henriques
- MRC-Laboratory for Molecular Cell Biology, University College London, London, UK.
- The Francis Crick Institute, London, UK.
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
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27
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Li D, Colin-York H, Barbieri L, Javanmardi Y, Guo Y, Korobchevskaya K, Moeendarbary E, Li D, Fritzsche M. Astigmatic traction force microscopy (aTFM). Nat Commun 2021; 12:2168. [PMID: 33846322 PMCID: PMC8042066 DOI: 10.1038/s41467-021-22376-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 03/12/2021] [Indexed: 01/23/2023] Open
Abstract
Quantifying small, rapidly progressing three-dimensional forces generated by cells remains a major challenge towards a more complete understanding of mechanobiology. Traction force microscopy is one of the most broadly applied force probing technologies but ascertaining three-dimensional information typically necessitates slow, multi-frame z-stack acquisition with limited sensitivity. Here, by performing traction force microscopy using fast single-frame astigmatic imaging coupled with total internal reflection fluorescence microscopy we improve the temporal resolution of three-dimensional mechanical force quantification up to 10-fold compared to its related super-resolution modalities. 2.5D astigmatic traction force microscopy (aTFM) thus enables live-cell force measurements approaching physiological sensitivity.
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Affiliation(s)
- Di Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Huw Colin-York
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Liliana Barbieri
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Yousef Javanmardi
- Department of Mechanical Engineering, University College London, London, UK
| | - Yuting Guo
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | | | - Emad Moeendarbary
- Department of Mechanical Engineering, University College London, London, UK.
| | - Dong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Marco Fritzsche
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK.
- Rosalind Franklin Institute, Harwell Campus, Didcot, UK.
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28
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Szeri F, Niaziorimi F, Donnelly S, Orndorff J, van de Wetering K. Generation of fully functional fluorescent fusion proteins to gain insights into ABCC6 biology. FEBS Lett 2021; 595:799-810. [PMID: 33058196 PMCID: PMC7987643 DOI: 10.1002/1873-3468.13957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/04/2020] [Accepted: 09/29/2020] [Indexed: 12/18/2022]
Abstract
ABCC6 mediates release of ATP from hepatocytes into the blood. Extracellularly, ATP is converted into the mineralization inhibitor pyrophosphate. Consequently, inactivating mutations in ABCC6 give low plasma pyrophosphate and underlie the ectopic mineralization disorder pseudoxanthoma elasticum. How ABCC6 mediates cellular ATP release is still unknown. Fluorescent ABCC6 fusion proteins would allow mechanistic studies, but fluorophores attached to the ABCC6 N- or C-terminus result in intracellular retention and degradation. Here we describe that intramolecular introduction of fluorophores yields fully functional ABCC6 fusion proteins. A corresponding ABCC6 variant in which the catalytic glutamate of the second nucleotide binding domain was mutated, correctly routed to the plasma membrane but was inactive. Finally, N-terminal His10 or FLAG tags did not affect activity of the fusion proteins, allowing their purification for biochemical characterization.
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Affiliation(s)
- Flora Szeri
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, 19107, Philadelphia (PA), USA
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary (current address)
| | - Fatemeh Niaziorimi
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, 19107, Philadelphia (PA), USA
| | - Sylvia Donnelly
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, 19107, Philadelphia (PA), USA
| | - Joseph Orndorff
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, 19107, Philadelphia (PA), USA
| | - Koen van de Wetering
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, 19107, Philadelphia (PA), USA
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29
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Touizer E, Sieben C, Henriques R, Marsh M, Laine RF. Application of Super-Resolution and Advanced Quantitative Microscopy to the Spatio-Temporal Analysis of Influenza Virus Replication. Viruses 2021; 13:233. [PMID: 33540739 PMCID: PMC7912985 DOI: 10.3390/v13020233] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 02/07/2023] Open
Abstract
With an estimated three to five million human cases annually and the potential to infect domestic and wild animal populations, influenza viruses are one of the greatest health and economic burdens to our society, and pose an ongoing threat of large-scale pandemics. Despite our knowledge of many important aspects of influenza virus biology, there is still much to learn about how influenza viruses replicate in infected cells, for instance, how they use entry receptors or exploit host cell trafficking pathways. These gaps in our knowledge are due, in part, to the difficulty of directly observing viruses in living cells. In recent years, advances in light microscopy, including super-resolution microscopy and single-molecule imaging, have enabled many viral replication steps to be visualised dynamically in living cells. In particular, the ability to track single virions and their components, in real time, now allows specific pathways to be interrogated, providing new insights to various aspects of the virus-host cell interaction. In this review, we discuss how state-of-the-art imaging technologies, notably quantitative live-cell and super-resolution microscopy, are providing new nanoscale and molecular insights into influenza virus replication and revealing new opportunities for developing antiviral strategies.
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Affiliation(s)
- Emma Touizer
- Division of Infection and Immunity, University College London, London WC1E 6AE, UK;
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
| | - Christian Sieben
- Department of Cell Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
- The Francis Crick Institute, London NW1 1AT, UK
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Mark Marsh
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
| | - Romain F. Laine
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
- The Francis Crick Institute, London NW1 1AT, UK
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30
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Yang Z, Li L, Ling J, Liu T, Huang X, Ying Y, Zhao Y, Zhao Y, Lei K, Chen L, Chen Z. Cyclooctatetraene-conjugated cyanine mitochondrial probes minimize phototoxicity in fluorescence and nanoscopic imaging. Chem Sci 2020; 11:8506-8516. [PMID: 34094186 PMCID: PMC8161535 DOI: 10.1039/d0sc02837a] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/25/2020] [Indexed: 12/27/2022] Open
Abstract
Modern fluorescence-imaging methods promise to unveil organelle dynamics in live cells. Phototoxicity, however, has become a prevailing issue when boosted illumination applies. Mitochondria are representative organelles whose research heavily relies on optical imaging, yet these membranous hubs of bioenergy are exceptionally vulnerable to photodamage. We report that cyclooctatetraene-conjugated cyanine dyes (PK Mito dyes), are ideal mitochondrial probes with remarkably low photodynamic damage for general use in fluorescence cytometry. In contrast, the nitrobenzene conjugate of Cy3 exhibits enhanced photostability but unaffected phototoxicity compared to parental Cy3. PK Mito Red, in conjunction with Hessian-structural illumination microscopy, enables 2000-frame time-lapse imaging with clearly resolvable crista structures, revealing rich mitochondrial dynamics. In a rigorous stem cell sorting and transplantation assay, PK Mito Red maximally retains the stemness of planarian neoblasts, exhibiting excellent multifaceted biocompatibility. Resonating with the ongoing theme of reducing photodamage using optical approaches, this work advocates the evaluation and minimization of phototoxicity when developing imaging probes.
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Affiliation(s)
- Zhongtian Yang
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University Beijing China
- Peking-Tsinghua Center for Life Sciences, Peking University Beijing China
| | - Liuju Li
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University Beijing China
- State Key Laboratory of Membrane Biology, Peking University Beijing China
| | - Jing Ling
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University Beijing China
- Peking-Tsinghua Center for Life Sciences, Peking University Beijing China
| | - Tianyan Liu
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University Beijing China
- Peking-Tsinghua Center for Life Sciences, Peking University Beijing China
| | - Xiaoshuai Huang
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University Beijing China
- State Key Laboratory of Membrane Biology, Peking University Beijing China
| | - Yuqing Ying
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation, Translational Research of Zhejiang ProvinceSchool of Life Sciences, Westlake University Hangzhou Zhejiang Province China
- Institute of Biology, Westlake Institute for Advanced Study Hangzhou Zhejiang Province China
| | - Yun Zhao
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation, Translational Research of Zhejiang ProvinceSchool of Life Sciences, Westlake University Hangzhou Zhejiang Province China
- Institute of Biology, Westlake Institute for Advanced Study Hangzhou Zhejiang Province China
| | - Yan Zhao
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University Beijing China
- Peking-Tsinghua Center for Life Sciences, Peking University Beijing China
| | - Kai Lei
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation, Translational Research of Zhejiang ProvinceSchool of Life Sciences, Westlake University Hangzhou Zhejiang Province China
- Institute of Biology, Westlake Institute for Advanced Study Hangzhou Zhejiang Province China
| | - Liangyi Chen
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University Beijing China
- State Key Laboratory of Membrane Biology, Peking University Beijing China
- PKU-Nanjing Institute of Translational Medicine Nanjing China
| | - Zhixing Chen
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University Beijing China
- Peking-Tsinghua Center for Life Sciences, Peking University Beijing China
- PKU-Nanjing Institute of Translational Medicine Nanjing China
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31
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Jacquemet G, Carisey AF, Hamidi H, Henriques R, Leterrier C. The cell biologist's guide to super-resolution microscopy. J Cell Sci 2020; 133:133/11/jcs240713. [PMID: 32527967 DOI: 10.1242/jcs.240713] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Fluorescence microscopy has become a ubiquitous method to observe the location of specific molecular components within cells. However, the resolution of light microscopy is limited by the laws of diffraction to a few hundred nanometers, blurring most cellular details. Over the last two decades, several techniques - grouped under the 'super-resolution microscopy' moniker - have been designed to bypass this limitation, revealing the cellular organization down to the nanoscale. The number and variety of these techniques have steadily increased, to the point that it has become difficult for cell biologists and seasoned microscopists alike to identify the specific technique best suited to their needs. Available techniques include image processing strategies that generate super-resolved images, optical imaging schemes that overcome the diffraction limit and sample manipulations that expand the size of the biological sample. In this Cell Science at a Glance article and the accompanying poster, we provide key pointers to help users navigate through the various super-resolution methods by briefly summarizing the principles behind each technique, highlighting both critical strengths and weaknesses, as well as providing example images.
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Affiliation(s)
- Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland .,Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland
| | - Alexandre F Carisey
- William T. Shearer Center for Human Immunobiology, Baylor College of Medicine and Texas Children's Hospital, 1102 Bates Street, Houston 77030 TX, USA
| | - Hellyeh Hamidi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Ricardo Henriques
- University College London, London WC1E 6BT, UK .,The Francis Crick Institute, London NW1 1AT, UK
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32
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Pereira PM, Gustafsson N, Marsh M, Mhlanga MM, Henriques R. Super-beacons: Open-source probes with spontaneous tuneable blinking compatible with live-cell super-resolution microscopy. Traffic 2020; 21:375-385. [PMID: 32170988 PMCID: PMC7643006 DOI: 10.1111/tra.12728] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 11/28/2022]
Abstract
Localization-based super-resolution microscopy relies on the detection of individual molecules cycling between fluorescent and non-fluorescent states. These transitions are commonly regulated by high-intensity illumination, imposing constrains to imaging hardware and producing sample photodamage. Here, we propose single-molecule self-quenching as a mechanism to generate spontaneous photoswitching. To demonstrate this principle, we developed a new class of DNA-based open-source super-resolution probes named super-beacons, with photoswitching kinetics that can be tuned structurally, thermally and chemically. The potential of these probes for live-cell compatible super-resolution microscopy without high-illumination or toxic imaging buffers is revealed by imaging interferon inducible transmembrane proteins (IFITMs) at sub-100 nm resolutions.
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Affiliation(s)
- Pedro M. Pereira
- MRC‐Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
- The Francis Crick InstituteLondonUK
- Bacterial Cell BiologyMOSTMICRO, ITQB‐NOVAOeirasPortugal
| | - Nils Gustafsson
- MRC‐Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
- Present address:
Department für Physik and CeNSLudwig‐Maximilians‐UniversitätMunichGermany
| | - Mark Marsh
- MRC‐Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
| | - Musa M. Mhlanga
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Ricardo Henriques
- MRC‐Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
- The Francis Crick InstituteLondonUK
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