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Cremer C, Szczurek A, Schock F, Gourram A, Birk U. Super-resolution microscopy approaches to nuclear nanostructure imaging. Methods 2017; 123:11-32. [PMID: 28390838 DOI: 10.1016/j.ymeth.2017.03.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/23/2017] [Indexed: 12/14/2022] Open
Abstract
The human genome has been decoded, but we are still far from understanding the regulation of all gene activities. A largely unexplained role in these regulatory mechanisms is played by the spatial organization of the genome in the cell nucleus which has far-reaching functional consequences for gene regulation. Until recently, it appeared to be impossible to study this problem on the nanoscale by light microscopy. However, novel developments in optical imaging technology have radically surpassed the limited resolution of conventional far-field fluorescence microscopy (ca. 200nm). After a brief review of available super-resolution microscopy (SRM) methods, we focus on a specific SRM approach to study nuclear genome structure at the single cell/single molecule level, Spectral Precision Distance/Position Determination Microscopy (SPDM). SPDM, a variant of localization microscopy, makes use of conventional fluorescent proteins or single standard organic fluorophores in combination with standard (or only slightly modified) specimen preparation conditions; in its actual realization mode, the same laser frequency can be used for both photoswitching and fluorescence read out. Presently, the SPDM method allows us to image nuclear genome organization in individual cells down to few tens of nanometer (nm) of structural resolution, and to perform quantitative analyses of individual small chromatin domains; of the nanoscale distribution of histones, chromatin remodeling proteins, and transcription, splicing and repair related factors. As a biomedical research application, using dual-color SPDM, it became possible to monitor in mouse cardiomyocyte cells quantitatively the effects of ischemia conditions on the chromatin nanostructure (DNA). These novel "molecular optics" approaches open an avenue to study the nuclear landscape directly in individual cells down to the single molecule level and thus to test models of functional genome architecture at unprecedented resolution.
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Affiliation(s)
- Christoph Cremer
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany; Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany. http://www.optics.imb-mainz.de
| | - Aleksander Szczurek
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Florian Schock
- Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany
| | - Amine Gourram
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Udo Birk
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany; Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany
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Eberle JP, Rapp A, Krufczik M, Eryilmaz M, Gunkel M, Erfle H, Hausmann M. Super-Resolution Microscopy Techniques and Their Potential for Applications in Radiation Biophysics. Methods Mol Biol 2017; 1663:1-13. [PMID: 28924654 DOI: 10.1007/978-1-4939-7265-4_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fluorescence microscopy is an essential tool for imaging tagged biological structures. Due to the wave nature of light, the resolution of a conventional fluorescence microscope is limited laterally to about 200 nm and axially to about 600 nm, which is often referred to as the Abbe limit. This hampers the observation of important biological structures and dynamics in the nano-scaled range ~10 nm to ~100 nm. Consequentially, various methods have been developed circumventing this limit of resolution. Super-resolution microscopy comprises several of those methods employing physical and/or chemical properties, such as optical/instrumental modifications and specific labeling of samples. In this article, we will give a brief insight into a variety of selected optical microscopy methods reaching super-resolution beyond the Abbe limit. We will survey three different concepts in connection to biological applications in radiation research without making a claim to be complete.
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Affiliation(s)
- Jan Philipp Eberle
- High-Content Analysis of the Cell (HiCell) and Advanced Biological Screening Facility, BioQuant, Heidelberg University, Heidelberg, Germany
| | - Alexander Rapp
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Matthias Krufczik
- Kirchhoff-Institute for Physics, Heidelberg University, In the Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Marion Eryilmaz
- Kirchhoff-Institute for Physics, Heidelberg University, In the Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Manuel Gunkel
- High-Content Analysis of the Cell (HiCell) and Advanced Biological Screening Facility, BioQuant, Heidelberg University, Heidelberg, Germany
| | - Holger Erfle
- High-Content Analysis of the Cell (HiCell) and Advanced Biological Screening Facility, BioQuant, Heidelberg University, Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, In the Neuenheimer Feld 227, 69120, Heidelberg, Germany.
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Compans B, Choquet D, Hosy E. Review on the role of AMPA receptor nano-organization and dynamic in the properties of synaptic transmission. NEUROPHOTONICS 2016; 3:041811. [PMID: 27981061 PMCID: PMC5109202 DOI: 10.1117/1.nph.3.4.041811] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/19/2016] [Indexed: 06/06/2023]
Abstract
Receptor trafficking and its regulation have appeared in the last two decades to be a major controller of basal synaptic transmission and its activity-dependent plasticity. More recently, considerable advances in super-resolution microscopy have begun deciphering the subdiffraction organization of synaptic elements and their functional roles. In particular, the dynamic nanoscale organization of neurotransmitter receptors in the postsynaptic membrane has recently been suggested to play a major role in various aspects of synapstic function. We here review the recent advances in our understanding of alpha-amino-3-hydroxy-5-méthyl-4-isoxazolepropionic acid subtype glutamate receptors subsynaptic organization and their role in short- and long-term synaptic plasticity.
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Affiliation(s)
- Benjamin Compans
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux F-33000, France
- Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, Bordeaux F-33000, France
| | - Daniel Choquet
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux F-33000, France
- Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, Bordeaux F-33000, France
- University of Bordeaux, Bordeaux Imaging Center, UMS 3420 CNRS, US4 INSERM, France
| | - Eric Hosy
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux F-33000, France
- Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, Bordeaux F-33000, France
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Application perspectives of localization microscopy in virology. Histochem Cell Biol 2014; 142:43-59. [DOI: 10.1007/s00418-014-1203-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2014] [Indexed: 01/07/2023]
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Quantitative analysis of individual hepatocyte growth factor receptor clusters in influenza A virus infected human epithelial cells using localization microscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:1191-8. [PMID: 24374315 DOI: 10.1016/j.bbamem.2013.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 11/26/2013] [Accepted: 12/20/2013] [Indexed: 01/25/2023]
Abstract
In this report, we applied a special localization microscopy technique (Spectral Precision Distance/Spatial Position Determination Microscopy/SPDM) to quantitatively analyze the effect of influenza A virus (IAV) infection on the spatial distribution of individual HGFR (Hepatocyte Growth Factor Receptor) proteins on the membrane of human epithelial cells at the single molecule resolution level. We applied this SPDM method to Alexa 488 labeled HGFR proteins with two different ligands. The ligands were either HGF (Hepatocyte Growth Factor), or IAV. In addition, the HGFR distribution in a control group of mock-incubated cells without any ligands was investigated. The spatial distribution of 1×10(6) individual HGFR proteins localized in large regions of interest on membranes of 240 cells was quantitatively analyzed and found to be highly non-random. Between 21% and 24% of the HGFR molecules were located in 44,304 small clusters with an average diameter of 54nm. The mean density of HGFR molecule signals per individual cluster was very similar in control cells, in cells with ligand only, and in IAV infected cells, independent of the incubation time. From the density of HGFR molecule signals in the clusters and the diameter of the clusters, the number of HGFR molecule signals per cluster was estimated to be in the range between 4 and 11 (means 5-6). This suggests that the membrane bound HGFR clusters form small molecular complexes with a maximum diameter of few tens of nm, composed of a relatively low number of HGFR molecules. This article is part of a Special Issue entitled: Viral Membrane Proteins - Channels for Cellular Networking.
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Rouquette J, Cremer C, Cremer T, Fakan S. Functional nuclear architecture studied by microscopy: present and future. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 282:1-90. [PMID: 20630466 DOI: 10.1016/s1937-6448(10)82001-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this review we describe major contributions of light and electron microscopic approaches to the present understanding of functional nuclear architecture. The large gap of knowledge, which must still be bridged from the molecular level to the level of higher order structure, is emphasized by differences of currently discussed models of nuclear architecture. Molecular biological tools represent new means for the multicolor visualization of various nuclear components in living cells. New achievements offer the possibility to surpass the resolution limit of conventional light microscopy down to the nanometer scale and require improved bioinformatics tools able to handle the analysis of large amounts of data. In combination with the much higher resolution of electron microscopic methods, including ultrastructural cytochemistry, correlative microscopy of the same cells in their living and fixed state is the approach of choice to combine the advantages of different techniques. This will make possible future analyses of cell type- and species-specific differences of nuclear architecture in more detail and to put different models to critical tests.
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Affiliation(s)
- Jacques Rouquette
- Biocenter, Ludwig Maximilians University (LMU), Martinsried, Germany
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High-precision structural analysis of subnuclear complexes in fixed and live cells via spatially modulated illumination (SMI) microscopy. Chromosome Res 2008; 16:367-82. [DOI: 10.1007/s10577-008-1238-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Tinnefeld P, Sauer M. Branching Out of Single‐Molecule Fluorescence Spectroscopy: Challenges for Chemistry and Influence on Biology. Angew Chem Int Ed Engl 2005; 44:2642-2671. [PMID: 15849689 DOI: 10.1002/anie.200300647] [Citation(s) in RCA: 182] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the last decade emerging single-molecule fluorescence-spectroscopy tools have been developed and adapted to analyze individual molecules under various conditions. Single-molecule-sensitive optical techniques are now well established and help to increase our understanding of complex problems in different disciplines ranging from materials science to cell biology. Previous dreams, such as the monitoring of the motility and structural changes of single motor proteins in living cells or the detection of single-copy genes and the determination of their distance from polymerase molecules in transcription factories in the nucleus of a living cell, no longer constitute unsolvable problems. In this Review we demonstrate that single-molecule fluorescence spectroscopy has become an independent discipline capable of solving problems in molecular biology. We outline the challenges and future prospects for optical single-molecule techniques which can be used in combination with smart labeling strategies to yield quantitative three-dimensional information about the dynamic organization of living cells.
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Affiliation(s)
- Philip Tinnefeld
- Applied Laserphysics und Laserspectroscopy, Faculty of Physics, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany, Fax: (+49) 521-106-2958
| | - Markus Sauer
- Applied Laserphysics und Laserspectroscopy, Faculty of Physics, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany, Fax: (+49) 521-106-2958
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Tinnefeld P, Sauer M. Neue Wege in der Einzelmolekül-Fluoreszenzspektroskopie: Herausforderungen für die Chemie und Einfluss auf die Biologie. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200300647] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Failla A, Albrecht B, Spöri U, Schweitzer A, Kroll A, Hildenbrand G, Bach M, Cremer C. Nanostructure Analysis Using Spatially Modulated Illumination Microscopy. ACTA ACUST UNITED AC 2003. [DOI: 10.1159/000070464] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Affiliation(s)
- James E N Jonkman
- Advanced Optical Microscopy Facility, Ontario Cancer Institute, Princess Margaret Hospital, Toronto, Canada
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Heintzmann R, Jovin TM, Cremer C. Saturated patterned excitation microscopy--a concept for optical resolution improvement. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2002; 19:1599-609. [PMID: 12152701 DOI: 10.1364/josaa.19.001599] [Citation(s) in RCA: 195] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The resolution of optical microscopy is limited by the numerical aperture and the wavelength of light. Many strategies for improving resolution such as 4Pi and I5M have focused on an increase of the numerical aperture. Other approaches have based resolution improvement in fluorescence microscopy on the establishment of a nonlinear relationship between local excitation light intensity in the sample and in the emitted light. However, despite their innovative character, current techniques such as stimulated emission depletion (STED) and ground-state depletion (GSD) microscopy require complex optical configurations and instrumentation to narrow the point-spread function. We develop the theory of nonlinear patterned excitation microscopy for achieving a substantial improvement in resolution by deliberate saturation of the fluorophore excited state. The postacquisition manipulation of the acquired data is computationally more complex than in STED or GSD, but the experimental requirements are simple. Simulations comparing saturated patterned excitation microscopy with linear patterned excitation microscopy (also referred to in the literature as structured illumination or harmonic excitation light microscopy) and ordinary widefield microscopy are presented and discussed. The effects of photon noise are included in the simulations.
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