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Cremer C, Schock F, Failla AV, Birk U. Modulated illumination microscopy: Application perspectives in nuclear nanostructure analysis. J Microsc 2024. [PMID: 38618985 DOI: 10.1111/jmi.13297] [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: 07/04/2023] [Revised: 02/26/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
Abstract
The structure of the cell nucleus of higher organisms has become a major topic of advanced light microscopy. So far, a variety of methods have been applied, including confocal laser scanning fluorescence microscopy, 4Pi, STED and localisation microscopy approaches, as well as different types of patterned illumination microscopy, modulated either laterally (in the object plane) or axially (along the optical axis). Based on our experience, we discuss here some application perspectives of Modulated Illumination Microscopy (MIM) and its combination with single-molecule localisation microscopy (SMLM). For example, spatially modulated illumination microscopy/SMI (illumination modulation along the optical axis) has been used to determine the axial extension (size) of small, optically isolated fluorescent objects between ≤ 200 nm and ≥ 40 nm diameter with a precision down to the few nm range; it also allows the axial positioning of such structures down to the 1 nm scale; combined with laterally structured illumination/SIM, a 3D localisation precision of ≤1 nm is expected using fluorescence yields typical for SMLM applications. Together with the nanosizing capability of SMI, this can be used to analyse macromolecular nuclear complexes with a resolution approaching that of cryoelectron microscopy.
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Affiliation(s)
- Christoph Cremer
- Kirchhoff Institute for Physics (KIP), Heidelberg, Germany
- Interdisciplinary Centre for Scientific Computing (IWR), University of Heidelberg, Heidelberg, Germany
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Florian Schock
- Kirchhoff Institute for Physics (KIP), Heidelberg, Germany
| | - Antonio Virgilio Failla
- UKE Microscopy Imaging Facility, University Medical Centre Hamburg Eppendorf, Hamburg, Germany
| | - Udo Birk
- Institute for Photonics and Robotics (IPR), Department of Applied Future Technologies, University of Applied Sciences of the Grisons (FH Graubünden), Chur, Switzerland
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2
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Cremer C, Birk U. Spatially modulated illumination microscopy: application perspectives in nuclear nanostructure analysis. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A: MATHEMATICAL, PHYSICAL AND ENGINEERING SCIENCES 2022; 380:20210152. [PMID: 0 DOI: 10.1098/rsta.2021.0152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/02/2021] [Indexed: 05/19/2023]
Abstract
Thousands of genes and the complex biochemical networks for their transcription are packed in the micrometer sized cell nucleus. To control biochemical processes, spatial organization plays a key role. Hence the structure of the cell nucleus of higher organisms has emerged as a main topic of advanced light microscopy. So far, a variety of methods have been applied for this, including confocal laser scanning fluorescence microscopy, 4Pi-, STED- and localization microscopy approaches, as well as (laterally) structured illumination microscopy (SIM). Here, we summarize the state of the art and discuss application perspectives for nuclear nanostructure analysis of spatially modulated illumination (SMI). SMI is a widefield-based approach to using axially structured illumination patterns to determine the axial extension (size) of small, optically isolated fluorescent objects between less than or equal to 200 nm and greater than or equal to 40 nm diameter with a precision down to the few nm range; in addition, it allows the axial positioning of such structures down to the 1 nm scale. Combined with SIM, a three-dimensional localization precision of less than or equal to 1 nm is expected to become feasible using fluorescence yields typical for single molecule localization microscopy applications. Together with its nanosizing capability, this may eventually be used to analyse macromolecular complexes and other nanostructures with a topological resolution, further narrowing the gap to Cryoelectron microscopy.
This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 2)’.
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Affiliation(s)
- Christoph Cremer
- Max-Planck Institute for Polymer Research, and Institute of Molecular Biology (IMB), D-55128 Mainz, Germany
- Kirchhoff Institute for Physics (KIP), Interdisciplinary Center for Scientific Computing (IWR), and Institute of Pharmacy and Molecular Biotechnology (IPMB), University Heidelberg, D-69120 Heidelberg, Germany
| | - Udo Birk
- Institute for Photonics and ICT (IPI), University of Applied Sciences (FH Graubünden), CH-7000 Chur, Switzerland
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Sahl SJ, Schönle A, Hell SW. Fluorescence Microscopy with Nanometer Resolution. SPRINGER HANDBOOK OF MICROSCOPY 2019. [DOI: 10.1007/978-3-030-00069-1_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Emerging views of the nucleus as a cellular mechanosensor. Nat Cell Biol 2018; 20:373-381. [PMID: 29467443 DOI: 10.1038/s41556-018-0038-y] [Citation(s) in RCA: 333] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/09/2018] [Indexed: 12/14/2022]
Abstract
The ability of cells to respond to mechanical forces is critical for numerous biological processes. Emerging evidence indicates that external mechanical forces trigger changes in nuclear envelope structure and composition, chromatin organization and gene expression. However, it remains unclear if these processes originate in the nucleus or are downstream of cytoplasmic signals. Here we discuss recent findings that support a direct role of the nucleus in cellular mechanosensing and highlight novel tools to study nuclear mechanotransduction.
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Birk U, Hase JV, Cremer C. Super-resolution microscopy with very large working distance by means of distributed aperture illumination. Sci Rep 2017; 7:3685. [PMID: 28623362 PMCID: PMC5473833 DOI: 10.1038/s41598-017-03743-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 05/05/2017] [Indexed: 02/03/2023] Open
Abstract
The limits of conventional light microscopy ("Abbe-Limit") depend critically on the numerical aperture (NA) of the objective lens. Imaging at large working distances or a large field-of-view typically requires low NA objectives, thereby reducing the optical resolution to the multi micrometer range. Based on numerical simulations of the intensity field distribution, we present an illumination concept for a super-resolution microscope which allows a three dimensional (3D) optical resolution around 150 nm for working distances up to the centimeter regime. In principle, the system allows great flexibility, because the illumination concept can be used to approximate the point-spread-function of conventional microscope optics, with the additional benefit of a customizable pupil function. Compared with the Abbe-limit using an objective lens with such a large working distance, a volume resolution enhancement potential in the order of 104 is estimated.
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Affiliation(s)
- Udo Birk
- Superresolution Microscopy, Institute of Molecular Biology (IMB), D-55128, Mainz, Germany
- Physics Department University Mainz (JGU), D-55128, Mainz, Germany
- Kirchhoff Institute for Physics, University Heidelberg, D-69120, Heidelberg, Germany
| | - Johann V Hase
- Institute of Pharmacy&Molecular Biotechnology (IPMB), University Heidelberg, D-69120, Heidelberg, Germany
| | - Christoph Cremer
- Superresolution Microscopy, Institute of Molecular Biology (IMB), D-55128, Mainz, Germany.
- Physics Department University Mainz (JGU), D-55128, Mainz, Germany.
- Kirchhoff Institute for Physics, University Heidelberg, D-69120, Heidelberg, Germany.
- Institute of Pharmacy&Molecular Biotechnology (IPMB), University Heidelberg, D-69120, Heidelberg, Germany.
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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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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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Baddeley D, Weiland Y, Batram C, Birk U, Cremer C. Model based precision structural measurements on barely resolved objects. J Microsc 2010; 237:70-8. [PMID: 20055920 DOI: 10.1111/j.1365-2818.2009.03304.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A model based method for the accurate quantification of the 3D structure of fluorescently labelled cellular objects similar in size to the optical resolution limit is presented. This method is applied to both simulated confocal images of chromatin structures and to real confocal data obtained on a Fluorescence in situ Hybridization (FISH) labelled gene domain. The model assumes that the object is composed of a small number of discrete points which are convolved with the microscope point spread function to give the image. Fitting this model to image data results in a method to assess object structure which is accurate, shows a low bias, and does not require user intervention or the potentially subjective setting of a threshold.
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Affiliation(s)
- D Baddeley
- Kirchhoff Institut für Physik, Universität Heidelberg, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany.
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10
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Model Convolution: A Computational Approach to Digital Image Interpretation. Cell Mol Bioeng 2010; 3:163-170. [PMID: 20461132 PMCID: PMC2864900 DOI: 10.1007/s12195-010-0101-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 01/26/2010] [Indexed: 01/16/2023] Open
Abstract
Digital fluorescence microscopy is commonly used to track individual proteins and their dynamics in living cells. However, extracting molecule-specific information from fluorescence images is often limited by the noise and blur intrinsic to the cell and the imaging system. Here we discuss a method called “model-convolution,” which uses experimentally measured noise and blur to simulate the process of imaging fluorescent proteins whose spatial distribution cannot be resolved. We then compare model-convolution to the more standard approach of experimental deconvolution. In some circumstances, standard experimental deconvolution approaches fail to yield the correct underlying fluorophore distribution. In these situations, model-convolution removes the uncertainty associated with deconvolution and therefore allows direct statistical comparison of experimental and theoretical data. Thus, if there are structural constraints on molecular organization, the model-convolution method better utilizes information gathered via fluorescence microscopy, and naturally integrates experiment and theory.
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11
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Lang M, Jegou T, Chung I, Richter K, Münch S, Udvarhelyi A, Cremer C, Hemmerich P, Engelhardt J, Hell SW, Rippe K. Three-dimensional organization of promyelocytic leukemia nuclear bodies. J Cell Sci 2010; 123:392-400. [PMID: 20130140 DOI: 10.1242/jcs.053496] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Promyelocytic leukemia nuclear bodies (PML-NBs) are mobile subnuclear organelles formed by PML and Sp100 protein. They have been reported to have a role in transcription, DNA replication and repair, telomere lengthening, cell cycle control and tumor suppression. We have conducted high-resolution 4Pi fluorescence laser-scanning microscopy studies complemented with correlative electron microscopy and investigations of the accessibility of the PML-NB subcompartment. During interphase PML-NBs adopt a spherical organization characterized by the assembly of PML and Sp100 proteins into patches within a 50- to 100-nm-thick shell. This spherical shell of PML and Sp100 imposes little constraint to the exchange of components between the PML-NB interior and the nucleoplasm. Post-translational SUMO modifications, telomere repeats and heterochromatin protein 1 were found to localize in characteristic patterns with respect to PML and Sp100. From our findings, we derived a model that explains how the three-dimensional organization of PML-NBs serves to concentrate different biological activities while allowing for an efficient exchange of components.
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Affiliation(s)
- Marion Lang
- Division of High Resolution Optical Microscopy, Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany
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12
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Baddeley D, Chagin VO, Schermelleh L, Martin S, Pombo A, Carlton PM, Gahl A, Domaing P, Birk U, Leonhardt H, Cremer C, Cardoso MC. Measurement of replication structures at the nanometer scale using super-resolution light microscopy. Nucleic Acids Res 2009; 38:e8. [PMID: 19864256 PMCID: PMC2811013 DOI: 10.1093/nar/gkp901] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
DNA replication, similar to other cellular processes, occurs within dynamic macromolecular structures. Any comprehensive understanding ultimately requires quantitative data to establish and test models of genome duplication. We used two different super-resolution light microscopy techniques to directly measure and compare the size and numbers of replication foci in mammalian cells. This analysis showed that replication foci vary in size from 210 nm down to 40 nm. Remarkably, spatially modulated illumination (SMI) and 3D-structured illumination microscopy (3D-SIM) both showed an average size of 125 nm that was conserved throughout S-phase and independent of the labeling method, suggesting a basic unit of genome duplication. Interestingly, the improved optical 3D resolution identified 3- to 5-fold more distinct replication foci than previously reported. These results show that optical nanoscopy techniques enable accurate measurements of cellular structures at a level previously achieved only by electron microscopy and highlight the possibility of high-throughput, multispectral 3D analyses.
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Affiliation(s)
- D Baddeley
- Kirchhoff Institut für Physik, University of Heidelberg, Germany
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13
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Hirvonen LM, Wicker K, Mandula O, Heintzmann R. Structured illumination microscopy of a living cell. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 38:807-12. [DOI: 10.1007/s00249-009-0501-6] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 05/26/2009] [Accepted: 05/27/2009] [Indexed: 11/28/2022]
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14
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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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15
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Baddeley D, Batram C, Weiland Y, Cremer C, Birk UJ. Nanostructure analysis using spatially modulated illumination microscopy. Nat Protoc 2008; 2:2640-6. [PMID: 17948007 DOI: 10.1038/nprot.2007.399] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe the usage of the spatially modulated illumination (SMI) microscope to estimate the sizes (and/or positions) of fluorescently labeled cellular nanostructures, including a brief introduction to the instrument and its handling. The principle setup of the SMI microscope will be introduced to explain the measures necessary for a successful nanostructure analysis, before the steps for sample preparation, data acquisition and evaluation are given. The protocol starts with cells already attached to the cover glass. The protocol and duration outlined here are typical for fixed specimens; however, considerably faster data acquisition and in vivo measurements are possible.
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Affiliation(s)
- David Baddeley
- Kirchhoff Institut für Physik, Universität Heidelberg, INF 227, D-69120 Heidelberg, Germany.
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17
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Pombo A. Advances in imaging the interphase nucleus using thin cryosections. Histochem Cell Biol 2007; 128:97-104. [PMID: 17636315 DOI: 10.1007/s00418-007-0310-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2007] [Indexed: 01/01/2023]
Abstract
The mammalian genome is partitioned amongst various chromosomes and encodes for approximately 30,000 protein-coding genes. Gene expression occurs after exit from mitosis, when chromosomes partially decondense within the cell nucleus to allow the enzymatic activities that work on chromatin to access each gene in a regulated fashion. Differential patterns of gene expression evolve during cell differentiation to give rise to the over 200 cell types in higher eukaryotes. The architectural organisation of the genome inside the interphase cell nucleus, and associated enzymatic activities, reveals dynamic and functional compartmentalization of the genome. In this review, I highlight the advantages of Tokuyasu cryosectioning on the investigation of nuclear structure and function.
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Affiliation(s)
- Ana Pombo
- Nuclear Organisation Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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18
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Gliko O, Reddy GD, Anvari B, Brownell WE, Saggau P. Standing wave total internal reflection fluorescence microscopy to measure the size of nanostructures in living cells. JOURNAL OF BIOMEDICAL OPTICS 2006; 11:064013. [PMID: 17212536 DOI: 10.1117/1.2372457] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We present the first application of standing wave fluorescence microscopy (SWFM) to determine the size of biological nanostructures in living cells. The improved lateral resolution of less than 100 nm enables superior quantification of the size of subcellular structures. We demonstrate the ability of SWFM by measuring the diameter of biological nanotubes (membrane tethers formed between cells). The combination of SWFM with total internal reflection (TIR), referred to as SW-TIRFM, allows additional improvement of axial resolution by selective excitation of fluorescence in a layer of about 100 nm.
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Affiliation(s)
- Olga Gliko
- Department of Otolaryngology-Head & Neck Surgery, Baylor College of Medicine, Houston, Texas 77030, USA
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Mathée H, Baddeley D, Wotzlaw C, Fandrey J, Cremer C, Birk U. Nanostructure of specific chromatin regions and nuclear complexes. Histochem Cell Biol 2005; 125:75-82. [PMID: 16284774 DOI: 10.1007/s00418-005-0096-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2005] [Indexed: 12/20/2022]
Abstract
Spatially modulated illumination (SMI) microscopy is a method of widefield fluorescence microscopy featuring interferometric illumination, which delivers structural information about nanoscale features in fluorescently labeled cells. Using this approach, structural changes in the context of gene activation and chromatin remodeling may be revealed. In this paper we present the application of SMI microscopy to size measurements of the 7q22 gene region, giving us a size estimate of 105+/-16 nm which corresponds to an average compaction ratio of 1:324. The results for the 7q22 domain are compared with the previously measured sizes of other fluorescently labeled gene regions, and to those obtained for transcription factories. The absence of a correlation between the measured and genomic sizes of the various gene regions indicate that a high variability in chromatin folding is present, with factors other than the sequence length contributing to the chromatin compaction. Measurements of the 7q22 region in different preparations and at different excitation wavelengths show a good agreement, thus demonstrating that the technique is robust when applied to biological samples.
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Affiliation(s)
- H Mathée
- Applied Optics and Information Processing, Kirchhoff Institute für Physik, Universität Heidelberg, INF 227, 69120, Heidelberg, Germany
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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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21
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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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22
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Hildenbrand G, Rapp A, Spöri U, Wagner C, Cremer C, Hausmann M. Nano-sizing of specific gene domains in intact human cell nuclei by spatially modulated illumination light microscopy. Biophys J 2005; 88:4312-8. [PMID: 15805170 PMCID: PMC1305660 DOI: 10.1529/biophysj.104.056796] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Although light microscopy and three-dimensional image analysis have made considerable progress during the last decade, it is still challenging to analyze the genome nano-architecture of specific gene domains in three-dimensional cell nuclei by fluorescence microscopy. Here, we present for the first time chromatin compaction measurements in human lymphocyte cell nuclei for three different, specific gene domains using a novel light microscopic approach called Spatially Modulated Illumination microscopy. Gene domains for p53, p58, and c-myc were labeled by fluorescence in situ hybridization and the sizes of the fluorescence in situ hybridization "spots" were measured. The mean diameters of the gene domains were determined to 103 nm (c-myc), 119 nm (p53), and 123 nm (p58) and did not correlate to the genomic, labeled sequence length. Assuming a spherical domain shape, these values would correspond to volumes of 5.7 x 10(-4) microm(3) (c-myc), 8.9 x 10(-4) microm(3) (p53), and 9.7 x 10(-4) microm(3) (p58). These volumes are approximately 2 orders of magnitude smaller than the diffraction limited illumination or observation volume, respectively, in a confocal laser scanning microscope using a high numerical aperture objective lens. By comparison of the labeled sequence length to the domain size, compaction ratios were estimated to 1:129 (p53), 1:235 (p58), and 1:396 (c-myc). The measurements demonstrate the advantage of the SMI technique for the analysis of gene domain nano-architecture in cell nuclei. The data indicate that chromatin compaction is subjected to a large variability which may be due to different states of genetic activity or reflect the cell cycle state.
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Affiliation(s)
- Georg Hildenbrand
- Applied Optics and Information Processing, Kirchhoff-Institute of Physics, University of Heidelberg, Germany
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Müller WG, Rieder D, Kreth G, Cremer C, Trajanoski Z, McNally JG. Generic features of tertiary chromatin structure as detected in natural chromosomes. Mol Cell Biol 2004; 24:9359-70. [PMID: 15485905 PMCID: PMC522243 DOI: 10.1128/mcb.24.21.9359-9370.2004] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Knowledge of tertiary chromatin structure in mammalian interphase chromosomes is largely derived from artificial tandem arrays. In these model systems, light microscope images reveal fibers or beaded fibers after high-density targeting of transactivators to insertional domains spanning several megabases. These images of fibers have lent support to chromonema fiber models of tertiary structure. To assess the relevance of these studies to natural mammalian chromatin, we identified two different approximately 400-kb regions on human chromosomes 6 and 22 and then examined light microscope images of interphase tertiary chromatin structure when the regions were transcriptionally active and inactive. When transcriptionally active, these natural chromosomal regions elongated, yielding images characterized by a series of adjacent puncta or "beads", referred to hereafter as beaded images. These elongated structures required transcription for their maintenance. Thus, despite marked differences in the density and the mode of transactivation, the natural and artificial systems showed similarities, suggesting that beaded images are generic features of transcriptionally active tertiary chromatin. We show here, however, that these images do not necessarily favor chromonema fiber models but can also be explained by a radial-loop model or even a simple nucleosome affinity, random-chain model. Thus, light microscope images of tertiary structure cannot distinguish among competing models, although they do impose key constraints: chromatin must be clustered to yield beaded images and then packaged within each cluster to enable decondensation into adjacent clusters.
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MESH Headings
- Base Sequence
- Cell Line
- Chromatin/chemistry
- Chromatin/genetics
- Chromatin/metabolism
- Chromosomes, Human, Pair 22/chemistry
- Chromosomes, Human, Pair 22/genetics
- Chromosomes, Human, Pair 22/metabolism
- Chromosomes, Human, Pair 6/chemistry
- Chromosomes, Human, Pair 6/genetics
- Chromosomes, Human, Pair 6/metabolism
- DNA/chemistry
- DNA/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Interferons/pharmacology
- Models, Biological
- Molecular Sequence Data
- Nucleic Acid Conformation
- Transcription, Genetic
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Affiliation(s)
- Waltraud G Müller
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Building 41, Room B516, 41 Library Dr., MSC 5055, Bethesda, MD 20892-5055, USA
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24
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Eggeling C. Nanotechnology and Single Molecules. Chemphyschem 2004; 5:1483-7. [PMID: 15535545 DOI: 10.1002/cphc.200400290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Christian Eggeling
- Max-Planck-Institute for Biophysical Chemistry, Department of NanoBiophotonics, Göttingen, Germany.
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25
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Martin S, Pombo A. Transcription factories: quantitative studies of nanostructures in the mammalian nucleus. Chromosome Res 2004; 11:461-70. [PMID: 12971722 DOI: 10.1023/a:1024926710797] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Transcription by the three nuclear RNA polymerases is carried out in transcription factories. This conclusion has been drawn from estimates of the total number of nascent transcripts or active polymerase molecules and the number of transcription sites within a cell. Here we summarise the variety of methods used to determine these parameters, discuss their associated problems and outline future prospects.
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Affiliation(s)
- Sonya Martin
- MRC-Clinical Sciences Centre, Faculty of Medicine, Imperial College School of Science, Technology and Medicine, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
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26
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Martin S, Failla AV, Spöri U, Cremer C, Pombo A. Measuring the size of biological nanostructures with spatially modulated illumination microscopy. Mol Biol Cell 2004; 15:2449-55. [PMID: 15020718 PMCID: PMC404036 DOI: 10.1091/mbc.e04-01-0045] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Spatially modulated illumination fluorescence microscopy can in theory measure the sizes of objects with a diameter ranging between 10 and 200 nm and has allowed accurate size measurement of subresolution fluorescent beads ( approximately 40-100 nm). Biological structures in this size range have so far been measured by electron microscopy. Here, we have labeled sites containing the active, hyperphosphorylated form of RNA polymerase II in the nucleus of HeLa cells by using the antibody H5. The spatially modulated illumination-microscope was compared with confocal laser scanning and electron microscopes and found to be suitable for measuring the size of cellular nanostructures in a biological setting. The hyperphosphorylated form of polymerase II was found in structures with a diameter of approximately 70 nm, well below the 200-nm resolution limit of standard fluorescence microscopes.
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Affiliation(s)
- Sonya Martin
- MRC, Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, United Kingdom
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27
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Sherman GW, Bradley CC. Interferometric laser diode probing of micrometer- and nanometer-scale materials. APPLIED OPTICS 2003; 42:6360-6366. [PMID: 14649279 DOI: 10.1364/ao.42.006360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We are developing a method for real-time detection, tracking, and categorization of micrometer- and nanometer-scale particles and materials using light scattered from a swept standing-wave probe. Synchronous, phase-sensitive detection of the weakly scattered optical field is exploited to provide interferometric sensitivity and improve the signal-to-noise ratio, allowing use of low-power laser diode sources and photodiode detectors. To demonstrate the technique, we probe a set of W, C, and Cu microfibers and determine diameters and refractive-index values from a detailed comparison of light-scattering data and a numerical model. We extrapolate these results and discuss the application of laser diode sources and photodiode receivers for the detection and study of nanoscale materials.
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Affiliation(s)
- Gregory W Sherman
- Department of Physics and Astronomy, Texas Christian University, TCU Box 298840, Fort Worth, Texas 76129, USA
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