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Carsten A, Failla AV, Aepfelbacher M. MINFLUX nanoscopy: Visualising biological matter at the nanoscale level. J Microsc 2024. [PMID: 38661499 DOI: 10.1111/jmi.13306] [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: 10/31/2023] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
Since its introduction in 2017, MINFLUX nanoscopy has shown that it can visualise fluorescent molecules with an exceptional localisation precision of a few nanometres. In this overview, we provide a brief insight into technical implementations, fluorescent marker developments and biological studies that have been conducted in connection with MINFLUX imaging and tracking. We also formulate ideas on how MINFLUX nanoscopy and derived technologies could influence bioimaging in the future. This insight is intended as a general starting point for an audience looking for a brief overview of MINFLUX nanoscopy from theory to application.
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Affiliation(s)
- Alexander Carsten
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Antonio Virgilio Failla
- UKE Microscopy Imaging Facility, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
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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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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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Huszka G, Gijs MA. Super-resolution optical imaging: A comparison. MICRO AND NANO ENGINEERING 2019. [DOI: 10.1016/j.mne.2018.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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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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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: 6] [Impact Index Per Article: 0.9] [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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Guzzinati G, Clark L, Béché A, Juchtmans R, Van Boxem R, Mazilu M, Verbeeck J. Prospects for versatile phase manipulation in the TEM: beyond aberration correction. Ultramicroscopy 2014; 151:85-93. [PMID: 25455416 DOI: 10.1016/j.ultramic.2014.10.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/06/2014] [Accepted: 10/06/2014] [Indexed: 11/16/2022]
Abstract
In this paper we explore the desirability of a transmission electron microscope in which the phase of the electron wave can be freely controlled. We discuss different existing methods to manipulate the phase of the electron wave and their limitations. We show how with the help of current techniques the electron wave can already be crafted into specific classes of waves each having their own peculiar properties. Assuming a versatile phase modulation device is feasible, we explore possible benefits and methods that could come into existence borrowing from light optics where the so-called spatial light modulators provide programmable phase plates for quite some time now. We demonstrate that a fully controllable phase plate building on Harald Rose׳s legacy in aberration correction and electron optics in general would open an exciting field of research and applications.
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Affiliation(s)
- Giulio Guzzinati
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Laura Clark
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Armand Béché
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Roeland Juchtmans
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Ruben Van Boxem
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Michael Mazilu
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, UK
| | - Jo Verbeeck
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
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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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11
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Spectrally coded optical nanosectioning (SpecON) with biocompatible metal-dielectric-coated substrates. Proc Natl Acad Sci U S A 2013; 110:20069-74. [PMID: 24277837 DOI: 10.1073/pnas.1307222110] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fluorescence nanosectioning within a submicron region above an interface is desirable for many disciplines in the life sciences. A drawback, however, to most current approaches is the a priori need to physically scan a sculptured point spread function in the axial dimension, which can be undesirable for optically sensitive or highly dynamic samples. Here we demonstrate a fluorescence imaging approach that can overcome the need for scanning by exploiting the position-dependent emission spectrum of fluorophores above a simple biocompatible nanostructure. To achieve this we have designed a thin metal-dielectric-coated substrate, where the spectral modification to the total measured fluorescence can be used to estimate the axial fluorophore distribution within distances of 10-150 nm above the substrate with an accuracy of up to 5-10 nm. The modeling and feasibility of the approach are verified and successfully applied to elucidate nanoscale adhesion protein and filopodia dynamics in migrating cells. It is likely that the general principle can find broader applications in, for example, single-molecule studies, biosensing, and studying fast dynamic processes.
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12
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Rapkin LM, Anchel DRP, Li R, Bazett-Jones DP. A view of the chromatin landscape. Micron 2011; 43:150-8. [PMID: 22172345 DOI: 10.1016/j.micron.2011.11.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 11/17/2011] [Accepted: 11/17/2011] [Indexed: 10/15/2022]
Abstract
The microscope has been indispensable to the last century of chromatin structure research. Microscopy techniques have revealed that the three-dimensional location of chromatin is not random but represents a further manifestation of a highly compartmentalized cell nucleus. Moreover, the structure and location of genetic loci display cell type-specific differences and relate directly to the state of differentiation. Advances to bridge imaging with genetic, molecular and biochemical approaches have greatly enhanced our understanding of the interdependence of chromatin structure and nuclear function in mammalian cells. In this review we discuss the current state of chromatin structure research in relationship to the variety of microscopy techniques that have contributed to this field.
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Affiliation(s)
- Lindsy M Rapkin
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
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Cremer C, Kaufmann R, Gunkel M, Pres S, Weiland Y, Müller P, Ruckelshausen T, Lemmer P, Geiger F, Degenhard S, Wege C, Lemmermann NAW, Holtappels R, Strickfaden H, Hausmann M. Superresolution imaging of biological nanostructures by spectral precision distance microscopy. Biotechnol J 2011; 6:1037-51. [DOI: 10.1002/biot.201100031] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores. Nat Methods 2011; 8:353-9. [DOI: 10.1038/nmeth.1583] [Citation(s) in RCA: 176] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 02/14/2011] [Indexed: 11/08/2022]
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Kaufmann R, Müller P, Hildenbrand G, Hausmann M, Cremer C. Analysis of Her2/neu membrane protein clusters in different types of breast cancer cells using localization microscopy. J Microsc 2010; 242:46-54. [PMID: 21118230 DOI: 10.1111/j.1365-2818.2010.03436.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The Her2/neu tyrosine kinase receptor is a member of the epidermal growth factor family. It plays an important role in tumour genesis of certain types of breast cancer and its overexpression correlates with distinct diagnostic and therapeutic decisions. Nevertheless, it is still under intense investigation to improve diagnostic outcome and therapy control. In this content, we applied spectral precision distance/position determination microscopy, a technique based on the general principles of localization microscopy in order to study tumour typical conformational changes of receptor clusters on cell membranes. We examined two different mamma carcinoma cell lines as well as cells of a breast biopsy of a healthy donor. The Her2/neu receptor sites were labelled by immunofluorescence using conventional fluorescent dyes (Alexa conjugated antibodies). The characterization of the Her2/neu distribution on plasma membrane sections of 176 different cells yielded a total amount of 20 637 clusters with a mean diameter of 67 nm. Statistical analysis on the single molecule level revealed differences in clustering of Her2/neu between all three different cell lines. We also showed that using spectral precision distance/position determination microscopy, a dual colour reconstruction of the 3D spatial arrangement of Her2/neu and Her3 is possible. This indicates that spectral precision distance/position determination microscopy could be used as an enhanced tool offering additional information of Her2/neu receptor status.
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Affiliation(s)
- R Kaufmann
- Applied Optics and Information Processing, Kirchhoff-Institute for Physics, University Heidelberg, Im Neuenheimer Feld, Heidelberg, Germany.
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Schermelleh L, Heintzmann R, Leonhardt H. A guide to super-resolution fluorescence microscopy. ACTA ACUST UNITED AC 2010; 190:165-75. [PMID: 20643879 PMCID: PMC2918923 DOI: 10.1083/jcb.201002018] [Citation(s) in RCA: 791] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
For centuries, cell biology has been based on light microscopy and at the same time been limited by its optical resolution. However, several new technologies have been developed recently that bypass this limit. These new super-resolution technologies are either based on tailored illumination, nonlinear fluorophore responses, or the precise localization of single molecules. Overall, these new approaches have created unprecedented new possibilities to investigate the structure and function of cells.
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Affiliation(s)
- Lothar Schermelleh
- Department of Biology and Center for Integrated Protein Science, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, 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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LEMMER P, GUNKEL M, WEILAND Y, MÜLLER P, BADDELEY D, KAUFMANN R, URICH A, EIPEL H, AMBERGER R, HAUSMANN M, CREMER C. Using conventional fluorescent markers for far-field fluorescence localization nanoscopy allows resolution in the 10-nm range. J Microsc 2009; 235:163-71. [DOI: 10.1111/j.1365-2818.2009.03196.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Batram C, Baddeley D, Kreth G, Cremer C. High precision size measurement of centromere 8 and the 8q24/c-myc gene region in metaphase and interphase human fibroblasts indicate differential condensation. J Struct Biol 2008; 164:293-303. [PMID: 18835450 DOI: 10.1016/j.jsb.2008.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 09/05/2008] [Accepted: 09/05/2008] [Indexed: 11/28/2022]
Abstract
The hypothesis that distinct chromatin domains expand and are remodelled differently when they undergo transcription, replication or cell cycle processes is well accepted. The condensation changes by which chromosomes are transformed at the metaphase-interphase transition are especially interesting and therefore extensively studied by light microscopy; however, quantitative information of the size on specific small chromatin domains during the cell cycle is scarce. In this respect, a serious problem is the determination of structural features close to the resolution limit. In this report we use a novel approach to quantify the lateral extent of the 8q24/c-myc gene domain and the centromeric region of chromosome 8 in doubly labelled normal human foreskin fibroblasts using confocal laser scanning microscopy (CLSM). The domains were analysed in both metaphase spreads and interphase nuclei. These high precision measurements revealed a somewhat smaller (few 10s of nm) lateral extension of the centromere region in metaphase compared to interphase. Surprisingly, within the same cells the lateral extension of the 8q24/c-myc region was significantly smaller in interphase than in metaphase. For comparison the centromere size was more condensed in metaphase than in interphase. This implies a different folding behaviour for specific chromatin domains with opposite condensation behaviour.
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Affiliation(s)
- C Batram
- Applied Optics and Information Processing, Kirchhoff Institute of Physics, University of Heidelberg, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany.
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Rodríguez PFG, Sepulveda E, Dubertret B, Loriette V. Axial coding in full-field microscopy using three-dimensional structured illumination implemented with no moving parts. OPTICS LETTERS 2008; 33:1617-1619. [PMID: 18628816 DOI: 10.1364/ol.33.001617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We report a simple optical setup to produce both axial and lateral structured illumination through a single objective lens. With a minimum of six full-field images obtained without moving either the sample or the microscope objective, 100 nm diameter fluorescent beads can be localized axially with an accuracy of 50 nm in a 1.76-microm-thick layer. We show that this axial localization improvement can easily be combined with classical lateral structured illumination, so that lateral resolution enhancement by a factor of 2 is maintained.
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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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22
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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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Rauch J, Knoch TA, Solovei I, Teller K, Stein S, Buiting K, Horsthemke B, Langowski J, Cremer T, Hausmann M, Cremer C. Light optical precision measurements of the active and inactive Prader-Willi syndrome imprinted regions in human cell nuclei. Differentiation 2007; 76:66-82. [PMID: 18039333 DOI: 10.1111/j.1432-0436.2007.00237.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Despite the major advancements during the last decade with respect to both knowledge of higher order chromatin organization in the cell nucleus and the elucidation of epigenetic mechanisms of gene control, the true three-dimensional (3D) chromatin structure of endogenous active and inactive gene loci is not known. The present study was initiated as an attempt to close this gap. As a model case, we compared the chromatin architecture between the genetically active and inactive domains of the imprinted Prader-Willi syndrome (PWS) locus in human fibroblast and lymphoblastoid cell nuclei by 3D fluorescence in situ hybridization and quantitative confocal laser scanning microscopy. The volumes and 3D compactions of identified maternal and paternal PWS domains were determined in stacks of light optical serial sections using a novel threshold-independent approach. Our failure to detect volume and compaction differences indicates that possible differences are below the limits of light optical resolution. To overcome this limitation, spectral precision distance microscopy, a method of localization microscopy at the nanometer scale, was used to measure 3D distances between differentially labeled probes located both within the PWS region and in its neighborhood. This approach allows the detection of intranuclear differences between 3D distances down to about 70-90 nm, but again did not reveal clearly detectable differences between active and inactive PWS domains. Despite this failure, a comparison of the experimental 3D distance measurements with computer simulations of chromatin folding strongly supports a non-random higher order chromatin configuration of the PWS locus and argues against 3D configurations based on giant chromatin loops. Our results indicate that the search for differences between endogenous active and inactive PWS domains must be continued at still smaller scales than hitherto possible with conventional light microscopic procedures. The possibilities to achieve this goal are discussed.
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Affiliation(s)
- Joachim Rauch
- Kirchhoff Institute of Physics, University of Heidelberg, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
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25
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Medda R, Jakobs S, Hell SW, Bewersdorf J. 4Pi microscopy of quantum dot-labeled cellular structures. J Struct Biol 2006; 156:517-23. [PMID: 17045487 DOI: 10.1016/j.jsb.2006.08.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2006] [Revised: 08/18/2006] [Accepted: 08/19/2006] [Indexed: 11/25/2022]
Abstract
The most prominent restrictions of fluorescence microscopy are the limited resolution and the finite signal. Established conventional, confocal, and multiphoton microscopes resolve at best approximately 200nm in the focal plane and only 500nm in depth. Additionally, organic fluorophores and fluorescent proteins are bleached after 10(4)-10(5) excitation cycles. To overcome these restrictions, we synergistically combine the 3- to 7-fold improved axial resolution of 4Pi microscopy with the greatly enhanced photostability of semiconductor quantum dots. Co-localization studies of immunolabeled microtubules and mitochondria demonstrate the feasibility of this approach for routine biological measurements. In particular, we visualize the three-dimensional entanglement of the two networks with unprecedented detail.
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Affiliation(s)
- Rebecca Medda
- Max Planck Institute for Biophysical Chemistry, Department of NanoBiophotonics, 37070 Göttingen, Germany
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26
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Abstract
The axial (z-) resolution of approximately 100 nm provided by 4Pi and I5M fluorescence microscopy relies on the coherent addition of spherical wavefronts of two opposing high aperture angle lenses. Both microscopes feature a point-spread function (PSF) with a sharp central spot that is accompanied by axially shifted sidelobes which leads to replication artefacts in the raw image data. In a 4Pi-microscope the sidelobes are less pronounced than in I5M and without relevant lateral (x,y) substructure, making their posterior removal in the image reliable and fast. On the other hand, high speeds of raw data acquisition are more easily gained by I5M. Moreover, I5M features a stronger signal as compared to the commonly employed two-photon excitation (2PE) 4Pi-imaging mode. We investigate here the capability of both techniques to image (aqueous) specimens without artefacts. To this end, we consider the optical transfer function (OTF) of the two microscopes in conjunction with the signal-to-noise-ratio (SNR) of the object to be imaged. The imaging of E. coli bacteria with an interconvertable setup enabled a direct comparison of the two imaging modes. As both systems rely on high aperture angles, water-immersion lenses of the largest numerical aperture available (NA = 1.2) were employed. The experimental results are corroborated by simulations assuming the signal strength encountered in the experiment. The comparison of the theoretical with the experimental PSFs/OTFs showed that our setup operated close to theory in both imaging modes. Although I5M provided about 10 times brighter raw image data as compared to (2PE) 4Pi-microscopy, the I5M data could not be entirely cleared of artefacts. In conclusion, with the current aperture angles and fluorescence signal strengths, it is not advisable to trade in the suppression of the sidelobes for a larger image signal.
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Affiliation(s)
- J Bewersdorf
- Max-Planck-Institute for Biophysical Chemistry, Department of NanoBiophotonics, Göttingen, Germany.
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27
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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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28
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Following are the abstracts from the Fourth Annual Meeting of the Society for Molecular Imaging. Mol Imaging 2005. [DOI: 10.1162/15353500200500210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Declaration of Financial Interests or Relationships To insure balance, independence, objectivity and scientific rigor in all CME programs it is the policy of the meeting's joint sponsors that any speaker or poster presenter who makes a presentation at a program designated for AMA Physician's Recognition Award (PRA) Category 1 or 2 credit must disclose any real or apparent financial interest or other relationship (i.e., grants, research support, consultant, honoraria) that the presenter may have with the manufacturers, distributors or providers of any commercial products or services that may be discussed in the presentation. ISMRM and SMI do not imply that such financial interests or relationships are inherently improper or that such interests or relationships would prevent the presenter from making an objective presentation. However, it is imperative that such financial interests or relationships be identified by the presenter so that participants at the CME activity may have these facts fully disclosed prior to the presentation, and may form their own judgments about the presentation. Towards this end, the information provided by each presenter can be found at the bottom of each abstract. Every speaker, abstract presenter, organizer or anyone else who has control over any content in this meeting has been required to submit a Declaration of Financial Interests or Relationships, even if there is no conflict or relationship to declare.
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29
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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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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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31
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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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32
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Dobrucki JW. Confocal Microscopy: Quantitative Analytical Capabilities. Methods Cell Biol 2004; 75:41-72. [PMID: 15603422 DOI: 10.1016/s0091-679x(04)75003-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Affiliation(s)
- Jurek W Dobrucki
- Laboratory of Confocal Microscopy and Image Analysis, Department of Biophysics, Faculty of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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33
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O'Brien TP, Bult CJ, Cremer C, Grunze M, Knowles BB, Langowski J, McNally J, Pederson T, Politz JC, Pombo A, Schmahl G, Spatz JP, van Driel R. Genome function and nuclear architecture: from gene expression to nanoscience. Genome Res 2003; 13:1029-41. [PMID: 12743020 DOI: 10.1101/gr.946403] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Biophysical, chemical, and nanoscience approaches to the study of nuclear structure and activity have been developing recently and hold considerable promise. A selection of fundamental problems in genome organization and function are reviewed and discussed in the context of these new perspectives and approaches. Advancing these concepts will require coordinated networks of physicists, chemists, and materials scientists collaborating with cell, developmental, and genome biologists.
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34
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Failla AV, Spoeri U, Albrecht B, Kroll A, Cremer C. Nanosizing of fluorescent objects by spatially modulated illumination microscopy. APPLIED OPTICS 2002; 41:7275-7283. [PMID: 12477118 DOI: 10.1364/ao.41.007275] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A new approach to measuring the sizes of small fluorescent objects by use of spatially modulated illumination (SMI) far-field light microscopy is presented. This method is based on SME measurements combined with a new SMI virtual microscopy (VIM) data analysis calibration algorithm. Here, experimental SMI measurements of fluorescent objects with known diameter (size) were made. From the SMI data obtained, the size was determined in an independent way by use of the SMI VIM algorithm. The results showed that with SMI microscopy in combination with SMI VIM calibration, subwavelength object size measurements as small as 40 nm are experimentally feasible with high accuracy.
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Affiliation(s)
- Antonio Virgillo Failla
- Applied Optics and Information Processing, Kirchhoff Institute for Physics, University of Heidelberg, Im Nevenheimer Feld 227, 69120 Heidelberg, Germany
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35
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Failla AV, Cavallo A, Cremer C. Subwavelength size determination by spatially modulated illumination virtual microscopy. APPLIED OPTICS 2002; 41:6651-6659. [PMID: 12412656 DOI: 10.1364/ao.41.006651] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A new approach for determining the sizes of individual, small fluorescent objects with diameters considerably below the optical resolution limit is described in which spatially modulated illumination (SMI) microscopy and 360-647-nm excitation wavelengths are used. The results of SMI virtual microscopy computer simulations indicate that, in this wavelength range, reliable measurements of sizes as small as approximately 20 nm are feasible if the low numbers of fluorescence photons that are usually detected from such small objects are taken into account. This method is based on the well-known fact that the modulation of the diffraction image in a SMI microscope is disturbed by the size of the object. Using appropriately calculated calibration functions, one can use this disturbance of the modulation to determine the size of the original object.
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