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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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Martinière A, Zelazny E. Membrane nanodomains and transport functions in plant. PLANT PHYSIOLOGY 2021; 187:1839-1855. [PMID: 35235669 PMCID: PMC8644385 DOI: 10.1093/plphys/kiab312] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/16/2021] [Indexed: 05/25/2023]
Abstract
Far from a homogeneous environment, biological membranes are highly structured with lipids and proteins segregating in domains of different sizes and dwell times. In addition, membranes are highly dynamics especially in response to environmental stimuli. Understanding the impact of the nanoscale organization of membranes on cellular functions is an outstanding question. Plant channels and transporters are tightly regulated to ensure proper cell nutrition and signaling. Increasing evidence indicates that channel and transporter nano-organization within membranes plays an important role in these regulation mechanisms. Here, we review recent advances in the field of ion, water, but also hormone transport in plants, focusing on protein organization within plasma membrane nanodomains and its cellular and physiological impacts.
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Affiliation(s)
| | - Enric Zelazny
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
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Cai W, Wang X, Yu T. Spatial-frequency encoded imaging of multangular and multispectral images. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:015111. [PMID: 33514201 DOI: 10.1063/5.0025112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
Modern imaging techniques increasingly require signals to be collected from multiple viewpoints and spectral bands to realize multi-dimensional and multi-species detections. For this purpose, multiple cameras are commonly required. Each camera collects signals from one viewpoint or one spectral band, resulting in a considerable experimental cost. Based on frequency modulation, this work proposes an encoded-imaging technique that can record multangular and multispectral images in one acquisition. The signals recorded from different viewpoints and spectral bands are superimposed in the spatial domain, while being separate in the frequency domain. This allows us to extract individual images based on their respective frequency components. In this work, a proof-of-concept experiment was conducted. The high correlation coefficient between the superimposition of the extracted images and a normal superimposed image demonstrates the effectiveness of this technique. In addition, an improved mathematical formulation was proposed to describe the higher spatial-frequency components, which were considered merely to be residual lines in previous studies. The proposed encoded-imaging technique may have potential for multangular and multispectral imaging, which is especially useful for tomographic reconstructions.
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Affiliation(s)
- Weiwei Cai
- Key Laboratory of Education Ministry for Power Machinery and Engineering, School of Mechanical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaolei Wang
- Institute of Modern Optics, Key Laboratory of Optical Information Science and Technology, Ministry of Education, Nankai University, Tianjin 300071, China
| | - Tao Yu
- Key Laboratory of Education Ministry for Power Machinery and Engineering, School of Mechanical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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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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Chekli L, Bayatsarmadi B, Sekine R, Sarkar B, Shen AM, Scheckel KG, Skinner W, Naidu R, Shon HK, Lombi E, Donner E. Analytical characterisation of nanoscale zero-valent iron: A methodological review. Anal Chim Acta 2015; 903:13-35. [PMID: 26709296 DOI: 10.1016/j.aca.2015.10.040] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 10/27/2015] [Accepted: 10/29/2015] [Indexed: 12/01/2022]
Abstract
Zero-valent iron nanoparticles (nZVI) have been widely tested as they are showing significant promise for environmental remediation. However, many recent studies have demonstrated that their mobility and reactivity in subsurface environments are significantly affected by their tendency to aggregate. Both the mobility and reactivity of nZVI mainly depends on properties such as particle size, surface chemistry and bulk composition. In order to ensure efficient remediation, it is crucial to accurately assess and understand the implications of these properties before deploying these materials into contaminated environments. Many analytical techniques are now available to determine these parameters and this paper provides a critical review of their usefulness and limitations for nZVI characterisation. These analytical techniques include microscopy and light scattering techniques for the determination of particle size, size distribution and aggregation state, and X-ray techniques for the characterisation of surface chemistry and bulk composition. Example characterisation data derived from commercial nZVI materials is used to further illustrate method strengths and limitations. Finally, some important challenges with respect to the characterisation of nZVI in groundwater samples are discussed.
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Affiliation(s)
- L Chekli
- School of Civil and Environmental Engineering, University of Technology, Sydney, Post Box 129, Broadway, NSW 2007, Australia; CRC CARE, PO Box 486, Salisbury, SA 5106, Australia
| | - B Bayatsarmadi
- School of Chemical Engineering, The University of Adelaide, Engineering North Building, Adelaide, SA 5005, Australia
| | - R Sekine
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Building X, Mawson Lakes Campus, SA 5095, Australia
| | - B Sarkar
- CRC CARE, PO Box 486, Salisbury, SA 5106, Australia; Centre for Environmental Risk Assessment and Remediation, University of South Australia, Building X, Mawson Lakes Campus, SA 5095, Australia
| | - A Maoz Shen
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Building X, Mawson Lakes Campus, SA 5095, Australia
| | - K G Scheckel
- U.S. Environmental Protection Agency, National Risk Management Research Laboratory, Land Remediation and Pollution Control Division, 5995 Center Hill Avenue, Cincinnati, OH, USA
| | - W Skinner
- Ian Wark Research Institute, University of South Australia, Building IW, Mawson Lakes Campus, SA 5095, Australia
| | - R Naidu
- CRC CARE, PO Box 486, Salisbury, SA 5106, Australia; Centre for Environmental Risk Assessment and Remediation, University of South Australia, Building X, Mawson Lakes Campus, SA 5095, Australia
| | - H K Shon
- School of Civil and Environmental Engineering, University of Technology, Sydney, Post Box 129, Broadway, NSW 2007, Australia; CRC CARE, PO Box 486, Salisbury, SA 5106, Australia
| | - E Lombi
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Building X, Mawson Lakes Campus, SA 5095, Australia.
| | - E Donner
- CRC CARE, PO Box 486, Salisbury, SA 5106, Australia; Centre for Environmental Risk Assessment and Remediation, University of South Australia, Building X, Mawson Lakes Campus, SA 5095, Australia
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8
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Super-resolution imaging in live cells. Dev Biol 2014; 401:175-81. [PMID: 25498481 PMCID: PMC4405210 DOI: 10.1016/j.ydbio.2014.11.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 11/23/2014] [Accepted: 11/25/2014] [Indexed: 12/26/2022]
Abstract
Over the last twenty years super-resolution fluorescence microscopy has gone from proof-of-concept experiments to commercial systems being available in many labs, improving the resolution achievable by up to a factor of 10 or more. There are three major approaches to super-resolution, stimulated emission depletion microscopy, structured illumination microscopy, and localisation microscopy, which have all produced stunning images of cellular structures. A major current challenge is optimising performance of each technique so that the same sort of data can be routinely taken in live cells. There are several major challenges, particularly phototoxicity and the speed with which images of whole cells, or groups of cells, can be acquired. In this review we discuss the various approaches which can be successfully used in live cells, the tradeoffs in resolution, speed, and ease of implementation which one must make for each approach, and the quality of results that one might expect from each technique. Super-resolution imaging of cell structures can achieve a resolution of tens of nm. There are three major techniques: STED, SIM, and localisation microscopy. Live cell super-resolution requires trading off resolution, speed, and light dose.
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Kuan KKY, Zhong Y, Chau PYK. Informational and Normative Social Influence in Group-Buying: Evidence from Self-Reported and EEG Data. J MANAGE INFORM SYST 2014. [DOI: 10.2753/mis0742-1222300406] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - Yingqin Zhong
- b Master of Finance program at the Business School, Chinese University of Hong Kong
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10
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Asiaei S, Nieva P, Vijayan MM. Fast Kinetics of Thiolic Self-Assembled Monolayer Adsorption on Gold: Modeling and Confirmation by Protein Binding. J Phys Chem B 2014; 118:13697-703. [DOI: 10.1021/jp509986s] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sasan Asiaei
- School
of Mechanical Engineering, Iran University of Science and Technology, Tehran, Iran 1684613114
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11
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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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12
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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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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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Botstein D. Technological innovation leads to fundamental understanding in cell biology. Mol Biol Cell 2011; 21:3791-2. [PMID: 21079013 PMCID: PMC2982132 DOI: 10.1091/mbc.e10-04-0366] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- David Botstein
- Lewis-Sigler Institute and Department of Molecular Biology, Princeton University, Princeton NJ 08544, USA.
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15
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Visualization and identification of the structures formed during early stages of fibrin polymerization. Blood 2011; 117:4609-14. [PMID: 21248064 DOI: 10.1182/blood-2010-07-297671] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We determined the sequence of events and identified and quantitatively characterized the mobility of moving structures present during the early stages of fibrin-clot formation from the beginning of polymerization to the gel point. Three complementary techniques were used in parallel: spinning-disk confocal microscopy, transmission electron microscopy, and turbidity measurements. At the beginning of polymerization the major structures were monomers, whereas at the middle of the lag period there were monomers, oligomers, protofibrils (defined as structures that consisted of more than 8 monomers), and fibers. At the end of the lag period, there were primarily monomers and fibers, giving way to mainly fibers at the gel point. Diffusion rates were calculated from 2 different results, one based on sizes and another on the velocity of the observed structures, with similar results in the range of 3.8-0.1 μm²/s. At the gel point, the diffusion coefficients corresponded to very large, slow-moving structures and individual protofibrils. The smallest moving structures visible by confocal microscopy during fibrin polymerization were identified as protofibrils with a length of approximately 0.5 μm. The sequence of early events of clotting and the structures present are important for understanding hemostasis and thrombosis.
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Weiland Y, Lemmer P, Cremer C. Combining FISH with localisation microscopy: Super-resolution imaging of nuclear genome nanostructures. Chromosome Res 2010; 19:5-23. [DOI: 10.1007/s10577-010-9171-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Birk UJ, Rieckher M, Konstantinides N, Darrell A, Sarasa-Renedo A, Meyer H, Tavernarakis N, Ripoll J. Correction for specimen movement and rotation errors for in-vivo Optical Projection Tomography. BIOMEDICAL OPTICS EXPRESS 2010; 1:87-96. [PMID: 21258448 PMCID: PMC3005161 DOI: 10.1364/boe.1.000087] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 06/27/2010] [Accepted: 06/30/2010] [Indexed: 05/18/2023]
Abstract
The application of optical projection tomography to in-vivo experiments is limited by specimen movement during the acquisition. We present a set of mathematical correction methods applied to the acquired data stacks to correct for movement in both directions of the image plane. These methods have been applied to correct experimental data taken from in-vivo optical projection tomography experiments in Caenorhabditis elegans. Successful reconstructions for both fluorescence and white light (absorption) measurements are shown. Since no difference between movement of the animal and movement of the rotation axis is made, this approach at the same time removes artifacts due to mechanical drifts and errors in the assumed center of rotation.
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Affiliation(s)
- Udo Jochen Birk
- Institute of Electronic Structure & Laser, Foundation for Research and Technology-Hellas (FORTH), P.O Box 1527, 71110 Heraklion, Greece
- Kirchhoff Institut für Physik, Universität Heidelberg, INF 227, 69120 Heidelberg, Germany
- Medizinisches Laserzentrum Lübeck GmbH, Peter-Monnik-Weg 4, D-23452 Lübeck, Germany
| | - Matthias Rieckher
- Institute of Molecular Biology and Biotechnology, FORTH, 71110 Heraklion, Greece
| | - Nikos Konstantinides
- Institute of Molecular Biology and Biotechnology, FORTH, 71110 Heraklion, Greece
| | - Alex Darrell
- Institute of Computer Science, FORTH, 71110 Heraklion, Greece
- Currently with the Medical Vision Laboratory, Department of Engineering Science, Oxford University, Parks Road, Oxford OX1 3PJ, UK
| | - Ana Sarasa-Renedo
- Institute of Molecular Biology and Biotechnology, FORTH, 71110 Heraklion, Greece
| | - Heiko Meyer
- Institute of Electronic Structure & Laser, Foundation for Research and Technology-Hellas (FORTH), P.O Box 1527, 71110 Heraklion, Greece
- Currently with the Laser Zentrum Hannover e.V., Hollerithallee 8, 30419 Hannover, Germany
| | | | - Jorge Ripoll
- Institute of Electronic Structure & Laser, Foundation for Research and Technology-Hellas (FORTH), P.O Box 1527, 71110 Heraklion, Greece
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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, 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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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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Pelletier MJ. Control of out-of-focus light intensity in confocal raman microscopy using optical preprocessing. APPLIED SPECTROSCOPY 2009; 63:591-596. [PMID: 19531285 DOI: 10.1366/000370209788559548] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Optical preprocessing, the manipulation of imaging-forming light prior to detection, is used in many forms of microscopy to enhance image information and interpretation. The rejection of out-of-focus light by a pinhole in confocal microscopy is an example of optical preprocessing, where spatial filtering is carried out in a plane conjugate to the object focal plane. The rejection efficiency afforded by this arrangement is, however, sometimes insufficient. Insufficient rejection of out-of-focus light intensity can lead to incorrect interpretations of confocal Raman depth and line maps. An alternative approach is to reject out-of-focus light by implementing spatial filtering in one of the several planes conjugate to the pupil plane. This paper shows that mapping enhanced by structured pupils (MESP) provides substantial additional rejection of out-of-focus intensity relative to traditional confocal microscopy, yielding a potential solution to the problem of misleading Raman maps. In addition, lossless MESP is proposed, wherein simple phase masks simultaneously direct in-focus and out-of-focus light intensity transmitted by confocal optics to different regions of a charge-coupled device (CCD) detector.
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Affiliation(s)
- Michael J Pelletier
- Analytical Technology, Pharmaceutical Sciences, Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, USA.
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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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