1
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Dencks S, Schmitz G. Ultrasound localization microscopy. Z Med Phys 2023; 33:292-308. [PMID: 37328329 PMCID: PMC10517400 DOI: 10.1016/j.zemedi.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 01/24/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Ultrasound Localization Microscopy (ULM) is an emerging technique that provides impressive super-resolved images of microvasculature, i.e., images with much better resolution than the conventional diffraction-limited ultrasound techniques and is already taking its first steps from preclinical to clinical applications. In comparison to the established perfusion or flow measurement methods, namely contrast-enhanced ultrasound (CEUS) and Doppler techniques, ULM allows imaging and flow measurements even down to the capillary level. As ULM can be realized as a post-processing method, conventional ultrasound systems can be used for. ULM relies on the localization of single microbubbles (MB) of commercial, clinically approved contrast agents. In general, these very small and strong scatterers with typical radii of 1-3 µm are imaged much larger in ultrasound images than they actually are due to the point spread function of the imaging system. However, by applying appropriate methods, these MBs can be localized with sub-pixel precision. Then, by tracking MBs over successive frames of image sequences, not only the morphology of vascular trees but also functional information such as flow velocities or directions can be obtained and visualized. In addition, quantitative parameters can be derived to describe pathological and physiological changes in the microvasculature. In this review, the general concept of ULM and conditions for its applicability to microvessel imaging are explained. Based on this, various aspects of the different processing steps for a concrete implementation are discussed. The trade-off between complete reconstruction of the microvasculature and the necessary measurement time as well as the implementation in 3D are reviewed in more detail, as they are the focus of current research. Through an overview of potential or already realized preclinical and clinical applications - pathologic angiogenesis or degeneration of vessels, physiological angiogenesis, or the general understanding of organ or tissue function - the great potential of ULM is demonstrated.
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Affiliation(s)
- Stefanie Dencks
- Lehrstuhl für Medizintechnik, Fakultät für Elektrotechnik und Informationstechnik, Ruhr-Universität Bochum, Bochum, Germany.
| | - Georg Schmitz
- Lehrstuhl für Medizintechnik, Fakultät für Elektrotechnik und Informationstechnik, Ruhr-Universität Bochum, Bochum, Germany
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2
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Colville M, Park S, Singh A, Paszek M, Zipfel WR. Azimuthal Beam Scanning Microscope Design and Implementation for Axial Localization with Scanning Angle Interference Microscopy. Methods Mol Biol 2022; 2393:127-152. [PMID: 34837177 DOI: 10.1007/978-1-0716-1803-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Azimuthal beam scanning, also referred to as circle scanning, is an effective way of eliminating coherence artifacts with laser illumination in widefield microscopy. With a static excitation spot, dirt on the optics and internal reflections can produce an uneven excitation field due to interference fringes. These artifacts become more pronounced in TIRF microscopy, where the excitation is confined to an evanescent field that extends a few hundred nanometers above the coverslip. Unwanted intensity patterns that arise from these imperfections vary with path of the excitation beam through the microscope optical train, so by rapidly rotating the beam through its azimuth the uneven illumination is eliminated by averaging over the camera exposure time. In addition to being useful from TIRF microscopy, it is also critical for scanning angle interference microscopy (SAIM), an axial localization technique with nanometer-scale precision that requires similar instrumentation to TIRF microscopy. For robust SAIM localization, laser excitation with a homogeneous profile over a range of polar angles is required. We have applied the circle scanning principle to SAIM, constructing an optimized instrument configuration and open-source hardware, enabling high-precision localization and significantly higher temporal resolution than previous implementations. In this chapter, we detail the design and construction of the SAIM instrument, including the optical configuration, required peripheral devices, and system calibration.
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Affiliation(s)
| | - Sangwoo Park
- Graduate Field of Biophysics, Cornell University, Ithaca, NY, USA
| | - Avtar Singh
- Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
- Broad Institute, Cambridge, MA, USA
| | - Matthew Paszek
- Graduate Field of Biophysics, Cornell University, Ithaca, NY, USA
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
- Field of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Kavli Institute for Nanoscale Science, Cornell University, Ithaca, NY, USA
| | - Warren R Zipfel
- Graduate Field of Biophysics, Cornell University, Ithaca, NY, USA.
- Applied and Engineering Physics, Cornell University, Ithaca, NY, USA.
- Kavli Institute for Nanoscale Science, Cornell University, Ithaca, NY, USA.
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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3
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Coelho S, Baek J, Gooding JJ, Gaus K. Building a Total Internal Reflection Microscope (TIRF) with Active Stabilization (Feedback SMLM). Bio Protoc 2021; 11:e4074. [PMID: 34327271 DOI: 10.21769/bioprotoc.4074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/16/2021] [Accepted: 04/05/2021] [Indexed: 11/02/2022] Open
Abstract
The data quality of high-resolution imaging can be markedly improved with active stabilization, which is based on feedback loops within the microscope that maintain the sample in the same location throughout the experiment. The purpose is to provide a highly accurate focus lock, therefore eliminating drift and improving localization precision. Here, we describe a step-by-step protocol for building a total internal reflection microscope combined with the feedback loops necessary for sample and detection stabilization, which we routinely use in single-molecule localization microscopy (SMLM). The performance of the final microscope with feedback loops, called feedback SMLM, has previously been described. We demonstrate how to build a replica of our system and include a list of the necessary optical components, tips, and an alignment strategy.
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Affiliation(s)
- Simao Coelho
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia.,Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Jongho Baek
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - J Justin Gooding
- School of Chemistry and Australian Centre of NanoMedicine, University of New South Wales, Sydney, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
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4
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Chen JH, Blanpied TA, Tang AH. Quantification of trans-synaptic protein alignment: A data analysis case for single-molecule localization microscopy. Methods 2019; 174:72-80. [PMID: 31325491 DOI: 10.1016/j.ymeth.2019.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/14/2019] [Accepted: 07/16/2019] [Indexed: 12/13/2022] Open
Abstract
Nanoscale distribution of proteins and their relative positioning within a defined subcellular region are key to their physiological functions. Thanks to the super-resolution imaging methods, especially single-molecule localization microscopy (SMLM), mapping the three-dimensional distribution of multiple proteins has been easier and more efficient than ever. Nevertheless, in spite of the many tools available for efficient localization detection and image rendering, it has been a challenge to quantitatively analyze the 3D distribution and relative positioning of proteins in these SMLM data. Here, using heterogeneously distributed synaptic proteins as examples, we describe in detail a series of analytical methods including detection of nanoscale density clusters, quantification of the trans-synaptic alignment between these protein densities, and automatic en face projection and averaging. These analyses were performed within customized Matlab routines and we make the full scripts available. The concepts behind these analytical methods and the scripts can be adapted for quantitative analysis of spatial organization of other macromolecular complexes.
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Affiliation(s)
- Jia-Hui Chen
- CAS Key Laboratory of Brain Function and Disease and Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Thomas A Blanpied
- Program in Neuroscience and Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ai-Hui Tang
- CAS Key Laboratory of Brain Function and Disease and Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.
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5
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Takeshima T, Takahashi T, Yamashita J, Okada Y, Watanabe S. A multi-emitter fitting algorithm for potential live cell super-resolution imaging over a wide range of molecular densities. J Microsc 2018; 271:266-281. [PMID: 29797718 DOI: 10.1111/jmi.12714] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 04/25/2018] [Accepted: 04/27/2018] [Indexed: 01/13/2023]
Abstract
Multi-emitter fitting algorithms have been developed to improve the temporal resolution of single-molecule switching nanoscopy, but the molecular density range they can analyse is narrow and the computation required is intensive, significantly limiting their practical application. Here, we propose a computationally fast method, wedged template matching (WTM), an algorithm that uses a template matching technique to localise molecules at any overlapping molecular density from sparse to ultrahigh density with subdiffraction resolution. WTM achieves the localization of overlapping molecules at densities up to 600 molecules μm-2 with a high detection sensitivity and fast computational speed. WTM also shows localization precision comparable with that of DAOSTORM (an algorithm for high-density super-resolution microscopy), at densities up to 20 molecules μm-2 , and better than DAOSTORM at higher molecular densities. The application of WTM to a high-density biological sample image demonstrated that it resolved protein dynamics from live cell images with subdiffraction resolution and a temporal resolution of several hundred milliseconds or less through a significant reduction in the number of camera images required for a high-density reconstruction. WTM algorithm is a computationally fast, multi-emitter fitting algorithm that can analyse over a wide range of molecular densities. The algorithm is available through the website. https://doi.org/10.17632/bf3z6xpn5j.1.
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Affiliation(s)
- T Takeshima
- System Division, Hamamatsu Photonics K.K., Hamamatsu City, Japan
| | - T Takahashi
- System Division, Hamamatsu Photonics K.K., Hamamatsu City, Japan
| | - J Yamashita
- System Division, Hamamatsu Photonics K.K., Hamamatsu City, Japan
| | - Y Okada
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan.,Department of Physics, Universal Biology Institute and International Research Center for Neurointelligence, University of Tokyo, Tokyo, Japan
| | - S Watanabe
- System Division, Hamamatsu Photonics K.K., Hamamatsu City, Japan
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6
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Staszowska AD, Fox-Roberts P, Foxall E, Jones GE, Cox S. Investigation of podosome ring protein arrangement using localization microscopy images. Methods 2017; 115:9-16. [PMID: 27840289 DOI: 10.1016/j.ymeth.2016.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/04/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022] Open
Abstract
Podosomes are adhesive structures formed on the plasma membrane abutting the extracellular matrix of macrophages, osteoclasts, and dendritic cells. They consist of an f-actin core and a ring structure composed of integrins and integrin-associated proteins. The podosome ring plays a major role in adhesion to the underlying extracellular matrix, but its detailed structure is poorly understood. Recently, it has become possible to study the nano-scale structure of podosome rings using localization microscopy. Unlike traditional microscopy images, localization microscopy images are reconstructed using discrete points, meaning that standard image analysis methods cannot be applied. Here, we present a pipeline for podosome identification, protein position calculation, and creating a podosome ring model for use with localization microscopy data.
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Affiliation(s)
- Adela D Staszowska
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Patrick Fox-Roberts
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Elizabeth Foxall
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Gareth E Jones
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Susan Cox
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK.
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7
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Abstract
Platinum replicas of unroofed mammalian cells can be imaged with a transmission electron microscope (TEM) to produce high contrast, high resolution images of the structure of the cytoplasmic side of a plasma membrane. A complementary approach, super-resolution fluorescence localization microscopy, can be used to localize labeled molecules with better than 20 nm precision in cells. Here, we describe a correlative method that couples these two techniques and produces images where localization microscopy data can be used to highlight specific proteins of interest within the structural context of the platinum replica TEM image. This combined method is uniquely suited to investigate the nanometer-scale structural organization of the plasma membrane and its associated organelles and proteins.
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Affiliation(s)
- Kem A Sochacki
- National Heart Lung and Blood Institute, National Institutes of Health, Bldg. 50, RM 3312, 50 South Drive, Bethesda, MD, 20892, USA
| | - Justin W Taraska
- National Heart Lung and Blood Institute, National Institutes of Health, Bldg. 50, RM 3312, 50 South Drive, Bethesda, MD, 20892, USA.
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8
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Wang R, Kamgoue A, Normand C, Léger-Silvestre I, Mangeat T, Gadal O. High resolution microscopy reveals the nuclear shape of budding yeast during cell cycle and in various biological states. J Cell Sci 2016; 129:4480-4495. [PMID: 27831493 PMCID: PMC5201014 DOI: 10.1242/jcs.188250] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 11/01/2016] [Indexed: 01/10/2023] Open
Abstract
How spatial organization of the genome depends on nuclear shape is unknown, mostly because accurate nuclear size and shape measurement is technically challenging. In large cell populations of the yeast Saccharomyces cerevisiae, we assessed the geometry (size and shape) of nuclei in three dimensions with a resolution of 30 nm. We improved an automated fluorescence localization method by implementing a post-acquisition correction of the spherical microscopic aberration along the z-axis, to detect the three dimensional (3D) positions of nuclear pore complexes (NPCs) in the nuclear envelope. Here, we used a method called NucQuant to accurately estimate the geometry of nuclei in 3D throughout the cell cycle. To increase the robustness of the statistics, we aggregated thousands of detected NPCs from a cell population in a single representation using the nucleolus or the spindle pole body (SPB) as references to align nuclei along the same axis. We could detect asymmetric changes of the nucleus associated with modification of nucleolar size. Stereotypical modification of the nucleus toward the nucleolus further confirmed the asymmetric properties of the nuclear envelope. Summary: This novel method to explore 3D geometry of the nuclear envelope with enhanced resolution and post-acquisition correction of z-axis aberration revealed increased NPC density near the SPB and the nucleolus.
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Affiliation(s)
- Renjie Wang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31000, France
| | - Alain Kamgoue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31000, France
| | - Christophe Normand
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31000, France
| | - Isabelle Léger-Silvestre
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31000, France
| | - Thomas Mangeat
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31000, France
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31000, France
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9
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Żurek-Biesiada D, Szczurek AT, Prakash K, Best G, Mohana GK, Lee HK, Roignant JY, Dobrucki JW, Cremer C, Birk U. Quantitative super-resolution localization microscopy of DNA in situ using Vybrant® DyeCycle™ Violet fluorescent probe. Data Brief 2016; 7:157-71. [PMID: 27054149 PMCID: PMC4802433 DOI: 10.1016/j.dib.2016.01.041] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 01/07/2016] [Accepted: 01/20/2016] [Indexed: 02/02/2023] Open
Abstract
Single Molecule Localization Microscopy (SMLM) is a recently emerged optical imaging method that was shown to achieve a resolution in the order of tens of nanometers in intact cells. Novel high resolution imaging methods might be crucial for understanding of how the chromatin, a complex of DNA and proteins, is arranged in the eukaryotic cell nucleus. Such an approach utilizing switching of a fluorescent, DNA-binding dye Vybrant® DyeCycle™ Violet has been previously demonstrated by us (Żurek-Biesiada et al., 2015) [1]. Here we provide quantitative information on the influence of the chemical environment on the behavior of the dye, discuss the variability in the DNA-associated signal density, and demonstrate direct proof of enhanced structural resolution. Furthermore, we compare different visualization approaches. Finally, we describe various opportunities of multicolor DNA/SMLM imaging in eukaryotic cell nuclei.
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Affiliation(s)
- Dominika Żurek-Biesiada
- Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | | | - Kirti Prakash
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Gerrit Best
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
| | - Giriram K Mohana
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Hyun-Keun Lee
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz, Germany
| | - Jean-Yves Roignant
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Jurek W Dobrucki
- Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany; Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany; Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz, Germany
| | - Udo Birk
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany; Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz, Germany
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10
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Lenn T, Leake MC. Single-molecule studies of the dynamics and interactions of bacterial OXPHOS complexes. Biochim Biophys Acta 2016; 1857:224-31. [PMID: 26498189 DOI: 10.1016/j.bbabio.2015.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 12/29/2022]
Abstract
Although significant insight has been gained into biochemical, genetic and structural features of oxidative phosphorylation (OXPHOS) at the single-enzyme level, relatively little was known of how the component complexes function together in time and space until recently. Several pioneering single-molecule studies have emerged over the last decade in particular, which have illuminated our knowledge of OXPHOS, most especially on model bacterial systems. Here, we discuss these recent findings of bacterial OXPHOS, many of which generate time-resolved information of the OXPHOS machinery with the native physiological context intact. These new investigations are transforming our knowledge not only of the molecular arrangement of OXPHOS components in live bacteria, but also of the way components dynamically interact with each other in a functional state. These new discoveries have important implications towards putative supercomplex formation in bacterial OXPHOS in particular. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Conrad Mullineaux.
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11
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Glasgow BJ, Ma L. Simultaneous two color image capture for sub-diffraction localization fluorescence microscopy. Micron 2015; 80:14-9. [PMID: 26409111 DOI: 10.1016/j.micron.2015.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/09/2015] [Accepted: 09/09/2015] [Indexed: 11/19/2022]
Abstract
A sub-diffraction limit fluorescence localization microscope was constructed using a standard cooled 1.4 mega-pixel fluorescence charge-coupled device (CCD) camera to simultaneously resolve closely adjacent paired quantum dots on a flat surface with emissions of 540 and 630 nm. The images of the overlapping Airy discs were analyzed to determine the center of the point spread function after noise reduction using Fourier transformation analysis. The Cartesian coordinates of the centers of the point spread functions were compared in serial images. Histograms constructed from serial images fit well to Gaussian functions for resolving two quantum dots separated by as little as 10nm in the x-y coordinates. Statistical analysis of multiple pairs validated discrimination of inter-fluorophore distances that vary by 10nm. The method is simple and developed for x-y resolution of dilute fluorophores on a flat surface, not serial z sectioning.
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Affiliation(s)
- Ben J Glasgow
- Departments of Ophthalmology, Pathology and Laboratory Medicine, Jules Stein Eye Institute, University of California, Los Angeles, 100 Stein Plaza Rm. BH 623, Los Angeles, CA 90095, USA.
| | - Lie Ma
- Departments of Ophthalmology, Pathology and Laboratory Medicine, Jules Stein Eye Institute, University of California, Los Angeles, 100 Stein Plaza Rm. BH 623, Los Angeles, CA 90095, USA
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12
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Erdélyi M, Sinkó J, Kákonyi R, Kelemen A, Rees E, Varga D, Szabó G. Origin and compensation of imaging artefacts in localization-based super-resolution microscopy. Methods 2015; 88:122-32. [PMID: 26036838 DOI: 10.1016/j.ymeth.2015.05.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/10/2015] [Accepted: 05/20/2015] [Indexed: 10/23/2022] Open
Abstract
Interpretation of high resolution images provided by localization-based microscopy techniques is a challenge due to imaging artefacts that can be categorized by their origin. They can be introduced by the optical system, by the studied sample or by the applied algorithms. Some artefacts can be eliminated via precise calibration procedures, others can be reduced only below a certain value. Images studied both theoretically and experimentally are qualified either by pattern specific metrics or by a more general metric based on fluorescence correlation spectroscopy.
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Affiliation(s)
- M Erdélyi
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Dóm tér 9, 6720, Hungary.
| | - J Sinkó
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Dóm tér 9, 6720, Hungary
| | - R Kákonyi
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Dóm tér 9, 6720, Hungary
| | - A Kelemen
- Department of Applied Informatics, University of Szeged, Boldogasszony sgt. 6, 6725, Hungary
| | - E Rees
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge CB2 3RA, UK
| | - D Varga
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Dóm tér 9, 6720, Hungary
| | - G Szabó
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Dóm tér 9, 6720, Hungary
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13
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Abstract
Super-resolution (SR) methodologies permit the visualization of cellular structures at near-molecular scale (1-30 nm), enabling novel mechanistic analysis of key events in cell biology not resolvable by conventional fluorescence imaging (∼300-nm resolution). When this level of detail is combined with computing power and fast and reliable analysis software, high-content screenings using SR becomes a practical option to address multiple biological questions. The importance of combining these powerful analytical techniques cannot be ignored, as they can address phenotypic changes on the molecular scale and in a statistically robust manner. In this work, we suggest an easy-to-implement protocol that can be applied to set up a high-content 3D SR experiment with user-friendly and freely available software. The protocol can be divided into two main parts: chamber and sample preparation, where a protocol to set up a direct STORM (dSTORM) sample is presented; and a second part where a protocol for image acquisition and analysis is described. We intend to take the reader step-by-step through the experimental process highlighting possible experimental bottlenecks and possible improvements based on recent developments in the field.
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Affiliation(s)
- Pedro M Pereira
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, London, UK
| | - Pedro Almada
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, London, UK
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, London, UK
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14
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Grab AL, Hagmann M, Dahint R, Cremer C. Localization microscopy (SPDM) facilitates high precision control of lithographically produced nanostructures. Micron 2015; 68:1-7. [PMID: 25212964 DOI: 10.1016/j.micron.2014.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 11/20/2022]
Abstract
Nanoscale resolution in material sciences is usually restricted to scanning electron beam microscopes. Here we present a procedure that allows single molecule resolution of the sample surface with visible light. Highlighting the performance we used electron beam lithography to generate highly regular nanostructures consisting of interconnected cubes. The samples were labeled with Alexa 647 dyes. The spatial organization of the dyes on nanostructured surfaces was localized with single molecule resolution using localization microscopy. This succeeded also in an absolute spatial calibration of the localization method applied (spectral precision distance microscopy/SPDM). The findings will contribute to the field of product control for industrial applications and long-term fluorescence imaging.
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Löschberger A, Franke C, Krohne G, van de Linde S, Sauer M. Correlative super-resolution fluorescence and electron microscopy of the nuclear pore complex with molecular resolution. J Cell Sci 2014; 127:4351-5. [PMID: 25146397 DOI: 10.1242/jcs.156620] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Here, we combine super-resolution fluorescence localization microscopy with scanning electron microscopy to map the position of proteins of nuclear pore complexes in isolated Xenopus laevis oocyte nuclear envelopes with molecular resolution in both imaging modes. We use the periodic molecular structure of the nuclear pore complex to superimpose direct stochastic optical reconstruction microscopy images with a precision of <20 nm on electron micrographs. The correlative images demonstrate quantitative molecular labeling and localization of nuclear pore complex proteins by standard immunocytochemistry with primary and secondary antibodies and reveal that the nuclear pore complex is composed of eight gp210 (also known as NUP210) protein homodimers. In addition, we find subpopulations of nuclear pore complexes with ninefold symmetry, which are found occasionally among the more typical eightfold symmetrical structures.
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Affiliation(s)
- Anna Löschberger
- Department of Biotechnology and Biophysics, Biozentrum, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Christian Franke
- Department of Biotechnology and Biophysics, Biozentrum, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Georg Krohne
- Department of Electron Microscopy, Biozentrum, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Sebastian van de Linde
- Department of Biotechnology and Biophysics, Biozentrum, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biozentrum, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
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Abstract
Super-resolution fluorescence imaging by single-molecule photoactivation or photoswitching and position determination (localization microscopy) has the potential to fundamentally revolutionize our understanding of how cellular function is encoded at the molecular level. Among all powerful, high-resolution imaging techniques introduced in recent years, localization microscopy excels because it delivers single-molecule information about molecular distributions, even giving absolute numbers of proteins present in subcellular compartments. This provides insight into biological systems at a molecular level that can yield direct experimental feedback for modeling the complexity of biological interactions. In addition, efficient new labeling methods and strategies to improve localization are emerging that promise to achieve true molecular resolution. This raises localization microscopy as a powerful complementary method for correlative light and electron microscopy experiments.
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Affiliation(s)
- Markus Sauer
- Department of Biotechnology and Biophysics, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany.
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Abstract
Conventional light and fluorescence microscopy techniques have offered tremendous insight into cellular processes and structures. Their resolution is however intrinsically limited by diffraction. Superresolution techniques achieve an order of magnitude higher resolution. Among these, localization microscopy relies on the position determination of single emitters with nanometer accuracy, which allows the subsequent reconstruction of an image of the target structure. In this chapter, we provide general guidelines for localization microscopy with a focus on Saccharomyces cerevisiae. Its different cellular architecture complicates efforts to directly transfer protocols established in mammalian cells to yeast. We compare different methodologies to label structures of interest and provide protocols for the respective sample preparation, which are not limited to yeast. Using these guidelines, nanoscopic subcellular structures in yeast can be investigated by localization microscopy, which perfectly complements live-cell fluorescence and electron microscopy.
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Affiliation(s)
- Markus Mund
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany
| | | | - Jonas Ries
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany
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Abstract
Visualization of subcellular structures and their temporal evolution is of utmost importance to understand a vast range of biological processes. Optical microscopy is the method of choice for imaging live cells and tissues; it is minimally invasive, so processes can be observed over extended periods of time without generating artifacts due to intense light irradiation. The use of fluorescence microscopy is advantageous because biomolecules or supramolecular structures of interest can be labeled specifically with fluorophores, so the images reveal information on processes involving only the labeled molecules. The key restriction of optical microscopy is its moderate resolution, which is limited to about half the wavelength of light (∼200 nm) due to fundamental physical laws governing wave optics. Consequently, molecular processes taking place at spatial scales between 1 and 100 nm cannot be studied by regular optical microscopy. In recent years, however, a variety of super-resolution fluorescence microscopy techniques have been developed that circumvent the resolution limitation. Here, we present a brief overview of these techniques and their application to cellular biophysics.
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