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Oudjedi L, Fiche JB, Abrahamsson S, Mazenq L, Lecestre A, Calmon PF, Cerf A, Nöllmann M. Astigmatic multifocus microscopy enables deep 3D super-resolved imaging. BIOMEDICAL OPTICS EXPRESS 2016; 7:2163-73. [PMID: 27375935 PMCID: PMC4918573 DOI: 10.1364/boe.7.002163] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/22/2016] [Accepted: 03/17/2016] [Indexed: 05/15/2023]
Abstract
We have developed a 3D super-resolution microscopy method that enables deep imaging in cells. This technique relies on the effective combination of multifocus microscopy and astigmatic 3D single-molecule localization microscopy. We describe the optical system and the fabrication process of its key element, the multifocus grating. Then, two strategies for localizing emitters with our imaging method are presented and compared with a previously described deep 3D localization algorithm. Finally, we demonstrate the performance of the method by imaging the nuclear envelope of eukaryotic cells reaching a depth of field of ~4µm.
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Affiliation(s)
- Laura Oudjedi
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Sara Abrahamsson
- Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Laurent Mazenq
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Aurélie Lecestre
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Pierre-François Calmon
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Aline Cerf
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Marcelo Nöllmann
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
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52
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Coles BC, Webb SED, Schwartz N, Rolfe DJ, Martin-Fernandez M, Lo Schiavo V. Characterisation of the effects of optical aberrations in single molecule techniques. BIOMEDICAL OPTICS EXPRESS 2016; 7:1755-67. [PMID: 27231619 PMCID: PMC4871079 DOI: 10.1364/boe.7.001755] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/25/2016] [Accepted: 04/03/2016] [Indexed: 05/17/2023]
Abstract
Optical aberrations degrade image quality in fluorescence microscopy, including for single-molecule based techniques. These depend on post-processing to localize individual molecules in an image series. Using simulated data, we show the impact of optical aberrations on localization success, accuracy and precision. The peak intensity and the proportion of successful localizations strongly reduces when the aberration strength is greater than 1.0 rad RMS, while the precision of each of those localisations is halved. The number of false-positive localisations exceeded 10% of the number of true-positive localisations at an aberration strength of only ~0.6 rad RMS when using the ThunderSTORM package, but at greater than 1.0 rad RMS with the Radial Symmetry package. In the presence of coma, the localization error reaches 100 nm at ~0.6 rad RMS of aberration strength. The impact of noise and of astigmatism for axial resolution are also considered. Understanding the effect of aberrations is crucial when deciding whether the addition of adaptive optics to a single-molecule microscope could significantly increase the information obtainable from an image series.
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Affiliation(s)
- Benjamin C. Coles
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0FA, UK
| | - Stephen E. D. Webb
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0FA, UK
| | - Noah Schwartz
- UK ATC, Royal Observatory Edinburgh, Blackford Hill, Edinburgh, EH9 3HJ, UK
| | - Daniel J. Rolfe
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0FA, UK
| | - Marisa Martin-Fernandez
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0FA, UK
| | - Valentina Lo Schiavo
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0FA, UK
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53
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Smith C, Huisman M, Siemons M, Grünwald D, Stallinga S. Simultaneous measurement of emission color and 3D position of single molecules. OPTICS EXPRESS 2016; 24:4996-5013. [PMID: 29092328 PMCID: PMC5499633 DOI: 10.1364/oe.24.004996] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/14/2016] [Accepted: 02/24/2016] [Indexed: 05/19/2023]
Abstract
We show that the position of single molecules in all three spatial dimensions can be estimated alongside its emission color by diffractive optics based design of the Point Spread Function (PSF). The phase in a plane conjugate to the aperture stop of the objective lens is modified by a diffractive structure that splits the spot on the camera into closely spaced diffraction orders. The distance between and the size of these sub-spots are a measure of the emission color. Estimation of the axial position is enabled by imprinting aberrations such as astigmatism and defocus onto the orders. The overall spot shape is fitted with a fully vectorial PSF model. Proof-of-principle experiments on quantum dots indicate that a spectral precision of 10 to 20 nm, an axial localization precision of 25 to 50 nm, and a lateral localization precision of 10 to 30 nm can be achieved over a 1 μm range of axial positions for on average 800 signal photons and 17 background photons/pixel. The method appears to be rather sensitive to PSF model errors such as aberrations, giving in particular rise to biases in the fitted wavelength of up to 15 nm.
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Affiliation(s)
- Carlas Smith
- University of Massachusetts Medical School, RNA Therapeutics Institute, Worcester, Massachusetts,
USA
| | - Max Huisman
- University of Massachusetts Medical School, RNA Therapeutics Institute, Worcester, Massachusetts,
USA
| | - Marijn Siemons
- Quantitative Imaging Group, Department of Imaging Physics, Delft University of Technology, Delft,
The Netherlands
| | - David Grünwald
- University of Massachusetts Medical School, RNA Therapeutics Institute, Worcester, Massachusetts,
USA
| | - Sjoerd Stallinga
- Quantitative Imaging Group, Department of Imaging Physics, Delft University of Technology, Delft,
The Netherlands
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54
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Hajj B, El Beheiry M, Dahan M. PSF engineering in multifocus microscopy for increased depth volumetric imaging. BIOMEDICAL OPTICS EXPRESS 2016; 7:726-31. [PMID: 27231584 PMCID: PMC4866451 DOI: 10.1364/boe.7.000726] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 01/27/2016] [Accepted: 01/27/2016] [Indexed: 05/15/2023]
Abstract
Imaging and localizing single molecules with high accuracy in a 3D volume is a challenging task. Here we combine multifocal microscopy, a recently developed volumetric imaging technique, with point spread function engineering to achieve an increased depth for single molecule imaging. Applications in 3D single molecule localization-based super-resolution imaging is shown over an axial depth of 4 µm as well as for the tracking of diffusing beads in a fluid environment over 8 µm.
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Affiliation(s)
- Bassam Hajj
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, 75005, Paris, France; Transcription Imaging Consortium, Janelia Research Campus, 19700 Helix Drive, Ashburn VA, 20147, USA;
| | - Mohamed El Beheiry
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, 75005, Paris, France; Transcription Imaging Consortium, Janelia Research Campus, 19700 Helix Drive, Ashburn VA, 20147, USA
| | - Maxime Dahan
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, 75005, Paris, France; Transcription Imaging Consortium, Janelia Research Campus, 19700 Helix Drive, Ashburn VA, 20147, USA;
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55
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Abstract
The majority of studies of the living cell rely on capturing images using fluorescence microscopy. Unfortunately, for centuries, diffraction of light was limiting the spatial resolution in the optical microscope: structural and molecular details much finer than about half the wavelength of visible light (~200 nm) could not be visualized, imposing significant limitations on this otherwise so promising method. The surpassing of this resolution limit in far-field microscopy is currently one of the most momentous developments for studying the living cell, as the move from microscopy to super-resolution microscopy or 'nanoscopy' offers opportunities to study problems in biophysical and biomedical research at a new level of detail. This review describes the principles and modalities of present fluorescence nanoscopes, as well as their potential for biophysical and cellular experiments. All the existing nanoscopy variants separate neighboring features by transiently preparing their fluorescent molecules in states of different emission characteristics in order to make the features discernible. Usually these are fluorescent 'on' and 'off' states causing the adjacent molecules to emit sequentially in time. Each of the variants can in principle reach molecular spatial resolution and has its own advantages and disadvantages. Some require specific transitions and states that can be found only in certain fluorophore subfamilies, such as photoswitchable fluorophores, while other variants can be realized with standard fluorescent labels. Similar to conventional far-field microscopy, nanoscopy can be utilized for dynamical, multi-color and three-dimensional imaging of fixed and live cells, tissues or organisms. Lens-based fluorescence nanoscopy is poised for a high impact on future developments in the life sciences, with the potential to help solve long-standing quests in different areas of scientific research.
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56
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Kuroda M, Murayama Y. Simple method to measure and analyze the fluctuations of a small particle in biopolymer solutions. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:125105. [PMID: 26724071 DOI: 10.1063/1.4936879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We developed a simple method to investigate the motion of a small particle in biopolymer solutions. Using optical tweezers with low stiffness, a trapped probe particle fluctuates widely for a long time along the light axis, which reflects the rheological properties of the surrounding environment. We present a convenient technique for three-dimensional position tracking and the analysis focused on the distribution of particle positions and its variance in a given time interval. It allows us to obtain useful information about the dynamics of a small particle in a wide range from a free diffusive motion to a constrained motion with statistical significance. We applied this method to investigate the dynamics in collagen and DNA solutions; it was found that a collagen solution behaves as a simple viscous liquid and a DNA solution has apparent elasticity due to the slow relaxation of the configuration of molecules.
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Affiliation(s)
- Masafumi Kuroda
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Yoshihiro Murayama
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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57
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Chien FC, Lien CH, Dai YH. Dual-color dynamic tracking of GM-CSF receptors/JAK2 kinases signaling activation using temporal focusing multiphoton fluorescence excitation and astigmatic imaging. OPTICS EXPRESS 2015; 23:30943-30955. [PMID: 26698726 DOI: 10.1364/oe.23.030943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The dual-color dynamic particle tracking approach that uses temporal focusing multiphoton fluorescence excitation and two-channel astigmatic imaging is utilized to track molecular trajectories in three dimensions to explore molecular interactions. Images of two fluorophores were obtained to extract their positions by optical sectioning excitation using a fast temporal focusing multiphoton excitation microscope (TFMPEM) and by the simultaneous collection of data in two channels. The presented pair of cylindrical lenses, which was used to adjust the astigmatism effect with the minimum shifting of the imaging plane, was more feasible and flexible than single cylindrical lens for aligning two separate detection channels in astigmatic imaging. The lateral and axial positioning resolutions were observed to be approximately 9-13 nm and 23-30 nm respectively, for the two fluorescence channels. The dynamic movement and binding behavior of clusters of GM-CSF receptors and JAK2 kinases in HeLa cells in the presence of GM-CSF ligands were observed. Therefore, the proposed dual-color tracking strategy is useful for the dynamic study of molecular interactions in living specimens with a fast frame rate, less photobleaching, better penetration depth, and minimum optical trapping force.
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58
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Imaging of molecular surface dynamics in brain slices using single-particle tracking. Nat Commun 2015; 5:3024. [PMID: 24429796 PMCID: PMC3905702 DOI: 10.1038/ncomms4024] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 11/26/2013] [Indexed: 12/03/2022] Open
Abstract
Organization of signalling molecules in biological membranes is crucial for cellular communication. Many receptors, ion channels and cell adhesion molecules are associated with proteins important for their trafficking, surface localization or function. These complexes are embedded in a lipid environment of varying composition. Binding affinities and stoichiometry of such complexes were so far experimentally accessible only in isolated systems or monolayers of cell culture. Visualization of molecular dynamics within signalling complexes and their correlation to specialized membrane compartments demand high temporal and spatial resolution and has been difficult to demonstrate in complex tissue like brain slices. Here we demonstrate the feasibility of single-particle tracking (SPT) in organotypic brain slices to measure molecular dynamics of lipids and transmembrane proteins in correlation to synaptic membrane compartments. This method will provide important information about the dynamics and organization of surface molecules in the complex environment of neuronal networks within brain slices. Lateral diffusion of transmembrane signalling molecules is implicated in neuronal communication but imaging in tissue is limited by poor temporal resolution. Here, the authors use quantum dots to label lipids and adhesion molecules, allowing them to track single-molecule motions in subcellular compartments.
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59
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Fast and Precise 3D Fluorophore Localization based on Gradient Fitting. Sci Rep 2015; 5:14335. [PMID: 26390959 PMCID: PMC4585720 DOI: 10.1038/srep14335] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/25/2015] [Indexed: 12/19/2022] Open
Abstract
Astigmatism imaging approach has been widely used to encode the fluorophore's 3D position in single-particle tracking and super-resolution localization microscopy. Here, we present a new high-speed localization algorithm based on gradient fitting to precisely decode the 3D subpixel position of the fluorophore. This algebraic algorithm determines the center of the fluorescent emitter by finding the position with the best-fit gradient direction distribution to the measured point spread function (PSF), and can retrieve the 3D subpixel position of the fluorophore in a single iteration. Through numerical simulation and experiments with mammalian cells, we demonstrate that our algorithm yields comparable localization precision to the traditional iterative Gaussian function fitting (GF) based method, while exhibits over two orders-of-magnitude faster execution speed. Our algorithm is a promising high-speed analyzing method for 3D particle tracking and super-resolution localization microscopy.
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60
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Zhang S, Chen D, Niu H. 3D localization of high particle density images using sparse recovery. APPLIED OPTICS 2015; 54:7859-64. [PMID: 26368955 DOI: 10.1364/ao.54.007859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
If particles are too close in space, their images may be overlapped when they are observed with microscopes because of diffraction limitation, which makes them difficult to be distinguished or localized. This limitation also affects the efficiency of localization of those single-particle-localization microcopies, such as stochastic optical reconstruction microscopy (STORM) and (fluorescence) photoactivated localization microscopy [(F)PALM]. In this work, we developed a 3D sparse recovery (3D-SR) method, with the aim of localizing particles with high density in three dimensions, which cannot be resolved using original STROM or (F)PALM. A cylindrical lens was introduced to a traditional wide-field microscope in order to form the 3D point spread function for 3D-SR. The performance of the 3D-SR method was evaluated using simulation. Simulated results demonstrated that, even for particle densities as high as 4 μm-2 on a transversal projection, particles could still be localized with high accuracy. The standard deviations were found to be 25.59 nm along the transverse direction and 50.42 nm along the axial direction. Compared with the existing 3D localization methods used in high particle density cases, such as 3D-DAOSTORM, 3D-SR allows a higher activated fluorophore density per frame.
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61
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Booth M, Andrade D, Burke D, Patton B, Zurauskas M. Aberrations and adaptive optics in super-resolution microscopy. Microscopy (Oxf) 2015; 64:251-61. [PMID: 26124194 PMCID: PMC4711293 DOI: 10.1093/jmicro/dfv033] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 05/29/2015] [Indexed: 12/05/2022] Open
Abstract
As one of the most powerful tools in the biological investigation of cellular structures and dynamic processes, fluorescence microscopy has undergone extraordinary developments in the past decades. The advent of super-resolution techniques has enabled fluorescence microscopy - or rather nanoscopy - to achieve nanoscale resolution in living specimens and unravelled the interior of cells with unprecedented detail. The methods employed in this expanding field of microscopy, however, are especially prone to the detrimental effects of optical aberrations. In this review, we discuss how super-resolution microscopy techniques based upon single-molecule switching, stimulated emission depletion and structured illumination each suffer from aberrations in different ways that are dependent upon intrinsic technical aspects. We discuss the use of adaptive optics as an effective means to overcome this problem.
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Affiliation(s)
- Martin Booth
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Débora Andrade
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK
| | - Daniel Burke
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK
| | - Brian Patton
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK
| | - Mantas Zurauskas
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK
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62
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Super-resolution microscopy approaches for live cell imaging. Biophys J 2015; 107:1777-1784. [PMID: 25418158 DOI: 10.1016/j.bpj.2014.08.028] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/01/2014] [Accepted: 08/07/2014] [Indexed: 11/21/2022] Open
Abstract
By delivering optical images with spatial resolutions below the diffraction limit, several super-resolution fluorescence microscopy techniques opened new opportunities to study biological structures with details approaching molecular structure sizes. They have now become methods of choice for imaging proteins and their nanoscale dynamic organizations in live cells. In this mini-review, we describe and compare the main far-field super-resolution approaches that allow studying endogenous or overexpressed proteins in live cells.
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63
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Normanno D, Boudarène L, Dugast-Darzacq C, Chen J, Richter C, Proux F, Bénichou O, Voituriez R, Darzacq X, Dahan M. Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher. Nat Commun 2015; 6:7357. [PMID: 26151127 PMCID: PMC4507003 DOI: 10.1038/ncomms8357] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 04/30/2015] [Indexed: 12/17/2022] Open
Abstract
Many cellular functions rely on DNA-binding proteins finding and associating to specific sites in the genome. Yet the mechanisms underlying the target search remain poorly understood, especially in the case of the highly organized mammalian cell nucleus. Using as a model Tet repressors (TetRs) searching for a multi-array locus, we quantitatively analyse the search process in human cells with single-molecule tracking and single-cell protein–DNA association measurements. We find that TetRs explore the nucleus and reach their target by 3D diffusion interspersed with transient interactions with non-cognate sites, consistent with the facilitated diffusion model. Remarkably, nonspecific binding times are broadly distributed, underlining a lack of clear delimitation between specific and nonspecific interactions. However, the search kinetics is not determined by diffusive transport but by the low association rate to nonspecific sites. Altogether, our results provide a comprehensive view of the recruitment dynamics of proteins at specific loci in mammalian cells. During transcription, replication and repair, DNA-binding proteins must find specific interaction sites hidden within a vast excess of genomic DNA. Here the authors use single-molecule tracking to quantitatively determine the contributions of the different processes that underlie target search in human cells.
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Affiliation(s)
- Davide Normanno
- Laboratoire Kastler Brossel, CNRS UMR 8552, École normale supérieure, Université Pierre et Marie Curie, Paris 6, 46 rue d'Ulm, 75005 Paris, France.,Functional Imaging of Transcription, CNRS UMR 8197, École normale supérieure, Institut de Biologie de l'ENS, IBENS, 46 rue d'Ulm, 75005 Paris, France.,Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA.,Physico-Chimie Curie, Institut Curie, CNRS UMR 168, Université Pierre et Marie Curie, Paris 6, 26 rue d'Ulm, 75005 Paris, France
| | - Lydia Boudarène
- Laboratoire Kastler Brossel, CNRS UMR 8552, École normale supérieure, Université Pierre et Marie Curie, Paris 6, 46 rue d'Ulm, 75005 Paris, France.,Functional Imaging of Transcription, CNRS UMR 8197, École normale supérieure, Institut de Biologie de l'ENS, IBENS, 46 rue d'Ulm, 75005 Paris, France
| | - Claire Dugast-Darzacq
- Functional Imaging of Transcription, CNRS UMR 8197, École normale supérieure, Institut de Biologie de l'ENS, IBENS, 46 rue d'Ulm, 75005 Paris, France.,Université Paris-Diderot, Paris 7, 5 rue Thomas Mann, 75013 Paris, France
| | - Jiji Chen
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Christian Richter
- Laboratoire Kastler Brossel, CNRS UMR 8552, École normale supérieure, Université Pierre et Marie Curie, Paris 6, 46 rue d'Ulm, 75005 Paris, France
| | - Florence Proux
- Functional Imaging of Transcription, CNRS UMR 8197, École normale supérieure, Institut de Biologie de l'ENS, IBENS, 46 rue d'Ulm, 75005 Paris, France
| | - Olivier Bénichou
- Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Paris 6, 4 place Jussieu, 75005 Paris, France
| | - Raphaël Voituriez
- Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Paris 6, 4 place Jussieu, 75005 Paris, France
| | - Xavier Darzacq
- Functional Imaging of Transcription, CNRS UMR 8197, École normale supérieure, Institut de Biologie de l'ENS, IBENS, 46 rue d'Ulm, 75005 Paris, France.,Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Maxime Dahan
- Laboratoire Kastler Brossel, CNRS UMR 8552, École normale supérieure, Université Pierre et Marie Curie, Paris 6, 46 rue d'Ulm, 75005 Paris, France.,Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA.,Physico-Chimie Curie, Institut Curie, CNRS UMR 168, Université Pierre et Marie Curie, Paris 6, 26 rue d'Ulm, 75005 Paris, France
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64
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Cattoni DI, Valeri A, Le Gall A, Nollmann M. A matter of scale: how emerging technologies are redefining our view of chromosome architecture. Trends Genet 2015; 31:454-64. [PMID: 26113398 DOI: 10.1016/j.tig.2015.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 11/25/2022]
Abstract
The 3D folding of the genome and its relation to fundamental processes such as gene regulation, replication, and segregation remains one of the most puzzling and exciting questions in genetics. In this review, we describe how the use of new technologies is starting to revolutionize the field of chromosome organization, and to shed light on the mechanisms of transcription, replication, and repair. In particular, we concentrate on recent studies using genome-wide methods, single-molecule technologies, and super-resolution microscopy (SRM). We summarize some of the main concerns when employing these techniques, and discuss potential new and exciting perspectives that illuminate the connection between 3D genomic organization and gene regulation.
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Affiliation(s)
- Diego I Cattoni
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Alessandro Valeri
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Antoine Le Gall
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France.
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65
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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] [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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66
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Tehrani KF, Xu J, Zhang Y, Shen P, Kner P. Adaptive optics stochastic optical reconstruction microscopy (AO-STORM) using a genetic algorithm. OPTICS EXPRESS 2015; 23:13677-92. [PMID: 26074617 DOI: 10.1364/oe.23.013677] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The resolution of Single Molecule Localization Microscopy (SML) is dependent on the width of the Point Spread Function (PSF) and the number of photons collected. However, biological samples tend to degrade the shape of the PSF due to the heterogeneity of the index of refraction. In addition, there are aberrations caused by imperfections in the optical components and alignment, and the refractive index mismatch between the coverslip and the sample, all of which directly reduce the accuracy of SML. Adaptive Optics (AO) can play a critical role in compensating for aberrations in order to increase the resolution. However the stochastic nature of single molecule emission presents a challenge for wavefront optimization because the large fluctuations in photon emission do not permit many traditional optimization techniques to be used. Here we present an approach that optimizes the wavefront during SML acquisition by combining an intensity independent merit function with a Genetic algorithm (GA) to optimize the PSF despite the fluctuating intensity. We demonstrate the use of AO with GA in tissue culture cells and through ~50µm of tissue in the Drosophila Central Nervous System (CNS) to achieve a 4-fold increase in the localization precision.
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67
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Hajj B, El Beheiry M, Izeddin I, Darzacq X, Dahan M. Accessing the third dimension in localization-based super-resolution microscopy. Phys Chem Chem Phys 2015; 16:16340-8. [PMID: 24901106 DOI: 10.1039/c4cp01380h] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Only a few years after its inception, localization-based super-resolution microscopy has become widely employed in biological studies. Yet, it is primarily used in two-dimensional imaging and accessing the organization of cellular structures at the nanoscale in three dimensions (3D) still poses important challenges. Here, we review optical and computational techniques that enable the 3D localization of individual emitters and the reconstruction of 3D super-resolution images. These techniques are grouped into three main categories: PSF engineering, multiple plane imaging and interferometric approaches. We provide an overview of their technical implementation as well as commentary on their applicability. Finally, we discuss future trends in 3D localization-based super-resolution microscopy.
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Affiliation(s)
- Bassam Hajj
- Laboratoire Physico-Chimie Curie, Institut Curie, CNRS UMR 168, Université Pierre et Marie Curie-Paris 6, 11 rue Pierre et Marie Curie, 75005 Paris, France.
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68
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Fraisier V, Clouvel G, Jasaitis A, Dimitrov A, Piolot T, Salamero J. Adaptive optics in spinning disk microscopy: improved contrast and brightness by a simple and fast method. J Microsc 2015; 259:219-27. [PMID: 25940062 DOI: 10.1111/jmi.12256] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/20/2015] [Indexed: 11/29/2022]
Abstract
Multiconfocal microscopy gives a good compromise between fast imaging and reasonable resolution. However, the low intensity of live fluorescent emitters is a major limitation to this technique. Aberrations induced by the optical setup, especially the mismatch of the refractive index and the biological sample itself, distort the point spread function and further reduce the amount of detected photons. Altogether, this leads to impaired image quality, preventing accurate analysis of molecular processes in biological samples and imaging deep in the sample. The amount of detected fluorescence can be improved with adaptive optics. Here, we used a compact adaptive optics module (adaptive optics box for sectioning optical microscopy), which was specifically designed for spinning disk confocal microscopy. The module overcomes undesired anomalies by correcting for most of the aberrations in confocal imaging. Existing aberration detection methods require prior illumination, which bleaches the sample. To avoid multiple exposures of the sample, we established an experimental model describing the depth dependence of major aberrations. This model allows us to correct for those aberrations when performing a z-stack, gradually increasing the amplitude of the correction with depth. It does not require illumination of the sample for aberration detection, thus minimizing photobleaching and phototoxicity. With this model, we improved both signal-to-background ratio and image contrast. Here, we present comparative studies on a variety of biological samples.
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Affiliation(s)
- V Fraisier
- UMR 144 CNRS Institut Curie, Cell and Tissue Imaging Platform (PICT-IBiSA), Nikon Imaging Centre, Paris, France
| | | | | | - A Dimitrov
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - T Piolot
- Institut Curie, Cell and Tissue Imaging platform (PICT-IBiSA), Paris, France
| | - J Salamero
- UMR 144 CNRS Institut Curie, Cell and Tissue Imaging Platform (PICT-IBiSA), Nikon Imaging Centre, Paris, France.,UMR 144 CNRS Institut Curie, Space Time Imaging of Endomembranes and Organelles Dynamics, Paris, France
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69
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Liu Z, Lavis L, Betzig E. Imaging Live-Cell Dynamics and Structure at the Single-Molecule Level. Mol Cell 2015; 58:644-59. [DOI: 10.1016/j.molcel.2015.02.033] [Citation(s) in RCA: 353] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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70
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Xu J, Tehrani KF, Kner P. Multicolor 3D super-resolution imaging by quantum dot stochastic optical reconstruction microscopy. ACS NANO 2015; 9:2917-25. [PMID: 25703291 DOI: 10.1021/nn506952g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We demonstrate multicolor three-dimensional super-resolution imaging with quantum dots (QSTORM). By combining quantum dot asynchronous spectral blueing with stochastic optical reconstruction microscopy and adaptive optics, we achieve three-dimensional imaging with 24 nm lateral and 37 nm axial resolution. By pairing two short-pass filters with two appropriate quantum dots, we are able to image single blueing quantum dots on two channels simultaneously, enabling multicolor imaging with high photon counts.
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Affiliation(s)
- Jianquan Xu
- College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Kayvan F Tehrani
- College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Peter Kner
- College of Engineering, University of Georgia, Athens, Georgia 30602, United States
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71
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Backer AS, Moerner WE. Determining the rotational mobility of a single molecule from a single image: a numerical study. OPTICS EXPRESS 2015; 23:4255-76. [PMID: 25836463 PMCID: PMC4394761 DOI: 10.1364/oe.23.004255] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/18/2015] [Accepted: 02/04/2015] [Indexed: 05/23/2023]
Abstract
Measurements of the orientational freedom with which a single molecule may rotate or 'wobble' about a fixed axis have provided researchers invaluable clues about the underlying behavior of a variety of biological systems. In this paper, we propose a measurement and data analysis procedure based on a widefield fluorescence microscope image for quantitatively distinguishing individual molecules that exhibit varying degrees of rotational mobility. Our proposed technique is especially applicable to cases in which the molecule undergoes rotational motions on a timescale much faster than the framerate of the camera used to record fluorescence images. Unlike currently available methods, sophisticated hardware for modulating the polarization of light illuminating the sample is not required. Additional polarization optics may be inserted in the microscope's imaging pathway to achieve superior measurement precision, but are not essential. We present a theoretical analysis, and benchmark our technique with numerical simulations using typical experimental parameters for single-molecule imaging.
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Affiliation(s)
- Adam S. Backer
- Institute for Computational and Mathematical Engineering, Stanford University, 475 Via Ortega, Stanford, CA 94305,
USA
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA 94305,
USA
| | - W. E. Moerner
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA 94305,
USA
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72
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Vu TQ, Lam WY, Hatch EW, Lidke DS. Quantum dots for quantitative imaging: from single molecules to tissue. Cell Tissue Res 2015; 360:71-86. [PMID: 25620410 DOI: 10.1007/s00441-014-2087-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/04/2014] [Indexed: 10/24/2022]
Abstract
Since their introduction to biological imaging, quantum dots (QDs) have progressed from a little known, but attractive, technology to one that has gained broad application in many areas of biology. The versatile properties of these fluorescent nanoparticles have allowed investigators to conduct biological studies with extended spatiotemporal capabilities that were previously not possible. In this review, we focus on QD applications that provide enhanced quantitative information concerning protein dynamics and localization, including single particle tracking and immunohistochemistry, and finish by examining the prospects of upcoming applications, such as correlative light and electron microscopy and super-resolution. Advances in single molecule imaging, including multi-color and three-dimensional QD tracking, have provided new insights into the mechanisms of cell signaling and protein trafficking. New forms of QD tracking in vivo have allowed the observation of biological processes at molecular level resolution in the physiological context of the whole animal. Further methodological development of multiplexed QD-based immunohistochemistry assays should enable more quantitative analysis of key proteins in tissue samples. These advances highlight the unique quantitative data sets that QDs can provide to further our understanding of biological and disease processes.
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Affiliation(s)
- Tania Q Vu
- Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, Ore., USA,
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73
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Hao Q, Cheng X, Kang J, Jiang Y. An image stabilization optical system using deformable freeform mirrors. SENSORS 2015; 15:1736-49. [PMID: 25599423 PMCID: PMC4327100 DOI: 10.3390/s150101736] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/05/2015] [Indexed: 11/16/2022]
Abstract
An image stabilization optical system using deformable freeform mirrors is proposed that enables the ray sets to couple dynamically in the object and image space. It aims to correct image blurring and degradation when there is relative movement between the imaging optical axis and the object. In this method, Fermat's principle and matrix methods are used to describe the optical path of the entire optical system with a shift object plane and a fixed corresponding image plane in the carrier coordinate system. A constant optical path length is determined for each ray set, so the correspondence between the object and the shift free image point is used to calculate the solution to the points on the surface profile of the deformable mirrors (DMs). Off-axis three-mirror anastigmats are used to demonstrate the benefits of optical image stabilization with one- and two-deformable mirrors.
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Affiliation(s)
- Qun Hao
- Beijing Key Lab. for Precision Optoelectronic Measurement Instrument and Technology, School of Optoelectronics, Beijing Institute of Technology, Beijing 100081, China.
| | - Xuemin Cheng
- Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China.
| | - Jiqiang Kang
- Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China.
| | - Yuhua Jiang
- Beijing Key Lab. for Precision Optoelectronic Measurement Instrument and Technology, School of Optoelectronics, Beijing Institute of Technology, Beijing 100081, China.
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74
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Spille JH, Kaminski TP, Scherer K, Rinne JS, Heckel A, Kubitscheck U. Direct observation of mobility state transitions in RNA trajectories by sensitive single molecule feedback tracking. Nucleic Acids Res 2015; 43:e14. [PMID: 25414330 PMCID: PMC4333372 DOI: 10.1093/nar/gku1194] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/01/2014] [Accepted: 11/03/2014] [Indexed: 11/12/2022] Open
Abstract
Observation and tracking of fluorescently labeled molecules and particles in living cells reveals detailed information about intracellular processes on the molecular level. Whereas light microscopic particle observation is usually limited to two-dimensional projections of short trajectory segments, we report here image-based real-time three-dimensional single particle tracking in an active feedback loop with single molecule sensitivity. We tracked particles carrying only 1-3 fluorophores deep inside living tissue with high spatio-temporal resolution. Using this approach, we succeeded to acquire trajectories containing several hundred localizations. We present statistical methods to find significant deviations from random Brownian motion in such trajectories. The analysis allowed us to directly observe transitions in the mobility of ribosomal (r)RNA and Balbiani ring (BR) messenger (m)RNA particles in living Chironomus tentans salivary gland cell nuclei. We found that BR mRNA particles displayed phases of reduced mobility, while rRNA particles showed distinct binding events in and near nucleoli.
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Affiliation(s)
- Jan-Hendrik Spille
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53115 Bonn, Germany
| | - Tim P Kaminski
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53115 Bonn, Germany
| | - Katharina Scherer
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53115 Bonn, Germany
| | - Jennifer S Rinne
- Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53115 Bonn, Germany
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75
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Lauer FM, Kaemmerer E, Meckel T. Single molecule microscopy in 3D cell cultures and tissues. Adv Drug Deliv Rev 2014; 79-80:79-94. [PMID: 25453259 DOI: 10.1016/j.addr.2014.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 09/20/2014] [Accepted: 10/03/2014] [Indexed: 12/19/2022]
Abstract
From the onset of the first microscopic visualization of single fluorescent molecules in living cells at the beginning of this century, to the present, almost routine application of single molecule microscopy, the method has well-proven its ability to contribute unmatched detailed insight into the heterogeneous and dynamic molecular world life is composed of. Except for investigations on bacteria and yeast, almost the entire story of success is based on studies on adherent mammalian 2D cell cultures. However, despite this continuous progress, the technique was not able to keep pace with the move of the cell biology community to adapt 3D cell culture models for basic research, regenerative medicine, or drug development and screening. In this review, we will summarize the progress, which only recently allowed for the application of single molecule microscopy to 3D cell systems and give an overview of the technical advances that led to it. While initially posing a challenge, we finally conclude that relevant 3D cell models will become an integral part of the on-going success of single molecule microscopy.
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Affiliation(s)
- Florian M Lauer
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 3-5, 64287 Darmstadt, Germany
| | - Elke Kaemmerer
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 3-5, 64287 Darmstadt, Germany; Institute of Health and Biomedical Innovation, Science and Engineering Faculty, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, 4059 QLD, Brisbane, Australia
| | - Tobias Meckel
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 3-5, 64287 Darmstadt, Germany.
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76
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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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77
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Whole-cell, multicolor superresolution imaging using volumetric multifocus microscopy. Proc Natl Acad Sci U S A 2014; 111:17480-5. [PMID: 25422417 DOI: 10.1073/pnas.1412396111] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Single molecule-based superresolution imaging has become an essential tool in modern cell biology. Because of the limited depth of field of optical imaging systems, one of the major challenges in superresolution imaging resides in capturing the 3D nanoscale morphology of the whole cell. Despite many previous attempts to extend the application of photo-activated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) techniques into three dimensions, effective localization depths do not typically exceed 1.2 µm. Thus, 3D imaging of whole cells (or even large organelles) still demands sequential acquisition at different axial positions and, therefore, suffers from the combined effects of out-of-focus molecule activation (increased background) and bleaching (loss of detections). Here, we present the use of multifocus microscopy for volumetric multicolor superresolution imaging. By simultaneously imaging nine different focal planes, the multifocus microscope instantaneously captures the distribution of single molecules (either fluorescent proteins or synthetic dyes) throughout an ∼ 4-µm-deep volume, with lateral and axial localization precisions of ∼ 20 and 50 nm, respectively. The capabilities of multifocus microscopy to rapidly image the 3D organization of intracellular structures are illustrated by superresolution imaging of the mammalian mitochondrial network and yeast microtubules during cell division.
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78
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Deschamps J, Mund M, Ries J. 3D superresolution microscopy by supercritical angle detection. OPTICS EXPRESS 2014; 22:29081-91. [PMID: 25402146 DOI: 10.1364/oe.22.029081] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We present a fundamentally new approach to 3D superresolution microscopy based on the principle of surface-generated fluorescence. This near-field fluorescence is strongly dependent on the distance of fluorophores from the coverslip and can therefore be used to estimate their axial positions. We established a robust and simple implementation of supercritical angle fluorescence detection for single-molecule localization microscopy, calibrated it using fluorescent bead samples, validated the method with DNA origami tetrahedra, and present proof-of-principle data on biological samples.
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79
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Lien CH, Lin CY, Chen SJ, Chien FC. Dynamic particle tracking via temporal focusing multiphoton microscopy with astigmatism imaging. OPTICS EXPRESS 2014; 22:27290-9. [PMID: 25401879 DOI: 10.1364/oe.22.027290] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A three-dimensional (3D) single fluorescent particle tracking strategy based on temporal focusing multiphoton excitation microscopy (TFMPEM) combined with astigmatism imaging is proposed for delivering nanoscale-level axial information that reveals 3D trajectories of single fluorospheres in the axially-resolved multiphoton excitation volume without z-axis scanning. Whereas other scanning spatial focusing multiphoton excitation schemes induce optical trapping interference, temporal focusing multiphoton excitation produces widefield illumination with minimum optical trapping force on the fluorospheres. Currently, the lateral and axial positioning resolutions of the dynamic particle tracking approach are about 14 nm and 21 nm in standard deviation, respectively. Furthermore, the motion behavior and diffusion coefficients of fluorospheres in glycerol solutions with different concentrations are dynamically measured at a frame rate up to 100 Hz. This TFMPEM with astigmatism imaging holds great promise for exploring dynamic molecular behavior deep inside biotissues via its superior penetration, reduced trapping effect, fast frame rate, and nanoscale-level positioning.
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80
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Ichimura T, Jin T, Fujita H, Higuchi H, Watanabe TM. Nano-scale measurement of biomolecules by optical microscopy and semiconductor nanoparticles. Front Physiol 2014; 5:273. [PMID: 25120488 PMCID: PMC4114191 DOI: 10.3389/fphys.2014.00273] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 07/05/2014] [Indexed: 12/14/2022] Open
Abstract
Over the past decade, great developments in optical microscopy have made this technology increasingly compatible with biological studies. Fluorescence microscopy has especially contributed to investigating the dynamic behaviors of live specimens and can now resolve objects with nanometer precision and resolution due to super-resolution imaging. Additionally, single particle tracking provides information on the dynamics of individual proteins at the nanometer scale both in vitro and in cells. Complementing advances in microscopy technologies has been the development of fluorescent probes. The quantum dot, a semi-conductor fluorescent nanoparticle, is particularly suitable for single particle tracking and super-resolution imaging. This article overviews the principles of single particle tracking and super resolution along with describing their application to the nanometer measurement/observation of biological systems when combined with quantum dot technologies.
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Affiliation(s)
- Taro Ichimura
- Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center Suita, Osaka, Japan
| | - Takashi Jin
- Laboratory for Nano-Bio Probes, RIKEN Quantitative Biology Center Suita, Osaka, Japan ; Graduate School of Frontier Biosciences, Osaka University Suita, Osaka, Japan ; WPI, Immunology Frontier Research Center, Osaka University Suita, Osaka, Japan
| | - Hideaki Fujita
- Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center Suita, Osaka, Japan ; WPI, Immunology Frontier Research Center, Osaka University Suita, Osaka, Japan
| | - Hideo Higuchi
- Department of Physics, School of Science, The University of Tokyo Bunkyo, Tokyo, Japan
| | - Tomonobu M Watanabe
- Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center Suita, Osaka, Japan ; Graduate School of Frontier Biosciences, Osaka University Suita, Osaka, Japan ; WPI, Immunology Frontier Research Center, Osaka University Suita, Osaka, Japan
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81
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Récamier V, Izeddin I, Bosanac L, Dahan M, Proux F, Darzacq X. Single cell correlation fractal dimension of chromatin: a framework to interpret 3D single molecule super-resolution. Nucleus 2014; 5:75-84. [PMID: 24637833 PMCID: PMC4028358 DOI: 10.4161/nucl.28227] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chromatin is a major nuclear component, and it is an active matter of debate to understand its different levels of spatial organization, as well as its implication in gene regulation. Measurements of nuclear chromatin compaction were recently used to understand how DNA is folded inside the nucleus and to detect cellular dysfunctions such as cancer. Super-resolution imaging opens new possibilities to measure chromatin organization in situ. Here, we performed a direct measure of chromatin compaction at the single cell level. We used histone H2B, one of the 4 core histone proteins forming the nucleosome, as a chromatin density marker. Using photoactivation localization microscopy (PALM) and adaptive optics, we measured the three-dimensional distribution of H2B with nanometric resolution. We computed the distribution of distances between every two points of the chromatin structure, namely the Ripley K(r) distribution. We found that the K(r) distribution of H2B followed a power law, leading to a precise measurement of the correlation fractal dimension of chromatin of 2.7. Moreover, using photoactivable GFP fused to H2B, we observed dynamic evolution of chromatin sub-regions compaction. As a result, the correlation fractal dimension of chromatin reported here can be interpreted as a dynamically maintained non-equilibrium state.
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Affiliation(s)
- Vincent Récamier
- Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France; Paris Descartes University; Paris, France
| | - Ignacio Izeddin
- Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France
| | - Lana Bosanac
- Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France; Molecular and Cellular Biology Department; University of California; Berkeley, CA USA
| | - Maxime Dahan
- Laboratoire Physico-Chimie Curie; Institut Curie; CNRS UMR168; Université Pierre et Marie Curie-Paris; Paris, France
| | - Florence Proux
- Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France
| | - Xavier Darzacq
- Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France
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82
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McGorty R, Schnitzbauer J, Zhang W, Huang B. Correction of depth-dependent aberrations in 3D single-molecule localization and super-resolution microscopy. OPTICS LETTERS 2014; 39:275-8. [PMID: 24562125 PMCID: PMC4030053 DOI: 10.1364/ol.39.000275] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Single-molecule switching based super-resolution microscopy techniques have been extended into three dimensions through various 3D single-molecule localization methods. However, the localization accuracy in z can be severely degraded by the presence of aberrations, particularly the spherical aberration introduced by the refractive index mismatch when imaging into an aqueous sample with an oil immersion objective. This aberration confines the imaging depth in most experiments to regions close to the coverslip. Here we show a method to obtain accurate, depth-dependent z calibrations by measuring the point spread function (PSF) at the coverslip surface, calculating the microscope pupil function through phase retrieval, and then computing the depth-dependent PSF with the addition of spherical aberrations. We demonstrate experimentally that this method can maintain z localization accuracy over a large range of imaging depths. Our super-resolution images of a mammalian cell nucleus acquired between 0 and 2.5 μm past the coverslip show that this method produces accurate z localizations even in the deepest focal plane.
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Affiliation(s)
- Ryan McGorty
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St, San Francisco, CA 94158
| | - Joerg Schnitzbauer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St, San Francisco, CA 94158
| | - Wei Zhang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St, San Francisco, CA 94158
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St, San Francisco, CA 94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, 1700 4th St, San Francisco, CA 94158
- Corresponding author:
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83
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Visualizing the Ultrastructures and Dynamics of Synapses by Single-Molecule Nanoscopy. NEUROMETHODS 2014. [DOI: 10.1007/978-1-4614-9179-8_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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84
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Specht CG, Izeddin I, Rodriguez PC, El Beheiry M, Rostaing P, Darzacq X, Dahan M, Triller A. Quantitative nanoscopy of inhibitory synapses: counting gephyrin molecules and receptor binding sites. Neuron 2013; 79:308-21. [PMID: 23889935 DOI: 10.1016/j.neuron.2013.05.013] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2013] [Indexed: 12/01/2022]
Abstract
The strength of synaptic transmission is controlled by the number and activity of neurotransmitter receptors. However, little is known about absolute numbers and densities of receptor and scaffold proteins and the stoichiometry of molecular interactions at synapses. Here, we conducted three-dimensional and quantitative nanoscopic imaging based on single-molecule detections to characterize the ultrastructure of inhibitory synapses and to count scaffold proteins and receptor binding sites. We observed a close correspondence between the spatial organization of gephyrin scaffolds and glycine receptors at spinal cord synapses. Endogenous gephyrin was clustered at densities of 5,000-10,000 molecules/μm(2). The stoichiometry between gephyrin molecules and receptor binding sites was approximately 1:1, consistent with a two-dimensional scaffold in which all gephyrin molecules can contribute to receptor binding. The competition of glycine and GABAA receptor complexes for synaptic binding sites highlights the potential of single-molecule imaging to quantify synaptic plasticity on the nanoscopic scale.
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Affiliation(s)
- Christian G Specht
- Biologie Cellulaire de la Synapse, Inserm U1024, Institute of Biology, École Normale Supérieure ENS, 46 rue d'Ulm, Paris 75005, France
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85
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Fluorescence nanoscopy. Methods and applications. J Chem Biol 2013; 6:97-120. [PMID: 24432127 DOI: 10.1007/s12154-013-0096-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 05/05/2013] [Indexed: 12/30/2022] Open
Abstract
Fluorescence nanoscopy refers to the experimental techniques and analytical methods used for fluorescence imaging at a resolution higher than conventional, diffraction-limited, microscopy. This review explains the concepts behind fluorescence nanoscopy and focuses on the latest and promising developments in acquisition techniques, labelling strategies to obtain highly detailed super-resolved images and in the quantitative methods to extract meaningful information from them.
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86
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Kamiyama D, Huang B. Development in the STORM. Dev Cell 2013; 23:1103-10. [PMID: 23237944 DOI: 10.1016/j.devcel.2012.10.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 10/01/2012] [Accepted: 10/01/2012] [Indexed: 12/13/2022]
Abstract
The recent invention of superresolution microscopy has brought up much excitement in the biological research community. Here, we focus on stochastic optical reconstruction microscopy/photoactivated localization microscopy (STORM/PALM) to discuss the challenges in applying superresolution microscopy to the study of developmental biology, including tissue imaging, sample preparation artifacts, and image interpretation. We also summarize new opportunities that superresolution microscopy could bring to the field of developmental biology.
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Affiliation(s)
- Daichi Kamiyama
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
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87
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Super-Resolution Imaging Through Stochastic Switching and Localization of Single Molecules: An Overview. SPRINGER SERIES ON FLUORESCENCE 2013. [DOI: 10.1007/4243_2013_61] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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88
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Gould TJ, Burke D, Bewersdorf J, Booth MJ. Adaptive optics enables 3D STED microscopy in aberrating specimens. OPTICS EXPRESS 2012; 20:20998-1009. [PMID: 23037223 PMCID: PMC3635694 DOI: 10.1364/oe.20.020998] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 07/31/2012] [Accepted: 08/02/2012] [Indexed: 05/18/2023]
Abstract
Stimulated emission depletion (STED) microscopy allows fluorescence far-field imaging with diffraction-unlimited resolution. Unfortunately, extending this technique to three-dimensional (3D) imaging of thick specimens has been inhibited by sample-induced aberrations. Here we present the first implementation of adaptive optics in STED microscopy to allow 3D super-resolution imaging in strongly aberrated imaging conditions, such as those introduced by thick biological tissue.
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Affiliation(s)
- Travis J. Gould
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520,
USA
| | - Daniel Burke
- Centre for Neural Circuits and Behaviour, University of Oxford, Mansfield Road, Oxford OX1 3SR,
UK
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520,
USA
- Department of Biomedical Engineering, Yale University School of Medicine, New Haven, CT 06520,
USA
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06520,
USA
| | - Martin J. Booth
- Centre for Neural Circuits and Behaviour, University of Oxford, Mansfield Road, Oxford OX1 3SR,
UK
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ,
UK
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89
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Spille JH, Kaminski T, Königshoven HP, Kubitscheck U. Dynamic three-dimensional tracking of single fluorescent nanoparticles deep inside living tissue. OPTICS EXPRESS 2012; 20:19697-707. [PMID: 23037022 DOI: 10.1364/oe.20.019697] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Three-dimensional (3D) spatial information can be encoded in two-dimensional images of fluorescent nanoparticles by astigmatic imaging. We combined this method with light sheet microscopy for high contrast single particle imaging up to 200 µm deep within living tissue and real-time image analysis to determine 3D particle localizations with nanometer precision and millisecond temporal resolution. Axial information was instantly directed to the sample stage to keep a moving particle within the focal plane in an active feedback loop. We demonstrated 3D tracking of nanoparticles at an unprecedented depth throughout large cell nuclei over several thousand frames and a range of more than 10 µm in each spatial dimension, while simultaneously acquiring optically sectioned wide field images. We conclude that this 3D particle tracking technique employing light sheet microscopy presents a valuable extension to the nanoscopy toolbox.
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Affiliation(s)
- Jan-Hendrik Spille
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität Bonn, Wegelerstrasse 12, D-53115 Bonn, Germany.
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90
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Ortega-Arroyo J, Kukura P. Interferometric scattering microscopy (iSCAT): new frontiers in ultrafast and ultrasensitive optical microscopy. Phys Chem Chem Phys 2012; 14:15625-36. [DOI: 10.1039/c2cp41013c] [Citation(s) in RCA: 205] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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