251
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Crossman DJ, Ruygrok PN, Hou YF, Soeller C. Next-generation endomyocardial biopsy: the potential of confocal and super-resolution microscopy. Heart Fail Rev 2015; 20:203-14. [PMID: 25112961 DOI: 10.1007/s10741-014-9455-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Confocal laser scanning microscopy and super-resolution microscopy provide high-contrast and high-resolution fluorescent imaging, which has great potential to increase the diagnostic yield of endomyocardial biopsy (EMB). EMB is currently the gold standard for identification of cardiac allograft rejection, myocarditis, and infiltrative and storage diseases. However, standard analysis is dominated by low-contrast bright-field light and electron microscopy (EM); this lack of contrast makes quantification of pathological features difficult. For example, assessment of cardiac allograft rejection relies on subjective grading of H&E histology, which may lead to diagnostic variability between pathologists. This issue could be solved by utilising the high contrast provided by fluorescence methods such as confocal to quantitatively assess the degree of lymphocytic infiltrate. For infiltrative diseases such as amyloidosis, the nanometre resolution provided by EM can be diagnostic in identifying disease-causing fibrils. The recent advent of super-resolution imaging, particularly direct stochastic optical reconstruction microscopy (dSTORM), provides high-contrast imaging at resolution approaching that of EM. Moreover, dSTORM utilises conventional fluorescence dyes allowing for the same structures to be routinely imaged at the cellular scale and then at the nanoscale. The key benefit of these technologies is that the high contrast facilitates quantitative digital analysis and thereby provides a means to robustly assess critical pathological features. Ultimately, this technology has the ability to provide greater accuracy and precision to EMB assessment, which could result in better outcomes for patients.
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Affiliation(s)
- David J Crossman
- Department of Physiology, University of Auckland, Auckland, New Zealand,
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252
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Sydor AM, Czymmek KJ, Puchner EM, Mennella V. Super-Resolution Microscopy: From Single Molecules to Supramolecular Assemblies. Trends Cell Biol 2015; 25:730-748. [DOI: 10.1016/j.tcb.2015.10.004] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/03/2015] [Accepted: 10/05/2015] [Indexed: 11/25/2022]
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253
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Manzo C, Garcia-Parajo MF. A review of progress in single particle tracking: from methods to biophysical insights. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:124601. [PMID: 26511974 DOI: 10.1088/0034-4885/78/12/124601] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Optical microscopy has for centuries been a key tool to study living cells with minimum invasiveness. The advent of single molecule techniques over the past two decades has revolutionized the field of cell biology by providing a more quantitative picture of the complex and highly dynamic organization of living systems. Amongst these techniques, single particle tracking (SPT) has emerged as a powerful approach to study a variety of dynamic processes in life sciences. SPT provides access to single molecule behavior in the natural context of living cells, thereby allowing a complete statistical characterization of the system under study. In this review we describe the foundations of SPT together with novel optical implementations that nowadays allow the investigation of single molecule dynamic events with increasingly high spatiotemporal resolution using molecular densities closer to physiological expression levels. We outline some of the algorithms for the faithful reconstruction of SPT trajectories as well as data analysis, and highlight biological examples where the technique has provided novel insights into the role of diffusion regulating cellular function. The last part of the review concentrates on different theoretical models that describe anomalous transport behavior and ergodicity breaking observed from SPT studies in living cells.
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Affiliation(s)
- Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain
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254
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Abstract
As of 2015, it has been 26 years since the first optical detection and spectroscopy of single molecules in condensed matter. This area of science has expanded far beyond the early low temperature studies in crystals to include single molecules in cells, polymers, and in solution. The early steps relied upon high-resolution spectroscopy of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral fine structure arising directly from the position-dependent fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 1990s, a variety of fascinating physical effects were observed for individual molecules, including imaging of the light from single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency. In the room temperature regime, researchers showed that bursts of light from single molecules could be detected in solution, leading to imaging and microscopy by a variety of methods. Studies of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. All of these early steps provided important fundamentals underpinning the development of super-resolution microscopy based on single-molecule localization and active control of emitting concentration. Current thrust areas include extensions to three-dimensional imaging with high precision, orientational analysis of single molecules, and direct measurements of photodynamics and transport properties for single molecules trapped in solution by suppression of Brownian motion. Without question, a huge variety of studies of single molecules performed by many talented scientists all over the world have extended our knowledge of the nanoscale and many microscopic mechanisms previously hidden by ensemble averaging.
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Affiliation(s)
- W E Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
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255
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von Diezmann A, Lee MY, Lew MD, Moerner WE. Correcting field-dependent aberrations with nanoscale accuracy in three-dimensional single-molecule localization microscopy. OPTICA 2015; 2:985-993. [PMID: 26973863 PMCID: PMC4782984 DOI: 10.1364/optica.2.000985] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The localization of single fluorescent molecules enables the imaging of molecular structure and dynamics with subdiffraction precision and can be extended to three dimensions using point spread function (PSF) engineering. However, the nanoscale accuracy of localization throughout a 3D single-molecule microscope's field of view has not yet been rigorously examined. By using regularly spaced subdiffraction apertures filled with fluorescent dyes, we reveal field-dependent aberrations as large as 50-100 nm and show that they can be corrected to less than 25 nm over an extended 3D focal volume. We demonstrate the applicability of this technique for two engineered PSFs, the double-helix PSF and the astigmatic PSF. We expect these results to be broadly applicable to 3D single-molecule tracking and superresolution methods demanding high accuracy.
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Affiliation(s)
- Alex von Diezmann
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Maurice Y. Lee
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
- Biophysics Program, Stanford University, Stanford, California 94305, USA
| | - Matthew D. Lew
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
- Corresponding author:
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256
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Abstract
In the course of a single decade single molecule microscopy has changed from being a secluded domain shared merely by physicists with a strong background in optics and laser physics to a discipline that is now enjoying vivid attention by life-scientists of all venues (1). This is because single molecule imaging has the unique potential to reveal protein behavior in situ in living cells and uncover cellular organization with unprecedented resolution below the diffraction limit of visible light (2). Glass-supported planar lipid bilayers (SLBs) are a powerful tool to bring cells otherwise growing in suspension in close enough proximity to the glass slide so that they can be readily imaged in noise-reduced Total Internal Reflection illumination mode (3,4). They are very useful to study the protein dynamics in plasma membrane-associated events as diverse as cell-cell contact formation, endocytosis, exocytosis and immune recognition. Simple procedures are presented how to generate highly mobile protein-functionalized SLBs in a reproducible manner, how to determine protein mobility within and how to measure protein densities with the use of single molecule detection. It is shown how to construct a cost-efficient single molecule microscopy system with TIRF illumination capabilities and how to operate it in the experiment.
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Affiliation(s)
- Markus Axmann
- Institute of Applied Physics - Biophysics, Vienna University of Technology
| | - Gerhard J Schütz
- Institute of Applied Physics - Biophysics, Vienna University of Technology
| | - Johannes B Huppa
- Institute for Hygiene and Applied Immunology, Immune Recognition Unit, Medical University of Vienna;
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257
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Sigal YM, Speer CM, Babcock HP, Zhuang X. Mapping Synaptic Input Fields of Neurons with Super-Resolution Imaging. Cell 2015; 163:493-505. [PMID: 26435106 PMCID: PMC4733473 DOI: 10.1016/j.cell.2015.08.033] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 07/22/2015] [Accepted: 08/12/2015] [Indexed: 01/28/2023]
Abstract
As a basic functional unit in neural circuits, each neuron integrates input signals from hundreds to thousands of synapses. Knowledge of the synaptic input fields of individual neurons, including the identity, strength, and location of each synapse, is essential for understanding how neurons compute. Here, we developed a volumetric super-resolution reconstruction platform for large-volume imaging and automated segmentation of neurons and synapses with molecular identity information. We used this platform to map inhibitory synaptic input fields of On-Off direction-selective ganglion cells (On-Off DSGCs), which are important for computing visual motion direction in the mouse retina. The reconstructions of On-Off DSGCs showed a GABAergic, receptor subtype-specific input field for generating direction selective responses without significant glycinergic inputs for mediating monosynaptic crossover inhibition. These results demonstrate unique capabilities of this super-resolution platform for interrogating neural circuitry.
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Affiliation(s)
- Yaron M Sigal
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Colenso M Speer
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hazen P Babcock
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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258
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Welsher K, Yang H. Imaging the behavior of molecules in biological systems: breaking the 3D speed barrier with 3D multi-resolution microscopy. Faraday Discuss 2015; 184:359-79. [PMID: 26426758 DOI: 10.1039/c5fd00090d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The overwhelming effort in the development of new microscopy methods has been focused on increasing the spatial and temporal resolution in all three dimensions to enable the measurement of the molecular scale phenomena at the heart of biological processes. However, there exists a significant speed barrier to existing 3D imaging methods, which is associated with the overhead required to image large volumes. This overhead can be overcome to provide nearly unlimited temporal precision by simply focusing on a single molecule or particle via real-time 3D single-particle tracking and the newly developed 3D Multi-resolution Microscopy (3D-MM). Here, we investigate the optical and mechanical limits of real-time 3D single-particle tracking in the context of other methods. In particular, we investigate the use of an optical cantilever for position sensitive detection, finding that this method yields system magnifications of over 3000×. We also investigate the ideal PID control parameters and their effect on the power spectrum of simulated trajectories. Taken together, these data suggest that the speed limit in real-time 3D single particle-tracking is a result of slow piezoelectric stage response as opposed to optical sensitivity or PID control.
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Affiliation(s)
- Kevin Welsher
- Department of Chemistry, Princeton University, New Jersey, USA.
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259
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Smith CS, Stallinga S, Lidke KA, Rieger B, Grunwald D. Probability-based particle detection that enables threshold-free and robust in vivo single-molecule tracking. Mol Biol Cell 2015; 26:4057-62. [PMID: 26424801 PMCID: PMC4710236 DOI: 10.1091/mbc.e15-06-0448] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/17/2015] [Indexed: 01/11/2023] Open
Abstract
Any single-molecule study starts with finding those single-molecule signals in recorded images. Currently, parameters such as filter and thresholds are user set, and errors are unknown and not observed or controlled. A framework is presented in which expert knowledge and parameter tweaking are replaced with a probability-based hypothesis test. Single-molecule detection in fluorescence nanoscopy has become a powerful tool in cell biology but can present vexing issues in image analysis, such as limited signal, unspecific background, empirically set thresholds, image filtering, and false-positive detection limiting overall detection efficiency. Here we present a framework in which expert knowledge and parameter tweaking are replaced with a probability-based hypothesis test. Our method delivers robust and threshold-free signal detection with a defined error estimate and improved detection of weaker signals. The probability value has consequences for downstream data analysis, such as weighing a series of detections and corresponding probabilities, Bayesian propagation of probability, or defining metrics in tracking applications. We show that the method outperforms all current approaches, yielding a detection efficiency of >70% and a false-positive detection rate of <5% under conditions down to 17 photons/pixel background and 180 photons/molecule signal, which is beneficial for any kind of photon-limited application. Examples include limited brightness and photostability, phototoxicity in live-cell single-molecule imaging, and use of new labels for nanoscopy. We present simulations, experimental data, and tracking of low-signal mRNAs in yeast cells.
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Affiliation(s)
- Carlas S Smith
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Sjoerd Stallinga
- Quantitative Imaging Group, Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
| | - Bernd Rieger
- Quantitative Imaging Group, Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
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260
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Yang B, Fang CY, Chang HC, Treussart F, Trebbia JB, Lounis B. Polarization effects in lattice-STED microscopy. Faraday Discuss 2015; 184:37-49. [PMID: 26407019 DOI: 10.1039/c5fd00092k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Massive parallelization of STED-like nanoscopies is now achievable using well-designed optical lattices for state depletion. Yet, only the lattice intensity distribution was considered for the description of the super-resolved point spread function. This holds for fast-rotating fluorescent emitters. Here, we study the effects of electric field topography in lattice-STED microscopy. The dependence of the super-resolved point spread function on the number of dipoles and their orientation is investigated. Single fluorescent nano-diamonds are imaged using different optical lattice configurations and the measured resolutions are compared to theoretical simulations.
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Affiliation(s)
- B Yang
- Univ Bordeaux, LP2N, F-33405 Talence, France.
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261
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Ji C, Zhang Y, Xu P, Xu T, Lou X. Nanoscale Landscape of Phosphoinositides Revealed by Specific Pleckstrin Homology (PH) Domains Using Single-molecule Superresolution Imaging in the Plasma Membrane. J Biol Chem 2015; 290:26978-26993. [PMID: 26396197 DOI: 10.1074/jbc.m115.663013] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Indexed: 11/06/2022] Open
Abstract
Both phosphatidylinositol 4-phosphate (PI4P) and phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) are independent plasma membrane (PM) determinant lipids that are essential for multiple cellular functions. However, their nanoscale spatial organization in the PM remains elusive. Using single-molecule superresolution microscopy and new photoactivatable fluorescence probes on the basis of pleckstrin homology domains that specifically recognize phosphatidylinositides in insulin-secreting INS-1 cells, we report that the PI(4,5)P2 probes exhibited a remarkably uniform distribution in the major regions of the PM, with some sparse PI(4,5)P2-enriched membrane patches/domains of diverse sizes (383 ± 14 nm on average). Quantitative analysis revealed a modest concentration gradient that was much less steep than previously thought, and no densely packed PI(4,5)P2 nanodomains were observed. Live-cell superresolution imaging further demonstrated the dynamic structural changes of those domains in the flat PM and membrane protrusions. PI4P and phosphatidylinositol (3,4,5)-trisphosphate (PI(3,4,5)P3) showed similar spatial distributions as PI(4,5)P2. These data reveal the nanoscale landscape of key inositol phospholipids in the native PM and imply a framework for local cellular signaling and lipid-protein interactions at a nanometer scale.
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Affiliation(s)
- Chen Ji
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705 and
| | - Yongdeng Zhang
- the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingyong Xu
- the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Xu
- the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuelin Lou
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705 and.
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262
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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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263
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Grover G, Mohrman W, Piestun R. Real-time adaptive drift correction for super-resolution localization microscopy. OPTICS EXPRESS 2015; 23:23887-23898. [PMID: 26368482 DOI: 10.1364/oe.23.023887] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Super-resolution localization microscopy involves acquiring thousands of image frames of sparse collections of single molecules in the sample. The long acquisition time makes the imaging setup prone to drift, affecting accuracy and precision. Localization accuracy is generally improved by a posteriori drift correction. However, localization precision lost due to sample drifting out of focus cannot be recovered as the signal is originally detected at a lower peak signal. Here, we demonstrate a method of stabilizing a super-resolution localization microscope in three dimensions for extended periods of time with nanometer precision. Hence, no localization correction after the experiment is required to obtain super-resolved reconstructions. The method incorporates a closed-loop with a feedback signal generated from camera images and actuation on a 3D nanopositioning stage holding the sample.
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264
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Mishin AS, Belousov VV, Solntsev KM, Lukyanov KA. Novel uses of fluorescent proteins. Curr Opin Chem Biol 2015; 27:1-9. [PMID: 26022943 DOI: 10.1016/j.cbpa.2015.05.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 05/07/2015] [Indexed: 11/28/2022]
Abstract
The field of genetically encoded fluorescent probes is developing rapidly. New chromophore structures were characterized in proteins of green fluorescent protein (GFP) family. A number of red fluorescent sensors, for example, for pH, Ca(2+) and H2O2, were engineered for multiparameter imaging. Progress in development of microscopy hardware and software together with specially designed FPs pushed superresolution fluorescence microscopy towards fast live-cell imaging. Deeper understanding of FPs structure and photophysics led to further development of imaging techniques. In addition to commonly used GFP-like proteins, unrelated types of FPs on the base of flavin-binding domains, bilirubin-binding domains or biliverdin-binding domains were designed. Their distinct biochemical and photophysical properties opened previously unexplored niches of FP uses such as labeling under anaerobic conditions, deep tissue imaging and even patients' blood analysis.
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Affiliation(s)
- Alexander S Mishin
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Nizhny Novgorod State Medical Academy, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia
| | - Vsevolod V Belousov
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Kyril M Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA 30332-0400, United States
| | - Konstantin A Lukyanov
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Nizhny Novgorod State Medical Academy, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia.
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265
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Wang X, Chen D, Yu B, Niu H. Fast stimulated emission nanoscopy based on single molecule localization. APPLIED OPTICS 2015; 54:6919-6923. [PMID: 26368110 DOI: 10.1364/ao.54.006919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
For super-resolution microscopy methods based on single molecule stochastic switching and localization, to simultaneously improve the spatial-temporal resolution, it is necessary to maximize the number of photons that can be collected from single molecules per unit time. Here, we describe a novel approach to enhance the signal intensity (collected photons per second) from fluorescence probes by introducing a stimulated emission (SE) optical process. This process is based on the following two properties: first, with reasonable parameters, the photon emission rate can be significantly increased with SE; and second, the SE photons, which are spatially coherent with the stimulation beam, are more favorable for collection than fluorescence. Theoretical results have shown that signal intensity from a single fluorescent molecule can be greatly improved with SE. We therefore showed, using SE in combination with single molecule localization methodology, that fast imaging at a rate of 0.05 s per reconstructed image with lateral resolutions of ∼30 nm can be obtained.
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266
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Jacak J, Schaller S, Borgmann D, Winkler SM. Characterization of the Distance Relationship Between Localized Serotonin Receptors and Glia Cells on Fluorescence Microscopy Images of Brain Tissue. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2015; 21:826-836. [PMID: 26173412 DOI: 10.1017/s1431927615013513] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We here present two new methods for the characterization of fluorescent localization microscopy images obtained from immunostained brain tissue sections. Direct stochastic optical reconstruction microscopy images of 5-HT1A serotonin receptors and glial fibrillary acidic proteins in healthy cryopreserved brain tissues are analyzed. In detail, we here present two image processing methods for characterizing differences in receptor distribution on glial cells and their distribution on neural cells: One variant relies on skeleton extraction and adaptive thresholding, the other on k-means based discrete layer segmentation. Experimental results show that both methods can be applied for distinguishing classes of images with respect to serotonin receptor distribution. Quantification of nanoscopic changes in relative protein expression on particular cell types can be used to analyze degeneration in tissues caused by diseases or medical treatment.
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Affiliation(s)
- Jaroslaw Jacak
- 1Department of Medical Engineering,University of Applied Sciences Upper Austria,Garnisonstraße 21,4020 Linz,Austria
| | - Susanne Schaller
- 3Bioinformatics Research Group,University of Applied Sciences Upper Austria,Softwarepark 11,4232 Hagenberg,Austria
| | - Daniela Borgmann
- 3Bioinformatics Research Group,University of Applied Sciences Upper Austria,Softwarepark 11,4232 Hagenberg,Austria
| | - Stephan M Winkler
- 3Bioinformatics Research Group,University of Applied Sciences Upper Austria,Softwarepark 11,4232 Hagenberg,Austria
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267
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Schneider J, Zahn J, Maglione M, Sigrist SJ, Marquard J, Chojnacki J, Kräusslich HG, Sahl SJ, Engelhardt J, Hell SW. Ultrafast, temporally stochastic STED nanoscopy of millisecond dynamics. Nat Methods 2015. [DOI: 10.1038/nmeth.3481] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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268
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Moerner WEWE. Single-Molecule Spectroscopy, Imaging, and Photocontrol: Foundations for Super-Resolution Microscopy (Nobel Lecture). Angew Chem Int Ed Engl 2015. [PMID: 26088273 DOI: 10.1103/revmodphys.87.1183] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
The initial steps toward optical detection and spectroscopy of single molecules in condensed matter arose out of the study of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 90s, many fascinating physical effects were observed for individual molecules, and the imaging of single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency provided important forerunners of the later super-resolution microscopy with single molecules. In the room temperature regime, imaging of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic observation and localization of individual fluorophores is a key ingredient to imaging beyond the optical diffraction limit. Combining this with active control of the number of emitting molecules in the pumped volume led to the super-resolution imaging of Eric Betzig and others, a new frontier for optical microscopy beyond the diffraction limit. The background leading up to these observations is described and current developments are summarized.
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Affiliation(s)
- W E William E Moerner
- Departments of Chemistry and (by Courtesy) of Applied Physics, Stanford University, Stanford, California 94305 (USA)
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269
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Hartmann A, Huckemann S, Dannemann J, Laitenberger O, Geisler C, Egner A, Munk A. Drift estimation in sparse sequential dynamic imaging, with application to nanoscale fluorescence microscopy. J R Stat Soc Series B Stat Methodol 2015. [DOI: 10.1111/rssb.12128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | | | | | | | | | | | - Axel Munk
- Georg-August-Universität; Göttingen Germany
- Max Planck Institute for Biophysical Chemistry; Göttingen Germany
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270
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Uno SN, Tiwari DK, Kamiya M, Arai Y, Nagai T, Urano Y. A guide to use photocontrollable fluorescent proteins and synthetic smart fluorophores for nanoscopy. Microscopy (Oxf) 2015; 64:263-77. [PMID: 26152215 DOI: 10.1093/jmicro/dfv037] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 06/12/2015] [Indexed: 12/28/2022] Open
Abstract
Recent advances in nanoscopy, which breaks the diffraction barrier and can visualize structures smaller than the diffraction limit in cells, have encouraged biologists to investigate cellular processes at molecular resolution. Since nanoscopy depends not only on special optics but also on 'smart' photophysical properties of photocontrollable fluorescent probes, including photoactivatability, photoswitchability and repeated blinking, it is important for biologists to understand the advantages and disadvantages of fluorescent probes and to choose appropriate ones for their specific requirements. Here, we summarize the characteristics of currently available fluorescent probes based on both proteins and synthetic compounds applicable to nanoscopy and provide a guideline for selecting optimal probes for specific applications.
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Affiliation(s)
- Shin-Nosuke Uno
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Dhermendra K Tiwari
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Yoshiyuki Arai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Takeharu Nagai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Yasuteru Urano
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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271
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Abstract
Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge in the mathematical form of biochemical reaction networks and understanding how higher level functions emerge from the combined action of biomolecules. However, there still remain formidable challenges in bridging the gap between bioimaging and mathematical modeling. Generally, measurements using fluorescence microscopy systems are influenced by systematic effects that arise from stochastic nature of biological cells, the imaging apparatus, and optical physics. Such systematic effects are always present in all bioimaging systems and hinder quantitative comparison between the cell model and bioimages. Computational tools for such a comparison are still unavailable. Thus, in this work, we present a computational framework for handling the parameters of the cell models and the optical physics governing bioimaging systems. Simulation using this framework can generate digital images of cell simulation results after accounting for the systematic effects. We then demonstrate that such a framework enables comparison at the level of photon-counting units.
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272
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Moerner WEWE. Spektroskopie, Visualisierung und Photomanipulation einzelner Moleküle: die Grundlage für superhochauflösende Mikroskopie (Nobel-Aufsatz). Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501949] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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273
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Moerner WEWE. Single-Molecule Spectroscopy, Imaging, and Photocontrol: Foundations for Super-Resolution Microscopy (Nobel Lecture). Angew Chem Int Ed Engl 2015; 54:8067-93. [PMID: 26088273 DOI: 10.1002/anie.201501949] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/10/2022]
Abstract
The initial steps toward optical detection and spectroscopy of single molecules in condensed matter arose out of the study of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 90s, many fascinating physical effects were observed for individual molecules, and the imaging of single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency provided important forerunners of the later super-resolution microscopy with single molecules. In the room temperature regime, imaging of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic observation and localization of individual fluorophores is a key ingredient to imaging beyond the optical diffraction limit. Combining this with active control of the number of emitting molecules in the pumped volume led to the super-resolution imaging of Eric Betzig and others, a new frontier for optical microscopy beyond the diffraction limit. The background leading up to these observations is described and current developments are summarized.
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Affiliation(s)
- W E William E Moerner
- Departments of Chemistry and (by Courtesy) of Applied Physics, Stanford University, Stanford, California 94305 (USA)
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274
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Sage D, Kirshner H, Pengo T, Stuurman N, Min J, Manley S, Unser M. Quantitative evaluation of software packages for single-molecule localization microscopy. Nat Methods 2015; 12:717-24. [PMID: 26076424 DOI: 10.1038/nmeth.3442] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 04/17/2015] [Indexed: 12/12/2022]
Abstract
The quality of super-resolution images obtained by single-molecule localization microscopy (SMLM) depends largely on the software used to detect and accurately localize point sources. In this work, we focus on the computational aspects of super-resolution microscopy and present a comprehensive evaluation of localization software packages. Our philosophy is to evaluate each package as a whole, thus maintaining the integrity of the software. We prepared synthetic data that represent three-dimensional structures modeled after biological components, taking excitation parameters, noise sources, point-spread functions and pixelation into account. We then asked developers to run their software on our data; most responded favorably, allowing us to present a broad picture of the methods available. We evaluated their results using quantitative and user-interpretable criteria: detection rate, accuracy, quality of image reconstruction, resolution, software usability and computational resources. These metrics reflect the various tradeoffs of SMLM software packages and help users to choose the software that fits their needs.
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Affiliation(s)
- Daniel Sage
- Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Hagai Kirshner
- Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Nico Stuurman
- 1] Howard Hughes Medical Institute, University of California (UCSF), San Francisco, California, USA. [2] Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, California, USA
| | - Junhong Min
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Suliana Manley
- Laboratory of Experimental Biophysics, EPFL, Lausanne, Switzerland
| | - Michael Unser
- Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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275
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Almada P, Culley S, Henriques R. PALM and STORM: Into large fields and high-throughput microscopy with sCMOS detectors. Methods 2015; 88:109-21. [PMID: 26079924 DOI: 10.1016/j.ymeth.2015.06.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/28/2015] [Accepted: 06/03/2015] [Indexed: 01/05/2023] Open
Abstract
Single Molecule Localization Microscopy (SMLM) techniques such as Photo-Activation Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) enable fluorescence microscopy super-resolution: the overcoming of the resolution barrier imposed by the diffraction of light. These techniques are based on acquiring hundreds or thousands of images of single molecules, locating them and reconstructing a higher-resolution image from the high-precision localizations. These methods generally imply a considerable trade-off between imaging speed and resolution, limiting their applicability to high-throughput workflows. Recent advancements in scientific Complementary Metal-Oxide Semiconductor (sCMOS) camera sensors and localization algorithms reduce the temporal requirements for SMLM, pushing it toward high-throughput microscopy. Here we outline the decisions researchers face when considering how to adapt hardware on a new system for sCMOS sensors with high-throughput in mind.
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Affiliation(s)
- Pedro Almada
- Quantitative Imaging and NanoBiophysics Group, MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, WC1E 6BT London, United Kingdom
| | - Siân Culley
- Quantitative Imaging and NanoBiophysics Group, MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, WC1E 6BT London, United Kingdom
| | - Ricardo Henriques
- Quantitative Imaging and NanoBiophysics Group, MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, WC1E 6BT London, United Kingdom.
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276
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Steady-state cross-correlations for live two-colour super-resolution localization data sets. Nat Commun 2015; 6:7347. [PMID: 26066572 PMCID: PMC4467025 DOI: 10.1038/ncomms8347] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 04/28/2015] [Indexed: 01/12/2023] Open
Abstract
Cross-correlation of super-resolution images gathered from point localizations allows for robust quantification of protein co-distributions in chemically fixed cells. Here this is extended to dynamic systems through an analysis that quantifies the steady-state cross-correlation between spectrally distinguishable probes. This methodology is used to quantify the co-distribution of several mobile membrane proteins in both vesicles and live cells, including Lyn kinase and the B-cell receptor during antigen stimulation.
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277
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Mennella V, Hanna R, Kim M. Subdiffraction resolution microscopy methods for analyzing centrosomes organization. Methods Cell Biol 2015; 129:129-152. [PMID: 26175437 DOI: 10.1016/bs.mcb.2015.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this chapter, we describe the current methods of examining the structure of centrosomes by fluorescence subdiffraction microscopy. By using recently developed microscopy techniques, centrosomal proteins can now be examined in cells with a resolution of only a few nanometers, a level of molecular detail beyond the reach of traditional cell biology methods as confocal and widefield microscopy. We emphasize imaging by three-dimensional structured illumination microscopy, stochastic optical reconstruction microscopy, and quantitative approaches to image data analysis.
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Affiliation(s)
- Vito Mennella
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
| | - Rachel Hanna
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Moshe Kim
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
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278
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Lin Y, Long JJ, Huang F, Duim WC, Kirschbaum S, Zhang Y, Schroeder LK, Rebane AA, Velasco MGM, Virrueta A, Moonan DW, Jiao J, Hernandez SY, Zhang Y, Bewersdorf J. Quantifying and optimizing single-molecule switching nanoscopy at high speeds. PLoS One 2015; 10:e0128135. [PMID: 26011109 PMCID: PMC4444241 DOI: 10.1371/journal.pone.0128135] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 04/23/2015] [Indexed: 12/12/2022] Open
Abstract
Single-molecule switching nanoscopy overcomes the diffraction limit of light by stochastically switching single fluorescent molecules on and off, and then localizing their positions individually. Recent advances in this technique have greatly accelerated the data acquisition speed and improved the temporal resolution of super-resolution imaging. However, it has not been quantified whether this speed increase comes at the cost of compromised image quality. The spatial and temporal resolution depends on many factors, among which laser intensity and camera speed are the two most critical parameters. Here we quantitatively compare the image quality achieved when imaging Alexa Fluor 647-immunolabeled microtubules over an extended range of laser intensities and camera speeds using three criteria - localization precision, density of localized molecules, and resolution of reconstructed images based on Fourier Ring Correlation. We found that, with optimized parameters, single-molecule switching nanoscopy at high speeds can achieve the same image quality as imaging at conventional speeds in a 5-25 times shorter time period. Furthermore, we measured the photoswitching kinetics of Alexa Fluor 647 from single-molecule experiments, and, based on this kinetic data, we developed algorithms to simulate single-molecule switching nanoscopy images. We used this software tool to demonstrate how laser intensity and camera speed affect the density of active fluorophores and influence the achievable resolution. Our study provides guidelines for choosing appropriate laser intensities for imaging Alexa Fluor 647 at different speeds and a quantification protocol for future evaluations of other probes and imaging parameters.
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Affiliation(s)
- Yu Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
| | - Jane J. Long
- Yale College, Yale University, New Haven, Connecticut, United States of America
| | - Fang Huang
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Whitney C. Duim
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Stefanie Kirschbaum
- Institute for Molecular Biophysics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Yongdeng Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Lena K. Schroeder
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Aleksander A. Rebane
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Physics, Yale University, New Haven, Connecticut, United States of America
| | - Mary Grace M. Velasco
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
| | - Alejandro Virrueta
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Mechanical Engineering and Material Science, Yale University, New Haven, Connecticut, United States of America
| | - Daniel W. Moonan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Junyi Jiao
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
| | - Sandy Y. Hernandez
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
| | - Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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279
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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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280
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Shepherd D. Life away from the coverslip: Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar. Phys Life Rev 2015; 13:144-5. [PMID: 25936616 DOI: 10.1016/j.plrev.2015.04.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Douglas Shepherd
- Department of Physics, University of Colorado Denver, Denver, CO 80204, United States; Pediatric Heart Lung Center, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO 80045, United States.
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281
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Bartke RM, Cameron EL, Cristie-David AS, Custer TC, Denies MS, Daher M, Dhakal S, Ghosh S, Heinicke LA, Hoff JD, Hou Q, Kahlscheuer ML, Karslake J, Krieger AG, Li J, Li X, Lund PE, Vo NN, Park J, Pitchiaya S, Rai V, Smith DJ, Suddala KC, Wang J, Widom JR, Walter NG. Meeting report: SMART timing--principles of single molecule techniques course at the University of Michigan 2014. Biopolymers 2015; 103:296-302. [PMID: 25546606 PMCID: PMC4613745 DOI: 10.1002/bip.22603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 12/17/2014] [Indexed: 11/07/2022]
Abstract
Four days after the announcement of the 2014 Nobel Prize in Chemistry for "the development of super-resolved fluorescence microscopy" based on single molecule detection, the Single Molecule Analysis in Real-Time (SMART) Center at the University of Michigan hosted a "Principles of Single Molecule Techniques 2014" course. Through a combination of plenary lectures and an Open House at the SMART Center, the course took a snapshot of a technology with an especially broad and rapidly expanding range of applications in the biomedical and materials sciences. Highlighting the continued rapid emergence of technical and scientific advances, the course underscored just how brightly the future of the single molecule field shines.
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Affiliation(s)
- Rebecca M Bartke
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055
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282
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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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283
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Palayret M, Armes H, Basu S, Watson AT, Herbert A, Lando D, Etheridge TJ, Endesfelder U, Heilemann M, Laue E, Carr AM, Klenerman D, Lee SF. Virtual-'light-sheet' single-molecule localisation microscopy enables quantitative optical sectioning for super-resolution imaging. PLoS One 2015; 10:e0125438. [PMID: 25884495 PMCID: PMC4401716 DOI: 10.1371/journal.pone.0125438] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 01/07/2015] [Indexed: 11/18/2022] Open
Abstract
Single-molecule super-resolution microscopy allows imaging of fluorescently-tagged proteins in live cells with a precision well below that of the diffraction limit. Here, we demonstrate 3D sectioning with single-molecule super-resolution microscopy by making use of the fitting information that is usually discarded to reject fluorophores that emit from above or below a virtual-'light-sheet', a thin volume centred on the focal plane of the microscope. We describe an easy-to-use routine (implemented as an open-source ImageJ plug-in) to quickly analyse a calibration sample to define and use such a virtual light-sheet. In addition, the plug-in is easily usable on almost any existing 2D super-resolution instrumentation. This optical sectioning of super-resolution images is achieved by applying well-characterised width and amplitude thresholds to diffraction-limited spots that can be used to tune the thickness of the virtual light-sheet. This allows qualitative and quantitative imaging improvements: by rejecting out-of-focus fluorophores, the super-resolution image gains contrast and local features may be revealed; by retaining only fluorophores close to the focal plane, virtual-'light-sheet' single-molecule localisation microscopy improves the probability that all emitting fluorophores will be detected, fitted and quantitatively evaluated.
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Affiliation(s)
- Matthieu Palayret
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Helen Armes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
- Genome Damage and Stability Centre, University of Sussex, Falmer, Sussex, BN1 9RQ, United Kingdom
| | - Srinjan Basu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Adam T. Watson
- Genome Damage and Stability Centre, University of Sussex, Falmer, Sussex, BN1 9RQ, United Kingdom
| | - Alex Herbert
- Genome Damage and Stability Centre, University of Sussex, Falmer, Sussex, BN1 9RQ, United Kingdom
| | - David Lando
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Thomas J. Etheridge
- Genome Damage and Stability Centre, University of Sussex, Falmer, Sussex, BN1 9RQ, United Kingdom
| | - Ulrike Endesfelder
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Ernest Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Antony M. Carr
- Genome Damage and Stability Centre, University of Sussex, Falmer, Sussex, BN1 9RQ, United Kingdom
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Steven F. Lee
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
- * E-mail:
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284
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Curthoys NM, Parent M, Mlodzianoski M, Nelson AJ, Lilieholm J, Butler MB, Valles M, Hess ST. Dances with Membranes: Breakthroughs from Super-resolution Imaging. CURRENT TOPICS IN MEMBRANES 2015; 75:59-123. [PMID: 26015281 PMCID: PMC5584789 DOI: 10.1016/bs.ctm.2015.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Biological membrane organization mediates numerous cellular functions and has also been connected with an immense number of human diseases. However, until recently, experimental methodologies have been unable to directly visualize the nanoscale details of biological membranes, particularly in intact living cells. Numerous models explaining membrane organization have been proposed, but testing those models has required indirect methods; the desire to directly image proteins and lipids in living cell membranes is a strong motivation for the advancement of technology. The development of super-resolution microscopy has provided powerful tools for quantification of membrane organization at the level of individual proteins and lipids, and many of these tools are compatible with living cells. Previously inaccessible questions are now being addressed, and the field of membrane biology is developing rapidly. This chapter discusses how the development of super-resolution microscopy has led to fundamental advances in the field of biological membrane organization. We summarize the history and some models explaining how proteins are organized in cell membranes, and give an overview of various super-resolution techniques and methods of quantifying super-resolution data. We discuss the application of super-resolution techniques to membrane biology in general, and also with specific reference to the fields of actin and actin-binding proteins, virus infection, mitochondria, immune cell biology, and phosphoinositide signaling. Finally, we present our hopes and expectations for the future of super-resolution microscopy in the field of membrane biology.
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Affiliation(s)
- Nikki M. Curthoys
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
| | - Matthew Parent
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
| | | | - Andrew J. Nelson
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
| | - Jennifer Lilieholm
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
| | - Michael B. Butler
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
| | - Matthew Valles
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
| | - Samuel T. Hess
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
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285
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Zahreddine RN, Cogswell CJ. Total variation regularized deconvolution for extended depth of field microscopy. APPLIED OPTICS 2015; 54:2244-54. [PMID: 25968507 DOI: 10.1364/ao.54.002244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 01/13/2015] [Indexed: 05/24/2023]
Abstract
The depth of field of an optical system can be extended through a combination of point spread function (PSF) engineering and image processing. A phase mask inserted in the back aperture of the system creates a PSF that is focus-invariant over an extended depth. A digital deconvolution is then used to restore transverse resolution. The application and analysis of this technique to fluorescence microscopy is limited in the literature. In this paper we formalize a microscopy specific imaging model, and experimentally demonstrate a total variation regularized deconvolution approach. Results are compared to the Wiener filter.
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286
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Spahn C, Cella-Zannacchi F, Endesfelder U, Heilemann M. Correlative super-resolution imaging of RNA polymerase distribution and dynamics, bacterial membrane and chromosomal structure inEscherichia coli. Methods Appl Fluoresc 2015; 3:014005. [DOI: 10.1088/2050-6120/3/1/014005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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287
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Diffraction-unlimited imaging: from pretty pictures to hard numbers. Cell Tissue Res 2015; 360:151-78. [DOI: 10.1007/s00441-014-2109-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 12/22/2014] [Indexed: 10/23/2022]
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288
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Zhong H. Applying superresolution localization-based microscopy to neurons. Synapse 2015; 69:283-94. [PMID: 25648102 DOI: 10.1002/syn.21806] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 01/19/2015] [Accepted: 01/26/2015] [Indexed: 01/15/2023]
Abstract
Proper brain function requires the precise localization of proteins and signaling molecules on a nanometer scale. The examination of molecular organization at this scale has been difficult in part because it is beyond the reach of conventional, diffraction-limited light microscopy. The recently developed method of superresolution, localization-based fluorescent microscopy (LBM), such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), has demonstrated a resolving power at a 10 nm scale and is poised to become a vital tool in modern neuroscience research. Indeed, LBM has revealed previously unknown cellular architectures and organizational principles in neurons. Here, we discuss the principles of LBM, its current applications in neuroscience, and the challenges that must be met before its full potential is achieved. We also present the unpublished results of our own experiments to establish a sample preparation procedure for applying LBM to study brain tissue.
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Affiliation(s)
- Haining Zhong
- Vollum Institute, Oregon Health & Science University, Portland, Oregon, 97239; Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, 20147
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289
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Helgesen E, Fossum-Raunehaug S, Sætre F, Schink KO, Skarstad K. Dynamic Escherichia coli SeqA complexes organize the newly replicated DNA at a considerable distance from the replisome. Nucleic Acids Res 2015; 43:2730-43. [PMID: 25722374 PMCID: PMC4357733 DOI: 10.1093/nar/gkv146] [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] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli SeqA protein binds to newly replicated, hemimethylated DNA behind replication forks and forms structures consisting of several hundred SeqA molecules bound to about 100 kb of DNA. It has been suggested that SeqA structures either direct the new sister DNA molecules away from each other or constitute a spacer that keeps the sisters together. We have developed an image analysis script that automatically measures the distance between neighboring foci in cells. Using this tool as well as direct stochastic optical reconstruction microscopy (dSTORM) we find that in cells with fluorescently tagged SeqA and replisome the sister SeqA structures were situated close together (less than about 30 nm apart) and relatively far from the replisome (on average 200–300 nm). The results support the idea that newly replicated sister molecules are kept together behind the fork and suggest the existence of a stretch of DNA between the replisome and SeqA which enjoys added stabilization. This could be important in facilitating DNA transactions such as recombination, mismatch repair and topoisomerase activity. In slowly growing cells without ongoing replication forks the SeqA protein was found to reside at the fully methylated origins prior to initiation of replication.
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Affiliation(s)
- Emily Helgesen
- Department of Cell Biology, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, 0310 Oslo, Norway
| | - Solveig Fossum-Raunehaug
- Department of Cell Biology, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, 0310 Oslo, Norway School of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Frank Sætre
- Department of Cell Biology, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, 0310 Oslo, Norway
| | - Kay Oliver Schink
- Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, 0310 Oslo, Norway
| | - Kirsten Skarstad
- Department of Cell Biology, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, 0310 Oslo, Norway School of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
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290
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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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291
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Whelan DR, Bell TDM. Super-Resolution Single-Molecule Localization Microscopy: Tricks of the Trade. J Phys Chem Lett 2015; 6:374-382. [PMID: 26261950 DOI: 10.1021/jz5019702] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Application of single-molecule fluorescence detection has led to the development of light microscopy techniques that make it possible to study fluorescent samples at spatial resolutions significantly improved upon the diffraction limit of light. The biological and materials science applications of these "super-resolution" microscopy methods are vast, causing current demand for them to be high. However, implementation, execution, and interpretation of these techniques, particularly involving biological samples, require a broad interdisciplinary skillset, not often found in a single laboratory. Those already used to interdisciplinary work as well as navigating communication and collaboration between more pure forms of physics, chemistry, and biology are well-positioned to spearhead such efforts. In this Perspective, we describe various aspects of single-molecule super-resolution imaging, discussing, in particular, the role that physical chemistry has so far played in its development and establishment. We also highlight a selection of some of the remarkable recent research achievements in this vibrant field.
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Affiliation(s)
- Donna R Whelan
- School of Chemistry, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Toby D M Bell
- School of Chemistry, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
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292
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Fornasiero EF, Opazo F. Super-resolution imaging for cell biologists: concepts, applications, current challenges and developments. Bioessays 2015; 37:436-51. [PMID: 25581819 DOI: 10.1002/bies.201400170] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The recent 2014 Nobel Prize in chemistry honored an era of discoveries and technical advancements in the field of super-resolution microscopy. However, the applications of diffraction-unlimited imaging in biology have a long road ahead and persistently engage scientists with new challenges. Some of the bottlenecks that restrain the dissemination of super-resolution techniques are tangible, and include the limited performance of affinity probes and the yet not capillary diffusion of imaging setups. Likewise, super-resolution microscopy has introduced new paradigms in the design of projects that require imaging with nanometer-resolution and in the interpretation of biological images. Besides structural or morphological characterization, super-resolution imaging is quickly expanding towards interaction mapping, multiple target detection and live imaging. Here we review the recent progress of biologists employing super-resolution imaging, some pitfalls, implications and new trends, with the purpose of animating the field and spurring future developments.
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Affiliation(s)
- Eugenio F Fornasiero
- STED Microscopy Group, European Neuroscience Institute, Göttingen, Germany; Department of Neuro- and Sensory-physiology, University of Göttingen, Göttingen, Germany
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293
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Pereira PM, Almada P, Henriques R. High-content 3D multicolor super-resolution localization microscopy. Methods Cell Biol 2015; 125:95-117. [PMID: 25640426 DOI: 10.1016/bs.mcb.2014.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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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294
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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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295
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Jayasinghe ID, Clowsley AH, Munro M, Hou Y, Crossman DJ, Soeller C. Revealing T-Tubules in Striated Muscle with New Optical Super-Resolution Microscopy Techniquess. Eur J Transl Myol 2014; 25:4747. [PMID: 26913143 PMCID: PMC4748971 DOI: 10.4081/ejtm.2015.4747] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/18/2014] [Indexed: 01/03/2023] Open
Abstract
The t-tubular system plays a central role in the synchronisation of calcium signalling and excitation-contraction coupling in most striated muscle cells. Light microscopy has been used for imaging t-tubules for well over 100 years and together with electron microscopy (EM), has revealed the three-dimensional complexities of the t-system topology within cardiomyocytes and skeletal muscle fibres from a range of species. The emerging super-resolution single molecule localisation microscopy (SMLM) techniques are offering a near 10-fold improvement over the resolution of conventional fluorescence light microscopy methods, with the ability to spectrally resolve nanometre scale distributions of multiple molecular targets. In conjunction with the next generation of electron microscopy, SMLM has allowed the visualisation and quantification of intricate t-tubule morphologies within large areas of muscle cells at an unprecedented level of detail. In this paper, we review recent advancements in the t-tubule structural biology with the utility of various microscopy techniques. We outline the technical considerations in adapting SMLM to study t-tubules and its potential to further our understanding of the molecular processes that underlie the sub-micron scale structural alterations observed in a range of muscle pathologies.
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Affiliation(s)
| | | | - Michelle Munro
- Department of Physiology, The University of Auckland , New Zealand
| | - Yufeng Hou
- Department of Physiology, The University of Auckland , New Zealand
| | - David J Crossman
- Department of Physiology, The University of Auckland , New Zealand
| | - Christian Soeller
- Biomedical Physics, University of Exeter, UK, New Zealand; Biomedical Physics, University of Exeter, UK, New Zealand
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296
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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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297
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Schoen I. Localization precision in stepwise photobleaching experiments. Biophys J 2014; 107:2122-9. [PMID: 25418097 PMCID: PMC4223207 DOI: 10.1016/j.bpj.2014.09.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 09/26/2014] [Accepted: 09/30/2014] [Indexed: 01/19/2023] Open
Abstract
The precise determination of the position of fluorescent labels is essential for the quantitative study of biomolecular structures by various localization microscopy techniques. Localization by stepwise photobleaching is especially suited for measuring nanometer-scale distances between two labels; however, the precision of this method has remained elusive. Here, we show that shot noise from other emitters and error propagation compromise the localization precision in stepwise photobleaching. Incorporation of point spread function-shaped shot noise into the variance term in the Fisher matrix yielded fundamental Cràmer-Rao lower bounds (CRLBs) that were in general anisotropic and depended on emitter intensity and position. We performed simulations to benchmark the extent to which different analysis procedures reached these ideal CRLBs. The accumulation of noise from several images accounted for the worse localization precision in image subtraction. Propagation of fitting errors compromised the CRLBs in sequential fitting using fixed parameters. Global fitting of all images was also governed by error propagation, but made optimal use of the available information. The precision of individual distance measurements depended critically on the exact bleaching kinetics and was correctly quantified by the CRLBs. The methods presented here provide a consistent framework for quantitatively analyzing stepwise photobleaching experiments and shed light on the localization precision in some other bleaching- or blinking-assisted techniques.
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Affiliation(s)
- Ingmar Schoen
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
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298
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Möckl L, Lamb DC, Bräuchle C. Superhochauflösende Mikroskopie: Nobelpreis in Chemie 2014 für Eric Betzig, Stefan Hell und William E. Moerner. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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299
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Möckl L, Lamb DC, Bräuchle C. Super-resolved fluorescence microscopy: Nobel Prize in Chemistry 2014 for Eric Betzig, Stefan Hell, and William E. Moerner. Angew Chem Int Ed Engl 2014; 53:13972-7. [PMID: 25371081 DOI: 10.1002/anie.201410265] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/22/2022]
Abstract
A big honor for small objects: The Nobel Prize in Chemistry 2014 was jointly awarded to Eric Betzig, Stefan Hell, and William E. Moerner "for the development of super-resolved fluorescence microscopy". This Highlight describes how the field of super-resolution microscopy developed from the first detection of a single molecule in 1989 to the sophisticated techniques of today.
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Affiliation(s)
- Leonhard Möckl
- Department for Chemistry and Center for NanoScience (CeNS), University of Munich (LMU), Butenandtstrasse 5-13 (E), 81377 Munich (Germany)
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300
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Min J, Holden SJ, Carlini L, Unser M, Manley S, Ye JC. 3D high-density localization microscopy using hybrid astigmatic/ biplane imaging and sparse image reconstruction. BIOMEDICAL OPTICS EXPRESS 2014; 5:3935-48. [PMID: 26526603 PMCID: PMC4242028 DOI: 10.1364/boe.5.003935] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Localization microscopy achieves nanoscale spatial resolution by iterative localization of sparsely activated molecules, which generally leads to a long acquisition time. By implementing advanced algorithms to treat overlapping point spread functions (PSFs), imaging of densely activated molecules can improve the limited temporal resolution, as has been well demonstrated in two-dimensional imaging. However, three-dimensional (3D) localization of high-density data remains challenging since PSFs are far more similar along the axial dimension than the lateral dimensions. Here, we present a new, high-density 3D imaging system and algorithm. The hybrid system is implemented by combining astigmatic and biplane imaging. The proposed 3D reconstruction algorithm is extended from our state-of-the art 2D high-density localization algorithm. Using mutual coherence analysis of model PSFs, we validated that the hybrid system is more suitable than astigmatic or biplane imaging alone for 3D localization of high-density data. The efficacy of the proposed method was confirmed via simulation and real data of microtubules. Furthermore, we also successfully demonstrated fluorescent-protein-based live cell 3D localization microscopy with a temporal resolution of just 3 seconds, capturing fast dynamics of the endoplasmic recticulum.
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Affiliation(s)
- Junhong Min
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon,
Republic of Korea
| | - Seamus J. Holden
- Institute of the Physics of Biological Systems, École polytechnique Fédérale de Lausanne,
Switzerland
| | - Lina Carlini
- Institute of the Physics of Biological Systems, École polytechnique Fédérale de Lausanne,
Switzerland
| | - Michael Unser
- Biomedical Imaging Group, École polytechnique fédérale de Lausanne,
Switzerland
| | - Suliana Manley
- Institute of the Physics of Biological Systems, École polytechnique Fédérale de Lausanne,
Switzerland
| | - Jong Chul Ye
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon,
Republic of Korea
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