151
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Nazari R, Zaare S, Alvarez RC, Karpos K, Engelman T, Madsen C, Nelson G, Spence JCH, Weierstall U, Adrian RJ, Kirian RA. 3D printing of gas-dynamic virtual nozzles and optical characterization of high-speed microjets. OPTICS EXPRESS 2020; 28:21749-21765. [PMID: 32752448 PMCID: PMC7470680 DOI: 10.1364/oe.390131] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 05/22/2023]
Abstract
Gas dynamic virtual nozzles (GDVNs) produce microscopic flow-focused liquid jets and droplets and play an important role at X-ray free-electron laser (XFEL) facilities where they are used to steer a stream of hydrated biomolecules into an X-ray focus during diffraction measurements. Highly stable and reproducible microjet and microdroplets are desired, as are flexible fabrication methods that enable integrated mixing microfluidics, droplet triggering mechanisms, laser illumination, and other customized features. In this study, we develop the use of high-resolution 3D nano-printing for the production of monolithic, asymmetric GDVN designs that are difficult to fabricate by other means. We also develop a dual-pulsed nanosecond image acquisition and analysis platform for the characterization of GDVN performance, including jet speed, length, diameter, and directionality, among others. We show that printed GDVNs can form microjets with very high degree of reproducibility, down to sub-micron diameters, and with water jet speeds beyond 170 m/s.
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Affiliation(s)
- Reza Nazari
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Sahba Zaare
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Roberto C. Alvarez
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- School of Mathematics and Statistical Sciences, Arizona State University, Tempe, AZ 85287, USA
| | | | - Trent Engelman
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Caleb Madsen
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - John C. H. Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Ronald J. Adrian
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
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152
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Hoelzel CA, Zhang X. Visualizing and Manipulating Biological Processes by Using HaloTag and SNAP-Tag Technologies. Chembiochem 2020; 21:1935-1946. [PMID: 32180315 PMCID: PMC7367766 DOI: 10.1002/cbic.202000037] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/27/2020] [Indexed: 12/25/2022]
Abstract
Visualizing and manipulating the behavior of proteins is crucial to understanding the physiology of the cell. Methods of biorthogonal protein labeling are important tools to attain this goal. In this review, we discuss advances in probe technology specific for self-labeling protein tags, focusing mainly on the application of HaloTag and SNAP-tag systems. We describe the latest developments in small-molecule probes that enable fluorogenic (no wash) imaging and super-resolution fluorescence microscopy. In addition, we cover several methodologies that enable the perturbation or manipulation of protein behavior and function towards the control of biological pathways. Thus, current technical advances in the HaloTag and SNAP-tag systems means that they are becoming powerful tools to enable the visualization and manipulation of biological processes, providing invaluable scientific insights that are difficult to obtain by traditional methodologies. As the multiplex of self-labeling protein tag systems continues to be developed and expanded, the utility of these protein tags will allow researchers to address previously inaccessible questions at the forefront of biology.
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Affiliation(s)
- Conner A Hoelzel
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, PA 16802, USA
| | - Xin Zhang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, PA 16802, USA
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153
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Abstract
Recent advances in super-resolution (sub-diffraction limited) microscopy have yielded remarkable insights into the nanoscale architecture and behavior of cells. In addition to the capacity to provide sub 100 nm resolution, these technologies offer unique quantitative opportunities with particular relevance to platelet and megakaryocyte biology. In this review, we provide a short introduction to modern super-resolution microscopy, its applications in the field of platelet and megakaryocyte biology, and emerging quantitative approaches which will allow for unprecedented insights into the biology of these unique cell types.
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Affiliation(s)
- Abdullah O Khan
- Institute of Cardiovascular Sciences, College of Medical and Dental Science, University of Birmingham , Birmingham, UK
| | - Jeremy A Pike
- Institute of Cardiovascular Sciences, College of Medical and Dental Science, University of Birmingham , Birmingham, UK.,Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham , UK
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154
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Godoy BI, Lin Y, Andersson SB. A time-varying approach to single particle tracking with a nonlinear observation model. PROCEEDINGS OF THE ... AMERICAN CONTROL CONFERENCE. AMERICAN CONTROL CONFERENCE 2020; 2020:5151-5156. [PMID: 34483467 PMCID: PMC8411988 DOI: 10.23919/acc45564.2020.9147877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Single Particle Tracking (SPT) is a powerful class of tools for analyzing the dynamics of individual biological macromolecules moving inside living cells. The acquired data is typically in the form of a sequence of camera images that are then post-processed to reveal details about the motion. In this work, we develop a local time-varying estimation algorithm for estimating motion model parameters from the data considering nonlinear observations. Our approach uses several well-known existing tools, namely the Expectation Maximization (EM) algorithm combined with an Unscented Kalman filter (UKF) and an Unscented Rauch-Tung-Striebel smoother (URTSS), and applies them to the time-varying case through a sliding window methodology. Due to the shot noise characteristics of the photon generation process, this model uses a Poisson distribution to capture the measurement noise inherent in imaging. In order to apply our time-varying approach to the UKF, we first need to transform the measurements into a model with additive Gaussian noise. This is carried out using a variance stabilizing transform. Results from simulations show that our approach is successful in tracing time-varying diffusion constants at a range of physically relevant signal levels. We also discuss the initialization for the EM algorithm based on the available data.
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Affiliation(s)
- Boris I Godoy
- Department of Mechanical Engineering, Boston University, Boston, MA 02215, USA
| | - Ye Lin
- Division of Systems Engineering, Boston University, Boston, MA 02215, USA
| | - Sean B Andersson
- Division of Systems Engineering, Boston University, Boston, MA 02215, USA
- Department of Mechanical Engineering, Boston University, Boston, MA 02215, USA
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155
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Zhang O, Lew MD. Quantum limits for precisely estimating the orientation and wobble of dipole emitters. PHYSICAL REVIEW RESEARCH 2020; 2:033114. [PMID: 32832916 PMCID: PMC7440618 DOI: 10.1103/physrevresearch.2.033114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Precisely measuring molecular orientation is key to understanding how molecules organize and interact in soft matter, but the maximum theoretical limit of measurement precision has yet to be quantified. We use quantum estimation theory and Fisher information (QFI) to derive a fundamental bound on the precision of estimating the orientations of rotationally fixed molecules. While direct imaging of the microscope pupil achieves the quantum bound, it is not compatible with wide-field imaging, so we propose an interferometric imaging system that also achieves QFI-limited measurement precision. Extending our analysis to rotationally diffusing molecules, we derive conditions that enable a subset of second-order dipole orientation moments to be measured with quantum-limited precision. Interestingly, we find that no existing techniques can measure all second moments simultaneously with QFI-limited precision; there exists a fundamental trade-off between precisely measuring the mean orientation of a molecule versus its wobble. This theoretical analysis provides crucial insight for optimizing the design of orientation-sensitive imaging systems.
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Affiliation(s)
- Oumeng Zhang
- Department of Electrical and Systems Engineering, Washington University in St. Louis, Missouri 63130, USA
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering, Washington University in St. Louis, Missouri 63130, USA
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156
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Franch N, Canals J, Moro V, Vilá A, Romano-Rodríguez A, Prades JD, Gülink J, Bezshlyakh D, Waag A, Kluczyk-Korch K, Auf der Maur M, di Carlo A, Diéguez Á. Nano illumination microscopy: a technique based on scanning with an array of individually addressable nanoLEDs. OPTICS EXPRESS 2020; 28:19044-19057. [PMID: 32672190 DOI: 10.1364/oe.391497] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
In lensless microscopy, spatial resolution is usually provided by the pixel density of current digital cameras, which are reaching a hard-to-surpass pixel size / resolution limit over 1 µm. As an alternative, the dependence of the resolving power can be moved from the detector to the light sources, offering a new kind of lensless microscopy setups. The use of continuously scaled-down Light-Emitting Diode (LED) arrays to scan the sample allows resolutions on order of the LED size, giving rise to compact and low-cost microscopes without mechanical scanners or optical accessories. In this paper, we present the operation principle of this new approach to lensless microscopy, with simulations that demonstrate the possibility to use it for super-resolution, as well as a first prototype. This proof-of-concept setup integrates an 8 × 8 array of LEDs, each 5 × 5 μm2 pixel size and 10 μm pitch, and an optical detector. We characterize the system using Electron-Beam Lithography (EBL) pattern. Our prototype validates the imaging principle and opens the way to improve resolution by further miniaturizing the light sources.
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157
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Petrov PN, Moerner WE. Addressing systematic errors in axial distance measurements in single-emitter localization microscopy. OPTICS EXPRESS 2020; 28:18616-18632. [PMID: 32672159 PMCID: PMC7340385 DOI: 10.1364/oe.391496] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 05/05/2023]
Abstract
Nanoscale localization of point emitters is critical to several methods in optical fluorescence microscopy, including single-molecule super-resolution imaging and tracking. While the precision of the localization procedure has been the topic of extensive study, localization accuracy has been less emphasized, in part due to the challenge of producing an experimental sample containing unperturbed point emitters at known three-dimensional positions in a relevant geometry. We report a new experimental system which reproduces a widely-adopted geometry in high-numerical aperture localization microscopy, in which molecules are situated in an aqueous medium above a glass coverslip imaged with an oil-immersion objective. We demonstrate a calibration procedure that enables measurement of the depth-dependent point spread function (PSF) for open aperture imaging as well as imaging with engineered PSFs with index mismatch. We reveal the complicated, depth-varying behavior of the focal plane position in this system and discuss the axial localization biases incurred by common approximations of this behavior. We compare our results to theoretical calculations.
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Affiliation(s)
- Petar N. Petrov
- 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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158
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DeepSTORM3D: dense 3D localization microscopy and PSF design by deep learning. Nat Methods 2020; 17:734-740. [PMID: 32541853 PMCID: PMC7610486 DOI: 10.1038/s41592-020-0853-5] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 05/06/2020] [Indexed: 12/24/2022]
Abstract
An outstanding challenge in single-molecule localization microscopy is the accurate and precise localization of individual point emitters in three dimensions in densely labeled samples. One established approach for three-dimensional single-molecule localization is point-spread-function (PSF) engineering, in which the PSF is engineered to vary distinctively with emitter depth using additional optical elements. However, images of dense emitters, which are desirable for improving temporal resolution, pose a challenge for algorithmic localization of engineered PSFs, due to lateral overlap of the emitter PSFs. Here we train a neural network to localize multiple emitters with densely overlapping Tetrapod PSFs over a large axial range. We then use the network to design the optimal PSF for the multi-emitter case. We demonstrate our approach experimentally with super-resolution reconstructions of mitochondria and volumetric imaging of fluorescently labeled telomeres in cells. Our approach, DeepSTORM3D, enables the study of biological processes in whole cells at timescales that are rarely explored in localization microscopy.
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159
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Zhong Y, Wang G. Three-Dimensional Single Particle Tracking and Its Applications in Confined Environments. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:381-403. [PMID: 32097571 DOI: 10.1146/annurev-anchem-091819-100409] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Single particle tracking (SPT) has proven to be a powerful technique in studying molecular dynamics in complicated systems. We review its recent development, including three-dimensional (3D) SPT and its applications in probing nanostructures and molecule-surface interactions that are important to analytical chemical processes. Several frequently used 3D SPT techniques are introduced. Especially of interest are those based on point spread function engineering, which are simple in instrumentation and can be easily adapted and used in analytical labs. Corresponding data analysis methods are briefly discussed. We present several important case studies, with a focus on probing mass transport and molecule-surface interactions in confined environments. The presented studies demonstrate the great potential of 3D SPT for understanding fundamental phenomena in confined space, which will enable us to predict basic principles involved in chemical recognition, separation, and analysis, and to optimize mass transport and responses by structural design and optimization.
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Affiliation(s)
- Yaning Zhong
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - Gufeng Wang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA;
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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160
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Luo F, Qin G, Xia T, Fang X. Single-Molecule Imaging of Protein Interactions and Dynamics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:337-361. [PMID: 32228033 DOI: 10.1146/annurev-anchem-091619-094308] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Live-cell single-molecule fluorescence imaging has become a powerful analytical tool to investigate cellular processes that are not accessible to conventional biochemical approaches. This has greatly enriched our understanding of the behaviors of single biomolecules in their native environments and their roles in cellular events. Here, we review recent advances in fluorescence-based single-molecule bioimaging of proteins in living cells. We begin with practical considerations of the design of single-molecule fluorescence imaging experiments such as the choice of imaging modalities, fluorescent probes, and labeling methods. We then describe analytical observables from single-molecule data and the associated molecular parameters along with examples of live-cell single-molecule studies. Lastly, we discuss computational algorithms developed for single-molecule data analysis.
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Affiliation(s)
- Fang Luo
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Gege Qin
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tie Xia
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaohong Fang
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
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161
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Jacquemet G, Carisey AF, Hamidi H, Henriques R, Leterrier C. The cell biologist's guide to super-resolution microscopy. J Cell Sci 2020; 133:133/11/jcs240713. [PMID: 32527967 DOI: 10.1242/jcs.240713] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Fluorescence microscopy has become a ubiquitous method to observe the location of specific molecular components within cells. However, the resolution of light microscopy is limited by the laws of diffraction to a few hundred nanometers, blurring most cellular details. Over the last two decades, several techniques - grouped under the 'super-resolution microscopy' moniker - have been designed to bypass this limitation, revealing the cellular organization down to the nanoscale. The number and variety of these techniques have steadily increased, to the point that it has become difficult for cell biologists and seasoned microscopists alike to identify the specific technique best suited to their needs. Available techniques include image processing strategies that generate super-resolved images, optical imaging schemes that overcome the diffraction limit and sample manipulations that expand the size of the biological sample. In this Cell Science at a Glance article and the accompanying poster, we provide key pointers to help users navigate through the various super-resolution methods by briefly summarizing the principles behind each technique, highlighting both critical strengths and weaknesses, as well as providing example images.
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Affiliation(s)
- Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland .,Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland
| | - Alexandre F Carisey
- William T. Shearer Center for Human Immunobiology, Baylor College of Medicine and Texas Children's Hospital, 1102 Bates Street, Houston 77030 TX, USA
| | - Hellyeh Hamidi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Ricardo Henriques
- University College London, London WC1E 6BT, UK .,The Francis Crick Institute, London NW1 1AT, UK
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162
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Zhang Y, Raymo FM. Photoactivatable fluorophores for single-molecule localization microscopy of live cells. Methods Appl Fluoresc 2020; 8:032002. [PMID: 32325443 DOI: 10.1088/2050-6120/ab8c5c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Photochemical reactions can be designed to convert either irreversibly or reversibly a nonemissive reactant into an emissive product. The irreversible disconnection of a photocleavable group from an emissive chromophore or the reversible interconversion of a photochromic component is generally exploited to implement these operating principles for fluorescence switching. In both instances, the interplay of activating radiation, to convert the nonemissive state into the emissive species, and exciting radiation, to produce fluorescence from the latter, can be exploited to switch fluorescence on in a given area of interest at a precise interval of time. Such a level of spatiotemporal control provides the opportunity to reconstruct sub-diffraction images with resolution at the nanometer level. Indeed, closely-spaced emitters can be switched on under photochemical control at distinct intervals of time and localized independently at the single-molecule level. In combination with appropriate intracellular targeting strategies, some of these photoactivatable fluorophores can be switched and localized inside live cells to permit the visualization of sub-cellular structures with a spatial resolution that would be impossible to achieve with conventional fluorophores. As a result, photoactivatable fluorophores can become invaluable probes for the implementation of super-resolution imaging schemes aimed at the elucidation of the fundamental factors controlling cellular functions at the molecular level.
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Affiliation(s)
- Yang Zhang
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, Coral Gables, FL, United States of America
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163
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Zhou Y, Zammit P, Zickus V, Taylor JM, Harvey AR. Twin-Airy Point-Spread Function for Extended-Volume Particle Localization. PHYSICAL REVIEW LETTERS 2020; 124:198104. [PMID: 32469536 DOI: 10.1103/physrevlett.124.198104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 11/11/2019] [Accepted: 04/08/2020] [Indexed: 06/11/2023]
Abstract
The localization of point sources in optical microscopy enables nm-precision imaging of single-molecules and biological dynamics. We report a new method of localization microscopy using twin Airy beams that yields precise 3D localization with the key advantages of extended depth range, higher optical throughput, and potential for imaging higher emitter densities than are possible using other techniques. A precision of better than 30 nm was achieved over a depth range in excess of 7 μm using a 60×, 1.4 NA objective. An illustrative application to extended-depth-range blood-flow imaging in a live zebrafish is also demonstrated.
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Affiliation(s)
- Yongzhuang Zhou
- School of Physics & Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Paul Zammit
- School of Physics & Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Vytautas Zickus
- School of Physics & Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Jonathan M Taylor
- School of Physics & Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Andrew R Harvey
- School of Physics & Astronomy, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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164
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Yao B, Li W, Pan W, Yang Z, Chen D, Li J, Qu J. Image reconstruction with a deep convolutional neural network in high-density super-resolution microscopy. OPTICS EXPRESS 2020; 28:15432-15446. [PMID: 32403571 DOI: 10.1364/oe.392358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
An accurate and fast reconstruction algorithm is crucial for the improvement of temporal resolution in high-density super-resolution microscopy, particularly in view of the challenges associated with live-cell imaging. In this work, we design a deep network based on a convolutional neural network to take advantage of its enhanced ability in high-density molecule localization, and introduce a residual layer into the network to reduce noise. The proposed scheme also incorporates robustness against variations of both the full width at half maximum (FWHM) and the pixel size. We validate our algorithm on both simulated and experimental data by achieving performance improvement in terms of loss value and image quality, and demonstrate live-cell imaging with temporal resolution of 0.5 seconds by recovering mitochondria dynamics.
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165
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Liu S, Huang F. Enhanced 4Pi single-molecule localization microscopy with coherent pupil based localization. Commun Biol 2020; 3:220. [PMID: 32385402 PMCID: PMC7210115 DOI: 10.1038/s42003-020-0908-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/24/2020] [Indexed: 01/05/2023] Open
Abstract
Over the last decades, super-resolution techniques have revolutionized the field of fluorescence microscopy. Among them, interferometric or 4Pi microscopy methods exhibit supreme resolving power in the axial dimension. Combined with single-molecule detection/localization and adaptive optics, current 4Pi microscopy methods enabled 10–15 nm isotropic 3D resolution throughout whole cells. However, further improving the achieved 3D resolution poses challenges arising from the complexity of single-molecule emission patterns generated by these coherent single-molecule imaging systems. These complex emission patterns render a large portion of information carrying photons unusable. Here, we introduce a localization algorithm that achieves the theoretical precision limit for a 4Pi based single-molecule switching nanoscopy (4Pi-SMSN) system, and demonstrate improvements in localization precision, accuracy as well as stability comparing with state-of-the-art 4Pi-SMSN methods. To further improve localisation precision and biases in all the three dimensions of 4Pi single molecule localisation microscopy, Huang and Liu develop a method based on coherent pupil functions and an algorithm to extract the position information content at the theoretical information limit while dynamically compensating the temperature-induced cavity drift.
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Affiliation(s)
- Sheng Liu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA. .,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA. .,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.
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166
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Möckl L. The Emerging Role of the Mammalian Glycocalyx in Functional Membrane Organization and Immune System Regulation. Front Cell Dev Biol 2020; 8:253. [PMID: 32351961 PMCID: PMC7174505 DOI: 10.3389/fcell.2020.00253] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/25/2020] [Indexed: 12/17/2022] Open
Abstract
All cells in the human body are covered by a dense layer of sugars and the proteins and lipids to which they are attached, collectively termed the "glycocalyx." For decades, the organization of the glycocalyx and its interplay with the cellular state have remained enigmatic. This changed in recent years. Latest research has shown that the glycocalyx is an organelle of vital significance, actively involved in and functionally relevant for various cellular processes, that can be directly targeted in therapeutic contexts. This review gives a brief introduction into glycocalyx biology and describes the specific challenges glycocalyx research faces. Then, the traditional view of the role of the glycocalyx is discussed before several recent breakthroughs in glycocalyx research are surveyed. These results exemplify a currently unfolding bigger picture about the role of the glycocalyx as a fundamental cellular agent.
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Affiliation(s)
- Leonhard Möckl
- Department of Chemistry, Stanford University, Stanford, CA, United States
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167
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168
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Anthonisen M, Zhang Y, Hussain Sangji M, Grütter P. Quantifying bio-filament morphology below the diffraction limit of an optical microscope using out-of-focus images. APPLIED OPTICS 2020; 59:2914-2923. [PMID: 32225847 DOI: 10.1364/ao.388265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
A method to measure the dimensions of objects below the optical diffraction limit using diffraction analysis of out-of-focus bright-field images is presented. The method relies on the comparison of the diffraction patterns of an object of unknown size to those of calibration objects of known size. Correlative scanning electron microscope measurements are used to demonstrate the applicability of this method to measure 100 nm microbeads as well as objects with a geometry different from the calibration objects. This technique is important in the context of tethered particle experiments, in which bio-filaments are bound between a substrate and a microbead. This procedure is applied to obtain the diameters of axonal extensions or neurites that are mechanically created in samples of rat hippocampal neurons. The dependence of neurite geometry on mechanical pull speed is investigated, and the diameter is found to be rate independent.
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169
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Möckl L, Roy AR, Moerner WE. Deep learning in single-molecule microscopy: fundamentals, caveats, and recent developments [Invited]. BIOMEDICAL OPTICS EXPRESS 2020; 11:1633-1661. [PMID: 32206433 PMCID: PMC7075610 DOI: 10.1364/boe.386361] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 05/08/2023]
Abstract
Deep learning-based data analysis methods have gained considerable attention in all fields of science over the last decade. In recent years, this trend has reached the single-molecule community. In this review, we will survey significant contributions of the application of deep learning in single-molecule imaging experiments. Additionally, we will describe the historical events that led to the development of modern deep learning methods, summarize the fundamental concepts of deep learning, and highlight the importance of proper data composition for accurate, unbiased results.
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170
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Marar A, Kner P. Three-dimensional nanoscale localization of point-like objects using self-interference digital holography. OPTICS LETTERS 2020; 45:591-594. [PMID: 33116345 PMCID: PMC7590946 DOI: 10.1364/ol.379047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/18/2019] [Indexed: 06/11/2023]
Abstract
We propose localizing point-like fluorescent emitters in three dimensions with nanometer precision throughout large volumes using self-interference digital holography (SIDH). SIDH enables imaging of incoherently emitting objects over large axial ranges without refocusing, and single molecule localization techniques allow sub-50 nm resolution in the lateral and axial dimensions. We demonstrate three-dimensional localization with SIDH by imaging 100 and 40 nm fluorescent nanospheres. With 49,000 photons detected, SIDH achieves a localization precision of 5 nm laterally and 40 nm axially. We are able to detect the nanospheres from as few as 13,000 detected photons.
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171
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Hao R, Peng Z, Zhang B. Single-Molecule Fluorescence Microscopy for Probing the Electrochemical Interface. ACS OMEGA 2020; 5:89-97. [PMID: 31956755 PMCID: PMC6963970 DOI: 10.1021/acsomega.9b03763] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/10/2019] [Indexed: 05/17/2023]
Abstract
The electrochemical interface is an ultrathin interfacial region between the electrode and solution where electrochemical reactions occur. The study of the electrochemical interface continues to be one of the most exciting directions in modern electrochemistry research. Much of our existing knowledge about the electrochemical interface comes from ensemble measurements and ex situ imaging of the electrode surface. Due to its enormous complexity and highly dynamic nature, however, new imaging tools that can probe the interface in situ with ultrahigh spatial and temporal resolution and single-molecule sensitivity are apparently needed. Single-molecule fluorescence microscopy (SMFM) has emerged as a powerful tool that is uniquely suited for studying the electrochemical interface. In this mini-review, we first give a brief overview of various existing SMFM methods for studying electrochemical problems. We then discuss several exciting research topics involving the use of SMFM methods for studying surface-immobilized molecules, single freely diffusing molecules, single molecules as catalytic reaction indicators, and single-molecule labeling and imaging of interfacial nanobubbles. We anticipate that we will continue to see a rapid increase in publications on stochastic electrochemistry of single molecules and nanoparticles. The increased use of SMFM will likely bring new information to our study of the electrochemical interface.
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172
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Möckl L, Roy AR, Petrov PN, Moerner WE. Accurate and rapid background estimation in single-molecule localization microscopy using the deep neural network BGnet. Proc Natl Acad Sci U S A 2020; 117:60-67. [PMID: 31871202 PMCID: PMC6955367 DOI: 10.1073/pnas.1916219117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background fluorescence, especially when it exhibits undesired spatial features, is a primary factor for reduced image quality in optical microscopy. Structured background is particularly detrimental when analyzing single-molecule images for 3-dimensional localization microscopy or single-molecule tracking. Here, we introduce BGnet, a deep neural network with a U-net-type architecture, as a general method to rapidly estimate the background underlying the image of a point source with excellent accuracy, even when point-spread function (PSF) engineering is in use to create complex PSF shapes. We trained BGnet to extract the background from images of various PSFs and show that the identification is accurate for a wide range of different interfering background structures constructed from many spatial frequencies. Furthermore, we demonstrate that the obtained background-corrected PSF images, for both simulated and experimental data, lead to a substantial improvement in localization precision. Finally, we verify that structured background estimation with BGnet results in higher quality of superresolution reconstructions of biological structures.
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Affiliation(s)
- Leonhard Möckl
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Anish R Roy
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Petar N Petrov
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305
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173
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Fast and accurate sCMOS noise correction for fluorescence microscopy. Nat Commun 2020; 11:94. [PMID: 31901080 PMCID: PMC6941997 DOI: 10.1038/s41467-019-13841-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/29/2019] [Indexed: 12/12/2022] Open
Abstract
The rapid development of scientific CMOS (sCMOS) technology has greatly advanced optical microscopy for biomedical research with superior sensitivity, resolution, field-of-view, and frame rates. However, for sCMOS sensors, the parallel charge-voltage conversion and different responsivity at each pixel induces extra readout and pattern noise compared to charge-coupled devices (CCD) and electron-multiplying CCD (EM-CCD) sensors. This can produce artifacts, deteriorate imaging capability, and hinder quantification of fluorescent signals, thereby compromising strategies to reduce photo-damage to live samples. Here, we propose a content-adaptive algorithm for the automatic correction of sCMOS-related noise (ACsN) for fluorescence microscopy. ACsN combines camera physics and layered sparse filtering to significantly reduce the most relevant noise sources in a sCMOS sensor while preserving the fine details of the signal. The method improves the camera performance, enabling fast, low-light and quantitative optical microscopy with video-rate denoising for a broad range of imaging conditions and modalities. Scientific complementary metal-oxide semiconductor (sCMOS) cameras have advanced the imaging field, but they often suffer from additional noise compared to CCD sensors. Here the authors present a content-adaptive algorithm for the automatic correction of sCMOS-related noise for fluorescence microscopy.
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174
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Bennett HW, Gustavsson AK, Bayas CA, Petrov PN, Mooney N, Moerner WE, Jackson PK. Novel fibrillar structure in the inversin compartment of primary cilia revealed by 3D single-molecule superresolution microscopy. Mol Biol Cell 2020; 31:619-639. [PMID: 31895004 PMCID: PMC7202064 DOI: 10.1091/mbc.e19-09-0499] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Primary cilia in many cell types contain a periaxonemal subcompartment called the inversin compartment. Four proteins have been found to assemble within the inversin compartment: INVS, ANKS6, NEK8, and NPHP3. The function of the inversin compartment is unknown, but it appears to be critical for normal development, including left–right asymmetry and renal tissue homeostasis. Here we combine superresolution imaging of human RPE1 cells, a classic model for studying primary cilia in vitro, with a genetic dissection of the protein–protein binding relationships that organize compartment assembly to develop a new structural model. We observe that INVS is the core structural determinant of a compartment composed of novel fibril-like substructures, which we identify here by three-dimensional single-molecule superresolution imaging. We find that NEK8 and ANKS6 depend on INVS for localization to these fibrillar assemblies and that ANKS6-NEK8 density within the compartment is regulated by NEK8. Together, NEK8 and ANKS6 are required downstream of INVS to localize and concentrate NPHP3 within the compartment. In the absence of these upstream components, NPHP3 is redistributed within cilia. These results provide a more detailed structure for the inversin compartment and introduce a new example of a membraneless compartment organized by protein–protein interactions.
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Affiliation(s)
- Henrietta W Bennett
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - Anna-Karin Gustavsson
- Department of Chemistry, Stanford University, Stanford, CA 94305.,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm SE 17177, Sweden
| | - Camille A Bayas
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Petar N Petrov
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Nancie Mooney
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
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175
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Li M, Xi N, Wang Y, Liu L. Atomic Force Microscopy as a Powerful Multifunctional Tool for Probing the Behaviors of Single Proteins. IEEE Trans Nanobioscience 2020; 19:78-99. [DOI: 10.1109/tnb.2019.2954099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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176
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Liu W, Kuang C, Yuan Y, Zhang Z, Chen Y, Han Y, Xu L, Zhang M, Zhang YH, Xu Y, Liu X. Simultaneous Two-Angle Axial Ratiometry for Fast Live and Long-Term Three-Dimensional Super-Resolution Fluorescence Imaging. J Phys Chem Lett 2019; 10:7811-7816. [PMID: 31804831 DOI: 10.1021/acs.jpclett.9b03093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The application of optical microscopy in four-dimensional (spatial and temporal) super-resolution imaging poses challenges because of the requirement of a long acquisition time or high illumination intensity. In this paper, we introduce simultaneous two-angle axial ratiometry (STARII) for <20 nm axial super-resolution imaging and for fast and long-term imaging of live cells up to hundreds of frames per second. This method involves recording two raw images in two incident angle channels in the context of evanescent wave illumination and obtaining the corresponding intensity ratio. Furthermore, we demonstrate the combination of STARII with the lateral super-resolution method to resolve three-dimensional nanoscale structures of microtubules and to visualize the long-term dynamical plasma membrane curvature and fast remodeling of endoplasmic reticulum tubule meshwork and three-way junctions. These demonstrations indicate an important potential application of STARII in investigating nanoscale cellular complex processes in the native state.
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Affiliation(s)
- Wenjie Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering , Zhejiang University , Hangzhou , Zhejiang 310027 , China
| | - Cuifang Kuang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering , Zhejiang University , Hangzhou , Zhejiang 310027 , China
- Ningbo Research Institute , Zhejiang University , Ningbo , Zhejiang 315100 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Yifan Yuan
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering , Zhejiang University , Hangzhou , Zhejiang 310027 , China
| | - Zhimin Zhang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering , Zhejiang University , Hangzhou , Zhejiang 310027 , China
| | - Youhua Chen
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering , Zhejiang University , Hangzhou , Zhejiang 310027 , China
- Shanxi Provincial Key Laboratory for Biomedical Imaging and Big Data , North University of China , Taiyuan , Shanxi 030051 , China
| | - Yubing Han
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering , Zhejiang University , Hangzhou , Zhejiang 310027 , China
| | - Liang Xu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering , Zhejiang University , Hangzhou , Zhejiang 310027 , China
| | - Meng Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Yu-Hui Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Yingke Xu
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Xu Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering , Zhejiang University , Hangzhou , Zhejiang 310027 , China
- Ningbo Research Institute , Zhejiang University , Ningbo , Zhejiang 315100 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
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177
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Möckl L, Petrov PN, Moerner WE. Accurate phase retrieval of complex 3D point spread functions with deep residual neural networks. APPLIED PHYSICS LETTERS 2019; 115:251106. [PMID: 32127719 PMCID: PMC7043838 DOI: 10.1063/1.5125252] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/09/2019] [Indexed: 05/03/2023]
Abstract
Phase retrieval, i.e., the reconstruction of phase information from intensity information, is a central problem in many optical systems. Imaging the emission from a point source such as a single molecule is one example. Here, we demonstrate that a deep residual neural net is able to quickly and accurately extract the hidden phase for general point spread functions (PSFs) formed by Zernike-type phase modulations. Five slices of the 3D PSF at different focal positions within a two micrometer range around the focus are sufficient to retrieve the first six orders of Zernike coefficients.
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178
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Abstract
Fluorescence microscopy has long been a valuable tool for biological and medical imaging. Control of optical parameters such as the amplitude, phase, polarization and propagation angle of light gives fluorescence imaging great capabilities ranging from super-resolution imaging to long-term real-time observation of living organisms. In this review, we discuss current fluorescence imaging techniques in terms of the use of tailored or structured light for the sample illumination and fluorescence detection, providing a clear overview of their working principles and capabilities.
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Affiliation(s)
- Jialei Tang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
- These authors contributed equally to this work
| | - Jinhan Ren
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
- These authors contributed equally to this work
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
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179
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Smith SJ, Sümbül U, Graybuck LT, Collman F, Seshamani S, Gala R, Gliko O, Elabbady L, Miller JA, Bakken TE, Rossier J, Yao Z, Lein E, Zeng H, Tasic B, Hawrylycz M. Single-cell transcriptomic evidence for dense intracortical neuropeptide networks. eLife 2019; 8:47889. [PMID: 31710287 PMCID: PMC6881117 DOI: 10.7554/elife.47889] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/10/2019] [Indexed: 12/19/2022] Open
Abstract
Seeking new insights into the homeostasis, modulation and plasticity of cortical synaptic networks, we have analyzed results from a single-cell RNA-seq study of 22,439 mouse neocortical neurons. Our analysis exposes transcriptomic evidence for dozens of molecularly distinct neuropeptidergic modulatory networks that directly interconnect all cortical neurons. This evidence begins with a discovery that transcripts of one or more neuropeptide precursor (NPP) and one or more neuropeptide-selective G-protein-coupled receptor (NP-GPCR) genes are highly abundant in all, or very nearly all, cortical neurons. Individual neurons express diverse subsets of NP signaling genes from palettes encoding 18 NPPs and 29 NP-GPCRs. These 47 genes comprise 37 cognate NPP/NP-GPCR pairs, implying the likelihood of local neuropeptide signaling. Here, we use neuron-type-specific patterns of NP gene expression to offer specific, testable predictions regarding 37 peptidergic neuromodulatory networks that may play prominent roles in cortical homeostasis and plasticity.
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Affiliation(s)
| | - Uygar Sümbül
- Allen Institute for Brain Science, Seattle, United States
| | | | | | | | - Rohan Gala
- Allen Institute for Brain Science, Seattle, United States
| | - Olga Gliko
- Allen Institute for Brain Science, Seattle, United States
| | - Leila Elabbady
- Allen Institute for Brain Science, Seattle, United States
| | | | | | - Jean Rossier
- Neuroscience Paris Seine, Sorbonne Université, Paris, France
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, United States
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, United States
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, United States
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, United States
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180
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Řeháček J, Paúr M, Stoklasa B, Koutný D, Hradil Z, Sánchez-Soto LL. Intensity-Based Axial Localization at the Quantum Limit. PHYSICAL REVIEW LETTERS 2019; 123:193601. [PMID: 31765209 DOI: 10.1103/physrevlett.123.193601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Indexed: 06/10/2023]
Abstract
We derive fundamental precision bounds for single-point axial localization. For Gaussian beams, this ultimate limit can be achieved with a single intensity scan, provided the camera is placed at one of two optimal transverse detection planes. Hence, for axial localization there is no need of more complicated detection schemes. The theory is verified with an experimental demonstration of axial resolution 3 orders of magnitude below the classical depth of focus.
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Affiliation(s)
- J Řeháček
- Department of Optics, Palacký University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - M Paúr
- Department of Optics, Palacký University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - B Stoklasa
- Department of Optics, Palacký University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - D Koutný
- Department of Optics, Palacký University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Z Hradil
- Department of Optics, Palacký University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - L L Sánchez-Soto
- Departamento de Óptica, Facultad de Física, Universidad Complutense, 28040 Madrid, Spain
- Max-Planck-Institut für die Physik des Lichts, Staudtstraße 2, 91058 Erlangen, Germany
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181
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Wang C, Ballard G, Plemmons R, Prasad S. Joint 3D localization and classification of space debris using a multispectral rotating point spread function. APPLIED OPTICS 2019; 58:8598-8611. [PMID: 31873353 DOI: 10.1364/ao.58.008598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
We consider the problem of joint three-dimensional (3D) localization and material classification of unresolved space debris using a multispectral rotating point spread function (RPSF). The use of RPSF allows one to estimate the 3D locations of point sources from their rotated images acquired by a single 2D sensor array, since the amount of rotation of each source image about its x, y location depends on its axial distance z. Using multispectral images, with one RPSF per spectral band, we are able not only to localize the 3D positions of the space debris but also classify their material composition. We propose a three-stage method for achieving joint localization and classification. In stage 1, we adopt an optimization scheme for localization in which the spectral signature of each material is assumed to be uniform, which significantly improves efficiency and yields better localization results than possible with a single spectral band. In stage 2, we estimate the spectral signature and refine the localization result via an alternating approach. We process classification in the final stage. Both Poisson noise and Gaussian noise models are considered, and the implementation of each is discussed. Numerical tests using multispectral data from NASA show the efficiency of our three-stage approach and illustrate the improvement of point source localization and spectral classification from using multiple bands over a single band.
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182
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Kovari DT, Dunlap D, Weeks ER, Finzi L. Model-free 3D localization with precision estimates for brightfield-imaged particles. OPTICS EXPRESS 2019; 27:29875-29895. [PMID: 31684243 PMCID: PMC6825595 DOI: 10.1364/oe.27.029875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/28/2019] [Accepted: 06/29/2019] [Indexed: 06/10/2023]
Abstract
Volumetric imaging and 3D particle tracking are becoming increasingly common and have a variety of microscopy applications including in situ fluorescent imaging, in-vitro single-molecule characterization, and analysis of colloidal systems. While recent interest has generated discussion of optimal schemes for localizing diffraction-limited fluorescent puncta, there have been relatively few published routines for tracking particles imaged with bright-field illumination. To address this, we outline a simple, look-up-table based 3D tracking strategy, which can be adapted to most commercially available wide-field microscopes, and present two image processing algorithms that together yield high-precision localization and return estimates of statistical accuracy. Under bright-field illumination, a particle's depth can be determined based on the size and shape of its diffractive pattern due to Mie scattering. Contrary to typical "super-resolution" fluorescence tracking routines, which typically fit a diffraction-limited spot to a model point-spread-function, the lateral (XY) tracking routine relies on symmetry to locate a particle without prior knowledge of the form of the particle. At low noise levels (signal:noise > 1000), the symmetry routine estimates particle positions with accuracy better than 0.01 pixel. Depth localization is accomplished by matching images of particles to those in a pre-recorded look-up-table. The routine presented here optimally interpolates between LUT entries with better than 0.05 step accuracy. Both routines are tolerant of high levels of image noise, yielding sub-pixel/step accuracy with signal-to-noise ratios as small as 1, and, by design, return confidence intervals indicating the expected accuracy of each calculated position. The included implementations operate extremely quickly and are amenable to real-time analysis at frame rates exceeding several hundred frames per second.
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183
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Wang X, Yi H, Gdor I, Hereld M, Scherer NF. Nanoscale Resolution 3D Snapshot Particle Tracking by Multifocal Microscopy. NANO LETTERS 2019; 19:6781-6787. [PMID: 31490694 DOI: 10.1021/acs.nanolett.9b01734] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Accurate, precise, and rapid particle tracking in three dimensions remains a challenge; yet, its achievement will significantly enhance our understanding of living systems. We developed a multifocal microscopy (MFM) that allows snapshot acquisition of the imaging data, and an associated image processing approach, that together allow simultaneous 3D tracking of many fluorescent particles with nanoscale resolution. The 3D tracking was validated by measuring a known trajectory of a fluorescent bead with an axial accuracy of 19 nm through an image depth (axial range) of 3 μm and 4 nm precision of axial localization through an image depth of 4 μm. A second test obtained a uniform axial probability distribution and Brownian dynamics of beads diffusing in solution. We also validated the MFM approach by imaging fluorescent beads immobilized in gels and comparing the 3D localizations to their "ground truth" positions obtained from a confocal microscopy z-stack of finely spaced images. Finally, we applied our MFM and image processing approach to obtain 3D trajectories of insulin granules in pseudoislets of MIN6 cells to demonstrate its compatibility with complex biological systems. Our study demonstrates that multifocal microscopy allows rapid (video rate) and simultaneous 3D tracking of many "particles" with nanoscale accuracy and precision in a wide range of systems, including over spatial scales relevant to whole live cells.
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Affiliation(s)
- Xiaolei Wang
- James Franck Institute , University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States
| | - Hannah Yi
- Department of Chemistry , University of Chicago , 5801 South Ellis Avenue , Chicago , Illinois 60637 , United States
| | - Itay Gdor
- James Franck Institute , University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States
| | - Mark Hereld
- Mathematics and Computer Science Division , Argonne National Laboratory , 9700 South Cass Avenue , Lemont , Illinois 60439 , United States
| | - Norbert F Scherer
- James Franck Institute , University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States
- Department of Chemistry , University of Chicago , 5801 South Ellis Avenue , Chicago , Illinois 60637 , United States
- Institute for Biophysical Dynamics , University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States
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184
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Choi J, Grosely R, Puglisi EV, Puglisi JD. Expanding single-molecule fluorescence spectroscopy to capture complexity in biology. Curr Opin Struct Biol 2019; 58:233-240. [PMID: 31213390 PMCID: PMC6778503 DOI: 10.1016/j.sbi.2019.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/03/2019] [Accepted: 05/08/2019] [Indexed: 11/16/2022]
Abstract
Fundamental biological processes are driven by diverse molecular machineries. In recent years, single-molecule fluorescence spectroscopy has matured as a unique tool in biology to study how structural dynamics of molecular complexes drive various biochemical reactions. In this review, we highlight underlying developments in single-molecule fluorescence methods that enable deep biological investigations. Recent progress in these methods points toward increasing complexity of measurements to capture biological processes in a living cell, where multiple processes often occur simultaneously and are mechanistically coupled.
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Affiliation(s)
- Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305-4090, USA
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Elisabetta V Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
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185
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Gardini L, Arbore C, Capitanio M, Pavone FS. A protocol for single molecule imaging and tracking of processive myosin motors. MethodsX 2019; 6:1854-1862. [PMID: 31508322 PMCID: PMC6726715 DOI: 10.1016/j.mex.2019.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 08/13/2019] [Indexed: 10/31/2022] Open
Abstract
Myosin is a large family of actin-based molecular motors, which includes efficient intracellular transporters that move cargoes and material essential for cell's life. Here, we describe protocols for labelling single myosin motors with quantum dots, tracking them in an in vitro reconstituted single-molecule motility assay, acquiring image stacks and analyzing them. We describe the required steps to obtain trajectories of single myosin motors from which fundamental biophysical parameters such as the motor velocity, run length and step size can be derived. We also describe protocols for an ensemble actin gliding assay, which is valuable to test the motor viability and its ensemble properties. The protocols allow probing the effect of changes in nucleotides, ions, and buffer composition on the motor properties and are easily generalizable to track the movements of different motor proteins.
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Affiliation(s)
- Lucia Gardini
- LENS - European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019, Sesto Fiorentino, Italy.,National Institute of Optics-National Research Council, Largo Fermi 6, 50125, Florence, Italy
| | - Claudia Arbore
- LENS - European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019, Sesto Fiorentino, Italy
| | - Marco Capitanio
- LENS - European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019, Sesto Fiorentino, Italy.,Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019, Sesto Fiorentino, Italy
| | - Francesco Saverio Pavone
- LENS - European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019, Sesto Fiorentino, Italy.,National Institute of Optics-National Research Council, Largo Fermi 6, 50125, Florence, Italy.,Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019, Sesto Fiorentino, Italy
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186
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Real-Time 3D Single Particle Tracking: Towards Active Feedback Single Molecule Spectroscopy in Live Cells. Molecules 2019; 24:molecules24152826. [PMID: 31382495 PMCID: PMC6695621 DOI: 10.3390/molecules24152826] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/27/2019] [Accepted: 08/01/2019] [Indexed: 01/25/2023] Open
Abstract
Single molecule fluorescence spectroscopy has been largely implemented using methods which require tethering of molecules to a substrate in order to make high temporal resolution measurements. However, the act of tethering a molecule requires that the molecule be removed from its environment. This is especially perturbative when measuring biomolecules such as enzymes, which may rely on the non-equilibrium and crowded cellular environment for normal function. A method which may be able to un-tether single molecule fluorescence spectroscopy is real-time 3D single particle tracking (RT-3D-SPT). RT-3D-SPT uses active feedback to effectively lock-on to freely diffusing particles so they can be measured continuously with up to photon-limited temporal resolution over large axial ranges. This review gives an overview of the various active feedback 3D single particle tracking methods, highlighting specialized detection and excitation schemes which enable high-speed real-time tracking. Furthermore, the combination of these active feedback methods with simultaneous live-cell imaging is discussed. Finally, the successes in real-time 3D single molecule tracking (RT-3D-SMT) thus far and the roadmap going forward for this promising family of techniques are discussed.
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187
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Kazemipour A, Novak O, Flickinger D, Marvin JS, Abdelfattah AS, King J, Borden PM, Kim JJ, Al-Abdullatif SH, Deal PE, Miller EW, Schreiter ER, Druckmann S, Svoboda K, Looger LL, Podgorski K. Kilohertz frame-rate two-photon tomography. Nat Methods 2019; 16:778-786. [PMID: 31363222 PMCID: PMC6754705 DOI: 10.1038/s41592-019-0493-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/14/2019] [Indexed: 11/25/2022]
Abstract
Point-scanning two-photon microscopy enables high-resolution imaging within scattering specimens such as the mammalian brain, but sequential acquisition of voxels fundamentally limits its speed. We developed a two-photon imaging technique that scans lines of excitation across a focal plane at multiple angles and computationally recovers high-resolution images, attaining voxel rates of over 1 billion Hz in structured samples. Using a static image as a prior for recording neural activity, we imaged visually evoked and spontaneous glutamate release across hundreds of dendritic spines in mice at depths over 250 µm and frame rates over 1 kHz. Dendritic glutamate transients in anesthetized mice are synchronized within spatially contiguous domains spanning tens of micrometers at frequencies ranging from 1-100 Hz. We demonstrate millisecond-resolved recordings of acetylcholine and voltage indicators, three-dimensional single-particle tracking and imaging in densely labeled cortex. Our method surpasses limits on the speed of raster-scanned imaging imposed by fluorescence lifetime.
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Affiliation(s)
- Abbas Kazemipour
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Ondrej Novak
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Second Medical Faculty, Charles University, Prague, Czech Republic
| | - Daniel Flickinger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jonathan S Marvin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | | | - Philip M Borden
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jeong Jun Kim
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Parker E Deal
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Evan W Miller
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Eric R Schreiter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Shaul Druckmann
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Kaspar Podgorski
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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188
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Belkahla H, Boudjemaa R, Caorsi V, Pineau D, Curcio A, Lomas JS, Decorse P, Chevillot-Biraud A, Azaïs T, Wilhelm C, Randriamahazaka H, Hémadi M. Carbon dots, a powerful non-toxic support for bioimaging by fluorescence nanoscopy and eradication of bacteria by photothermia. NANOSCALE ADVANCES 2019; 1:2571-2579. [PMID: 36132715 PMCID: PMC9418816 DOI: 10.1039/c9na00140a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/17/2019] [Indexed: 05/02/2023]
Abstract
Carbon Dots (CDs) are innovative materials which have potential applications in many fields, including nanomedicine, energy and catalysis. Here CDs were produced by the alkali-assisted ultrasonic route and characterized by several techniques to determine their composition and properties. Fluorescence nanoscopy using single-molecule localization microscopy shows that they have very good photophysical properties and a remarkable blinking behaviour at 405 nm. Moreover, these CDs are a safe material, non-toxic towards different cell lines (cancer and non-cancer cells) even at very high concentration, reflecting an excellent biocompatibility. Photothermia, i.e. their heating capacity under laser irradiation, was evaluated at two wavelengths and at several power densities. The resulting temperature increment was high (5 < ΔT < 45 °C) and appropriate for biomedical applications. Bioimaging and photothermia were then performed on E. coli, a Gram(-) bacterium, incubated with CDs. Remarkably, by photothermia at 680 nm (0.3, 1 and 1.9 W cm-2) or 808 nm (1.9 W cm-2), CDs are able to eradicate bacteria in their exponential and stationary phases. Images obtained by 3D super-resolution microscopy clearly show the different CD distributions in surviving bacteria after mild photothermal treatment. These results confirm that CDs are multifunctional materials with a wide range of biomedical applications.
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Affiliation(s)
- H Belkahla
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - R Boudjemaa
- Abbelight 6 rue Jean Calvin 75005 Paris France
| | - V Caorsi
- Abbelight 6 rue Jean Calvin 75005 Paris France
| | - D Pineau
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - A Curcio
- Laboratoire Matières et Systèmes Complexes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7057, 10 rue Alice Domon et Léonie Duquet 75205 Paris Cedex 13 France
| | - J S Lomas
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - P Decorse
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - A Chevillot-Biraud
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - T Azaïs
- Laboratoire de Chimie de la Matière Condensée de Paris, Sorbonne Université, CNRS-UMR 7574, Collège de France 4 place Jussieu 75005 Paris France
| | - C Wilhelm
- Laboratoire Matières et Systèmes Complexes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7057, 10 rue Alice Domon et Léonie Duquet 75205 Paris Cedex 13 France
| | - H Randriamahazaka
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - M Hémadi
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
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189
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Mao X, Liu C, Hesari M, Zou N, Chen P. Super-resolution imaging of non-fluorescent reactions via competition. Nat Chem 2019; 11:687-694. [DOI: 10.1038/s41557-019-0288-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 05/31/2019] [Indexed: 11/09/2022]
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190
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Topologically-guided continuous protein crystallization controls bacterial surface layer self-assembly. Nat Commun 2019; 10:2731. [PMID: 31227690 PMCID: PMC6588578 DOI: 10.1038/s41467-019-10650-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/16/2019] [Indexed: 12/22/2022] Open
Abstract
Many bacteria and most archaea possess a crystalline protein surface layer (S-layer), which surrounds their growing and topologically complicated outer surface. Constructing a macromolecular structure of this scale generally requires localized enzymatic machinery, but a regulatory framework for S-layer assembly has not been identified. By labeling, superresolution imaging, and tracking the S-layer protein (SLP) from C. crescentus, we show that 2D protein self-assembly is sufficient to build and maintain the S-layer in living cells by efficient protein crystal nucleation and growth. We propose a model supported by single-molecule tracking whereby randomly secreted SLP monomers diffuse on the lipopolysaccharide (LPS) outer membrane until incorporated at the edges of growing 2D S-layer crystals. Surface topology creates crystal defects and boundaries, thereby guiding S-layer assembly. Unsupervised assembly poses challenges for therapeutics targeting S-layers. However, protein crystallization as an evolutionary driver rationalizes S-layer diversity and raises the potential for biologically inspired self-assembling macromolecular nanomaterials. Bacteria assemble the surface layer (S-layer), a crystalline protein coat surrounding the curved surface, using protein self-assembly. Here authors image native and purified RsaA, the S-layer protein from C. crescentus, and show that protein crystallization alone is sufficient to assemble and maintain the S-layer in vivo.
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191
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Chasing Uptake: Super-Resolution Microscopy in Endocytosis and Phagocytosis. Trends Cell Biol 2019; 29:727-739. [PMID: 31227311 DOI: 10.1016/j.tcb.2019.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/14/2019] [Accepted: 05/23/2019] [Indexed: 11/21/2022]
Abstract
Since their invention about two decades ago, super-resolution microscopes have become a method of choice in cell biology. Owing to a spatial resolution below 50 nm, smaller than the size of most organelles, and an order of magnitude better than the diffraction limit of conventional light microscopes, super-resolution microscopy is a powerful technique for resolving intracellular trafficking. In this review we discuss discoveries in endocytosis and phagocytosis that have been made possible by super-resolution microscopy - from uptake at the plasma membrane, endocytic coat formation, and cytoskeletal rearrangements to endosomal maturation. The detailed visualization of the diverse molecular assemblies that mediate endocytic uptake will provide a better understanding of how cells ingest extracellular material.
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192
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Pan Q, Zhao H, Lin X, He Y. Spatiotemporal Heterogeneity of Reactions in Solution Observed with High‐Speed Single‐Nanorod Rotational Sensing. Angew Chem Int Ed Engl 2019; 58:8389-8393. [DOI: 10.1002/anie.201901550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Qi Pan
- Department of ChemistryKey Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)Tsinghua University Beijing 100084 China
| | - Hansen Zhao
- Department of ChemistryKey Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)Tsinghua University Beijing 100084 China
| | - Xijian Lin
- Department of ChemistryKey Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)Tsinghua University Beijing 100084 China
| | - Yan He
- Department of ChemistryKey Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)Tsinghua University Beijing 100084 China
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193
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Gardini L, Arbore C, Pavone FS, Capitanio M. Myosin V fluorescence imaging dataset for single-molecule localization and tracking. Data Brief 2019; 25:103973. [PMID: 31194150 PMCID: PMC6552026 DOI: 10.1016/j.dib.2019.103973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/18/2019] [Accepted: 04/26/2019] [Indexed: 11/11/2022] Open
Abstract
Myosin-5B is one of three members of the myosin-5 family of actin-based molecular motors fundamental in recycling endosome trafficking and collective actin network dynamics. Through single-molecule motility assays, we recently demonstrated that myosin-5B can proceed in 36-nm steps along actin filaments as single motor. By analyzing trajectories of single myosin-5B along actin filaments we showed that its velocity is dependent on ATP concentration, while its run length is independent on ATP concentration, as a landmark of processivity. Here, we share image stacks acquired under total internal reflection fluorescence (TIRF) microscopy and representative trajectories of single myosin-5B molecules labelled with Quantum Dots (QD-myo-5B) moving along actin filaments at different ATP concentrations (0.3–1000 μM). Localization of QD-myo-5B was performed with the PROOF software, which is freely available [1]. The data can be valuable for researchers interested in molecular motors motility, both from an experimental and modeling point of view, as well as to researchers developing single particle tracking algorithms. The data is related to the research article “Dissecting myosin-5B mechanosensitivity and calcium regulation at the single molecule level” Gardini et al., 2015.
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Affiliation(s)
- Lucia Gardini
- LENS - European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy.,National Institute of Optics-National Research Council, Largo Fermi 6, 50125 Florence, Italy
| | - Claudia Arbore
- LENS - European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Francesco Saverio Pavone
- LENS - European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy.,National Institute of Optics-National Research Council, Largo Fermi 6, 50125 Florence, Italy.,Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Italy
| | - Marco Capitanio
- LENS - European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy.,Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Italy
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194
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Extended-Depth 3D Super-Resolution Imaging Using Probe-Refresh STORM. Biophys J 2019; 114:1980-1987. [PMID: 29694874 DOI: 10.1016/j.bpj.2018.03.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/17/2018] [Accepted: 03/20/2018] [Indexed: 12/14/2022] Open
Abstract
Single-molecule localization microscopy methods for super-resolution fluorescence microscopy such as STORM (stochastic optical reconstruction microscopy) are generally limited to thin three-dimensional (3D) sections (≤600 nm) because of photobleaching of molecules outside the focal plane. Although multiple focal planes may be imaged before photobleaching by focusing progressively deeper within the sample, image quality is compromised in this approach because the total number of measurable localizations is divided between detection planes. Here, we solve this problem on fixed samples by developing an imaging method that we call probe-refresh STORM (prSTORM), which allows bleached fluorophores to be straightforwardly replaced with nonbleached fluorophores. We accomplish this by immunostaining the sample with DNA-conjugated antibodies and then reading out their distribution using fluorescently-labeled DNA-reporter oligonucleotides that can be fully replaced in successive rounds of imaging. We demonstrate that prSTORM can acquire 3D images over extended depths without sacrificing the density of localizations at any given plane. We also show that prSTORM can be adapted to obtain high-quality, 3D multichannel images with extended depth that would be challenging or impossible to achieve using established probe methods.
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195
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Li Y, Wu YL, Hoess P, Mund M, Ries J. Depth-dependent PSF calibration and aberration correction for 3D single-molecule localization. BIOMEDICAL OPTICS EXPRESS 2019; 10:2708-2718. [PMID: 31259045 PMCID: PMC6583355 DOI: 10.1364/boe.10.002708] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/02/2019] [Accepted: 04/09/2019] [Indexed: 05/22/2023]
Abstract
Three-dimensional single molecule localization microscopy relies on the fitting of the individual molecules with a point spread function (PSF) model. The reconstructed images often show local squeezing or expansion in z. A common cause is depth-induced aberrations in conjunction with an imperfect PSF model calibrated from beads on a coverslip, resulting in a mismatch between measured PSF and real PSF. Here, we developed a strategy for accurate z-localization in which we use the imperfect PSF model for fitting, determine the fitting errors and correct for them in a post-processing step. We present an open-source software tool and a simple experimental calibration procedure that allow retrieving accurate z-positions in any PSF engineering approach or fitting modality, even at large imaging depths.
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Affiliation(s)
- Yiming Li
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Yu-Le Wu
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Philipp Hoess
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Markus Mund
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
- Current affiliation: Department of Biochemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Jonas Ries
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
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196
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Pan Q, Zhao H, Lin X, He Y. Spatiotemporal Heterogeneity of Reactions in Solution Observed with High‐Speed Single‐Nanorod Rotational Sensing. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Qi Pan
- Department of ChemistryKey Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)Tsinghua University Beijing 100084 China
| | - Hansen Zhao
- Department of ChemistryKey Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)Tsinghua University Beijing 100084 China
| | - Xijian Lin
- Department of ChemistryKey Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)Tsinghua University Beijing 100084 China
| | - Yan He
- Department of ChemistryKey Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)Tsinghua University Beijing 100084 China
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197
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Liu S, Mlodzianoski MJ, Hu Z, Ren Y, McElmurry K, Suter DM, Huang F. sCMOS noise-correction algorithm for microscopy images. Nat Methods 2019; 14:760-761. [PMID: 28753600 DOI: 10.1038/nmeth.4379] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sheng Liu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Michael J Mlodzianoski
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Zhenhua Hu
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Yuan Ren
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Kristi McElmurry
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Daniel M Suter
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana, USA.,Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, USA.,Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana, USA
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA.,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana, USA.,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA
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198
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Qi Q, Chi W, Li Y, Qiao Q, Chen J, Miao L, Zhang Y, Li J, Ji W, Xu T, Liu X, Yoon J, Xu Z. A H-bond strategy to develop acid-resistant photoswitchable rhodamine spirolactams for super-resolution single-molecule localization microscopy. Chem Sci 2019; 10:4914-4922. [PMID: 31160962 PMCID: PMC6510312 DOI: 10.1039/c9sc01284b] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/04/2019] [Indexed: 01/04/2023] Open
Abstract
Rhodamine spirolactam based photoswitches have been extensively applied in super-resolution single-molecule localization microscopy (SMLM). However, the ring-opening reactions of spirolactams are cross-sensitive to acid, limiting their photoswitch use to neutral pH conditions. In addition, the ring-closing reactions of spirolactams are environment-sensitive and slow (up to hours), virtually making rhodamine spirolactams caged fluorescent dyes instead of reversible photoswitches in SMLM. Herein, by introducing hydrogen bonds to stabilize spirolactams, we report a series of acid-resistant rhodamine spirolactams with accelerated ring-closing reactions from fluorescent xanthyliums to non-fluorescent spirolactams, endowing them with good photoswitchable properties even in acidic environments. By further substitution of 6-phenylethynyl naphthalimide on the spirolactam, we shifted the photoactivation wavelength into the visible region (>400 nm). Subsequently, we have successfully applied these dyes in labeling and imaging the cell surface of Bacillus subtilis at pH 4.5 using SMLM.
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Affiliation(s)
- Qingkai Qi
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China .
| | - Weijie Chi
- Singapore University of Technology and Design , 8 Somapah Road , Singapore 487372 , Singapore .
| | - Yuanyuan Li
- National Laboratory of Biomacromolecules , Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China .
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China .
| | - Jie Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China .
| | - Lu Miao
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China .
| | - Yi Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China .
| | - Jin Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China .
| | - Wei Ji
- National Laboratory of Biomacromolecules , Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China .
| | - Tao Xu
- National Laboratory of Biomacromolecules , Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China .
| | - Xiaogang Liu
- Singapore University of Technology and Design , 8 Somapah Road , Singapore 487372 , Singapore .
| | - Juyoung Yoon
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 120-750 , Korea .
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China .
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199
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Yokota H. Fluorescence microscopy for visualizing single-molecule protein dynamics. Biochim Biophys Acta Gen Subj 2019; 1864:129362. [PMID: 31078674 DOI: 10.1016/j.bbagen.2019.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/26/2019] [Accepted: 05/07/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND Single-molecule fluorescence imaging (smFI) has evolved into a valuable method used in biophysical and biochemical studies as it can observe the real-time behavior of individual protein molecules, enabling understanding of their detailed dynamic features. smFI is also closely related to other state-of-the-art microscopic methods, optics, and nanomaterials in that smFI and these technologies have developed synergistically. SCOPE OF REVIEW This paper provides an overview of the recently developed single-molecule fluorescence microscopy methods, focusing on critical techniques employed in higher-precision measurements in vitro and fluorescent nanodiamond, an emerging promising fluorophore that will improve single-molecule fluorescence microscopy. MAJOR CONCLUSIONS smFI will continue to improve regarding the photostability of fluorophores and will develop via combination with other techniques based on nanofabrication, single-molecule manipulation, and so on. GENERAL SIGNIFICANCE Quantitative, high-resolution single-molecule studies will help establish an understanding of protein dynamics and complex biomolecular systems.
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Affiliation(s)
- Hiroaki Yokota
- Biophotonics Laboratory, Graduate School for the Creation of New Photonics Industries, Kurematsu-cho, Nishi-ku, Hamamatsu, Shizuoka 431-1202, Japan.
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200
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Qiu K, Fato TP, Yuan B, Long YT. Toward Precision Measurement and Manipulation of Single-Molecule Reactions by a Confined Space. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805426. [PMID: 30924293 DOI: 10.1002/smll.201805426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/28/2019] [Indexed: 06/09/2023]
Abstract
All chemical reactions can be divided into a series of single molecule reactions (SMRs), the elementary steps that involve only isomerization of, dissociation from, and addition to an individual molecule. Analyzing SMRs is of paramount importance to identify the intrinsic molecular mechanism of a complex chemical reaction, which is otherwise implausible to reveal in an ensemble fashion, owing to the significant static and dynamic heterogeneity of real-world chemical systems. The single-molecule measurement and manipulation methods developed recently are playing an increasingly irreplaceable role to detect and recognize short-lived intermediates, visualize their transient existence, and determinate the kinetics and dynamics of single bond breaking and formation. Notably, none of the above SMRs characterizations can be realized without the aid of a confined space. Therefore, this Review aims to highlight the recent progress in the development of confined space enabled single-molecule sensing, imaging, and tuning methods to study chemical reactions. Future prospects of SMRs research are also included, including a push toward the physical limit on transduction of information to signals and vice versa, transmission and recording of signals, computational modeling and simulation, and rational design of a confined space for precise SMRs.
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Affiliation(s)
- Kaipei Qiu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Tano Patrice Fato
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Bo Yuan
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yi-Tao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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