201
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Kim T, Moon S, Xu K. Information-rich localization microscopy through machine learning. Nat Commun 2019; 10:1996. [PMID: 31040287 PMCID: PMC6491467 DOI: 10.1038/s41467-019-10036-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 04/11/2019] [Indexed: 02/07/2023] Open
Abstract
Recent years have witnessed the development of single-molecule localization microscopy as a generic tool for sampling diverse biologically relevant information at the super-resolution level. While current approaches often rely on the target-specific alteration of the point spread function to encode the multidimensional contents of single fluorophores, the details of the point spread function in an unmodified microscope already contain rich information. Here we introduce a data-driven approach in which artificial neural networks are trained to make a direct link between an experimental point spread function image and its underlying, multidimensional parameters, and compare results with alternative approaches based on maximum likelihood estimation. To demonstrate this concept in real systems, we decipher in fixed cells both the colors and the axial positions of single molecules in regular localization microscopy data.
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Affiliation(s)
- Taehwan Kim
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, 94720, USA
| | - Seonah Moon
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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202
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Abstract
Light microscopy has played a central role in science for the past couple of hundred years and will continue to do so. Multiple super-resolution microscopy techniques have been in the headlines for smashing what for more than 100+ years was believed to be the limits of optical microscopy. This resolution improvement enables the visualization of molecular structures and processes on the nano scale. While certain scientific questions in toxicology can benefit from modalities within the super-resolution suite, due diligence is required for efficiency and to achieve optimal results. For a given hypothesis being tested, there are biophysical issues that need to be considered before heading down the super-resolution road. All commercially available super-resolution modalities, along with cautions and tips, will be discussed. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Richard Cole
- Wadsworth Center, New York State Department of Health, Albany, New York.,Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, New York
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203
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Lin HY, Chu LA, Yang H, Hsu KJ, Lin YY, Lin KH, Chu SW, Chiang AS. Imaging through the Whole Brain of Drosophila at λ/20 Super-resolution. iScience 2019; 14:164-170. [PMID: 30978667 PMCID: PMC6460254 DOI: 10.1016/j.isci.2019.03.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/27/2019] [Accepted: 03/19/2019] [Indexed: 11/26/2022] Open
Abstract
Recently, many super-resolution technologies have been demonstrated, significantly affecting biological studies by observation of cellular structures down to nanometer precision. However, current super-resolution techniques mostly rely on wavefront engineering or wide-field imaging of signal blinking or fluctuation, and thus imaging depths are limited due to tissue scattering or aberration. Here we present a technique that is capable of imaging through an intact Drosophila brain with 20-nm lateral resolution at ∼200 μm depth. The spatial resolution is provided by molecular localization of a photoconvertible fluorescent protein Kaede, whose red form is found to exhibit blinking state. The deep-tissue observation is enabled by optical sectioning of spinning disk microscopy, as well as reduced scattering from optical clearing. Together these techniques are readily available for many biologists, providing three-dimensional resolution of densely entangled dendritic fibers in a complete Drosophila brain. The method paves the way toward whole-brain neural network studies and is applicable to other high-resolution bioimaging.
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Affiliation(s)
- Han-Yuan Lin
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Li-An Chu
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan; Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Hsuan Yang
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Kuo-Jen Hsu
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan; Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yen-Yin Lin
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Keng-Hui Lin
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan.
| | - Shi-Wei Chu
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan; Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan.
| | - Ann-Shyn Chiang
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan; Institute of Physics, Academia Sinica, Taipei 11529, Taiwan; Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu 30013, Taiwan; Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA 92093-0526, USA.
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204
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Croop B, Han KY. Facile single-molecule pull-down assay for analysis of endogenous proteins. Phys Biol 2019; 16:035002. [PMID: 30769341 DOI: 10.1088/1478-3975/ab0792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The single-molecule pull-down (SiMPull) assay analyzes molecular complexes in physiological conditions from cell or tissue lysates. Currently the approach requires a lengthy sample preparation process, which has largely prevented the widespread adoption of this technique in bioanalysis. Here, we present a simplified SiMPull assay based upon dichlorodimethylsilane-Tween-20 passivation and F(ab) fragment labeling. Our passivation is a much shorter process than the standard polyethylene glycol passivation used in most single-molecule studies. The use of F(ab) fragments for indirect fluorescent labeling rather than divalent F(ab')2 or whole IgG antibodies allows for the pre-incubation of the detection antibodies, reducing the sample preparation time for single-molecule immunoprecipitation samples. We examine the applicability of our approach to recombinant proteins and endogenous proteins from mammalian cell lysates.
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Affiliation(s)
- Benjamin Croop
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, FL, United States of America
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205
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Two-Dimensional and Three-Dimensional Single Particle Tracking of Upconverting Nanoparticles in Living Cells. Int J Mol Sci 2019; 20:ijms20061424. [PMID: 30901823 PMCID: PMC6471022 DOI: 10.3390/ijms20061424] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/10/2019] [Accepted: 03/19/2019] [Indexed: 01/10/2023] Open
Abstract
Lanthanide-doped upconversion nanoparticles (UCNPs) are inorganic nanomaterials in which the lanthanide cations embedded in the host matrix can convert incident near-infrared light to visible or ultraviolet light. These particles are often used for long-term and real-time imaging because they are extremely stable even when subjected to continuous irradiation for a long time. It is now possible to image their movement at the single particle level with a scale of a few nanometers and track their trajectories as a function of time with a scale of a few microseconds. Such UCNP-based single-particle tracking (SPT) technology provides information about the intracellular structures and dynamics in living cells. Thus far, most imaging techniques have been built on fluorescence microscopic techniques (epifluorescence, total internal reflection, etc.). However, two-dimensional (2D) images obtained using these techniques are limited in only being able to visualize those on the focal planes of the objective lens. On the contrary, if three-dimensional (3D) structures and dynamics are known, deeper insights into the biology of the thick cells and tissues can be obtained. In this review, we introduce the status of the fluorescence imaging techniques, discuss the mathematical description of SPT, and outline the past few studies using UCNPs as imaging probes or biologically functionalized carriers.
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206
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Zhang Y, Song KH, Dong B, Davis JL, Shao G, Sun C, Zhang HF. Multicolor super-resolution imaging using spectroscopic single-molecule localization microscopy with optimal spectral dispersion. APPLIED OPTICS 2019; 58:2248-2255. [PMID: 31044927 PMCID: PMC6620783 DOI: 10.1364/ao.58.002248] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We developed transmission diffraction grating-based spectroscopic single-molecule localization microscopy (sSMLM) to collect the spatial and spectral information of single-molecule blinking events concurrently. We characterized the spectral heterogeneities of multiple far-red emitting dyes in a high-throughput manner using sSMLM. We also investigated the influence of spectral dispersion on the single-molecule identification performance of fluorophores with large spectral overlapping. The careful tuning of spectral dispersion in grating-based sSMLM permitted simultaneous three-color super-resolution imaging in fixed cells with a single objective lens at a relatively low photon budget. Our sSMLM has a compact optical design and can be integrated with conventional localization microscopy to provide add-on spectroscopic analysis capability.
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Affiliation(s)
- Yang Zhang
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208 USA
- These authors contributed equally to this work
| | - Ki-Hee Song
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208 USA
- These authors contributed equally to this work
| | - Biqin Dong
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208 USA
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208 USA
| | - Janel l. Davis
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208 USA
| | - Guangbin Shao
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208 USA
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208 USA
| | - Hao F. Zhang
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208 USA
- corresponding author:
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207
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Liu W, Liu Q, Zhang Z, Han Y, Kuang C, Xu L, Yang H, Liu X. Three-dimensional super-resolution imaging of live whole cells using galvanometer-based structured illumination microscopy. OPTICS EXPRESS 2019; 27:7237-7248. [PMID: 30876291 DOI: 10.1364/oe.27.007237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Imaging and tracking three-dimensional (3D) nanoscale organizations and functions of live cells is essential for biological research but it remains challenging. Among different 3D super-resolution techniques, 3D structured illumination microscopy (SIM) has the intrinsic advantages for live-cell studies; it is based on wide-field imaging and does not require high light intensities or special fluorescent dyes to double 3D resolution. However, the 3D SIM system has developed relatively slowly, especially in live imaging. Here, we report a more flexible 3D SIM system based on two galvanometer sets conveniently controlling the structured illumination pattern's period and orientation, which is able to study dynamics of live whole cells with high speed. We demonstrate our microscope's capabilities with strong optical sectioning and lateral, axial, and volume temporal resolution of 104 nm, 320 nm and 4 s, respectively. We do this by imaging nanoparticle and microtubule organizations and mitochondria evolution. These characteristics enable our galvanometer-based 3D SIM system to broaden the accessible imaging content of SIM-family microscopes and further facilitate their applications in life sciences.
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208
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209
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Wang W, Ye F, Shen H, Moringo NA, Dutta C, Robinson JT, Landes CF. Generalized method to design phase masks for 3D super-resolution microscopy. OPTICS EXPRESS 2019; 27:3799-3816. [PMID: 30732394 DOI: 10.1364/oe.27.003799] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/20/2019] [Indexed: 05/20/2023]
Abstract
Point spread function (PSF) engineering by phase modulation is a novel approach to three-dimensional (3D) super-resolution microscopy, with different point spread functions being proposed for specific applications. It is often not easy to achieve the desired shape of engineered point spread functions because it is challenging to determine the correct phase mask. Additionally, a phase mask can either encode 3D space information or additional time information, but not both simultaneously. A robust algorithm for recovering a phase mask to generate arbitrary point spread functions is needed. In this work, a generalized phase mask design method is introduced by performing an optimization. A stochastic gradient descent algorithm and a Gauss-Newton algorithm are developed and compared for their ability to recover the phase masks for previously reported point spread functions. The new Gauss-Newton algorithm converges to a minimum at much higher speeds. This algorithm is used to design a novel stretching-lobe phase mask to encode temporal and 3D spatial information simultaneously. The stretching-lobe phase mask and other masks are fabricated in-house for proof-of-concept using multi-level light lithography and an optimized commercially sourced stretching-lobe phase mask (PM) is validated experimentally to encode 3D spatial and temporal information. The algorithms' generalizability is further demonstrated by generating a phase mask that comprises four different letters at different depths.
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210
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Yang J, Li BQ, Li R, Mei X. Quantum 3D thermal imaging at the micro-nanoscale. NANOSCALE 2019; 11:2249-2263. [PMID: 30656329 DOI: 10.1039/c8nr09096c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Real-time and accurate measurement of three-dimensional (3D) temperature field gradient maps of cells and tissues would provide an effective experimental method for analyzing the coupled correlation between metabolism and heat, as well as exploring the thermodynamic properties of nanoparticles under complex environments. In this work, a new principle of quantum 3D thermal imaging is proposed. The photoluminescence principle of quantum dots is expounded and CdTe QDs are prepared by aqueous phase synthesis. Fluorescence spectral characteristics of QDs at different temperatures are studied. The optimized algorithm of the optical spot double helix point spread function is proposed to improve the imaging, where optimized light energy increased by 27.36%. The design scheme of a quantum 3D thermal imaging system is presented. The measurement range is (-8 mm, +8 mm). The temperature is calculated according to the temperature-heat curve of quantum dots. The double helix point spread function has converted the defocus distance of QDs into the rotation angle of the double optical spot, thereby determining its position. The experimental results reveal that real-time 3D tracking and temperature measurements of quantum dots at the micro-nanoscale are achieved. Overall, the proposed nano-scale 3D quantum thermal imaging system with high-resolution may provide a new research direction and exploration of many frontier fields.
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Affiliation(s)
- Jun Yang
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China.
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211
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Clarke DT, Martin-Fernandez ML. A Brief History of Single-Particle Tracking of the Epidermal Growth Factor Receptor. Methods Protoc 2019; 2:mps2010012. [PMID: 31164594 PMCID: PMC6481046 DOI: 10.3390/mps2010012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/15/2022] Open
Abstract
Single-particle tracking (SPT) has been used and developed over the last 25 years as a method to investigate molecular dynamics, structure, interactions, and function in the cellular context. SPT is able to show how fast and how far individual molecules move, identify different dynamic populations, measure the duration and strength of intermolecular interactions, and map out structures on the nanoscale in cells. In combination with other techniques such as macromolecular crystallography and molecular dynamics simulation, it allows us to build models of complex structures, and develop and test hypotheses of how these complexes perform their biological roles in health as well as in disease states. Here, we use the example of the epidermal growth factor receptor (EGFR), which has been studied extensively by SPT, demonstrating how the method has been used to increase our understanding of the receptor’s organization and function, including its interaction with the plasma membrane, its activation, clustering, and oligomerization, and the role of other receptors and endocytosis. The examples shown demonstrate how SPT might be employed in the investigation of other biomolecules and systems.
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Affiliation(s)
- David T Clarke
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK.
| | - Marisa L Martin-Fernandez
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK.
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212
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Moerner WE. Viewpoint: Localization Microscopy of Single Molecules Enhanced by 3D Imaging and Light Sheet Illumination. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2019; 52:011001. [PMID: 31160828 PMCID: PMC6544387 DOI: 10.1088/1361-6463/aae632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Single-molecule super-resolution fluorescence microscopy has produced a revolution in the optical resolution available for study of the nanoscale details of cells and materials. The early work on two-dimensional imaging yielded images of samples that spanned only a small axial range on the order of ~500 nm. Much more useful information can be obtained in complex extended samples using three-dimensional (3D) single-molecule localization. Without 3D capability, visualization of structures extending in the axial direction can easily be missed or confused and the understanding of the science compromised. A variety of methods for obtaining 3D super-resolution images have been devised, each with their own strengths and weaknesses, ranging from point-spread-function engineering to steep axial illumination gradients. Imaging thicker samples, such as mammalian cells and tissue, in all three dimensions presents additional challenges due to increased background and large volumes to image. Light sheet illumination is a method that allows for selective irradiation of the image plane, and its inherent optical sectioning capability allows for imaging of biological samples with reduced background, photobleaching, and photodamage. Beyond these developments, there is a continuing need for better controllable fluorophores, additional novel optical system designs, and enhanced mathematical and statistical signal processing ideas to accurately extract the maximum information available from single emitters in the shortest possible time.
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213
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Talib AJ, Fisher A, Voronine DV, Sinyukov AM, Bustamante Lopez SC, Ambardar S, Meissner KE, Scully MO, Sokolov AV. Fluorescence imaging of stained red blood cells with simultaneous resonance Raman photostability analysis. Analyst 2019; 144:4362-4370. [DOI: 10.1039/c9an00757a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Simultaneous fluorescence and resonance Raman imaging of R6G-stained red blood cells with optimal laser power.
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Affiliation(s)
- Ansam J. Talib
- Institute for Quantum Science and Engineering
- Texas A&M University
- College Station
- USA
- Department of Physics
| | - Andrew Fisher
- Department of Physics
- Centre for Nanohealth
- Swansea University
- Wales
- UK
| | - Dmitri V. Voronine
- Department of Physics
- University of South Florida
- Tampa
- USA
- Department of Medical Engineering
| | | | - Sandra C. Bustamante Lopez
- Institute for Quantum Science and Engineering
- Texas A&M University
- College Station
- USA
- Department of Physics
| | - Sharad Ambardar
- Department of Physics
- University of South Florida
- Tampa
- USA
- Department of Medical Engineering
| | | | - Marlan O. Scully
- Institute for Quantum Science and Engineering
- Texas A&M University
- College Station
- USA
- Department of Physics
| | - Alexei V. Sokolov
- Institute for Quantum Science and Engineering
- Texas A&M University
- College Station
- USA
- Department of Physics
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214
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Yoon J, Comerci CJ, Weiss LE, Milenkovic L, Stearns T, Moerner WE. Revealing Nanoscale Morphology of the Primary Cilium Using Super-Resolution Fluorescence Microscopy. Biophys J 2018; 116:319-329. [PMID: 30598282 PMCID: PMC6349968 DOI: 10.1016/j.bpj.2018.11.3136] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/20/2018] [Accepted: 11/28/2018] [Indexed: 12/28/2022] Open
Abstract
Super-resolution (SR) microscopy has been used to observe structural details beyond the diffraction limit of ∼250 nm in a variety of biological and materials systems. By combining this imaging technique with both computer-vision algorithms and topological methods, we reveal and quantify the nanoscale morphology of the primary cilium, a tiny tubular cellular structure (∼2-6 μm long and 200-300 nm in diameter). The cilium in mammalian cells protrudes out of the plasma membrane and is important in many signaling processes related to cellular differentiation and disease. After tagging individual ciliary transmembrane proteins, specifically Smoothened, with single fluorescent labels in fixed cells, we use three-dimensional (3D) single-molecule SR microscopy to determine their positions with a precision of 10-25 nm. We gain a dense, pointillistic reconstruction of the surfaces of many cilia, revealing large heterogeneity in membrane shape. A Poisson surface reconstruction algorithm generates a fine surface mesh, allowing us to characterize the presence of deformations by quantifying the surface curvature. Upon impairment of intracellular cargo transport machinery by genetic knockout or small-molecule treatment of cells, our quantitative curvature analysis shows significant morphological differences not visible by conventional fluorescence microscopy techniques. Furthermore, using a complementary SR technique, two-color, two-dimensional stimulated emission depletion microscopy, we find that the cytoskeleton in the cilium, the axoneme, also exhibits abnormal morphology in the mutant cells, similar to our 3D results on the Smoothened-measured ciliary surface. Our work combines 3D SR microscopy and computational tools to quantitatively characterize morphological changes of the primary cilium under different treatments and uses stimulated emission depletion to discover correlated changes in the underlying structure. This approach can be useful for studying other biological or nanoscale structures of interest.
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Affiliation(s)
- Joshua Yoon
- Department of Applied Physics, Stanford University, Stanford, California; Department of Chemistry, Stanford University, Stanford, California
| | - Colin J Comerci
- Biophysics Program, Stanford University, Stanford, California
| | - Lucien E Weiss
- Department of Chemistry, Stanford University, Stanford, California
| | | | - Tim Stearns
- Department of Biology, Stanford University, Stanford, California
| | - W E Moerner
- Department of Applied Physics, Stanford University, Stanford, California; Department of Chemistry, Stanford University, Stanford, California.
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215
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VIPER is a genetically encoded peptide tag for fluorescence and electron microscopy. Proc Natl Acad Sci U S A 2018; 115:12961-12966. [PMID: 30518560 DOI: 10.1073/pnas.1808626115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many discoveries in cell biology rely on making specific proteins visible within their native cellular environment. There are various genetically encoded tags, such as fluorescent proteins, developed for fluorescence microscopy (FM). However, there are almost no genetically encoded tags that enable cellular proteins to be observed by both FM and electron microscopy (EM). Herein, we describe a technology for labeling proteins with diverse chemical reporters, including bright organic fluorophores for FM and electron-dense nanoparticles for EM. Our technology uses versatile interacting peptide (VIP) tags, a class of genetically encoded tag. We present VIPER, which consists of a coiled-coil heterodimer formed between the genetic tag, CoilE, and a probe-labeled peptide, CoilR. Using confocal FM, we demonstrate that VIPER can be used to highlight subcellular structures or to image receptor-mediated iron uptake. Additionally, we used VIPER to image the iron uptake machinery by correlative light and EM (CLEM). VIPER compared favorably with immunolabeling for imaging proteins by CLEM, and is an enabling technology for protein targets that cannot be immunolabeled. VIPER is a versatile peptide tag that can be used to label and track proteins with diverse chemical reporters observable by both FM and EM instrumentation.
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216
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Anderson CT. Finding order in a bustling construction zone: quantitative imaging and analysis of cell wall assembly in plants. CURRENT OPINION IN PLANT BIOLOGY 2018; 46:62-67. [PMID: 30107305 DOI: 10.1016/j.pbi.2018.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/16/2018] [Accepted: 07/25/2018] [Indexed: 06/08/2023]
Abstract
Assembly of polysaccharide-based walls by plant cells involves the rapid synthesis, trafficking, and deposition of complex biopolymers, but how these events are controlled and coordinated to achieve a strong, resilient extracellular matrix has remained obscure for decades. Recent quantitative analyses of fluorescence microscopy data have revealed details of the trafficking and synthetic activity of cellulose synthases, and new methods for labeling matrix polymers have unveiled aspects of their regulated deposition in the wall. Detailed studies of the identity, architecture, activity, and trafficking of the proteins and protein complexes that synthesize wall polymers, combined with advances in image acquisition and analysis, will aid future efforts to dissect wall assembly.
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Affiliation(s)
- Charles T Anderson
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Lignocellulose Structure and Formation, The Pennsylvania State University, University Park, PA 16802, USA.
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217
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Kou L, Jin L, Lei H, Hu C, Li H, Hu X, Hu X. Real-time parallel 3D multiple particle tracking with single molecule centrifugal force microscopy. J Microsc 2018; 273:178-188. [PMID: 30489640 DOI: 10.1111/jmi.12773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 11/16/2018] [Accepted: 11/20/2018] [Indexed: 12/20/2022]
Abstract
Real-time tracking of multiple particles is key for quantitative analysis of dynamic biophysical processes and materials science via time-lapse microscopy image data, especially for single molecule biophysical techniques, such as magnetic tweezers and centrifugal force microscopy. However, real-time multiple particle tracking with high resolution is limited by the current imaging processes or tracking algorithms. Here, we demonstrate 1 nm resolution in three dimensions in real-time with a graphics-processing unit (GPU) based on a compute unified device architecture (CUDA) parallel computing framework instead of only a central processing unit (CPU). We also explore the trade-offs between processing speed and size of the utilized regions of interest and a maximum speedup of 137 is achieved with the GPU compared with the CPU. Moreover, we utilize this method with our recently self-built centrifugal force microscope (CFM) in experiments that track multiple DNA-tethered particles. Our approach paves the way for high-throughput single molecule techniques with high resolution and efficiency. LAY DESCRIPTION: Particles are widely used as probes in life sciences through their motions. In single molecule techniques such as optical tweezers and magnetic tweezers, microbeads are used to study intermolecular or intramolecular interactions via beads tracking. Also tracking multiple beads' motions could study cell-cell or cell-ECM interactions in traction force microscopy. Therefore, particle tracking is of key important during these researches. However, parallel 3D multiple particle tracking in real-time with high resolution is a challenge either due to the algorithm or the program. Here, we combine the performance of CPU and CUDA-based GPU to make a hybrid implementation for particle tracking. In this way, a speedup of 137 is obtained compared the program before only with CPU without loss of accuracy. Moreover, we improve and build a new centrifugal force microscope for multiple single molecule force spectroscopy research in parallel. Then we employed our program into centrifugal force microscope for DNA stretching study. Our results not only demonstrate the application of this program in single molecule techniques, also indicate the capability of multiple single molecule study with centrifugal force microscopy.
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Affiliation(s)
- L Kou
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin, China
| | - L Jin
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin, China
| | - H Lei
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin, China
| | - C Hu
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin, China
| | - H Li
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin, China.,Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - X Hu
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin, China
| | - X Hu
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin, China
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218
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Analyzing complex single-molecule emission patterns with deep learning. Nat Methods 2018; 15:913-916. [PMID: 30377349 PMCID: PMC6624853 DOI: 10.1038/s41592-018-0153-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 08/09/2018] [Indexed: 11/28/2022]
Abstract
A fluorescent emitter simultaneously transmits its identity, location, and cellular context through its emission pattern. We developed smNet, a deep neural network for multiplexed single-molecule analysis to enable retrieving such information with high accuracy. We demonstrate that smNet can extract three-dimensional molecule location, orientation, and wavefront distortion with precision approaching the theoretical limit and therefore will allow multiplexed measurements through the emission pattern of a single molecule. The deep neural network smNet enables extraction of multiplexed parameters such as 3D position, orientation and wavefront distortion from emission patterns of single molecules.
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219
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Coceancigh H, Higgins DA, Ito T. Optical Microscopic Techniques for Synthetic Polymer Characterization. Anal Chem 2018; 91:405-424. [PMID: 30350610 DOI: 10.1021/acs.analchem.8b04694] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Herman Coceancigh
- Department of Chemistry , Kansas State University , 213 CBC Building , Manhattan , Kansas 66506-0401 , United States
| | - Daniel A Higgins
- Department of Chemistry , Kansas State University , 213 CBC Building , Manhattan , Kansas 66506-0401 , United States
| | - Takashi Ito
- Department of Chemistry , Kansas State University , 213 CBC Building , Manhattan , Kansas 66506-0401 , United States
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220
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Neves MMPDS, Martín-Yerga D. Advanced Nanoscale Approaches to Single-(Bio)entity Sensing and Imaging. BIOSENSORS 2018; 8:E100. [PMID: 30373209 PMCID: PMC6316691 DOI: 10.3390/bios8040100] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 01/01/2023]
Abstract
Individual (bio)chemical entities could show a very heterogeneous behaviour under the same conditions that could be relevant in many biological processes of significance in the life sciences. Conventional detection approaches are only able to detect the average response of an ensemble of entities and assume that all entities are identical. From this perspective, important information about the heterogeneities or rare (stochastic) events happening in individual entities would remain unseen. Some nanoscale tools present interesting physicochemical properties that enable the possibility to detect systems at the single-entity level, acquiring richer information than conventional methods. In this review, we introduce the foundations and the latest advances of several nanoscale approaches to sensing and imaging individual (bio)entities using nanoprobes, nanopores, nanoimpacts, nanoplasmonics and nanomachines. Several (bio)entities such as cells, proteins, nucleic acids, vesicles and viruses are specifically considered. These nanoscale approaches provide a wide and complete toolbox for the study of many biological systems at the single-entity level.
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Affiliation(s)
| | - Daniel Martín-Yerga
- Department of Chemical Engineering, KTH Royal Institute of Technology, 100-44 Stockholm, Sweden.
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221
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Abstract
In the past decades, advances in microscopy have made it possible to study the dynamics of individual biomolecules in vitro and resolve intramolecular kinetics that would otherwise be hidden in ensemble averages. More recently, single-molecule methods have been used to image, localize, and track individually labeled macromolecules in the cytoplasm of living cells, allowing investigations of intermolecular kinetics under physiologically relevant conditions. In this review, we illuminate the particular advantages of single-molecule techniques when studying kinetics in living cells and discuss solutions to specific challenges associated with these methods.
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Affiliation(s)
- Johan Elf
- Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden;
| | - Irmeli Barkefors
- Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden;
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222
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He H, Li S, Shi X, Wang X, Liu X, Wang Q, Guo A, Ge B, Khan NU, Huang F. Quantitative Nanoscopy of Small Blinking Graphene Nanocarriers in Drug Delivery. Bioconjug Chem 2018; 29:3658-3666. [DOI: 10.1021/acs.bioconjchem.8b00589] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Hua He
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Shan Li
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xinjian Shi
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiaojuan Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xu Liu
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Qian Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Aijun Guo
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Naseer Ullah Khan
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
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223
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Jiang Y, McNeill J. Superresolution mapping of energy landscape for single charge carriers in plastic semiconductors. Nat Commun 2018; 9:4314. [PMID: 30333490 PMCID: PMC6193038 DOI: 10.1038/s41467-018-06846-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/19/2018] [Indexed: 12/03/2022] Open
Abstract
The performance of conjugated polymer devices is largely dictated by charge transport processes. However, it is difficult to obtain a clear relationship between conjugated polymer structures and charge transport properties, due to the complexity of the structure and the dispersive nature of charge transport in conjugated polymers. Here, we develop a method to map the energy landscape for charge transport in conjugated polymers based on simultaneous, correlated charge carrier tracking and single-particle fluorescence spectroscopy. In nanoparticles of the conjugated polymer poly[9,9-dioctylfluorenyl-2,7-diyl)-co-1,4-benzo-{2,1′-3}-thiadiazole)], two dominant chain conformations were observed, a blue-emitting phase (λmax = 550 nm) and a red-emitting phase (λmax = 595 nm). Hole polarons were trapped within the red phase, only occasionally escaping into the blue phase. Polaron hopping between the red-emitting traps was observed, with transition time ranging from tens of milliseconds to several seconds. These results provide unprecedented nanoscale detail about charge transport at the single carrier level. To understand the complex nanoscale structure-property relationships in conjugated polymers for device applications, new methods for tracking charge transport are required. Here, the authors employ superresolution mapping to study the charge carrier dynamics in conjugated polymer nanoparticles.
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Affiliation(s)
- Yifei Jiang
- Department of Chemistry, Clemson University, Clemson, SC, 29634, USA
| | - Jason McNeill
- Department of Chemistry, Clemson University, Clemson, SC, 29634, USA.
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224
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Naumov AV, Gorshelev AA, Gladush MG, Anikushina TA, Golovanova AV, Köhler J, Kador L. Micro-Refractometry and Local-Field Mapping with Single Molecules. NANO LETTERS 2018; 18:6129-6134. [PMID: 30188725 DOI: 10.1021/acs.nanolett.8b01753] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The refractive index n is one of the most important materials parameters of solids and, in recent years, has become the subject of significant interdisciplinary interest, especially in nanostructures and meta-materials. It is, in principle, a macroscopic quantity, so its meaning on a length scale of a few nanometers, i.e., well below the wavelength of light, is not clear a priori and is related to methods of its measurement on this length scale. Here we introduce a novel experimental approach for mapping the effective local value [Formula: see text] of the refractive index in solid films and the analysis of related local-field enhancement effects. The approach is based on the imaging and spectroscopy of single chromophore molecules at cryogenic temperatures. Since the fluorescence lifetime T1 of dye molecules in a transparent matrix depends on the refractive index due to the local density of the electromagnetic field (i.e., of the photon states), one can obtain the local [Formula: see text] values in the surroundings of individual chromophores simply by measuring their T1 times. Spatial mapping of the local [Formula: see text] values is accomplished by localizing the corresponding chromophores with nanometer accuracy. We demonstrate this approach for a polycrystalline n-hexadecane film doped with terrylene. Unexpectedly large fluctuations of local-field effects and effective [Formula: see text] values (the latter between 1.1 and 1.9) were found.
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Affiliation(s)
- A V Naumov
- Institute for Spectroscopy, Russian Academy of Sciences , Moscow 108840 , Russia
- Moscow State Pedagogical University , Moscow , 119435 , Russia
| | - A A Gorshelev
- Institute for Spectroscopy, Russian Academy of Sciences , Moscow 108840 , Russia
| | - M G Gladush
- Institute for Spectroscopy, Russian Academy of Sciences , Moscow 108840 , Russia
- Moscow State Pedagogical University , Moscow , 119435 , Russia
| | - T A Anikushina
- Institute for Spectroscopy, Russian Academy of Sciences , Moscow 108840 , Russia
- Moscow State Pedagogical University , Moscow , 119435 , Russia
| | - A V Golovanova
- Institute for Spectroscopy, Russian Academy of Sciences , Moscow 108840 , Russia
- Moscow State Pedagogical University , Moscow , 119435 , Russia
| | - J Köhler
- University of Bayreuth, Institute of Physics , D-95440 Bayreuth , Germany
- University of Bayreuth, Spectroscopy of Soft Matter , D-95440 Bayreuth , Germany
- Bavarian Polymer Institute , D-95440 Bayreuth , Germany
| | - L Kador
- University of Bayreuth, Institute of Physics , D-95440 Bayreuth , Germany
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225
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Gronnier J, Gerbeau-Pissot P, Germain V, Mongrand S, Simon-Plas F. Divide and Rule: Plant Plasma Membrane Organization. TRENDS IN PLANT SCIENCE 2018; 23:899-917. [PMID: 30174194 DOI: 10.1016/j.tplants.2018.07.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/09/2018] [Accepted: 07/13/2018] [Indexed: 05/24/2023]
Abstract
Since the publication of the fluid mosaic as a relevant model for biological membranes, accumulating evidence has revealed the outstanding complexity of the composition and organization of the plant plasma membrane (PM). Powerful new methodologies have uncovered the remarkable multiscale and multicomponent heterogeneity of PM subcompartmentalization, and this is emerging as a general trait with different features and properties. It is now evident that the dynamics of such a complex organization are intrinsically related to signaling pathways that regulate key physiological processes. Listing and linking recent progress in precisely qualifying these heterogeneities will help to draw an integrated picture of the plant PM. Understanding the key principles governing such a complex dynamic organization will contribute to deciphering the crucial role of the PM in cell physiology.
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Affiliation(s)
- Julien Gronnier
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche (UMR) 5200, Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux, Bordeaux, France; Present address: Laboratory of Cyril Zipfel, Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Patricia Gerbeau-Pissot
- Agroécologie, Institut National Supérieur des Sciences Agronomiques, de l'Alimentation, et de l'Environnement (AgroSup) Dijon, CNRS, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, Dijon, France
| | - Véronique Germain
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche (UMR) 5200, Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux, Bordeaux, France
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche (UMR) 5200, Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux, Bordeaux, France; These authors contributed equally to this work
| | - Françoise Simon-Plas
- Agroécologie, Institut National Supérieur des Sciences Agronomiques, de l'Alimentation, et de l'Environnement (AgroSup) Dijon, CNRS, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, Dijon, France; These authors contributed equally to this work.
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226
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Bishop LDC, Landes CF. From a Protein's Perspective: Elution at the Single-Molecule Level. Acc Chem Res 2018; 51:2247-2254. [PMID: 30132321 DOI: 10.1021/acs.accounts.8b00211] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Column chromatography is a widely used analytical technique capable of identifying and isolating a desired chemical species from a more complicated mixture. Despite the method's prevalence, theoretical descriptions have not advanced to accommodate today's common analyte, proteins. Proteins are increasingly used as biologics, a term that refers to biological pharmaceuticals, and present new complexities for chromatographic separation. Large variations in surface charge, chemistry, and structure among protein analytes expose the limits in the current theoretical framework's ability to predict the efficiency of a column without empirical data. The bottleneck created by empirical optimization is a strong motivation for a renewed effort to achieve an in-depth understanding of the range of interactions that occur between a protein analyte and the stationary phase that together enable its selective separation from other constituents of a mixture. The physical and chemical processes that dictate the amount of time an analyte spends in the column are often abstracted by theory and treated as statistical distributions. Until recently, these distributions could not be mapped experimentally as traditional experimental techniques could not reveal underlying heterogeneity in structure, charge, and dynamics. Aligning the latest experimental and theoretical advances is thus a hurdle to be overcome so that significant progress can be made toward a predictive chromatographic theory. In this Account, we detail the work of the Landes Lab in developing single-molecule techniques that refine the stochastic theory of chromatography as a first step toward predictive chromatographic column design. We provide a brief review of the development of stochastic theory and establish a mathematical framework to put the discussed physical chemistry in context. We describe our investigations of three pertinent phenomena: mobile/stationary phase exchange, adsorption/desorption kinetics, and hindered diffusion. We highlight experimental evidence that points to nonuniform behavior. Then, we describe our work in developing single-molecule techniques that can evaluate these effects on a protein-by-protein basis. We highlight two developments: fast imaging via super temporal-resolved microscopy (STReM) and visualizing diffusion within pores via a combination of fluorescence correlation spectroscopy and super-resolution optical fluctuation imaging (fcsSOFI). Both methods offer new ways to study chromatographic elution at the single-protein level. Such methods can identify the rare heterogeneities that prevent efficient separations and advance the field closer to predictively optimized protein separations.
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227
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Minimizing Structural Bias in Single-Molecule Super-Resolution Microscopy. Sci Rep 2018; 8:13133. [PMID: 30177692 PMCID: PMC6120949 DOI: 10.1038/s41598-018-31366-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/17/2018] [Indexed: 11/08/2022] Open
Abstract
Single-molecule localization microscopy (SMLM) depends on sequential detection and localization of individual molecular blinking events. Due to the stochasticity of single-molecule blinking and the desire to improve SMLM’s temporal resolution, algorithms capable of analyzing frames with a high density (HD) of active molecules, or molecules whose images overlap, are a prerequisite for accurate location measurements. Thus far, HD algorithms are evaluated using scalar metrics, such as root-mean-square error, that fail to quantify the structure of errors caused by the structure of the sample. Here, we show that the spatial distribution of localization errors within super-resolved images of biological structures are vectorial in nature, leading to systematic structural biases that severely degrade image resolution. We further demonstrate that the shape of the microscope’s point-spread function (PSF) fundamentally affects the characteristics of imaging artifacts. We built a Robust Statistical Estimation algorithm (RoSE) to minimize these biases for arbitrary structures and PSFs. RoSE accomplishes this minimization by estimating the likelihood of blinking events to localize molecules more accurately and eliminate false localizations. Using RoSE, we measure the distance between crossing microtubules, quantify the morphology of and separation between vesicles, and obtain robust recovery using diverse 3D PSFs with unmatched accuracy compared to state-of-the-art algorithms.
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228
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Sigal YM, Zhou R, Zhuang X. Visualizing and discovering cellular structures with super-resolution microscopy. Science 2018; 361:880-887. [PMID: 30166485 DOI: 10.1126/science.aau1044] [Citation(s) in RCA: 359] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Super-resolution microscopy has overcome a long-held resolution barrier-the diffraction limit-in light microscopy and enabled visualization of previously invisible molecular details in biological systems. Since their conception, super-resolution imaging methods have continually evolved and can now be used to image cellular structures in three dimensions, multiple colors, and living systems with nanometer-scale resolution. These methods have been applied to answer questions involving the organization, interaction, stoichiometry, and dynamics of individual molecular building blocks and their integration into functional machineries in cells and tissues. In this Review, we provide an overview of super-resolution methods, their state-of-the-art capabilities, and their constantly expanding applications to biology, with a focus on the latter. We will also describe the current technical challenges and future advances anticipated in super-resolution imaging.
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Affiliation(s)
- Yaron M Sigal
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Ruobo Zhou
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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229
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Pick H, Alves AC, Vogel H. Single-Vesicle Assays Using Liposomes and Cell-Derived Vesicles: From Modeling Complex Membrane Processes to Synthetic Biology and Biomedical Applications. Chem Rev 2018; 118:8598-8654. [PMID: 30153012 DOI: 10.1021/acs.chemrev.7b00777] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The plasma membrane is of central importance for defining the closed volume of cells in contradistinction to the extracellular environment. The plasma membrane not only serves as a boundary, but it also mediates the exchange of physical and chemical information between the cell and its environment in order to maintain intra- and intercellular functions. Artificial lipid- and cell-derived membrane vesicles have been used as closed-volume containers, representing the simplest cell model systems to study transmembrane processes and intracellular biochemistry. Classical examples are studies of membrane translocation processes in plasma membrane vesicles and proteoliposomes mediated by transport proteins and ion channels. Liposomes and native membrane vesicles are widely used as model membranes for investigating the binding and bilayer insertion of proteins, the structure and function of membrane proteins, the intramembrane composition and distribution of lipids and proteins, and the intermembrane interactions during exo- and endocytosis. In addition, natural cell-released microvesicles have gained importance for early detection of diseases and for their use as nanoreactors and minimal protocells. Yet, in most studies, ensembles of vesicles have been employed. More recently, new micro- and nanotechnological tools as well as novel developments in both optical and electron microscopy have allowed the isolation and investigation of individual (sub)micrometer-sized vesicles. Such single-vesicle experiments have revealed large heterogeneities in the structure and function of membrane components of single vesicles, which were hidden in ensemble studies. These results have opened enormous possibilities for bioanalysis and biotechnological applications involving unprecedented miniaturization at the nanometer and attoliter range. This review will cover important developments toward single-vesicle analysis and the central discoveries made in this exciting field of research.
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Affiliation(s)
- Horst Pick
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Ana Catarina Alves
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Horst Vogel
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
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230
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Zhong Y, Li C, Zhou H, Wang G. Developing Noise-Resistant Three-Dimensional Single Particle Tracking Using Deep Neural Networks. Anal Chem 2018; 90:10748-10757. [DOI: 10.1021/acs.analchem.8b01334] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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231
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Couture O, Hingot V, Heiles B, Muleki-Seya P, Tanter M. Ultrasound Localization Microscopy and Super-Resolution: A State of the Art. IEEE TRANSACTIONS ON ULTRASONICS, FERROELECTRICS, AND FREQUENCY CONTROL 2018; 65:1304-1320. [PMID: 29994673 DOI: 10.1109/tuffc.2018.2850811] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Because it drives the compromise between resolution and penetration, the diffraction limit has long represented an unreachable summit to conquer in ultrasound imaging. Within a few years after the introduction of optical localization microscopy, we proposed its acoustic alter ego that exploits the micrometric localization of microbubble contrast agents to reconstruct the finest vessels in the body in-depth. Various groups now working on the subject are optimizing the localization precision, microbubble separation, acquisition time, tracking, and velocimetry to improve the capacity of ultrasound localization microscopy (ULM) to detect and distinguish vessels much smaller than the wavelength. It has since been used in vivo in the brain, the kidney, and tumors. In the clinic, ULM is bound to improve drastically our vision of the microvasculature, which could revolutionize the diagnosis of cancer, arteriosclerosis, stroke, and diabetes.
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232
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Reversible, Spatial and Temporal Control over Protein Activity Using Light. Trends Biochem Sci 2018; 43:567-575. [DOI: 10.1016/j.tibs.2018.05.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/03/2018] [Accepted: 05/27/2018] [Indexed: 12/22/2022]
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233
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Attota RK. Fidelity test for through-focus or volumetric type of optical imaging methods. OPTICS EXPRESS 2018; 26:19100-19114. [PMID: 30114170 PMCID: PMC6159218 DOI: 10.1364/oe.26.019100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 06/23/2018] [Indexed: 06/08/2023]
Abstract
Rapid increase in interest and applications of through-focus (TF) or volumetric type of optical imaging in biology and other areas has resulted in the development of several TF image collection methods. Achieving quantitative results from images requires standardization and optimization of image acquisition protocols. Several standardization protocols are available for conventional optical microscopy where a best-focus image is used, but to date, rigorous testing protocols do not exist for TF optical imaging. In this paper, we present a method to determine the fidelity of the TF optical data using the TF scanning optical microscopy images.
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Affiliation(s)
- Ravi Kiran Attota
- Engineering Physics Division, PML, NIST, Gaithersburg, MD 20899-8212, USA
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234
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Mlodzianoski MJ, Cheng-Hathaway PJ, Bemiller SM, McCray TJ, Liu S, Miller DA, Lamb BT, Landreth GE, Huang F. Active PSF shaping and adaptive optics enable volumetric localization microscopy through brain sections. Nat Methods 2018; 15:583-586. [PMID: 30013047 PMCID: PMC6071422 DOI: 10.1038/s41592-018-0053-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/17/2018] [Indexed: 12/21/2022]
Abstract
Single Molecule Switching Nanoscopy (SMSN) beyond the coverslip surface poses significant challenges. The sample-induced aberrations distort and blur single-molecule emission patterns. Combining active point-spread function shaping and efficient adaptive optics enables robust 3D-SMSN imaging at large depths. This development allowed us to image through 30-μm thick brain sections, visualize the morphology and the nanoscale details of amyloid-β filaments in a mouse model of Alzheimer’s disease and reconstruct their volumetric arrangements.
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Affiliation(s)
- Michael J Mlodzianoski
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.,Centre for Dynamic Imaging, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Paul J Cheng-Hathaway
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Shane M Bemiller
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tyler J McCray
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sheng Liu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - David A Miller
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Bruce T Lamb
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Neurosciences, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Gary E Landreth
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA. .,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA. .,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA.
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235
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Backlund MP, Shechtman Y, Walsworth RL. Fundamental Precision Bounds for Three-Dimensional Optical Localization Microscopy with Poisson Statistics. PHYSICAL REVIEW LETTERS 2018; 121:023904. [PMID: 30085695 DOI: 10.1103/physrevlett.121.023904] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Indexed: 05/23/2023]
Abstract
Point source localization is a problem of persistent interest in optical imaging. In particular, a number of widely used biological microscopy techniques rely on precise three-dimensional localization of single fluorophores. As emitter depth localization is more challenging than lateral localization, considerable effort has been spent on engineering the response of the microscope in a way that reveals increased depth information. Here, we prove the (sub)optimality of these approaches by deriving and comparing to the measurement-independent quantum Cramér-Rao bound (QCRB). We show that existing methods for depth localization with single-objective collection exceed the QCRB, and we gain insight into the bound by proposing an interferometer arrangement that approaches it. We also show that for light collection with two opposed objectives, an established interferometric technique globally reaches the QCRB in all three dimensions simultaneously, and so this represents an interesting case study from the point of view of quantum multiparameter estimation.
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Affiliation(s)
- Mikael P Backlund
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts 02138, USA
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Yoav Shechtman
- Department of Biomedical Engineering, Technion, Israel Institute of Technology, Haifa 32000, Israel
| | - Ronald L Walsworth
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts 02138, USA
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
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236
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Swinstead EE, Paakinaho V, Hager GL. Chromatin reprogramming in breast cancer. Endocr Relat Cancer 2018; 25:R385-R404. [PMID: 29692347 PMCID: PMC6029727 DOI: 10.1530/erc-18-0033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 04/24/2018] [Indexed: 02/06/2023]
Abstract
Reprogramming of the chromatin landscape is a critical component to the transcriptional response in breast cancer. Effects of sex hormones such as estrogens and progesterone have been well described to have a critical impact on breast cancer proliferation. However, the complex network of the chromatin landscape, enhancer regions and mode of function of steroid receptors (SRs) and other transcription factors (TFs), is an intricate web of signaling and functional processes that is still largely misunderstood at the mechanistic level. In this review, we describe what is currently known about the dynamic interplay between TFs with chromatin and the reprogramming of enhancer elements. Emphasis has been placed on characterizing the different modes of action of TFs in regulating enhancer activity, specifically, how different SRs target enhancer regions to reprogram chromatin in breast cancer cells. In addition, we discuss current techniques employed to study enhancer function at a genome-wide level. Further, we have noted recent advances in live cell imaging technology. These single-cell approaches enable the coupling of population-based assays with real-time studies to address many unsolved questions about SRs and chromatin dynamics in breast cancer.
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Affiliation(s)
- Erin E Swinstead
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, NIH, Bethesda, Maryland, USA
- Institute of BiomedicineUniversity of Eastern Finland, Kuopio, Finland
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, NIH, Bethesda, Maryland, USA
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237
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Attota RK. Through-focus or volumetric type of optical imaging methods: a review. JOURNAL OF BIOMEDICAL OPTICS 2018; 23:1-10. [PMID: 29981229 PMCID: PMC6157599 DOI: 10.1117/1.jbo.23.7.070901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/11/2018] [Indexed: 05/04/2023]
Abstract
In recent years, the use of through-focus (TF) or volumetric type of optical imaging has gained momentum in several areas such as biological imaging, microscopy, adaptive optics, material processing, optical data storage, and optical inspection. We provide a review of basic TF optical methods highlighting their design, major unique characteristics, and application space.
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Affiliation(s)
- Ravi Kiran Attota
- Engineering Physics Division, PML, National Institute of Standards and Technology Gaithersburg, MD 20899, USA
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238
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Baddeley D, Bewersdorf J. Biological Insight from Super-Resolution Microscopy: What We Can Learn from Localization-Based Images. Annu Rev Biochem 2018; 87:965-989. [PMID: 29272143 DOI: 10.1146/annurev-biochem-060815-014801] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Super-resolution optical imaging based on the switching and localization of individual fluorescent molecules [photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), etc.] has evolved remarkably over the last decade. Originally driven by pushing technological limits, it has become a tool of biological discovery. The initial demand for impressive pictures showing well-studied biological structures has been replaced by a need for quantitative, reliable data providing dependable evidence for specific unresolved biological hypotheses. In this review, we highlight applications that showcase this development, identify the features that led to their success, and discuss remaining challenges and difficulties. In this context, we consider the complex topic of defining resolution for this imaging modality and address some of the more common analytical methods used with this data.
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Affiliation(s)
- David Baddeley
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA; , .,Auckland Bioengineering Institute, University of Auckland, Auckland 1010, New Zealand
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA; , .,Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA
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239
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Aristov A, Lelandais B, Rensen E, Zimmer C. ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range. Nat Commun 2018; 9:2409. [PMID: 29921892 PMCID: PMC6008307 DOI: 10.1038/s41467-018-04709-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/16/2018] [Indexed: 11/23/2022] Open
Abstract
Single molecule localization microscopy can generate 3D super-resolution images without scanning by leveraging the axial variations of normal or engineered point spread functions (PSF). Successful implementation of these approaches for extended axial ranges remains, however, challenging. We present Zernike Optimized Localization Approach in 3D (ZOLA-3D), an easy-to-use computational and optical solution that achieves optimal resolution over a tunable axial range. We use ZOLA-3D to demonstrate 3D super-resolution imaging of mitochondria, nuclear pores and microtubules in entire nuclei or cells up to ~5 μm deep. 3D single-molecule localization is limited in depth and often requires using a wide range of point spread functions (PSFs). Here the authors present an optical solution featuring a deformable mirror to generate different PSFs and easy-to-use software for super-resolution imaging up to 5 µm deep.
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Affiliation(s)
- Andrey Aristov
- Unité Imagerie et Modélisation, Institut Pasteur, 25-28 rue du Docteur Roux, Paris, France.,UMR 3691, CNRS; C3BI, USR 3756, IP CNRS, Paris, France
| | - Benoit Lelandais
- Unité Imagerie et Modélisation, Institut Pasteur, 25-28 rue du Docteur Roux, Paris, France.,UMR 3691, CNRS; C3BI, USR 3756, IP CNRS, Paris, France.,Hub Bioinformatique et Biostatistique, Institut Pasteur, Paris, France
| | - Elena Rensen
- Unité Imagerie et Modélisation, Institut Pasteur, 25-28 rue du Docteur Roux, Paris, France.,UMR 3691, CNRS; C3BI, USR 3756, IP CNRS, Paris, France
| | - Christophe Zimmer
- Unité Imagerie et Modélisation, Institut Pasteur, 25-28 rue du Docteur Roux, Paris, France. .,UMR 3691, CNRS; C3BI, USR 3756, IP CNRS, Paris, France.
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240
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Eilers Y, Ta H, Gwosch KC, Balzarotti F, Hell SW. MINFLUX monitors rapid molecular jumps with superior spatiotemporal resolution. Proc Natl Acad Sci U S A 2018; 115:6117-6122. [PMID: 29844182 PMCID: PMC6004438 DOI: 10.1073/pnas.1801672115] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Compared with localization schemes solely based on evaluating patterns of molecular emission, the recently introduced single-molecule localization concept called MINFLUX and the fluorescence nanoscopies derived from it require up to orders of magnitude fewer emissions to attain single-digit nanometer resolution. Here, we demonstrate that the lower number of required fluorescence photons enables MINFLUX to detect molecular movements of a few nanometers at a temporal sampling of well below 1 millisecond. Using fluorophores attached to thermally fluctuating DNA strands as model systems, we demonstrate that measurement times as short as 400 microseconds suffice to localize fluorescent molecules with ∼2-nm precision. Such performance is out of reach for popular camera-based localization by centroid calculation of emission diffraction patterns. Since theoretical limits have not been reached, our results show that emerging MINFLUX nanoscopy bears great potential for dissecting the motions of individual (macro)molecules at hitherto-unattained combinations of spatial and temporal resolution.
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Affiliation(s)
- Yvan Eilers
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Haisen Ta
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Klaus C Gwosch
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Francisco Balzarotti
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Stefan W Hell
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
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241
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Observing DNA in live cells. Biochem Soc Trans 2018; 46:729-740. [PMID: 29871877 DOI: 10.1042/bst20170301] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/26/2018] [Accepted: 05/01/2018] [Indexed: 12/17/2022]
Abstract
The structural organization and dynamics of DNA are known to be of paramount importance in countless cellular processes, but capturing these events poses a unique challenge. Fluorescence microscopy is well suited for these live-cell investigations, but requires attaching fluorescent labels to the species under investigation. Over the past several decades, a suite of techniques have been developed for labeling and imaging DNA, each with various advantages and drawbacks. Here, we provide an overview of the labeling and imaging tools currently available for visualizing DNA in live cells, and discuss their suitability for various applications.
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242
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A method for optical imaging and monitoring of the excretion of fluorescent nanocomposites from the body using artificial neural networks. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 14:1371-1380. [DOI: 10.1016/j.nano.2018.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/19/2018] [Accepted: 03/31/2018] [Indexed: 11/17/2022]
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243
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Gustavsson AK, Petrov PN, Moerner WE. Light sheet approaches for improved precision in 3D localization-based super-resolution imaging in mammalian cells [Invited]. OPTICS EXPRESS 2018; 26:13122-13147. [PMID: 29801343 PMCID: PMC6005674 DOI: 10.1364/oe.26.013122] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/30/2018] [Indexed: 05/08/2023]
Abstract
The development of imaging techniques beyond the diffraction limit has paved the way for detailed studies of nanostructures and molecular mechanisms in biological systems. Imaging thicker samples, such as mammalian cells and tissue, in all three dimensions, is challenging due to increased background and volumes to image. Light sheet illumination is a method that allows for selective irradiation of the image plane, and its inherent optical sectioning capability allows for imaging of biological samples with reduced background, photobleaching, and photodamage. In this review, we discuss the advantage of combining single-molecule imaging with light sheet illumination. We begin by describing the principles of single-molecule localization microscopy and of light sheet illumination. Finally, we present examples of designs that successfully have married single-molecule super-resolution imaging with light sheet illumination for improved precision in mammalian cells.
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244
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Dlasková A, Engstová H, Špaček T, Kahancová A, Pavluch V, Smolková K, Špačková J, Bartoš M, Hlavatá LP, Ježek P. 3D super-resolution microscopy reflects mitochondrial cristae alternations and mtDNA nucleoid size and distribution. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:829-844. [PMID: 29727614 DOI: 10.1016/j.bbabio.2018.04.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/10/2018] [Accepted: 04/24/2018] [Indexed: 12/13/2022]
Abstract
3D super-resolution microscopy based on the direct stochastic optical reconstruction microscopy (dSTORM) with primary Alexa-Fluor-647-conjugated antibodies is a powerful method for accessing changes of objects that could be normally resolved only by electron microscopy. Despite the fact that mitochondrial cristae yet to become resolved, we have indicated changes in cristae width and/or morphology by dSTORM of ATP-synthase F1 subunit α (F1α). Obtained 3D images were analyzed with the help of Ripley's K-function modeling spatial patterns or transferring them into distance distribution function. Resulting histograms of distances frequency distribution provide most frequent distances (MFD) between the localized single antibody molecules. In fasting state of model pancreatic β-cells, INS-1E, MFD between F1α were ~80 nm at 0 and 3 mM glucose, whereas decreased to 61 nm and 57 nm upon glucose-stimulated insulin secretion (GSIS) at 11 mM and 20 mM glucose, respectively. Shorter F1α interdistances reflected cristae width decrease upon GSIS, since such repositioning of F1α correlated to average 20 nm and 15 nm cristae width at 0 and 3 mM glucose, and 9 nm or 8 nm after higher glucose simulating GSIS (11, 20 mM glucose, respectively). Also, submitochondrial entities such as nucleoids of mtDNA were resolved e.g. after bromo-deoxyuridine (BrDU) pretreatment using anti-BrDU dSTORM. MFD in distances distribution histograms reflected an average nucleoid diameter (<100 nm) and average distances between nucleoids (~1000 nm). Double channel PALM/dSTORM with Eos-lactamase-β plus anti-TFAM dSTORM confirmed the latter average inter-nucleoid distance. In conclusion, 3D single molecule (dSTORM) microscopy is a reasonable tool for studying mitochondrion.
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Affiliation(s)
- Andrea Dlasková
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Engstová
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Špaček
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Anežka Kahancová
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vojtěch Pavluch
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Katarína Smolková
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jitka Špačková
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Bartoš
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic; Alef Ltd, Prague, Czech Republic
| | - Lydie Plecitá Hlavatá
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Ježek
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic.
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245
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Keller AM, DeVore MS, Stich DG, Vu DM, Causgrove T, Werner JH. Multicolor Three-Dimensional Tracking for Single-Molecule Fluorescence Resonance Energy Transfer Measurements. Anal Chem 2018; 90:6109-6115. [DOI: 10.1021/acs.analchem.8b00244] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Aaron M. Keller
- Department of Chemistry, William Jewell College, Liberty, Missouri 64068, United States
| | - Matthew S. DeVore
- Department of Natural & Applied Sciences, Evangel University, Springfield, Missouri 65802, United States
| | - Dominik G. Stich
- Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado 80045, United States
| | - Dung M. Vu
- Physical Chemistry & Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Timothy Causgrove
- Department of Physical & Environmental Sciences, Texas A&M University—Corpus Christi, Corpus Christi, Texas 78412, United States
| | - James H. Werner
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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246
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Abstract
In 2016, the Nobel Prize in Chemistry was awarded for pioneering work on molecular machines. Half a year later, in Toulouse, the first molecular car race, a "nanocar race", was held by using the tip of a scanning tunneling microscope as an electrical remote control. In this Focus Review, we discuss the current state-of-the-art in research on molecular machines at interfaces. In the first section, we briefly explain the science behind the nanocar race, followed by a selection of recent examples of controlling molecules on surfaces. Finally, motion synchronization and the functions of molecular machines at liquid interfaces are discussed. This new concept of molecular tuning at interfaces is also introduced as a method for the continuous modification and optimization of molecular structure for target functions.
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Affiliation(s)
- Katsuhiko Ariga
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan.,Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Taizo Mori
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
| | - Waka Nakanishi
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
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247
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Birkholz O, Burns JR, Richter CP, Psathaki OE, Howorka S, Piehler J. Multi-functional DNA nanostructures that puncture and remodel lipid membranes into hybrid materials. Nat Commun 2018; 9:1521. [PMID: 29670084 PMCID: PMC5906680 DOI: 10.1038/s41467-018-02905-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 01/08/2018] [Indexed: 02/06/2023] Open
Abstract
Synthetically replicating key biological processes requires the ability to puncture lipid bilayer membranes and to remodel their shape. Recently developed artificial DNA nanopores are one possible synthetic route due to their ease of fabrication. However, an unresolved fundamental question is how DNA nanopores bind to and dynamically interact with lipid bilayers. Here we use single-molecule fluorescence microscopy to establish that DNA nanopores carrying cholesterol anchors insert via a two-step mechanism into membranes. Nanopores are furthermore shown to locally cluster and remodel membranes into nanoscale protrusions. Most strikingly, the DNA pores can function as cytoskeletal components by stabilizing autonomously formed lipid nanotubes. The combination of membrane puncturing and remodeling activity can be attributed to the DNA pores’ tunable transition between two orientations to either span or co-align with the lipid bilayer. This insight is expected to catalyze the development of future functional nanodevices relevant in synthetic biology and nanobiotechnology. DNA nanopores can span lipid bilayers but how they interact with lipids is not known. Here the authors establish at single-molecule level the insertion mechanism and show that DNA nanopores can locally cluster and remodel membranes, and stabilize autonomously formed lipid nanotubes.
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248
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Maurice L, Bilenca A. Maximum-likelihood analysis of axial displacement in fluorescence phase-shifting interferometry. OPTICS EXPRESS 2018; 26:7965-7978. [PMID: 29715771 DOI: 10.1364/oe.26.007965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
Fluorescence phase-shifting interferometry (FPSI) is an optical technique that coherently combines the phase-shifted 4π steradian emission wavefronts of a single fluorescent emitter to obtain multiple interferograms from which the emitter axial displacement can be retrieved with high precision. Here, we study the axial displacement sensitivity in 4-step FPSI within the framework of maximum-likelihood (ML) phase estimation. Using Monte-Carlo simulations, we show that regardless of the method used to preprocess the measured interferograms, the variance of the ML estimate of the axial displacement approaches the Cramér-Rao lower bound and is closely limited from above by the variance of the classical 4-step phase shifting estimator. The difference between these lower and upper bounds depends on the interferogram visibility and signal-to-noise-ratio (SNR), with a percentage change of up to 29% that yields an absolute change of a few sub-nanometers to some nanometers for SNRs larger than ~5. Our results suggest that for these levels of SNR, the use of the computationally simpler classical 4-step phase shifting estimation can be adequate to accurately determine axial displacements in FPSI, as we also experimentally verified. FPSI interferograms with lower SNR but good visibility can benefit from the use of the ML estimator, provided that the spatiotemporal phase stability of the FPSI system is high.
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249
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Spatial organization and dynamics of RNase E and ribosomes in Caulobacter crescentus. Proc Natl Acad Sci U S A 2018; 115:E3712-E3721. [PMID: 29610352 DOI: 10.1073/pnas.1721648115] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We report the dynamic spatial organization of Caulobacter crescentus RNase E (RNA degradosome) and ribosomal protein L1 (ribosome) using 3D single-particle tracking and superresolution microscopy. RNase E formed clusters along the central axis of the cell, while weak clusters of ribosomal protein L1 were deployed throughout the cytoplasm. These results contrast with RNase E and ribosome distribution in Escherichia coli, where RNase E colocalizes with the cytoplasmic membrane and ribosomes accumulate in polar nucleoid-free zones. For both RNase E and ribosomes in Caulobacter, we observed a decrease in confinement and clustering upon transcription inhibition and subsequent depletion of nascent RNA, suggesting that RNA substrate availability for processing, degradation, and translation facilitates confinement and clustering. Importantly, RNase E cluster positions correlated with the subcellular location of chromosomal loci of two highly transcribed rRNA genes, suggesting that RNase E's function in rRNA processing occurs at the site of rRNA synthesis. Thus, components of the RNA degradosome and ribosome assembly are spatiotemporally organized in Caulobacter, with chromosomal readout serving as the template for this organization.
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250
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Moringo NA, Shen H, Bishop LDC, Wang W, Landes CF. Enhancing Analytical Separations Using Super-Resolution Microscopy. Annu Rev Phys Chem 2018; 69:353-375. [PMID: 29490205 DOI: 10.1146/annurev-physchem-052516-045018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Super-resolution microscopy is becoming an invaluable tool to investigate structure and dynamics driving protein interactions at interfaces. In this review, we highlight the applications of super-resolution microscopy for quantifying the physics and chemistry that occur between target proteins and stationary-phase supports during chromatographic separations. Our discussion concentrates on the newfound ability of super-resolved single-protein spectroscopy to inform theoretical parameters via quantification of adsorption-desorption dynamics, protein unfolding, and nanoconfined transport.
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Affiliation(s)
| | - Hao Shen
- Department of Chemistry, Rice University, Houston, Texas 77251, USA;
| | - Logan D C Bishop
- Department of Chemistry, Rice University, Houston, Texas 77251, USA;
| | - Wenxiao Wang
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77251, USA
| | - Christy F Landes
- Department of Chemistry, Rice University, Houston, Texas 77251, USA; .,Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77251, USA.,Smalley-Curl Institute, Rice University, Houston, Texas 77251, USA
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