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Xu Y, Jin L, Toomre D. Imaging Single-Vesicle Exocytosis with Total Internal Reflection Fluorescence Microscopy (TIRFM). Methods Mol Biol 2022; 2473:157-164. [PMID: 35819765 DOI: 10.1007/978-1-0716-2209-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Total internal reflection fluorescence microscopy (TIRFM) provides extremely thin optical sectioning with excellent signal-to-noise ratios, which allows for visualization of membrane dynamics at the cell surface with superb spatiotemporal resolution. In this chapter, TIRFM is used to record and analyze exocytosis of single glucose transporter-4 (GLUT4) containing vesicles in 3T3-L1 adipocytes.
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Affiliation(s)
- Yingke Xu
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, China.
| | - Luhong Jin
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, China
| | - Derek Toomre
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
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2
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Liu Z, Jin L, Chen J, Fang Q, Ablameyko S, Yin Z, Xu Y. A survey on applications of deep learning in microscopy image analysis. Comput Biol Med 2021; 134:104523. [PMID: 34091383 DOI: 10.1016/j.compbiomed.2021.104523] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 01/12/2023]
Abstract
Advanced microscopy enables us to acquire quantities of time-lapse images to visualize the dynamic characteristics of tissues, cells or molecules. Microscopy images typically vary in signal-to-noise ratios and include a wealth of information which require multiple parameters and time-consuming iterative algorithms for processing. Precise analysis and statistical quantification are often needed for the understanding of the biological mechanisms underlying these dynamic image sequences, which has become a big challenge in the field. As deep learning technologies develop quickly, they have been applied in bioimage processing more and more frequently. Novel deep learning models based on convolution neural networks have been developed and illustrated to achieve inspiring outcomes. This review article introduces the applications of deep learning algorithms in microscopy image analysis, which include image classification, region segmentation, object tracking and super-resolution reconstruction. We also discuss the drawbacks of existing deep learning-based methods, especially on the challenges of training datasets acquisition and evaluation, and propose the potential solutions. Furthermore, the latest development of augmented intelligent microscopy that based on deep learning technology may lead to revolution in biomedical research.
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Affiliation(s)
- Zhichao Liu
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 310058, China
| | - Luhong Jin
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 310058, China
| | - Jincheng Chen
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 310058, China
| | - Qiuyu Fang
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China
| | - Sergey Ablameyko
- National Academy of Sciences, United Institute of Informatics Problems, Belarusian State University, Minsk, 220012, Belarus
| | - Zhaozheng Yin
- AI Institute, Department of Biomedical Informatics and Department of Computer Science, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Yingke Xu
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China; Department of Endocrinology, The Affiliated Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 310058, China.
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3
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Three-dimensional total-internal reflection fluorescence nanoscopy with nanometric axial resolution by photometric localization of single molecules. Nat Commun 2021; 12:517. [PMID: 33483489 PMCID: PMC7822951 DOI: 10.1038/s41467-020-20863-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 12/17/2020] [Indexed: 01/06/2023] Open
Abstract
Single-molecule localization microscopy enables far-field imaging with lateral resolution in the range of 10 to 20 nanometres, exploiting the fact that the centre position of a single-molecule’s image can be determined with much higher accuracy than the size of that image itself. However, attaining the same level of resolution in the axial (third) dimension remains challenging. Here, we present Supercritical Illumination Microscopy Photometric z-Localization with Enhanced Resolution (SIMPLER), a photometric method to decode the axial position of single molecules in a total internal reflection fluorescence microscope. SIMPLER requires no hardware modification whatsoever to a conventional total internal reflection fluorescence microscope and complements any 2D single-molecule localization microscopy method to deliver 3D images with nearly isotropic nanometric resolution. Performance examples include SIMPLER-direct stochastic optical reconstruction microscopy images of the nuclear pore complex with sub-20 nm axial localization precision and visualization of microtubule cross-sections through SIMPLER-DNA points accumulation for imaging in nanoscale topography with sub-10 nm axial localization precision. Achieving high axial resolution is challenging in single-molecule localization microscopy. Here, the authors present a photometric method to decode the axial position of single molecules in a total internal reflection fluorescence microscope without hardware modification, and show nearly isotropic nanometric resolution.
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4
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Yin S, Tien M, Yang H. Prior-Apprised Unsupervised Learning of Subpixel Curvilinear Features in Low Signal/Noise Images. Biophys J 2020; 118:2458-2469. [PMID: 32359407 PMCID: PMC7231927 DOI: 10.1016/j.bpj.2020.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/07/2020] [Accepted: 04/09/2020] [Indexed: 11/16/2022] Open
Abstract
Many biophysical problems involve molecular and nanoscale targets moving next to a curvilinear track, e.g., a cytosolic cargo transported by motor proteins moving along a microtubule. For this type of problem, fluorescence imaging is usually the primary tool of choice. There is, however, an ∼20-fold mismatch between target-localization precision and track-imaging resolution such that questions requiring high-fidelity definition of the target's track remain inaccessible. On the other hand, if the contextual image of the tracks can be refined to a level comparable to that of the target, many intuitive yet mechanistically important issues can begin to be addressed. This work demonstrates that it is possible to statistically infer, to subpixel precision, curvilinear features in a low signal/noise image. This is achieved by a framework that consists of three stages: the Hessian-based feature enhancement, the subimage feature sampling and registration, and the statistical learning of the underlying curvilinear structure using a new, to our knowledge, method developed here for inferring the principal curves. In each stage, the descriptive prior information that the features come from curvilinear elements is explicitly taken into account. It is fully automated without user supervision, which is distinctly different from approaches that require user seeding or well-defined training data sets. Computer simulations of realistic images are used to investigate the performance of the framework and its implementation. The characterization results suggest that curvilinear features are refined to the same order of precision as that of the target and that the bootstrap confidence intervals from the analysis allow an estimate for the statistical bounds of the simulated "true" curve. Also shown are analyses of experimental images from three different microscopy modalities: two-photon laser-scanning microscopy, epifluorescence microscopy, and total internal reflection fluorescence microscopy. The practical application of this prior-apprised unsupervised learning framework as well as its potential outlook are discussed.
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Affiliation(s)
- Shuhui Yin
- Department of Chemistry, Princeton University, Princeton, New Jersey
| | - Ming Tien
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania
| | - Haw Yang
- Department of Chemistry, Princeton University, Princeton, New Jersey.
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5
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Stehr F, Stein J, Schueder F, Schwille P, Jungmann R. Flat-top TIRF illumination boosts DNA-PAINT imaging and quantification. Nat Commun 2019; 10:1268. [PMID: 30894522 PMCID: PMC6426843 DOI: 10.1038/s41467-019-09064-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/19/2019] [Indexed: 11/09/2022] Open
Abstract
Super-resolution (SR) techniques have extended the optical resolution down to a few nanometers. However, quantitative treatment of SR data remains challenging due to its complex dependence on a manifold of experimental parameters. Among the different SR variants, DNA-PAINT is relatively straightforward to implement, since it achieves the necessary ‘blinking’ without the use of rather complex optical or chemical activation schemes. However, it still suffers from image and quantification artifacts caused by inhomogeneous optical excitation. Here we demonstrate that several experimental challenges can be alleviated by introducing a segment-wise analysis approach and ultimately overcome by implementing a flat-top illumination profile for TIRF microscopy using a commercially-available beam-shaping device. The improvements with regards to homogeneous spatial resolution and precise kinetic information over the whole field-of-view were quantitatively assayed using DNA origami and cell samples. Our findings open the door to high-throughput DNA-PAINT studies with thus far unprecedented accuracy for quantitative data interpretation. The use of TIRF microscopy for DNA-PAINT experiments is limited by inhomogeneous illumination. Here the authors show that quantitative analysis of single-molecule TIRF experiments can be improved by using a segment-wise analysis approach and overcome by using a beam-shaping device to give a flat-top illumination profile.
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Affiliation(s)
- Florian Stehr
- Max Planck Institute of Biochemistry, 82152, Martinsried, Munich, Germany
| | - Johannes Stein
- Max Planck Institute of Biochemistry, 82152, Martinsried, Munich, Germany
| | - Florian Schueder
- Max Planck Institute of Biochemistry, 82152, Martinsried, Munich, Germany.,Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539, Munich, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, 82152, Martinsried, Munich, Germany.
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, 82152, Martinsried, Munich, Germany. .,Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539, Munich, Germany.
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6
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Archetti A, Glushkov E, Sieben C, Stroganov A, Radenovic A, Manley S. Waveguide-PAINT offers an open platform for large field-of-view super-resolution imaging. Nat Commun 2019; 10:1267. [PMID: 30894525 PMCID: PMC6427008 DOI: 10.1038/s41467-019-09247-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/19/2019] [Indexed: 11/18/2022] Open
Abstract
Super-resolution microscopies based on the localization of single molecules have been widely adopted due to their demonstrated performance and their accessibility resulting from open software and simple hardware. The PAINT method for localization microscopy offers improved resolution over photoswitching methods, since it is less prone to sparse sampling of structures and provides higher localization precision. Here, we show that waveguides enable increased throughput and data quality for PAINT, by generating a highly uniform ~100 × 2000 µm2 area evanescent field for TIRF illumination. To achieve this, we designed and fabricated waveguides optimized for efficient light coupling and propagation, incorporating a carefully engineered input facet and taper. We also developed a stable, low-cost microscope and 3D-printable waveguide chip holder for easy alignment and imaging. We demonstrate the capabilities of our open platform by using DNA-PAINT to image multiple whole cells or hundreds of origami structures in a single field of view. TIRF imaging is limited by the size and uniformity of the illumination. Here the authors present a waveguide solution to create a large area of uniform evanescent illumination suitable for single molecule imaging coupled with a customised sample holder containing a reservoir for DNA-PAINT solutions.
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Affiliation(s)
- Anna Archetti
- Laboratory of Experimental Biophysics, Institutes of Physics and Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Evgenii Glushkov
- Laboratory of Nanoscale Biology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Christian Sieben
- Laboratory of Experimental Biophysics, Institutes of Physics and Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Anton Stroganov
- Laboratory of Experimental Biophysics, Institutes of Physics and Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.,Laboratory of Nanoscale Biology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institutes of Physics and Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
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7
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Soubies E, Radwanska A, Grall D, Blanc-Féraud L, Van Obberghen-Schilling E, Schaub S. Nanometric axial resolution of fibronectin assembly units achieved with an efficient reconstruction approach for multi-angle-TIRF microscopy. Sci Rep 2019; 9:1926. [PMID: 30760745 PMCID: PMC6374485 DOI: 10.1038/s41598-018-36119-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/08/2018] [Indexed: 02/01/2023] Open
Abstract
High resolution imaging of molecules at the cell-substrate interface is required for understanding key biological processes. Here we propose a complete pipeline for multi-angle total internal reflection fluorescence microscopy (MA-TIRF) going from instrument design and calibration procedures to numerical reconstruction. Our custom setup is endowed with a homogeneous field illumination and precise excitation beam angle. Given a set of MA-TIRF acquisitions, we deploy an efficient joint deconvolution/reconstruction algorithm based on a variational formulation of the inverse problem. This algorithm offers the possibility of using various regularizations and can run on graphics processing unit (GPU) for rapid reconstruction. Moreover, it can be easily used with other MA-TIRF devices and we provide it as an open-source software. This ensemble has enabled us to visualize and measure with unprecedented nanometric resolution, the depth of molecular components of the fibronectin assembly machinery at the basal surface of endothelial cells.
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Affiliation(s)
- Emmanuel Soubies
- Université Côte d'Azur, CNRS, Inria, I3S, France. .,Biomedical Imaging Group, EPFL, Lausanne, Switzerland.
| | | | | | | | | | - Sébastien Schaub
- Université Côte d'Azur, CNRS, Inria, I3S, France. .,Université Côte d'Azur, CNRS, Inserm, iBV, France.
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8
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Li J, Han W, Li Y, Chen Y, Shang Y, Chen Y, Gui Z. Inverse problem based on the fast alternating direction method of multipliers algorithm in multiangle total internal reflection fluorescence microscopy. APPLIED OPTICS 2018; 57:9828-9834. [PMID: 30462018 DOI: 10.1364/ao.57.009828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/22/2018] [Indexed: 06/09/2023]
Abstract
Multiangle total internal reflection fluorescence microscopy (TIRFM) has become one of the most important techniques for achieving axial superresolution. The key process in this technique is solving the inverse problem. This paper applies an improved alternating direction method of multipliers algorithm to solve the inverse problem and validates the accuracy of the algorithm by reconstructing simulated microtubule structures in multiangle TIRFM images. The reconstruction times for different algorithms and the convergence speeds of the improved and original algorithms are compared. Experimental results show that the improved algorithm can achieve an axial resolution of 40 nm, reduce the influence of the penalty parameter on convergence, and improve the convergence speed of the iterative process while ensuring image reconstruction quality. Based on the algorithm, a three-dimensional image with the depth information of microtubules and mitochondria is reconstructed.
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9
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Zhang Z, Xia S, Kanchanawong P. An integrated enhancement and reconstruction strategy for the quantitative extraction of actin stress fibers from fluorescence micrographs. BMC Bioinformatics 2017; 18:268. [PMID: 28532442 PMCID: PMC5440974 DOI: 10.1186/s12859-017-1684-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 05/11/2017] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The stress fibers are prominent organization of actin filaments that perform important functions in cellular processes such as migration, polarization, and traction force generation, and whose collective organization reflects the physiological and mechanical activities of the cells. Easily visualized by fluorescence microscopy, the stress fibers are widely used as qualitative descriptors of cell phenotypes. However, due to the complexity of the stress fibers and the presence of other actin-containing cellular features, images of stress fibers are relatively challenging to quantitatively analyze using previously developed approaches, requiring significant user intervention. This poses a challenge for the automation of their detection, segmentation, and quantitative analysis. RESULT Here we describe an open-source software package, SFEX (Stress Fiber Extractor), which is geared for efficient enhancement, segmentation, and analysis of actin stress fibers in adherent tissue culture cells. Our method made use of a carefully chosen image filtering technique to enhance filamentous structures, effectively facilitating the detection and segmentation of stress fibers by binary thresholding. We subdivided the skeletons of stress fiber traces into piecewise-linear fragments, and used a set of geometric criteria to reconstruct the stress fiber networks by pairing appropriate fiber fragments. Our strategy enables the trajectory of a majority of stress fibers within the cells to be comprehensively extracted. We also present a method for quantifying the dimensions of the stress fibers using an image gradient-based approach. We determine the optimal parameter space using sensitivity analysis, and demonstrate the utility of our approach by analyzing actin stress fibers in cells cultured on various micropattern substrates. CONCLUSION We present an open-source graphically-interfaced computational tool for the extraction and quantification of stress fibers in adherent cells with minimal user input. This facilitates the automated extraction of actin stress fibers from fluorescence images. We highlight their potential uses by analyzing images of cells with shapes constrained by fibronectin micropatterns. The method we reported here could serve as the first step in the detection and characterization of the spatial properties of actin stress fibers to enable further detailed morphological analysis.
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Affiliation(s)
- Zhen Zhang
- Mechanobiology Institute, Singapore, 117411, Republic of Singapore
| | - Shumin Xia
- Mechanobiology Institute, Singapore, 117411, Republic of Singapore
| | - Pakorn Kanchanawong
- Mechanobiology Institute, Singapore, 117411, Republic of Singapore.
- Department of Biomedical Engineering, National University of Singapore, Singapore, 117411, Republic of Singapore.
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10
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Axial superresolution via multiangle TIRF microscopy with sequential imaging and photobleaching. Proc Natl Acad Sci U S A 2016; 113:4368-73. [PMID: 27044072 DOI: 10.1073/pnas.1516715113] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report superresolution optical sectioning using a multiangle total internal reflection fluorescence (TIRF) microscope. TIRF images were constructed from several layers within a normal TIRF excitation zone by sequentially imaging and photobleaching the fluorescent molecules. The depth of the evanescent wave at different layers was altered by tuning the excitation light incident angle. The angle was tuned from the highest (the smallest TIRF depth) toward the critical angle (the largest TIRF depth) to preferentially photobleach fluorescence from the lower layers and allow straightforward observation of deeper structures without masking by the brighter signals closer to the coverglass. Reconstruction of the TIRF images enabled 3D imaging of biological samples with 20-nm axial resolution. Two-color imaging of epidermal growth factor (EGF) ligand and clathrin revealed the dynamics of EGF-activated clathrin-mediated endocytosis during internalization. Furthermore, Bayesian analysis of images collected during the photobleaching step of each plane enabled lateral superresolution (<100 nm) within each of the sections.
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11
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Chowdary PD, Che DL, Zhang K, Cui B. Retrograde NGF axonal transport--motor coordination in the unidirectional motility regime. Biophys J 2016; 108:2691-703. [PMID: 26039170 DOI: 10.1016/j.bpj.2015.04.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 04/26/2015] [Accepted: 04/29/2015] [Indexed: 10/23/2022] Open
Abstract
We present a detailed motion analysis of retrograde nerve growth factor (NGF) endosomes in axons to show that mechanical tugs-of-war and intracellular motor regulation are complimentary features of the near-unidirectional endosome directionality. We used quantum dots to fluorescently label NGF and acquired trajectories of retrograde quantum-dot-NGF-endosomes with <20-nm accuracy at 32 Hz in microfluidic neuron cultures. Using a combination of transient motion analysis and Bayesian parsing, we partitioned the trajectories into sustained periods of retrograde (dynein-driven) motion, constrained pauses, and brief anterograde (kinesin-driven) reversals. The data shows many aspects of mechanical tugs-of-war and multiple-motor mechanics in NGF-endosome transport. However, we found that stochastic mechanical models based on in vitro parameters cannot simulate the experimental data, unless the microtubule-binding affinity of kinesins on the endosome is tuned down by 10 times. Specifically, the simulations suggest that the NGF-endosomes are driven on average by 5-6 active dyneins and 1-2 downregulated kinesins. This is also supported by the dynamics of endosomes detaching under load in axons, showcasing the cooperativity of multiple dyneins and the subdued activity of kinesins. We discuss the possible motor coordination mechanism consistent with motor regulation and tugs-of-war for future investigations.
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Affiliation(s)
| | - Daphne L Che
- Department of Chemistry, Stanford University, Stanford, California
| | - Kai Zhang
- Department of Chemistry, Stanford University, Stanford, California
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, California.
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12
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Mutch LJ, Howden JD, Jenner EPL, Poulter NS, Rappoport JZ. Polarised clathrin-mediated endocytosis of EGFR during chemotactic invasion. Traffic 2015; 15:648-64. [PMID: 24921075 PMCID: PMC4309520 DOI: 10.1111/tra.12165] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Directed cell migration is critical for numerous physiological processes including development and wound healing. However chemotaxis is also exploited during cancer progression. Recent reports have suggested links between vesicle trafficking pathways and directed cell migration. Very little is known about the potential roles of endocytosis pathways during metastasis. Therefore we performed a series of studies employing a previously characterised model for chemotactic invasion of cancer cells to assess specific hypotheses potentially linking endocytosis to directed cell migration. Our results demonstrate that clathrin-mediated endocytosis is indispensable for epidermal growth factor (EGF) directed chemotactic invasion of MDA-MB-231 cells. Conversely, caveolar endocytosis is not required in this mode of migration. We further found that chemoattractant receptor (EGFR) trafficking occurs by clathrin-mediated endocytosis and is polarised towards the front of migrating cells. However, we found no role for clathrin-mediated endocytosis in focal adhesion disassembly in this migration model. Thus, this study has characterised the role of endocytosis during chemotactic invasion and has identified functions mechanistically linking clathrin-mediated endocytosis to directed cell motility.
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Affiliation(s)
- Laura Jane Mutch
- School of Biosciences, The University of BirminghamEdgbaston, Birmingham, B15 2TT, UK
| | - Jake Davey Howden
- School of Biosciences, The University of BirminghamEdgbaston, Birmingham, B15 2TT, UK
| | | | - Natalie Sarah Poulter
- Centre for Cardiovascular Research, Institute for Biomedical Research, The College of Medical and Dental Sciences, The University of BirminghamEdgbaston, Birmingham, B15 2TT, UK
| | - Joshua Zachary Rappoport
- School of Biosciences, The University of BirminghamEdgbaston, Birmingham, B15 2TT, UK
- *Corresponding author: Joshua Z. Rappoport,
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13
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Boulanger J, Gueudry C, Münch D, Cinquin B, Paul-Gilloteaux P, Bardin S, Guérin C, Senger F, Blanchoin L, Salamero J. Fast high-resolution 3D total internal reflection fluorescence microscopy by incidence angle scanning and azimuthal averaging. Proc Natl Acad Sci U S A 2014; 111:17164-9. [PMID: 25404337 PMCID: PMC4260613 DOI: 10.1073/pnas.1414106111] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Total internal reflection fluorescence microscopy (TIRFM) is the method of choice to visualize a variety of cellular processes in particular events localized near the plasma membrane of live adherent cells. This imaging technique not relying on particular fluorescent probes provides a high sectioning capability. It is, however, restricted to a single plane. We present here a method based on a versatile design enabling fast multiwavelength azimuthal averaging and incidence angles scanning to computationally reconstruct 3D images sequences. We achieve unprecedented 50-nm axial resolution over a range of 800 nm above the coverslip. We apply this imaging modality to obtain structural and dynamical information about 3D actin architectures. We also temporally decipher distinct Rab11a-dependent exocytosis events in 3D at a rate of seven stacks per second.
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Affiliation(s)
| | - Charles Gueudry
- Plateforme Imagerie Cellulaire et Tissulaire-Infrastructure en Biologie Santé et Agronomie Institut Curie, 75005 Paris, France; Roper Scientific SAS, 91017 Evry, France; and
| | - Daniel Münch
- Plateforme Imagerie Cellulaire et Tissulaire-Infrastructure en Biologie Santé et Agronomie Institut Curie, 75005 Paris, France; Roper Scientific SAS, 91017 Evry, France; and
| | | | - Perrine Paul-Gilloteaux
- UMR144 CNRS/Institut Curie, 75005 Paris, France; Plateforme Imagerie Cellulaire et Tissulaire-Infrastructure en Biologie Santé et Agronomie Institut Curie, 75005 Paris, France
| | | | - Christophe Guérin
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, CNRS/Commissariat à l'Energie Atomique/Institut National de la Recherche Agronomique/Université Joseph Fourier, Grenoble 38054, France
| | - Fabrice Senger
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, CNRS/Commissariat à l'Energie Atomique/Institut National de la Recherche Agronomique/Université Joseph Fourier, Grenoble 38054, France
| | - Laurent Blanchoin
- Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire et Végétale, CNRS/Commissariat à l'Energie Atomique/Institut National de la Recherche Agronomique/Université Joseph Fourier, Grenoble 38054, France
| | - Jean Salamero
- UMR144 CNRS/Institut Curie, 75005 Paris, France; Plateforme Imagerie Cellulaire et Tissulaire-Infrastructure en Biologie Santé et Agronomie Institut Curie, 75005 Paris, France;
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14
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Liang L, Shen H, De Camilli P, Duncan JS. A novel multiple hypothesis based particle tracking method for clathrin mediated endocytosis analysis using fluorescence microscopy. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2014; 23:1844-57. [PMID: 24808351 PMCID: PMC4373089 DOI: 10.1109/tip.2014.2303633] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In order to quantitatively analyze biological images and study underlying mechanisms of the cellular and subcellular processes, it is often required to track a large number of particles involved in these processes. Manual tracking can be performed by the biologists, but the workload is very heavy. In this paper, we present an automatic particle tracking method for analyzing an essential subcellular process, namely clathrin mediated endocytosis. The framework of the tracking method is an extension of the classical multiple hypothesis tracking (MHT), and it is designed to manage trajectories, solve data association problems, and handle pseudo-splitting/merging events. In the extended MHT framework, particle tracking becomes evaluating two types of hypotheses. The first one is the trajectory-related hypothesis, to test whether a recovered trajectory is correct, and the second one is the observation-related hypothesis, to test whether an observation from an image belongs to a real particle. Here, an observation refers to a detected particle and its feature vector. To detect the particles in 2D fluorescence images taken using total internal reflection microscopy, the images are segmented into regions, and the features of the particles are obtained by fitting Gaussian mixture models into each of the image regions. Specific models are developed according to the properties of the particles. The proposed tracking method is demonstrated on synthetic data under different scenarios and applied to real data.
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Affiliation(s)
- Liang Liang
- Department of Electrical Engineering, Yale University, New Haven, CT 06511 USA
| | - Hongying Shen
- Department of Cell Biology, Yale University, New Haven, CT 06511 USA
| | - Pietro De Camilli
- Department of Cell Biology, Yale University, New Haven, CT 06511 USA
| | - James S. Duncan
- Department of Electrical Engineering, Biomedical Engineering and Diagnostic Radiology, Yale University, New Haven, CT 06511 USA
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15
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Rohou A, Grigorieff N. Frealix: model-based refinement of helical filament structures from electron micrographs. J Struct Biol 2014; 186:234-44. [PMID: 24657230 DOI: 10.1016/j.jsb.2014.03.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/12/2014] [Accepted: 03/13/2014] [Indexed: 12/20/2022]
Abstract
The structures of many helical protein filaments can be derived from electron micrographs of their suspensions in thin films of vitrified aqueous solutions. The most successful and generally-applicable approach treats short segments of these filaments as independent "single particles", yielding near-atomic resolution for rigid and well-ordered filaments. The single-particle approach can also accommodate filament deformations, yielding sub-nanometer resolution for more flexible filaments. However, in the case of thin and flexible filaments, such as some amyloid-β (Aβ) fibrils, the single-particle approach may fail because helical segments can be curved or otherwise distorted and their alignment can be inaccurate due to low contrast in the micrographs. We developed new software called Frealix that allows the use of arbitrarily short filament segments during alignment to approximate even high curvatures. All segments in a filament are aligned simultaneously with constraints that ensure that they connect to each other in space to form a continuous helical structure. In this paper, we describe the algorithm and benchmark it against datasets of Aβ(1-40) fibrils and tobacco mosaic virus (TMV), both analyzed in earlier work. In the case of TMV, our algorithm achieves similar results to single-particle analysis. In the case of Aβ(1-40) fibrils, we match the previously-obtained resolution but we are also able to obtain reliable alignments and ∼8-Å reconstructions from curved filaments. Our algorithm also offers a detailed characterization of filament deformations in three dimensions and enables a critical evaluation of the worm-like chain model for biological filaments.
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Affiliation(s)
- Alexis Rohou
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA; Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Nikolaus Grigorieff
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA; Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
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16
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Stender AS, Marchuk K, Liu C, Sander S, Meyer MW, Smith EA, Neupane B, Wang G, Li J, Cheng JX, Huang B, Fang N. Single cell optical imaging and spectroscopy. Chem Rev 2013; 113:2469-527. [PMID: 23410134 PMCID: PMC3624028 DOI: 10.1021/cr300336e] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Anthony S. Stender
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Kyle Marchuk
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Chang Liu
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Suzanne Sander
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Matthew W. Meyer
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Emily A. Smith
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Bhanu Neupane
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Gufeng Wang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Junjie Li
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Ji-Xin Cheng
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Bo Huang
- Department of Pharmaceutical Chemistry and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Ning Fang
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
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Liang L, Shen H, De Camilli P, Toomre DK, Duncan JS. An expectation maximization based method for subcellular particle tracking using multi-angle TIRF microscopy. MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION : MICCAI ... INTERNATIONAL CONFERENCE ON MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION 2011; 14:629-36. [PMID: 22003671 PMCID: PMC3648983 DOI: 10.1007/978-3-642-23623-5_79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Multi-angle total internal reflection fluorescence microscopy (MA-TIRFM) is a new generation of TIRF microscopy to study cellular processes near dorsal cell membrane in 4 dimensions (3D+t). To perform quantitative analysis using MA-TIRFM, it is necessary to track subcellular particles in these processes. In this paper, we propose a method based on a MAP framework for automatic particle tracking and apply it to track clathrin coated pits (CCPs). The expectation maximization (EM) algorithm is employed to solve the MAP problem. To provide the initial estimations for the EM algorithm, we develop a forward filter based on the most probable trajectory (MPT) filter. Multiple linear models are used to model particle dynamics. For CCP tracking, we use two linear models to describe constrained Brownian motion and fluorophore variation according to CCP properties. The tracking method is evaluated on synthetic data and results show that it has high accuracy. The result on real data confirmed by human expert cell biologists is also presented.
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