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Chen X, Li Y, Chen P, Yao H, Ye T. High speed two-photon laser scanning stereomicroscopy for three-dimension tracking multiple particles simultaneously in three-dimension. FRONTIERS IN PHOTONICS 2022; 3:985474. [PMID: 38784836 PMCID: PMC11112984 DOI: 10.3389/fphot.2022.985474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
In this paper, we will describe a video rate two-photon laser scanning stereomicroscopy for imaging-based three-dimensional particle tracking. Using a resonant galvanometer, we have now achieved 30 volumes per second (frame size 512 × 512) in volumetric imaging. Owing to the pulse multiplexing and demultiplexing techniques, the system does not suffer the speed loss for taking two parallax views of a volume. The switching time between left and right views is reduced to several nanoseconds. The extremely fast view switching and high volumetric imaging speed allow us to track fast transport processes of nanoparticles in deep light-scattering media. For instance, in 1%-intralipid solution and fibrillar scaffolds, the tracking penetration depth can be around 400 μm.
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Affiliation(s)
- Xun Chen
- Department of Bioengineering, CU-MUSC Bioengineering Program, Clemson University, Charleston, SC, United States
- School of Engineering Medicine, Beihang University, Beijing, China
| | - Yang Li
- Department of Bioengineering, CU-MUSC Bioengineering Program, Clemson University, Charleston, SC, United States
| | - Peng Chen
- Department of Bioengineering, CU-MUSC Bioengineering Program, Clemson University, Charleston, SC, United States
| | - Hai Yao
- Department of Bioengineering, CU-MUSC Bioengineering Program, Clemson University, Charleston, SC, United States
| | - Tong Ye
- Department of Bioengineering, CU-MUSC Bioengineering Program, Clemson University, Charleston, SC, United States
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, United States
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2
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Gagliano G, Nelson T, Saliba N, Vargas-Hernández S, Gustavsson AK. Light Sheet Illumination for 3D Single-Molecule Super-Resolution Imaging of Neuronal Synapses. Front Synaptic Neurosci 2021; 13:761530. [PMID: 34899261 PMCID: PMC8651567 DOI: 10.3389/fnsyn.2021.761530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/27/2021] [Indexed: 01/02/2023] Open
Abstract
The function of the neuronal synapse depends on the dynamics and interactions of individual molecules at the nanoscale. With the development of single-molecule super-resolution microscopy over the last decades, researchers now have a powerful and versatile imaging tool for mapping the molecular mechanisms behind the biological function. However, imaging of thicker samples, such as mammalian cells and tissue, in all three dimensions is still challenging due to increased fluorescence background and imaging volumes. The combination of single-molecule imaging with light sheet illumination is an emerging approach that allows for imaging of biological samples with reduced fluorescence background, photobleaching, and photodamage. In this review, we first present a brief overview of light sheet illumination and previous super-resolution techniques used for imaging of neurons and synapses. We then provide an in-depth technical review of the fundamental concepts and the current state of the art in the fields of three-dimensional single-molecule tracking and super-resolution imaging with light sheet illumination. We review how light sheet illumination can improve single-molecule tracking and super-resolution imaging in individual neurons and synapses, and we discuss emerging perspectives and new innovations that have the potential to enable and improve single-molecule imaging in brain tissue.
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Affiliation(s)
- Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Tyler Nelson
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Sofía Vargas-Hernández
- Department of Chemistry, Rice University, Houston, TX, United States
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
- Department of Biosciences, Rice University, Houston, TX, United States
- Laboratory for Nanophotonics, Rice University, Houston, TX, United States
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3
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Bernardello M, Gora RJ, Van Hage P, Castro-Olvera G, Gualda EJ, Schaaf MJM, Loza-Alvarez P. Analysis of intracellular protein dynamics in living zebrafish embryos using light-sheet fluorescence single-molecule microscopy. BIOMEDICAL OPTICS EXPRESS 2021; 12:6205-6227. [PMID: 34745730 PMCID: PMC8547987 DOI: 10.1364/boe.435103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Single-molecule microscopy techniques have emerged as useful tools to image individual molecules and analyze their dynamics inside cells, but their application has mostly been restricted to cell cultures. Here, a light-sheet fluorescence microscopy setup is presented for imaging individual proteins inside living zebrafish embryos. The optical configuration makes this design accessible to many laboratories and a dedicated sample-mounting system ensures sample viability and mounting flexibility. Using this setup, we have analyzed the dynamics of individual glucocorticoid receptors, which demonstrates that this approach creates multiple possibilities for the analysis of intracellular protein dynamics in intact living organisms.
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Affiliation(s)
- Matteo Bernardello
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, 08860, Spain
- Equal contribution
| | - Radoslaw J Gora
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Equal contribution
| | - Patrick Van Hage
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Gustavo Castro-Olvera
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, 08860, Spain
| | - Emilio J Gualda
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, 08860, Spain
| | - Marcel J M Schaaf
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Equal contribution
| | - Pablo Loza-Alvarez
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, 08860, Spain
- Equal contribution
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4
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Chen X, Liu T, Qin X, Nguyen QQ, Lee SK, Lee C, Ren Y, Chu J, Zhu G, Yoon TY, Park CY, Park H. Simultaneous Real-Time Three-Dimensional Localization and FRET Measurement of Two Distinct Particles. NANO LETTERS 2021; 21:7479-7485. [PMID: 34491760 DOI: 10.1021/acs.nanolett.1c01328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Many biological processes employ mechanisms involving the locations and interactions of multiple components. Given that most biological processes occur in three dimensions, the simultaneous measurement of three-dimensional locations and interactions is necessary. However, the simultaneous three-dimensional precise localization and measurement of interactions in real time remains challenging. Here, we report a new microscopy technique to localize two spectrally distinct particles in three dimensions with an accuracy (2.35σ) of tens of nanometers with an exposure time of 100 ms and to measure their real-time interactions using fluorescence resonance energy transfer (FRET) simultaneously. Using this microscope, we tracked two distinct vesicles containing t-SNAREs or v-SNARE in three dimensions and observed FRET simultaneously during single-vesicle fusion in real time, revealing the nanoscale motion and interactions of single vesicles in vesicle fusion. Thus, this study demonstrates that our microscope can provide detailed information about real-time three-dimensional nanoscale locations, motion, and interactions in biological processes.
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Affiliation(s)
- Xingxiang Chen
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Teng Liu
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xianan Qin
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Quang Quan Nguyen
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Sang Kwon Lee
- Department of Biological Sciences, School of Life Sciences, UNIST, 44919, Ulsan, Republic of Korea
| | - Chanwoo Lee
- School of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Yaguang Ren
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jun Chu
- Research Lab for Biomedical Optics and Molecular Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Tae-Young Yoon
- School of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Chan Young Park
- Department of Biological Sciences, School of Life Sciences, UNIST, 44919, Ulsan, Republic of Korea
| | - Hyokeun Park
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- State Key Laboratory of Molecular Neuroscience The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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5
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Inamoto J, Fukuda T, Inoue T, Shimizu K, Nishio K, Xia P, Matoba O, Awatsuji Y. Modularized microscope based on parallel phase-shifting digital holography for imaging of living biospecimens. JOURNAL OF BIOMEDICAL OPTICS 2020; 25:JBO-200277SSR. [PMID: 33277888 PMCID: PMC7716092 DOI: 10.1117/1.jbo.25.12.123706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
SIGNIFICANCE Parallel phase-shifting digital holographic microscope (PPSDHM) is powerful for three-dimensional (3D) measurements of dynamic specimens. However, the PPSDHM reported previously was directly fixed on the optical bench and imposed difficulties case, thus it is required to modify the specification of the microscope or transport the microscope to another location. AIM We present a modularized PPSDHM. We construct the proposed PPSDHM and demonstrate the 3D measurement capability of the PPSDHM. APPROACH The PPSDHM was designed as an inverted microscope to record transparent objects and modularized by integrating the optical elements of the PPSDHM on an optical breadboard. To demonstrate the effectiveness of the PPSDHM, we recorded a 3D motion-picture of moving Volvoxes at 1000 frames / s and carried out 3D tracking of the Volvoxes. RESULTS The PPSDHM was practically realized and 3D images of objects were successfully reconstructed from holograms recorded with a single-shot exposure. The 3D trajectories of Volvoxes were obtained from the reconstructed images. CONCLUSIONS We established a modularized PPSDHM that is capable of 3D image acquisition by integrating the optical elements of the PPSDHM on an optical breadboard. The recording capability of 3D motion-pictures of dynamic specimens was experimentally demonstrated by the PPSDHM.
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Affiliation(s)
- Junya Inamoto
- Kyoto Institute of Technology, Graduate School of Science and Technology, Kyoto, Japan
| | - Takahito Fukuda
- Kyoto Institute of Technology, Graduate School of Science and Technology, Kyoto, Japan
| | - Tomoyoshi Inoue
- Kyoto Institute of Technology, Graduate School of Science and Technology, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Kazuki Shimizu
- Kyoto Institute of Technology, Graduate School of Science and Technology, Kyoto, Japan
| | - Kenzo Nishio
- Kyoto Institute of Technology, Graduate School of Science and Technology, Kyoto, Japan
| | - Peng Xia
- National Institute of Advanced Industrial Science and Technology, National Metrology Institute of Japan, Tsukuba, Japan
| | - Osamu Matoba
- Kobe University, Graduate School of System Informatics, Department of Systems Science, Kobe, Japan
| | - Yasuhiro Awatsuji
- Kyoto Institute of Technology, Graduate School of Science and Technology, Kyoto, Japan
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6
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Sharma KK, Marzinek JK, Tantirimudalige SN, Bond PJ, Wohland T. Single-molecule studies of flavivirus envelope dynamics: Experiment and computation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 143:38-51. [PMID: 30223001 DOI: 10.1016/j.pbiomolbio.2018.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/06/2018] [Accepted: 09/11/2018] [Indexed: 12/11/2022]
Abstract
Flaviviruses are simple enveloped viruses exhibiting complex structural and functional heterogeneities. Decades of research have provided crucial basic insights, antiviral medication and moderately successful gene therapy trials. The most infectious particle is, however, not always the most abundant one in a population, questioning the utility of classic ensemble-averaging virology approaches. Indeed, viral replication is often not particularly efficient, prone to errors or containing parallel routes. Here, we review different single-molecule sensitive fluorescence methods that are employed to investigate flaviviruses. In particular, we review how (i) time-resolved Förster resonance energy transfer (trFRET) was applied to probe dengue envelope conformations; (ii) FRET-fluorescence correlation spectroscopy to investigate dengue envelope intrinsic dynamics and (iii) single particle tracking to follow the path of dengue viruses in cells. We also discuss how such methods may be supported by molecular dynamics (MD) simulations over a range of spatio-temporal scales, to provide complementary data on the structure and dynamics of flaviviral systems. We describe recent improvements in multiscale MD approaches that allowed the simulation of dengue particle envelopes in near-atomic resolution. We hope this review is an incentive for setting up and applying similar single-molecule studies and combine them with MD simulations to investigate structural dynamics of entire flavivirus particles over the nanosecond-to-millisecond time-scale and follow viruses during infection in cells over milliseconds to minutes.
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Affiliation(s)
- Kamal Kant Sharma
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Jan K Marzinek
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Sarala Neomi Tantirimudalige
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Peter J Bond
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Department of Chemistry, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore.
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7
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Shen H, Tauzin LJ, Baiyasi R, Wang W, Moringo N, Shuang B, Landes CF. Single Particle Tracking: From Theory to Biophysical Applications. Chem Rev 2017; 117:7331-7376. [PMID: 28520419 DOI: 10.1021/acs.chemrev.6b00815] [Citation(s) in RCA: 264] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
After three decades of developments, single particle tracking (SPT) has become a powerful tool to interrogate dynamics in a range of materials including live cells and novel catalytic supports because of its ability to reveal dynamics in the structure-function relationships underlying the heterogeneous nature of such systems. In this review, we summarize the algorithms behind, and practical applications of, SPT. We first cover the theoretical background including particle identification, localization, and trajectory reconstruction. General instrumentation and recent developments to achieve two- and three-dimensional subdiffraction localization and SPT are discussed. We then highlight some applications of SPT to study various biological and synthetic materials systems. Finally, we provide our perspective regarding several directions for future advancements in the theory and application of SPT.
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Affiliation(s)
- Hao Shen
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Lawrence J Tauzin
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Rashad Baiyasi
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Wenxiao Wang
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Nicholas Moringo
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Bo Shuang
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Christy F Landes
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
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8
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Lin M, Qiao X, Liu Q, Shao C, Su X. Light-sheet-based 2D light scattering cytometry for label-free characterization of senescent cells. BIOMEDICAL OPTICS EXPRESS 2016; 7:5170-5181. [PMID: 28018733 PMCID: PMC5175560 DOI: 10.1364/boe.7.005170] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/03/2016] [Accepted: 11/11/2016] [Indexed: 05/24/2023]
Abstract
A light-sheet-based 2D light scattering cytometer is developed for label-free characterization of senescent cells. The light-sheet provides an illumination beam with controlled thickness for single cell excitation, and 2D light scattering patterns are obtained by using a defocused imaging method. The principle of this cytometer is validated by distinguishing microspheres with submicron resolution. Automatic classification of senescent and normal cells is achieved at single cell level by using the support vector machine (SVM) algorithm, where a sensitivity of 89.1% and a specificity of 96.4% are obtained. Our results suggest that the light-sheet-based 2D light scattering label-free cytometry has the capability to perform size differentiation of beads with submicron resolution and to classify different groups of cells without fluorescent labeling, showing the potential for clinical diagnosis of senescence-related diseases.
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Affiliation(s)
- Meiai Lin
- Institute of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong, 250061, China
| | - Xu Qiao
- Institute of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong, 250061, China
| | - Qiao Liu
- Key Laboratory of Experimental Teratology (Ministry of Education); Department of Molecular Medicine and Genetics, School of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Changshun Shao
- Key Laboratory of Experimental Teratology (Ministry of Education); Department of Molecular Medicine and Genetics, School of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xuantao Su
- Institute of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong, 250061, China
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9
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Ding Y, Li C. Dual-color multiple-particle tracking at 50-nm localization and over 100-µm range in 3D with temporal focusing two-photon microscopy. BIOMEDICAL OPTICS EXPRESS 2016; 7:4187-4197. [PMID: 27867724 PMCID: PMC5102526 DOI: 10.1364/boe.7.004187] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/09/2016] [Accepted: 09/14/2016] [Indexed: 05/12/2023]
Abstract
Nanoscale particle tracking in three dimensions is crucial to directly observe dynamics of molecules and nanoparticles in living cells. Here we present a three-dimensional particle tracking method based on temporally focused two-photon excitation. Multiple particles are imaged at 30 frames/s in volume up to 180 × 180 × 100 µm3. The spatial localization precision can reach 50 nm. We demonstrate its capability of tracking fast swimming microbes at speed of ~200 µm/s. Two-photon dual-color tracking is achieved by simultaneously exciting two kinds of fluorescent beads at 800 nm to demonstrate its potential in molecular interaction studies. Our method provides a simple wide-field fluorescence imaging approach for deep multiple-particle tracking.
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Affiliation(s)
- Yu Ding
- Department of Physics, The University of Texas at El Paso, 500 W University Avenue, El Paso, TX 79968, USA
| | - Chunqiang Li
- Department of Physics, The University of Texas at El Paso, 500 W University Avenue, El Paso, TX 79968, USA
- Border Biomedical Research Center, The University of Texas at El Paso, 500 W University Avenue, El Paso, TX 79968, USA
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10
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Yu B, Yu J, Li W, Cao B, Li H, Chen D, Niu H. Nanoscale three-dimensional single particle tracking by light-sheet-based double-helix point spread function microscopy. APPLIED OPTICS 2016; 55:449-53. [PMID: 26835916 DOI: 10.1364/ao.55.000449] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The double-helix point spread function (DH-PSF) microscopy has become an essential tool for nanoscale three-dimensional (3D) localization and tracking of single molecules in living cells. However, its localization precision is limited by fluorescent contrast in thick samples because the signal-to-noise ratio of the system is low due to the inherent low transfer function efficiency and background fluorescence. Here we combine DH-PSF microscopy with light-sheet illumination to eliminate out-of-focus background fluorescence for high-precision 3D single particle tracking. To demonstrate the capability of the method, we obtain the single fluorescent bead image with light-sheet illumination, with three-dimensional localization accuracy better than that of epi-illumination. We also show that the single fluorescent beads in agarose solution can be tracked, which demonstrates the possibility of our method for the study of dynamic processes in complex biological specimens.
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11
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Chien FC, Lien CH, Dai YH. Dual-color dynamic tracking of GM-CSF receptors/JAK2 kinases signaling activation using temporal focusing multiphoton fluorescence excitation and astigmatic imaging. OPTICS EXPRESS 2015; 23:30943-30955. [PMID: 26698726 DOI: 10.1364/oe.23.030943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The dual-color dynamic particle tracking approach that uses temporal focusing multiphoton fluorescence excitation and two-channel astigmatic imaging is utilized to track molecular trajectories in three dimensions to explore molecular interactions. Images of two fluorophores were obtained to extract their positions by optical sectioning excitation using a fast temporal focusing multiphoton excitation microscope (TFMPEM) and by the simultaneous collection of data in two channels. The presented pair of cylindrical lenses, which was used to adjust the astigmatism effect with the minimum shifting of the imaging plane, was more feasible and flexible than single cylindrical lens for aligning two separate detection channels in astigmatic imaging. The lateral and axial positioning resolutions were observed to be approximately 9-13 nm and 23-30 nm respectively, for the two fluorescence channels. The dynamic movement and binding behavior of clusters of GM-CSF receptors and JAK2 kinases in HeLa cells in the presence of GM-CSF ligands were observed. Therefore, the proposed dual-color tracking strategy is useful for the dynamic study of molecular interactions in living specimens with a fast frame rate, less photobleaching, better penetration depth, and minimum optical trapping force.
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12
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Perillo EP, Liu YL, Huynh K, Liu C, Chou CK, Hung MC, Yeh HC, Dunn AK. Deep and high-resolution three-dimensional tracking of single particles using nonlinear and multiplexed illumination. Nat Commun 2015. [PMID: 26219252 PMCID: PMC4532916 DOI: 10.1038/ncomms8874] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Molecular trafficking within cells, tissues and engineered three-dimensional multicellular models is critical to the understanding of the development and treatment of various diseases including cancer. However, current tracking methods are either confined to two dimensions or limited to an interrogation depth of ∼15 μm. Here we present a three-dimensional tracking method capable of quantifying rapid molecular transport dynamics in highly scattering environments at depths up to 200 μm. The system has a response time of 1 ms with a temporal resolution down to 50 μs in high signal-to-noise conditions, and a spatial localization precision as good as 35 nm. Built on spatiotemporally multiplexed two-photon excitation, this approach requires only one detector for three-dimensional particle tracking and allows for two-photon, multicolour imaging. Here we demonstrate three-dimensional tracking of epidermal growth factor receptor complexes at a depth of ∼100 μm in tumour spheroids. Existing single-particle tracking techniques are limited in terms of penetration depth, tracking range or temporal resolution. Here, Perillo et al. demonstrate three-dimensional particle tracking up to 200-μm depth, with 35-nm spatial localization and 50-μs resolution using multiplexed two-photon excitation.
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Affiliation(s)
- Evan P Perillo
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton Street, C0800, Austin, Texas 78712, USA
| | - Yen-Liang Liu
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton Street, C0800, Austin, Texas 78712, USA
| | - Khang Huynh
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton Street, C0800, Austin, Texas 78712, USA
| | - Cong Liu
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton Street, C0800, Austin, Texas 78712, USA
| | - Chao-Kai Chou
- 1] Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holocombe, Boulevard, Unit 108, Houston, Texas 77030-4009, USA [2] Center for Molecular Medicine and Graduate Institute of Cancer Biology, China Medical University, No. 91 Hsueh-Shih Road, Taichung 40402, Taiwan
| | - Mien-Chie Hung
- 1] Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holocombe, Boulevard, Unit 108, Houston, Texas 77030-4009, USA [2] Center for Molecular Medicine and Graduate Institute of Cancer Biology, China Medical University, No. 91 Hsueh-Shih Road, Taichung 40402, Taiwan
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton Street, C0800, Austin, Texas 78712, USA
| | - Andrew K Dunn
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton Street, C0800, Austin, Texas 78712, USA
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13
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Scherer KM, Spille JH, Sahl HG, Grein F, Kubitscheck U. The lantibiotic nisin induces lipid II aggregation, causing membrane instability and vesicle budding. Biophys J 2015; 108:1114-24. [PMID: 25762323 PMCID: PMC4375720 DOI: 10.1016/j.bpj.2015.01.020] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 12/19/2014] [Accepted: 01/23/2015] [Indexed: 10/23/2022] Open
Abstract
The antimicrobial peptide nisin exerts its activity by a unique dual mechanism. It permeates the cell membranes of Gram-positive bacteria by binding to the cell wall precursor Lipid II and inhibits cell wall synthesis. Binding of nisin to Lipid II induces the formation of large nisin-Lipid II aggregates in the membrane of bacteria as well as in Lipid II-doped model membranes. Mechanistic details of the aggregation process and its impact on membrane permeation are still unresolved. In our experiments, we found that fluorescently labeled nisin bound very inhomogeneously to bacterial membranes as a consequence of the strong aggregation due to Lipid II binding. A correlation between cell membrane damage and nisin aggregation was observed in vivo. To further investigate the aggregation process of Lipid II and nisin, we assessed its dynamics by single-molecule microscopy of fluorescently labeled Lipid II molecules in giant unilamellar vesicles using light-sheet illumination. We observed a continuous reduction of Lipid II mobility due to a steady growth of nisin-Lipid II aggregates as a function of time and nisin concentration. From the measured diffusion constants of Lipid II, we estimated that the largest aggregates contained tens of thousands of Lipid II molecules. Furthermore, we observed that the formation of large nisin-Lipid II aggregates induced vesicle budding in giant unilamellar vesicles. Thus, we propose a membrane permeation mechanism that is dependent on the continuous growth of nisin-Lipid II aggregation and probably involves curvature effects on the membrane.
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Affiliation(s)
- Katharina M Scherer
- Institute for Physical and Theoretical Chemistry, Pharmaceutical Microbiology Unit, Rheinische Friedrich-Wilhelms University Bonn, Bonn, Germany.
| | - Jan-Hendrik Spille
- Institute for Physical and Theoretical Chemistry, Pharmaceutical Microbiology Unit, Rheinische Friedrich-Wilhelms University Bonn, Bonn, Germany
| | - Hans-Georg Sahl
- Institute for Medical Microbiology, Immunology and Parasitology, Pharmaceutical Microbiology Unit, Rheinische Friedrich-Wilhelms University Bonn, Bonn, Germany
| | - Fabian Grein
- Institute for Medical Microbiology, Immunology and Parasitology, Pharmaceutical Microbiology Unit, Rheinische Friedrich-Wilhelms University Bonn, Bonn, Germany
| | - Ulrich Kubitscheck
- Institute for Physical and Theoretical Chemistry, Pharmaceutical Microbiology Unit, Rheinische Friedrich-Wilhelms University Bonn, Bonn, Germany
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14
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Zagato E, Forier K, Martens T, Neyts K, Demeester J, De Smedt S, Remaut K, Braeckmans K. Single-particle tracking for studying nanomaterial dynamics: applications and fundamentals in drug delivery. Nanomedicine (Lond) 2015; 9:913-27. [PMID: 24981654 DOI: 10.2217/nnm.14.43] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Many macromolecular therapeutics could potentially treat genetic disorders and cancer. They have, however, not yet reached the clinical stage owing to a lack of suitable carriers that can bring the therapeutics from the administration site to the subcellular site in target cells. One of the reasons that is hindering the development of such carriers is the limited knowledge of their transport dynamics and intracellular processing. Single-particle tracking (SPT) microscopy, thanks to its single molecule sensitivity and its broad applicability, has found its entry in the field of drug delivery to get an answer to these questions. This review aims to introduce the fundamentals of SPT to the drug delivery community and highlight the most recent discoveries obtained with SPT in the field of drug delivery.
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Affiliation(s)
- Elisa Zagato
- Laboratory of General Biochemistry & Physical Pharmacy, Ghent University, Ghent, Belgium
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15
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Li H, Chen D, Xu G, Yu B, Niu H. Three dimensional multi-molecule tracking in thick samples with extended depth-of-field. OPTICS EXPRESS 2015; 23:787-794. [PMID: 25835838 DOI: 10.1364/oe.23.000787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a non-z-scanning multi-molecule tracking system with nano-resolution in all three dimensions and extended depth of field (DOF), which based on distorted grating (DG) and double-helix point spread function (DH-PSF) combination microscopy (DDCM). The critical component in DDCM is a custom designed composite phase mask (PM) combining the functions of DG and DH-PSF. The localization precision and the effective DOF of the home-built DDCM system based on the designed PM were tested. Our experimental results show that the three-dimensional (3D) localization precision for the three diffraction orders of the grating are σ(-1st)(x, y, z) = (6.5 nm, 9.2nm, 23.4 nm), σ(0th)(x, y, z) = (3.7 nm, 2.8nm, 10.3 nm), and σ(+1s)(x, y, z) = (5.8 nm, 6.9 nm, 18.4 nm), respectively. Furthermore, the total effective DOF of the DDCM system is extended to 14 μm. Tracking experiment demonstrated that beads separated over 12 μm along the axial direction at some instants can be localized and tracked successfully.
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16
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Spille JH, Kaminski TP, Scherer K, Rinne JS, Heckel A, Kubitscheck U. Direct observation of mobility state transitions in RNA trajectories by sensitive single molecule feedback tracking. Nucleic Acids Res 2015; 43:e14. [PMID: 25414330 PMCID: PMC4333372 DOI: 10.1093/nar/gku1194] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/01/2014] [Accepted: 11/03/2014] [Indexed: 11/12/2022] Open
Abstract
Observation and tracking of fluorescently labeled molecules and particles in living cells reveals detailed information about intracellular processes on the molecular level. Whereas light microscopic particle observation is usually limited to two-dimensional projections of short trajectory segments, we report here image-based real-time three-dimensional single particle tracking in an active feedback loop with single molecule sensitivity. We tracked particles carrying only 1-3 fluorophores deep inside living tissue with high spatio-temporal resolution. Using this approach, we succeeded to acquire trajectories containing several hundred localizations. We present statistical methods to find significant deviations from random Brownian motion in such trajectories. The analysis allowed us to directly observe transitions in the mobility of ribosomal (r)RNA and Balbiani ring (BR) messenger (m)RNA particles in living Chironomus tentans salivary gland cell nuclei. We found that BR mRNA particles displayed phases of reduced mobility, while rRNA particles showed distinct binding events in and near nucleoli.
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Affiliation(s)
- Jan-Hendrik Spille
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53115 Bonn, Germany
| | - Tim P Kaminski
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53115 Bonn, Germany
| | - Katharina Scherer
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53115 Bonn, Germany
| | - Jennifer S Rinne
- Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53115 Bonn, Germany
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17
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Spille JH, Kubitscheck U. Labelling and imaging of single endogenous messenger RNA particles in vivo. J Cell Sci 2015; 128:3695-706. [DOI: 10.1242/jcs.166728] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
ABSTRACT
RNA molecules carry out widely diverse functions in numerous different physiological processes in living cells. The RNA life cycle from transcription, through the processing of nascent RNA, to the regulatory function of non-coding RNA and cytoplasmic translation of messenger RNA has been studied extensively using biochemical and molecular biology techniques. In this Commentary, we highlight how single molecule imaging and particle tracking can yield further insight into the dynamics of RNA particles in living cells. In the past few years, a variety of bright and photo-stable labelling techniques have been developed to generate sufficient contrast for imaging of single endogenous RNAs in vivo. New imaging modalities allow determination of not only lateral but also axial positions with high precision within the cellular context, and across a wide range of specimen from yeast and bacteria to cultured cells, and even multicellular organisms or live animals. A whole range of methods to locate and track single particles, and to analyze trajectory data are available to yield detailed information about the kinetics of all parts of the RNA life cycle. Although the concepts presented are applicable to all types of RNA, we showcase here the wealth of information gained from in vivo imaging of single particles by discussing studies investigating dynamics of intranuclear trafficking, nuclear pore transport and cytoplasmic transport of endogenous messenger RNA.
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Affiliation(s)
- Jan-Hendrik Spille
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, Bonn 53115, Germany
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, Bonn 53115, Germany
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18
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Lauer FM, Kaemmerer E, Meckel T. Single molecule microscopy in 3D cell cultures and tissues. Adv Drug Deliv Rev 2014; 79-80:79-94. [PMID: 25453259 DOI: 10.1016/j.addr.2014.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 09/20/2014] [Accepted: 10/03/2014] [Indexed: 12/19/2022]
Abstract
From the onset of the first microscopic visualization of single fluorescent molecules in living cells at the beginning of this century, to the present, almost routine application of single molecule microscopy, the method has well-proven its ability to contribute unmatched detailed insight into the heterogeneous and dynamic molecular world life is composed of. Except for investigations on bacteria and yeast, almost the entire story of success is based on studies on adherent mammalian 2D cell cultures. However, despite this continuous progress, the technique was not able to keep pace with the move of the cell biology community to adapt 3D cell culture models for basic research, regenerative medicine, or drug development and screening. In this review, we will summarize the progress, which only recently allowed for the application of single molecule microscopy to 3D cell systems and give an overview of the technical advances that led to it. While initially posing a challenge, we finally conclude that relevant 3D cell models will become an integral part of the on-going success of single molecule microscopy.
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Affiliation(s)
- Florian M Lauer
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 3-5, 64287 Darmstadt, Germany
| | - Elke Kaemmerer
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 3-5, 64287 Darmstadt, Germany; Institute of Health and Biomedical Innovation, Science and Engineering Faculty, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, 4059 QLD, Brisbane, Australia
| | - Tobias Meckel
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 3-5, 64287 Darmstadt, Germany.
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19
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Lien CH, Lin CY, Chen SJ, Chien FC. Dynamic particle tracking via temporal focusing multiphoton microscopy with astigmatism imaging. OPTICS EXPRESS 2014; 22:27290-9. [PMID: 25401879 DOI: 10.1364/oe.22.027290] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A three-dimensional (3D) single fluorescent particle tracking strategy based on temporal focusing multiphoton excitation microscopy (TFMPEM) combined with astigmatism imaging is proposed for delivering nanoscale-level axial information that reveals 3D trajectories of single fluorospheres in the axially-resolved multiphoton excitation volume without z-axis scanning. Whereas other scanning spatial focusing multiphoton excitation schemes induce optical trapping interference, temporal focusing multiphoton excitation produces widefield illumination with minimum optical trapping force on the fluorospheres. Currently, the lateral and axial positioning resolutions of the dynamic particle tracking approach are about 14 nm and 21 nm in standard deviation, respectively. Furthermore, the motion behavior and diffusion coefficients of fluorospheres in glycerol solutions with different concentrations are dynamically measured at a frame rate up to 100 Hz. This TFMPEM with astigmatism imaging holds great promise for exploring dynamic molecular behavior deep inside biotissues via its superior penetration, reduced trapping effect, fast frame rate, and nanoscale-level positioning.
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20
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Arbel E, Praiz A, Bilenca A. Fluorescence phase-shifting interferometry for axial single particle tracking: a numerical simulation study. OPTICS EXPRESS 2014; 22:19641-19652. [PMID: 25321047 DOI: 10.1364/oe.22.019641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Tracking of single fluorescent probes along the axial (depth) dimension is an important task in the biological and physical sciences. In this paper, we propose and analyze the use of fluorescence phase-shifting interferometry (FPSI) for axial single particle tracking (SPT) along 1 μm-depth (z) trajectories. FPSI is a photon-efficient, self-interference method that collects and coherently combines the 4π steradian emission wavefronts of a single fluorescent particle while introducing multiple phase shifts between the wavefronts to axially localize the particle with high precision over an extended depth-of-field. We employ vectorial imaging analysis and Monte-Carlo simulations of diffusive and directed motions to present a detailed comparative study of spatial and temporal FPSI for axial SPT based on simultaneous and time sequential collection of four phase-shifted interferograms using a single camera, respectively. The results of the numerical simulations show that for ≤0.105 μm2/s diffusion, spatial FPSI attains a maximal twofold improvement in the trajectory reconstruction precision at the expense of a fourfold reduced field-of-view compared to temporal FPSI. Furthermore, the analysis predicts that for sufficiently slow random linear motions, temporal FPSI is superior to spatial FPSI and achieves a smaller trajectory reconstruction error.
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21
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Pitchiaya S, Heinicke LA, Custer TC, Walter NG. Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev 2014; 114:3224-65. [PMID: 24417544 PMCID: PMC3968247 DOI: 10.1021/cr400496q] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Laurie A. Heinicke
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thomas C. Custer
- Program in Chemical Biology, University of Michigan,
Ann Arbor, MI 48109-1055, USA
| | - Nils G. Walter
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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22
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Lee YK, Kim S, Oh JW, Nam JM. Massively Parallel and Highly Quantitative Single-Particle Analysis on Interactions between Nanoparticles on Supported Lipid Bilayer. J Am Chem Soc 2014; 136:4081-8. [DOI: 10.1021/ja501225p] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Young Kwang Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, South Korea
| | - Sungi Kim
- Department of Chemistry, Seoul National University, Seoul 151-747, South Korea
| | - Jeong-Wook Oh
- Department of Chemistry, Seoul National University, Seoul 151-747, South Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul 151-747, South Korea
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23
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Fucikova A, Valenta J, Pelant I, Kalbacova MH, Broz A, Rezek B, Kromka A, Bakaeva Z. Silicon nanocrystals and nanodiamonds in live cells: photoluminescence characteristics, cytotoxicity and interaction with cell cytoskeleton. RSC Adv 2014. [DOI: 10.1039/c3ra47574c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Our study on biological interaction of silicon nanocrystals (a) and nanodiamonds (b) with cells encourages their use in human medicine.
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Affiliation(s)
- A. Fucikova
- Department of Chemical Physics and Optics
- Faculty of Mathematics and Physics
- Charles University
- Prague 2, Czech Republic
| | - J. Valenta
- Department of Chemical Physics and Optics
- Faculty of Mathematics and Physics
- Charles University
- Prague 2, Czech Republic
| | - I. Pelant
- Institute of Physics AS CR
- v. v. i
- Prague 6, Czech Republic
| | - M. Hubalek Kalbacova
- Institute of Inherited Metabolic Disorders
- 1st Faculty of Medicine
- Charles University
- Prague, Czech Republic
| | - A. Broz
- Institute of Inherited Metabolic Disorders
- 1st Faculty of Medicine
- Charles University
- Prague, Czech Republic
| | - B. Rezek
- Institute of Physics AS CR
- v. v. i
- Prague 6, Czech Republic
| | - A. Kromka
- Institute of Physics AS CR
- v. v. i
- Prague 6, Czech Republic
| | - Z. Bakaeva
- Institute of Macromolecular Chemistry AV CR
- v. v. i
- Prague 6, Czech Republic
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24
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Deschout H, Raemdonck K, Stremersch S, Maoddi P, Mernier G, Renaud P, Jiguet S, Hendrix A, Bracke M, Van den Broecke R, Röding M, Rudemo M, Demeester J, De Smedt SC, Strubbe F, Neyts K, Braeckmans K. On-chip light sheet illumination enables diagnostic size and concentration measurements of membrane vesicles in biofluids. NANOSCALE 2014; 6:1741-7. [PMID: 24346038 DOI: 10.1039/c3nr04432g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cell-derived membrane vesicles that are released in biofluids, like blood or saliva, are emerging as potential non-invasive biomarkers for diseases, such as cancer. Techniques capable of measuring the size and concentration of membrane vesicles directly in biofluids are urgently needed. Fluorescence single particle tracking microscopy has the potential of doing exactly that by labelling the membrane vesicles with a fluorescent label and analysing their Brownian motion in the biofluid. However, an unbound dye in the biofluid can cause high background intensity that strongly biases the fluorescence single particle tracking size and concentration measurements. While such background intensity can be avoided with light sheet illumination, current set-ups require specialty sample holders that are not compatible with high-throughput diagnostics. Here, a microfluidic chip with integrated light sheet illumination is reported, and accurate fluorescence single particle tracking size and concentration measurements of membrane vesicles in cell culture medium and in interstitial fluid collected from primary human breast tumours are demonstrated.
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Affiliation(s)
- Hendrik Deschout
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Belgium.
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25
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Heidernätsch M, Bauer M, Radons G. Characterizing N-dimensional anisotropic Brownian motion by the distribution of diffusivities. J Chem Phys 2013; 139:184105. [DOI: 10.1063/1.4828860] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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26
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Mueller F, Stasevich TJ, Mazza D, McNally JG. Quantifying transcription factor kinetics: at work or at play? Crit Rev Biochem Mol Biol 2013; 48:492-514. [PMID: 24025032 DOI: 10.3109/10409238.2013.833891] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Transcription factors (TFs) interact dynamically in vivo with chromatin binding sites. Here we summarize and compare the four different techniques that are currently used to measure these kinetics in live cells, namely fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS), single molecule tracking (SMT) and competition ChIP (CC). We highlight the principles underlying each of these approaches as well as their advantages and disadvantages. A comparison of data from each of these techniques raises an important question: do measured transcription kinetics reflect biologically functional interactions at specific sites (i.e. working TFs) or do they reflect non-specific interactions (i.e. playing TFs)? To help resolve this dilemma we discuss five key unresolved biological questions related to the functionality of transient and prolonged binding events at both specific promoter response elements as well as non-specific sites. In support of functionality, we review data suggesting that TF residence times are tightly regulated, and that this regulation modulates transcriptional output at single genes. We argue that in addition to this site-specific regulatory role, TF residence times also determine the fraction of promoter targets occupied within a cell thereby impacting the functional status of cellular gene networks. Thus, TF residence times are key parameters that could influence transcription in multiple ways.
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Affiliation(s)
- Florian Mueller
- Institut Pasteur, Computational Imaging and Modeling Unit, CNRS , Paris , France
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27
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Kaminski T, Siebrasse JP, Kubitscheck U. A single molecule view on Dbp5 and mRNA at the nuclear pore. Nucleus 2013; 4:8-13. [PMID: 23324459 DOI: 10.4161/nucl.23386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Numerous molecular details of intracellular mRNA processing have been revealed in recent years. However, the export process of single native mRNA molecules, the actual translocation through the nuclear pore complex (NPC), could not yet be examined in vivo. The problem is observing mRNA molecules without interfering with their native behavior. We used a protein-based labeling approach to visualize single native mRNPs in live salivary gland cells of Chironomus tentans, an iconic system used for decades to study the mRNA life cycle. Recombinant hrp36, the C. tentans homolog of mammalian hnRNP A1, was fluorescence labeled and microinjected into living cells, where it was integrated into nascent mRNPs. Intranuclear trajectories of single mRNPs, including their NPC passage, were observed with high space and time resolution employing a custom-built light sheet fluorescence microscope. We analyzed the kinetics and dynamics of mRNP export and started to study its mechanism and regulation by measuring the turnover-kinetics of single Dbp5 at the NPC.
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Affiliation(s)
- Tim Kaminski
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Bonn, Germany
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