1
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Houston JP, Valentino S, Bitton A. Fluorescence Lifetime Measurements and Analyses: Protocols Using Flow Cytometry and High-Throughput Microscopy. Methods Mol Biol 2024; 2779:323-351. [PMID: 38526793 DOI: 10.1007/978-1-0716-3738-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
This chapter focuses on applications and protocols that involve the measurement of the fluorescence lifetime as an informative cytometric parameter. The timing of fluorescence decay has been well-studied for cell counting, sorting, and imaging. Therefore, provided herein is an overview of the techniques used, how they enhance cytometry protocols, and the modern techniques used for lifetime analysis. The background and theory behind fluorescence decay kinetic measurements in cells is first discussed followed by the history of the development of time-resolved flow cytometry. These sections are followed by a review of applications that benefit from the quantitative nature of fluorescence lifetimes as a photophysical trait. Lastly, perspectives on the modern ways in which the fluorescence lifetime is scanned at high throughputs which include high-speed microscopy and machine learning are provided.
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Affiliation(s)
- Jessica P Houston
- Department of Chemical & Materials Engineering, New Mexico State University, Las Cruces, NM, USA.
| | - Samantha Valentino
- Department of Chemical & Materials Engineering, New Mexico State University, Las Cruces, NM, USA
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2
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Gottlieb D, Asadipour B, Kostina P, Ung TPL, Stringari C. FLUTE: A Python GUI for interactive phasor analysis of FLIM data. BIOLOGICAL IMAGING 2023; 3:e21. [PMID: 38487690 PMCID: PMC10936343 DOI: 10.1017/s2633903x23000211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/16/2023] [Accepted: 10/25/2023] [Indexed: 03/17/2024]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) is a powerful technique used to probe the local environment of fluorophores. The fit-free phasor approach to FLIM data is increasingly being used due to its ease of interpretation. To date, no open-source graphical user interface (GUI) for phasor analysis of FLIM data is available in Python, thus limiting the widespread use of phasor analysis in biomedical research. Here, we present Fluorescence Lifetime Ultimate Explorer (FLUTE), a Python GUI that is designed to fill this gap. FLUTE simplifies and automates many aspects of the analysis of FLIM data acquired in the time domain, such as calibrating the FLIM data, performing interactive exploration of the phasor plot, displaying phasor plots and FLIM images with different lifetime contrasts simultaneously, and calculating the distance from known molecular species. After applying desired filters and thresholds, the final edited datasets can be exported for further user-specific analysis. FLUTE has been tested using several FLIM datasets including autofluorescence of zebrafish embryos and in vitro cells. In summary, our user-friendly GUI extends the advantages of phasor plotting by making the data visualization and analysis easy and interactive, allows for analysis of large FLIM datasets, and accelerates FLIM analysis for non-specialized labs.
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Affiliation(s)
- Dale Gottlieb
- Laboratory for Optics and Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Bahar Asadipour
- Laboratory for Optics and Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Polina Kostina
- Laboratory for Optics and Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Thi Phuong Lien Ung
- Laboratory for Optics and Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Chiara Stringari
- Laboratory for Optics and Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
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3
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Smith JT, Rudkouskaya A, Gao S, Gupta JM, Ulku A, Bruschini C, Charbon E, Weiss S, Barroso M, Intes X, Michalet X. In vitro and in vivo NIR fluorescence lifetime imaging with a time-gated SPAD camera. OPTICA 2022; 9:532-544. [PMID: 35968259 PMCID: PMC9368735 DOI: 10.1364/optica.454790] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/27/2022] [Indexed: 05/20/2023]
Abstract
Near-infrared (NIR) fluorescence lifetime imaging (FLI) provides a unique contrast mechanism to monitor biological parameters and molecular events in vivo. Single-photon avalanche diode (SPAD) cameras have been recently demonstrated in FLI microscopy (FLIM) applications, but their suitability for in vivo macroscopic FLI (MFLI) in deep tissues remains to be demonstrated. Herein, we report in vivo NIR MFLI measurement with SwissSPAD2, a large time-gated SPAD camera. We first benchmark its performance in well-controlled in vitro experiments, ranging from monitoring environmental effects on fluorescence lifetime, to quantifying Förster resonant energy transfer (FRET) between dyes. Next, we use it for in vivo studies of target-drug engagement in live and intact tumor xenografts using FRET. Information obtained with SwissSPAD2 was successfully compared to that obtained with a gated intensified charge-coupled device (ICCD) camera, using two different approaches. Our results demonstrate that SPAD cameras offer a powerful technology for in vivo preclinical applications in the NIR window.
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Affiliation(s)
- Jason T. Smith
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Alena Rudkouskaya
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York 12208, USA
| | - Shan Gao
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Juhi M. Gupta
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Arin Ulku
- AQUA Lab, Ecole Polytechnique Fédérale de Lausanne (EPFL), Neuchâtel, Switzerland
| | - Claudio Bruschini
- AQUA Lab, Ecole Polytechnique Fédérale de Lausanne (EPFL), Neuchâtel, Switzerland
| | - Edoardo Charbon
- AQUA Lab, Ecole Polytechnique Fédérale de Lausanne (EPFL), Neuchâtel, Switzerland
| | - Shimon Weiss
- Department of Chemistry & Biochemistry, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York 12208, USA
| | - Xavier Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Xavier Michalet
- Department of Chemistry & Biochemistry, University of California at Los Angeles, Los Angeles, California 90095, USA
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4
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Michalet X. Continuous and discrete phasor analysis of binned or time-gated periodic decays. AIP ADVANCES 2021; 11:035331. [PMID: 33786208 PMCID: PMC7990508 DOI: 10.1063/5.0027834] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/22/2021] [Indexed: 05/29/2023]
Abstract
The time-resolved analysis of periodically excited luminescence decays by the phasor method in the presence of time-gating or binning is revisited. Analytical expressions for discrete configurations of square gates are derived, and the locus of the phasors of such modified periodic single-exponential decays is compared to the canonical universal semicircle. The effects of instrument response function offset, decay truncation, and gate shape are also discussed. Finally, modified expressions for the phase and modulus lifetimes are provided for some simple cases. A discussion of a modified phasor calibration approach is presented, and an illustration of the new concepts with examples from the literature concludes this work.
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Affiliation(s)
- Xavier Michalet
- Department of Chemistry and Biochemistry, 607 Charles E. Young Drive E., Los Angeles, California 90095, USA
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5
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van Rijssel MJ, Froeling M, van Lier AL, Verhoeff JJ, Pluim JP. Untangling the diffusion signal using the phasor transform. NMR IN BIOMEDICINE 2020; 33:e4372. [PMID: 32701224 PMCID: PMC7685171 DOI: 10.1002/nbm.4372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 05/21/2023]
Abstract
Separating the decay signal from diffusion-weighted scans into two or more components can be challenging. The phasor technique is well established in the field of optical microscopy for visualization and separation of fluorescent dyes with different lifetimes. The use of the phasor technique for separation of diffusion-weighted decay signals was recently proposed. In this study, we investigate the added value of this technique for fitting decay models and visualization of decay rates. Phasor visualization was performed in five glioblastoma patients. Using simulations, the influence of incorrect diffusivity values and of the number of b-values on fitting a three-component model with fixed diffusivities (dubbed "unmixing") was investigated for both a phasor-based fit and a linear least squares (LLS) fit. Phasor-based intravoxel incoherent motion (IVIM) fitting was compared with nonlinear least squares (NLLS) and segmented fitting (SF) methods in terms of accuracy and precision. The distributions of the parameter estimates of simulated data were compared with those obtained in a healthy volunteer. In the phasor visualizations of two glioblastoma patients, a cluster of points was observed that was not seen in healthy volunteers. The identified cluster roughly corresponded to the enhanced edge region of the tumor of two glioblastoma patients visible on fluid-attenuated inversion recovery (FLAIR) images. For fitting decay models the usefulness of the phasor transform is less pronounced, but the additional knowledge gained from the geometrical configuration of phasor space can aid fitting routines. This has led to slightly improved fitting results for the IVIM model: phasor-based fitting yielded parameter maps with higher precision than the NLLS and SF methods for parameters f and D (interquartile range [IQR] for f: NLLS 27, SF 12, phasor 5.7%; IQR for D: NLLS 0.28, SF 0.18, phasor 0.10 μm2 /s). For unmixing, LLS fitting slightly but consistently outperformed phasor-based fitting in all of the tested scenarios.
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Affiliation(s)
| | | | | | | | - Josien P.W. Pluim
- Center for Image Sciences, UMC UtrechtUtrechtthe Netherlands
- Department of Biomedical EngineeringTechnische Universiteit EindhovenEindhoventhe Netherlands
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6
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Tavakoli M, Jazani S, Sgouralis I, Heo W, Ishii K, Tahara T, Pressé S. Direct Photon-by-Photon Analysis of Time-Resolved Pulsed Excitation Data using Bayesian Nonparametrics. CELL REPORTS. PHYSICAL SCIENCE 2020; 1:100234. [PMID: 34414380 PMCID: PMC8373049 DOI: 10.1016/j.xcrp.2020.100234] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Lifetimes of chemical species are typically estimated by either fitting time-correlated single-photon counting (TCSPC) histograms or phasor analysis from time-resolved photon arrivals. While both methods yield lifetimes in a computationally efficient manner, their performance is limited by choices made on the number of distinct chemical species contributing photons. However, the number of species is encoded in the photon arrival times collected for each illuminated spot and need not be set by hand a priori. Here, we propose a direct photon-by-photon analysis of data drawn from pulsed excitation experiments to infer, simultaneously and self-consistently, the number of species and their associated lifetimes from a few thousand photons. We do so by leveraging new mathematical tools within the Bayesian nonparametric. We benchmark our method for both simulated and experimental data for 1-4 species.
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Affiliation(s)
- Meysam Tavakoli
- Department of Physics, Indiana University-Purdue University, Indianapolis, IN 46202, USA
| | - Sina Jazani
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Ioannis Sgouralis
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wooseok Heo
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Steve Pressé
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Lead Contact
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7
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Lagarto JL, Villa F, Tisa S, Zappa F, Shcheslavskiy V, Pavone FS, Cicchi R. Real-time multispectral fluorescence lifetime imaging using Single Photon Avalanche Diode arrays. Sci Rep 2020; 10:8116. [PMID: 32415224 PMCID: PMC7229199 DOI: 10.1038/s41598-020-65218-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022] Open
Abstract
Autofluorescence spectroscopy has emerged in recent years as a powerful tool to report label-free contrast between normal and diseased tissues, both in vivo and ex vivo. We report the development of an instrument employing Single Photon Avalanche Diode (SPAD) arrays to realize real-time multispectral autofluorescence lifetime imaging at a macroscopic scale using handheld single-point fibre optic probes, under bright background conditions. At the detection end, the fluorescence signal is passed through a transmission grating and both spectral and temporal information are encoded in the SPAD array. This configuration allows interrogation in the spectral range of interest in real time. Spatial information is provided by an external camera together with a guiding beam that provides a visual reference that is tracked in real-time. Through fast image processing and data analysis, fluorescence lifetime maps are augmented on white light images to provide feedback of the measurements in real-time. We validate and demonstrate the practicality of this technique in the reference fluorophores and in articular cartilage samples mimicking the degradation that occurs in osteoarthritis. Our results demonstrate that SPADs together with fibre probes can offer means to report autofluorescence spectral and lifetime contrast in real-time and thus are suitable candidates for in situ tissue diagnostics.
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Affiliation(s)
- João L Lagarto
- National Institute of Optics National Research Council (INO-CNR), Largo Enrico Fermi 6, 50125, Florence, Italy.
- European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 1, 50019, Sesto Fiorentino, Italy.
| | - Federica Villa
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, 20133, Milan, Italy
| | - Simone Tisa
- Micro Photon Device SRL, Via Waltraud Gebert Deeg 3g, I-39100, Bolzano, Italy
| | - Franco Zappa
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, 20133, Milan, Italy
| | - Vladislav Shcheslavskiy
- Becker & Hickl GmbH, Nunsdorfer Ring 7-9, 12277, Berlin, Germany
- Privolzhskiy Medical Research University, 603005, Nizhny Novgorod, Russia
| | - Francesco S Pavone
- National Institute of Optics National Research Council (INO-CNR), Largo Enrico Fermi 6, 50125, Florence, Italy
- European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 1, 50019, Sesto Fiorentino, Italy
- Department of Physics, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy
| | - Riccardo Cicchi
- National Institute of Optics National Research Council (INO-CNR), Largo Enrico Fermi 6, 50125, Florence, Italy
- European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 1, 50019, Sesto Fiorentino, Italy
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8
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Datta R, Heaster TM, Sharick JT, Gillette AA, Skala MC. Fluorescence lifetime imaging microscopy: fundamentals and advances in instrumentation, analysis, and applications. JOURNAL OF BIOMEDICAL OPTICS 2020; 25:1-43. [PMID: 32406215 PMCID: PMC7219965 DOI: 10.1117/1.jbo.25.7.071203] [Citation(s) in RCA: 326] [Impact Index Per Article: 81.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/24/2020] [Indexed: 05/18/2023]
Abstract
SIGNIFICANCE Fluorescence lifetime imaging microscopy (FLIM) is a powerful technique to distinguish the unique molecular environment of fluorophores. FLIM measures the time a fluorophore remains in an excited state before emitting a photon, and detects molecular variations of fluorophores that are not apparent with spectral techniques alone. FLIM is sensitive to multiple biomedical processes including disease progression and drug efficacy. AIM We provide an overview of FLIM principles, instrumentation, and analysis while highlighting the latest developments and biological applications. APPROACH This review covers FLIM principles and theory, including advantages over intensity-based fluorescence measurements. Fundamentals of FLIM instrumentation in time- and frequency-domains are summarized, along with recent developments. Image segmentation and analysis strategies that quantify spatial and molecular features of cellular heterogeneity are reviewed. Finally, representative applications are provided including high-resolution FLIM of cell- and organelle-level molecular changes, use of exogenous and endogenous fluorophores, and imaging protein-protein interactions with Förster resonance energy transfer (FRET). Advantages and limitations of FLIM are also discussed. CONCLUSIONS FLIM is advantageous for probing molecular environments of fluorophores to inform on fluorophore behavior that cannot be elucidated with intensity measurements alone. Development of FLIM technologies, analysis, and applications will further advance biological research and clinical assessments.
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Affiliation(s)
- Rupsa Datta
- Morgridge Institute for Research, Madison, Wisconsin, United States
| | - Tiffany M. Heaster
- Morgridge Institute for Research, Madison, Wisconsin, United States
- University of Wisconsin, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | - Joe T. Sharick
- Morgridge Institute for Research, Madison, Wisconsin, United States
| | - Amani A. Gillette
- Morgridge Institute for Research, Madison, Wisconsin, United States
- University of Wisconsin, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | - Melissa C. Skala
- Morgridge Institute for Research, Madison, Wisconsin, United States
- University of Wisconsin, Department of Biomedical Engineering, Madison, Wisconsin, United States
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9
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Esposito A. How many photons are needed for FRET imaging? BIOMEDICAL OPTICS EXPRESS 2020; 11:1186-1202. [PMID: 32133242 PMCID: PMC7041441 DOI: 10.1364/boe.379305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/15/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
Förster resonance energy transfer (FRET) imaging is an essential analytical method in biomedical research. The limited photon-budget experimentally available, however, imposes compromises between spatiotemporal and biochemical resolutions, photodamage and phototoxicity. The study of photon-statistics in biochemical imaging is thus important in guiding the efficient design of instrumentation and assays. Here, we show a comparative analysis of photon-statistics in FRET imaging demonstrating how the precision of FRET imaging varies vastly with imaging parameters. Therefore, we provide analytical and numerical tools for assay optimization. Fluorescence lifetime imaging microscopy (FLIM) is a very robust technique with excellent photon-efficiencies. However, we show that also intensity-based FRET imaging can reach high precision by utilizing information from both donor and acceptor fluorophores.
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Affiliation(s)
- Alessandro Esposito
- MRC Cancer Unit, University of Cambridge, Biomedical Campus, Cambridge, CB20XY, UK
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10
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Ankri R, Basu A, Ulku AC, Bruschini C, Charbon E, Weiss S, Michalet X. Single-Photon, Time-Gated, Phasor-Based Fluorescence Lifetime Imaging through Highly Scattering Medium. ACS PHOTONICS 2020; 7:68-79. [PMID: 35936550 PMCID: PMC9355389 DOI: 10.1021/acsphotonics.9b00874] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Fluorescence lifetime imaging (FLI) is increasingly recognized as a powerful tool for biochemical and cellular investigations, including in vivo applications. Fluorescence lifetime is an intrinsic characteristic of any fluorescent dye which, to a large extent, does not depend on excitation intensity and signal level. In particular, it allows distinguishing dyes with similar emission spectra, offering additional multiplexing capabilities. However, in vivo FLI in the visible range is complicated by the contamination by (i) tissue autofluorescence, which decreases contrast, and by (ii) light scattering and absorption in tissues, which significantly reduce fluorescence intensity and modify the temporal profile of the signal. Here, we demonstrate how these issues can be accounted for and overcome, using a new time-gated single-photon avalanche diode array camera, SwissSPAD2, combined with phasor analysis to provide a simple and fast visual method for lifetime imaging. In particular, we show how phasor dispersion increases with increasing scattering and/or decreasing fluorescence intensity. Next, we show that as long as the fluorescence signal of interest is larger than the phantom autofluorescence, the presence of a distinct lifetime can be clearly identified with appropriate background correction. We use these results to demonstrate the detection of A459 cells expressing the fluorescent protein mCyRFP1 through highly scattering and autofluorescent phantom layers. These results showcase the possibility to perform FLI in challenging conditions, using standard, bright, visible fluorophore or fluorescence proteins.
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Affiliation(s)
- Rinat Ankri
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, California 90095, United States
- Corresponding Authors:.
| | - Arkaprabha Basu
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Arin Can Ulku
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel 1015, Switzerland
| | - Claudio Bruschini
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel 1015, Switzerland
| | - Edoardo Charbon
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel 1015, Switzerland
| | - Shimon Weiss
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Xavier Michalet
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, California 90095, United States
- Corresponding Authors:.
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11
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Smith JT, Yao R, Sinsuebphon N, Rudkouskaya A, Un N, Mazurkiewicz J, Barroso M, Yan P, Intes X. Fast fit-free analysis of fluorescence lifetime imaging via deep learning. Proc Natl Acad Sci U S A 2019; 116:24019-24030. [PMID: 31719196 PMCID: PMC6883809 DOI: 10.1073/pnas.1912707116] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Fluorescence lifetime imaging (FLI) provides unique quantitative information in biomedical and molecular biology studies but relies on complex data-fitting techniques to derive the quantities of interest. Herein, we propose a fit-free approach in FLI image formation that is based on deep learning (DL) to quantify fluorescence decays simultaneously over a whole image and at fast speeds. We report on a deep neural network (DNN) architecture, named fluorescence lifetime imaging network (FLI-Net) that is designed and trained for different classes of experiments, including visible FLI and near-infrared (NIR) FLI microscopy (FLIM) and NIR gated macroscopy FLI (MFLI). FLI-Net outputs quantitatively the spatially resolved lifetime-based parameters that are typically employed in the field. We validate the utility of the FLI-Net framework by performing quantitative microscopic and preclinical lifetime-based studies across the visible and NIR spectra, as well as across the 2 main data acquisition technologies. These results demonstrate that FLI-Net is well suited to accurately quantify complex fluorescence lifetimes in cells and, in real time, in intact animals without any parameter settings. Hence, FLI-Net paves the way to reproducible and quantitative lifetime studies at unprecedented speeds, for improved dissemination and impact of FLI in many important biomedical applications ranging from fundamental discoveries in molecular and cellular biology to clinical translation.
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Affiliation(s)
- Jason T Smith
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180;
| | - Ruoyang Yao
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Nattawut Sinsuebphon
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Alena Rudkouskaya
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208
| | - Nathan Un
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Joseph Mazurkiewicz
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208
| | - Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208
| | - Pingkun Yan
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Xavier Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180;
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12
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Chen SJ, Sinsuebphon N, Rudkouskaya A, Barroso M, Intes X, Michalet X. In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using short-lifetime near-infrared dyes and time-gated imaging. JOURNAL OF BIOPHOTONICS 2019; 12:e201800185. [PMID: 30421551 PMCID: PMC6559731 DOI: 10.1002/jbio.201800185] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/08/2018] [Accepted: 11/11/2018] [Indexed: 05/22/2023]
Abstract
We introduce a simple new approach for time-resolved multiplexed analysis of complex systems using near-infrared (NIR) dyes, applicable to in vitro and in vivo studies. We show that fast and precise in vitro quantification of NIR fluorophores' short (subnanosecond) lifetime and stoichiometry can be done using phasor analysis, a computationally efficient and user-friendly representation of complex fluorescence intensity decays obtained with pulsed laser excitation and time-gated camera imaging. We apply this approach to the study of binding equilibria by Förster resonant energy transfer using two different model systems: primary/secondary antibody binding in vitro and ligand/receptor binding in cell cultures. We then extend it to dynamic imaging of the pharmacokinetics of transferrin engagement with the transferrin receptor in live mice, elucidating the kinetics of differential transferrin accumulation in specific organs, straightforwardly differentiating specific from nonspecific binding. Our method, implemented in a freely-available software, has the advantage of time-resolved NIR imaging, including better tissue penetration and background-free imaging, but simplifies and considerably speeds up data processing and interpretation, while remaining quantitative. These advances make this method attractive and of broad applicability for in vitro and in vivo molecular imaging and could be extended to applications as diverse as image-guided surgery or optical tomography.
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Affiliation(s)
- Sez-Jade Chen
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Nattawut Sinsuebphon
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Alena Rudkouskaya
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Xavier Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, California
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13
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Ardelean A, Ulku AC, Michalet X, Charbon E, Bruschini C. Fluorescence lifetime imaging with a single-photon SPAD array using long overlapping gates: an experimental and theoretical study. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2019; 10882:108820Y. [PMID: 33833477 PMCID: PMC8026147 DOI: 10.1117/12.2511287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Developing large arrays of single-photon avalanche diodes (SPADs) with on-chip time-correlated single-photon counting (TCSPC) capabilities continues to be a difficult task due to stringent silicon real estate constraints, high data rates and system complexity. As an alternative to TCSPC, time-gated architectures have been proposed, where the numbers of photons detected within different time gates are used as a replacement to the usual time-resolved luminescence decay. However, because of technological limitations, the minimum gate length implement is on the order of nanoseconds, longer than most fluorophore lifetimes of interest. However, recent FLIM measurements have shown that it is mainly the gate step and rise/fall time, rather than its length, which determine lifetime resolution. In addition, the large number of photons captured by longer gates results in higher SNR. In this paper, we study the effects of using long, overlapping gates on lifetime extraction by phasor analysis, using a recently developed 512×512 time-gated SPAD array. The experiments used Cy3B, Rhodamine 6G and Atto550 dyes as test samples. The gate window length was varied between 11.3 ns and 23 ns while the gate step was varied between 17.86 ps and 3 ns. We validated the results with a standard TCSPC setup and investigated the case of multi-exponential samples through simulations. Results indicate that lifetime extraction is not degraded by the use of longer gates, nor is the ability to resolve multi-exponential decays.
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Affiliation(s)
- Andrei Ardelean
- AQUA Laboratory, EPFL, 71b Rue de la Maladière, Neuchâtel, Switzerland
| | - Arin Can Ulku
- AQUA Laboratory, EPFL, 71b Rue de la Maladière, Neuchâtel, Switzerland
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, USA
| | - Edoardo Charbon
- AQUA Laboratory, EPFL, 71b Rue de la Maladière, Neuchâtel, Switzerland
| | - Claudio Bruschini
- AQUA Laboratory, EPFL, 71b Rue de la Maladière, Neuchâtel, Switzerland
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Ulku AC, Bruschini C, Antolovic IM, Charbon E, Kuo Y, Ankri R, Weiss S, Michalet X. A 512×512 SPAD Image Sensor with Integrated Gating for Widefield FLIM. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS : A PUBLICATION OF THE IEEE LASERS AND ELECTRO-OPTICS SOCIETY 2019; 25:6801212. [PMID: 31156324 PMCID: PMC6541425 DOI: 10.1109/jstqe.2018.2867439] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We report on SwissSPAD2, an image sensor with 512×512 photon-counting pixels, each comprising a single-photon avalanche diode (SPAD), a 1-bit memory, and a gating mechanism capable of turning the SPAD on and off, with a skew of 250ps and 344ps, respectively, for a minimum duration of 5.75ns. The sensor is designed to achieve a frame rate of up to 97,700 binary frames per second and sub-40ps gate shifts. By synchronizing it with a pulsed laser and using multiple successive overlapping gates, one can reconstruct a molecule's fluorescent response with picosecond temporal resolution. Thanks to the sensor's number of pixels (the largest to date) and the fully integrated gated operation, SwissSPAD2 enables widefield FLIM with an all-solid-state solution and at relatively high frame rates. This was demonstrated with preliminary results on organic dyes and semiconductor quantum dots using both decay fitting and phasor analysis. Furthermore, pixels with an exceptionally low dark count rate and high photon detection probability enable uniform and high quality imaging of biologically relevant fluorescent samples stained with multiple dyes. While future versions will feature the addition of microlenses and optimize firmware speed, our results open the way to low-cost alternatives to commercially available scientific time-resolved imagers.
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Affiliation(s)
- Arin C Ulku
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel, 2002, Switzerland
| | - Claudio Bruschini
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel, 2002, Switzerland
| | - Ivan Michel Antolovic
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel, 2002, Switzerland
| | - Edoardo Charbon
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel, 2002, Switzerland
| | - Yung Kuo
- Department of Chemistry and Biochemistry, University of California at Los Angeles (UCLA), Los Angeles, CA, 90095-1569
| | - Rinat Ankri
- Department of Chemistry and Biochemistry, University of California at Los Angeles (UCLA), Los Angeles, CA, 90095-1569
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California at Los Angeles (UCLA), Los Angeles, CA, 90095-1569
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California at Los Angeles (UCLA), Los Angeles, CA, 90095-1569
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Santra K, Smith EA, Song X, Petrich JW. A Bayesian Approach for Extracting Fluorescence Lifetimes from Sparse Data Sets and Its Significance for Imaging Experiments. Photochem Photobiol 2018; 95:773-779. [DOI: 10.1111/php.13057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/06/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Kalyan Santra
- Department of Chemistry Iowa State University Ames IA
- Ames Laboratory U.S. Department of Energy Ames IA
| | - Emily A. Smith
- Department of Chemistry Iowa State University Ames IA
- Ames Laboratory U.S. Department of Energy Ames IA
| | - Xueyu Song
- Department of Chemistry Iowa State University Ames IA
- Ames Laboratory U.S. Department of Energy Ames IA
| | - Jacob W. Petrich
- Department of Chemistry Iowa State University Ames IA
- Ames Laboratory U.S. Department of Energy Ames IA
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16
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Ranjit S, Malacrida L, Gratton E. Differences between FLIM phasor analyses for data collected with the Becker and Hickl SPC830 card and with the FLIMbox card. Microsc Res Tech 2018; 81:980-989. [PMID: 30295346 PMCID: PMC6240382 DOI: 10.1002/jemt.23061] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/13/2018] [Indexed: 01/31/2023]
Abstract
The phasor approach to FLIM (Fluorescence Lifetime Imaging Microscopy) is becoming popular due to the powerful fit free analysis and the visualization of the decay at each point in images of cells and tissues. However, although several implementation of the method are offered by manufactures of FLIM accessories for microscopes, the details of the conversion of the decay to phasors at each point in an image requires some consideration. Here, we show that if the decay is not properly acquired, the apparently simple phasor transformation can provide incorrect phasor plots and the results may be misinterpreted. In particular, we show the disagreement in experimental data acquired on the same samples using the two cards (FLIMbox, frequency domain and Becker & Hickl BH 830, time domain) and the effect produced by using the BH 830 card with different settings. This difference in data acquisition translates to the assignment of phasor components calculated using different acquisition parameters. This effect is already present in the original data that are not acquired with the proper parameters for the phasor conversion. We also show that the difference in the resolution of components already exists in the data acquired in the time domain when used with settings that do not allow acquisition of the fluorescence decay on a sufficient large time scale. RESEARCH HIGHLIGHTS: This paper is intended to made researchers aware of some simple requirements for the conversion of time-domain data (typically TCSPC) to phasors. The use of phasors for FLIM analysis has seen a surge of popularity. Since the phasor approach is a fit free method and has a powerful visualization of the data, it appears very simple to use. This paper shows that when the original data in the time domain is not acquired with the proper time range to cover the lifetimes in a sample, the conversion to phasors can produce very erroneous results. These results are appearing more frequently in the literature since many of the manufacturers of FLIM accessories for microscopes are now offering the phasor analysis in their software. Here, we show that the phasor transformation per se cannot correct for the problems with data acquisition and that one is misled to think that the "phasor approach" is a universal fix for the lack of the proper time range for data acquisition.
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Affiliation(s)
- Suman Ranjit
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, California
| | - Leonel Malacrida
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, California
- Departamento de Fisiopatología, Hospital de Clínicas, Universidad de la República, Montevideo, Uruguay
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, California
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Wang L, Chen B, Yan W, Yang Z, Peng X, Lin D, Weng X, Ye T, Qu J. Resolution improvement in STED super-resolution microscopy at low power using a phasor plot approach. NANOSCALE 2018; 10:16252-16260. [PMID: 30124714 DOI: 10.1039/c8nr03584a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Stimulated emission depletion (STED) microscopy is a powerful super-resolution microscopy technique that has achieved significant results in breaking the resolution limit and relevant applications. In principle, STED super resolution is obtained by stimulated emission partially inhibiting the spontaneous emission in the periphery of a diffraction-limited area. However, very high depletion laser power is generally necessary for the enhancement of imaging resolution, which is harmful to live biological specimens due to its high phototoxicity and photo-bleaching effects. Therefore, further improving the STED resolution at a lower depletion power level has recently attracted increasing interest from researchers in various fields. In this work, a phasor plot approach combined with fluorescence lifetime imaging microscopy (FLIM) is used to resolve the abovementioned problem based on a long- and short-lifetime criterion. Firstly, the time-resolved data obtained by STED-FLIM is converted to the frequency domain via a phasor approach. Next, partial data is extracted according to the information on the phase and amplitude for resolution improvement. Then, fluorescent microspheres (100 nm in diameter) are observed under different depletion powers, resulting in a series of improved resolution through phasor plots. Finally, this method is applied to image human Nup153 in fixed HeLa cells, providing a 86 nm higher resolution than that in traditional STED imaging at a depletion power of 20 mW.
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Affiliation(s)
- Luwei Wang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
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18
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Fereidouni F, Griffin C, Todd A, Levenson R. Multispectral analysis tools can increase utility of RGB color images in histology. JOURNAL OF OPTICS (2010) 2018; 20:044007. [PMID: 30847052 PMCID: PMC6398595 DOI: 10.1088/2040-8986/aab0e8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Multispectral imaging (MSI) is increasingly finding application in the study and characterization of biological specimens. However, the methods typically used come with challenges on both the acquisition and the analysis front. MSI can be slow and photon-inefficient, leading to long imaging times and possible phototoxicity and photobleaching. The resulting datasets can be large and complex, prompting the development of a number of mathematical approaches for segmentation and signal unmixing. We show that under certain circumstances, just three spectral channels provided by standard color cameras, coupled with multispectral analysis tools, including a more recent spectral phasor approach, can efficiently provide useful insights. These findings are supported with a mathematical model relating spectral bandwidth and spectral channel number to achievable spectral accuracy. The utility of 3-band RGB and MSI analysis tools are demonstrated on images acquired using brightfield and fluorescence techniques, as well as a novel microscopy approach employing UV-surface excitation. Supervised linear unmixing, automated non-negative matrix factorization and phasor analysis tools all provide useful results, with phasors generating particularly helpful spectral display plots for sample exploration.
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Affiliation(s)
- Farzad Fereidouni
- Department of Pathology and Laboratory Medicine, University of California Davis, 4400 V Street, Sacramento, CA 95817, United States of America
| | - Croix Griffin
- School of Veterinary Medicine, University of California Davis, 944 Garrod Drive, Davis, CA 95616, United States of America
| | - Austin Todd
- Department of Pathology and Laboratory Medicine, University of California Davis, 4400 V Street, Sacramento, CA 95817, United States of America
| | - Richard Levenson
- Department of Pathology and Laboratory Medicine, University of California Davis, 4400 V Street, Sacramento, CA 95817, United States of America
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19
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Fereidouni F, Gorpas D, Ma D, Fatakdawala H, Marcu L. Rapid fluorescence lifetime estimation with modified phasor approach and Laguerre deconvolution: a comparative study. Methods Appl Fluoresc 2017; 5:035003. [PMID: 28644150 PMCID: PMC6043162 DOI: 10.1088/2050-6120/aa7b62] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fluorescence lifetime imaging has been shown to serve as a valuable tool for interrogating and diagnosis of biological tissue at a mesoscopic level. The ability to analyze fluorescence decay curves to extract lifetime values in real-time is crucial for clinical translation and applications such as tumor margin delineation or intracoronary imaging of atherosclerotic plaques. In this work, we compare the performance of two popular non-parametric (fit-free) methods for determining lifetime values from fluorescence decays in real-time-the Phasor approach and Laguerre deconvolution. We demonstrate results from simulated and experimental data to compare the accuracy and speed of both methods and their dependence on noise and model parameters.
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Affiliation(s)
- Farzad Fereidouni
- Department of Pathology and Laboratory Medicine, 4400 V Street, CA 95817, United States of America
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20
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Silberberg M, Grecco HE. pawFLIM: reducing bias and uncertainty to enable lower photon count in FLIM experiments. Methods Appl Fluoresc 2017. [DOI: 10.1088/2050-6120/aa72ab] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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21
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Vergeldt FJ, Prusova A, Fereidouni F, Amerongen HV, Van As H, Scheenen TWJ, Bader AN. Multi-component quantitative magnetic resonance imaging by phasor representation. Sci Rep 2017; 7:861. [PMID: 28408740 PMCID: PMC5429833 DOI: 10.1038/s41598-017-00864-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/20/2017] [Indexed: 12/02/2022] Open
Abstract
Quantitative magnetic resonance imaging (qMRI) is a versatile, non-destructive and non-invasive tool in life, material, and medical sciences. When multiple components contribute to the signal in a single pixel, however, it is difficult to quantify their individual contributions and characteristic parameters. Here we introduce the concept of phasor representation to qMRI to disentangle the signals from multiple components in imaging data. Plotting the phasors allowed for decomposition, unmixing, segmentation and quantification of our in vivo data from a plant stem, a human and mouse brain and a human prostate. In human brain images, we could identify 3 main T2 components and 3 apparent diffusion coefficients; in human prostate 5 main contributing spectral shapes were distinguished. The presented phasor analysis is model-free, fast and accurate. Moreover, we also show that it works for undersampled data.
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Affiliation(s)
- Frank J Vergeldt
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands.,Wageningen NMR Centre, Wageningen University & Research, Wageningen, The Netherlands
| | - Alena Prusova
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Farzad Fereidouni
- Department of Pathology and Laboratory Medicine, UC Davis Medical Center, Sacramento, CA, USA
| | - Herbert van Amerongen
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands.,MicroSpectroscopy Centre, Wageningen University and Research, Wageningen, The Netherlands
| | - Henk Van As
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands. .,Wageningen NMR Centre, Wageningen University & Research, Wageningen, The Netherlands.
| | - Tom W J Scheenen
- Department of Radiology and Nuclear Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Arjen N Bader
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands. .,MicroSpectroscopy Centre, Wageningen University and Research, Wageningen, The Netherlands.
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22
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Chen SJ, Sinsuebphon N, Barroso M, Intes X, Michalet X. AlliGator: A Phasor Computational Platform for Fast in vivo Lifetime Analysis. OPTICAL MOLECULAR PROBES, IMAGING AND DRUG DELIVERY 2017; 2017:OmTu2D.2. [PMID: 35072178 PMCID: PMC8772506 DOI: 10.1364/omp.2017.omtu2d.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A fast time-gated phasor analysis tool was developed and used to monitor kinetics of NIR FLIM-FRET in vitro and in vivo. The results were validated by comparison with standard two-component fluorescence decay fitting analysis.
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Affiliation(s)
- Sez-Jade Chen
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Nattawut Sinsuebphon
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Margarida Barroso
- Center for Cardiovascular Sciences, Albany Medical College, Albany, NY, 12208, USA
| | - Xavier Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA
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23
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Lakner PH, Monaghan MG, Möller Y, Olayioye MA, Schenke-Layland K. Applying phasor approach analysis of multiphoton FLIM measurements to probe the metabolic activity of three-dimensional in vitro cell culture models. Sci Rep 2017; 7:42730. [PMID: 28211922 PMCID: PMC5304149 DOI: 10.1038/srep42730] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/13/2017] [Indexed: 01/25/2023] Open
Abstract
Fluorescence lifetime imaging microscopy (FLIM) can measure and discriminate endogenous fluorophores present in biological samples. This study seeks to identify FLIM as a suitable method to non-invasively detect a shift in cellular metabolic activity towards glycolysis or oxidative phosphorylation in 3D Caco-2 models of colorectal carcinoma. These models were treated with potassium cyanide or hydrogen peroxide as controls, and epidermal growth factor (EGF) as a physiologically-relevant influencer of cell metabolic behaviour. Autofluorescence, attributed to nicotinamide adenine dinucleotide (NADH), was induced by two-photon laser excitation and its lifetime decay was analysed using a standard multi-exponential decay approach and also a novel custom-written code for phasor-based analysis. While both methods enabled detection of a statistically significant shift of metabolic activity towards glycolysis using potassium cyanide, and oxidative phosphorylation using hydrogen peroxide, employing the phasor approach required fewer initial assumptions to quantify the lifetimes of contributing fluorophores. 3D Caco-2 models treated with EGF had increased glucose consumption, production of lactate, and presence of ATP. FLIM analyses of these cultures revealed a significant shift in the contribution of protein-bound NADH towards free NADH, indicating increased glycolysis-mediated metabolic activity. This data demonstrate that FLIM is suitable to interpret metabolic changes in 3D in vitro models.
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Affiliation(s)
- Pirmin H Lakner
- Department of Women's Health, Research Institute for Women's Health, University Hospital of the Eberhard Karls University Tübingen, Tübingen, Germany
| | - Michael G Monaghan
- Department of Women's Health, Research Institute for Women's Health, University Hospital of the Eberhard Karls University Tübingen, Tübingen, Germany
- Trinity Centre for Bioengineering, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- Department of Mechanical and Manufacturing Engineering, School of Engineering, Trinity College Dublin, Dublin, Ireland
- Department of Cell and Tissue Engineering, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
| | - Yvonne Möller
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
- Center for Personalised Medicine (ZPM), University Hospital of the Eberhard Karls University Tübingen, Tübingen, Germany
| | - Monilola A Olayioye
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
- Stuttgart Research Center Systems Biology, University of Stuttgart, Stuttgart, Germany
| | - Katja Schenke-Layland
- Department of Women's Health, Research Institute for Women's Health, University Hospital of the Eberhard Karls University Tübingen, Tübingen, Germany
- Department of Cell and Tissue Engineering, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
- Department of Medicine/Cardiology, University of California Los Angeles (UCLA), Los Angeles/CA, USA
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Ranjit S, Dvornikov A, Levi M, Furgeson S, Gratton E. Characterizing fibrosis in UUO mice model using multiparametric analysis of phasor distribution from FLIM images. BIOMEDICAL OPTICS EXPRESS 2016; 7:3519-3530. [PMID: 27699117 PMCID: PMC5030029 DOI: 10.1364/boe.7.003519] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/09/2016] [Accepted: 08/12/2016] [Indexed: 05/22/2023]
Abstract
Phasor approach to fluorescence lifetime microscopy is used to study development of fibrosis in the unilateral ureteral obstruction model (UUO) of kidney in mice. Traditional phasor analysis has been modified to create a multiparametric analysis scheme that splits the phasor points in four equidistance segments based on the height of peak of the phasor distribution and calculates six parameters including average phasor positions, the shape of each segment, the angle of the distribution and the number of points in each segment. These parameters are used to create a spectrum of twenty four points specific to the phasor distribution of each sample. Comparisons of spectra from diseased and healthy tissues result in quantitative separation and calculation of statistical parameters including AUC values, positive prediction values and sensitivity. This is a new method in the evolving field of analyzing phasor distribution of FLIM data and provides further insights. Additionally, the progression of fibrosis with time is detected using this multiparametric approach to phasor analysis.
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Affiliation(s)
- Suman Ranjit
- Laboratory Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA
| | - Alexander Dvornikov
- Laboratory Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA
| | - Moshe Levi
- Departments of Medicine, University of Colorado-Anschutz Medical Campus, Aurora, Colorado, USA
| | - Seth Furgeson
- Departments of Medicine, University of Colorado-Anschutz Medical Campus, Aurora, Colorado, USA
| | - Enrico Gratton
- Laboratory Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA
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25
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Iermak I, Vink J, Bader AN, Wientjes E, van Amerongen H. Visualizing heterogeneity of photosynthetic properties of plant leaves with two-photon fluorescence lifetime imaging microscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1473-1478. [PMID: 27239747 DOI: 10.1016/j.bbabio.2016.05.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/09/2016] [Accepted: 05/21/2016] [Indexed: 01/09/2023]
Abstract
Two-photon fluorescence lifetime imaging microscopy (FLIM) was used to analyse the distribution and properties of Photosystem I (PSI) and Photosystem II (PSII) in palisade and spongy chloroplasts of leaves from the C3 plant Arabidopsis thaliana and the C4 plant Miscanthus x giganteus. This was achieved by separating the time-resolved fluorescence of PSI and PSII in the leaf. It is found that the PSII antenna size is larger on the abaxial side of A. thaliana leaves, presumably because chloroplasts in the spongy mesophyll are "shaded" by the palisade cells. The number of chlorophylls in PSI on the adaxial side of the A. thaliana leaf is slightly higher. The C4 plant M. x giganteus contains both mesophyll and bundle sheath cells, which have a different PSI/PSII ratio. It is shown that the time-resolved fluorescence of bundle sheath and mesophyll cells can be analysed separately. The relative number of chlorophylls, which belong to PSI (as compared to PSII) in the bundle sheath cells is at least 2.5 times higher than in mesophyll cells. FLIM is thus demonstrated to be a useful technique to study the PSI/PSII ratio and PSII antenna size in well-defined regions of plant leaves without having to isolate pigment-protein complexes.
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Affiliation(s)
- Ievgeniia Iermak
- Laboratory of Biophysics, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, The Netherlands; BioSolar Cells Project Office, P.O. Box 98, 6700 AB Wageningen, The Netherlands
| | - Jochem Vink
- Laboratory of Biophysics, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, The Netherlands
| | - Arjen N Bader
- Laboratory of Biophysics, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, The Netherlands; MicroSpectroscopy Centre, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, The Netherlands
| | - Emilie Wientjes
- Laboratory of Biophysics, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, The Netherlands
| | - Herbert van Amerongen
- Laboratory of Biophysics, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, The Netherlands; BioSolar Cells Project Office, P.O. Box 98, 6700 AB Wageningen, The Netherlands; MicroSpectroscopy Centre, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, The Netherlands
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26
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Sharma A, Kiripolsky J, Klimatcheva E, Howell A, Fereidouni F, Levenson R, Rothstein TL, Kramer JM. Early BAFF receptor blockade mitigates murine Sjögren's syndrome: Concomitant targeting of CXCL13 and the BAFF receptor prevents salivary hypofunction. Clin Immunol 2016; 164:85-94. [PMID: 26826598 DOI: 10.1016/j.clim.2016.01.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 01/23/2016] [Accepted: 01/25/2016] [Indexed: 12/28/2022]
Abstract
Sjögren's syndrome (SS) is a debilitating autoimmune disease. Patients with SS may develop xerostomia. This process is progressive, and there are no therapeutics that target disease etiology. We hypothesized BAFF receptor (BAFFR) blockade would mitigate SS disease development, and neutralization of CXCL13 and BAFF signaling would be more efficacious than BAFFR blockade alone. We treated NOD/ShiLtJ SS mice with soluble BAFF receptor (BAFFR-Fc) or anti-CXCL13/BAFFR-Fc in combination, prior to the development of clinical disease. Our results show treatment with BAFFR-Fc reduced peripheral B cell numbers and decreased sialadenitis. In addition, this treatment reduced total serum immunoglobulin as well as IgG and IgM specific anti-nuclear autoantibodies. NOD/ShiLtJ mice treated with BAFFR-Fc and anti-CXCL13 antibody were protected from salivary deficits. Results from this study suggest blockade of CXCL13 and BAFFR together may be an effective therapeutic strategy in preventing salivary hypofunction and reducing autoantibody titers and sialadenitis in patients with SS.
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Affiliation(s)
- Arjun Sharma
- Department of Oral Biology, School of Dental Medicine, University of Buffalo, The State University of New York, Buffalo, NY USA 14214
| | - Jeremy Kiripolsky
- Department of Oral Biology, School of Dental Medicine, University of Buffalo, The State University of New York, Buffalo, NY USA 14214
| | | | | | - Farzad Fereidouni
- Department of Pathology and Laboratory Medicine, UC Davis Medical Center, Sacramento, CA 95817
| | - Richard Levenson
- Department of Pathology and Laboratory Medicine, UC Davis Medical Center, Sacramento, CA 95817
| | - Thomas L Rothstein
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY 11030.,Department of Molecular Medicine, School of Medicine, Manhasset, NY 11030.,Department of Medicine, Hofstra North Shore-LIJ, School of Medicine, Manhasset, NY 11030
| | - Jill M Kramer
- Department of Oral Biology, School of Dental Medicine, University of Buffalo, The State University of New York, Buffalo, NY USA 14214.,Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY 11030.,Department of Molecular Medicine, School of Medicine, Manhasset, NY 11030.,Department of Dental Medicine, Division of Oral and Maxillofacial Pathology, North Shore-LIJ Health System, Manhasset, NY 11030
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27
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Fitzgerald C, Hosny NA, Tong H, Seville PC, Gallimore PJ, Davidson NM, Athanasiadis A, Botchway SW, Ward AD, Kalberer M, Kuimova MK, Pope FD. Fluorescence lifetime imaging of optically levitated aerosol: a technique to quantitatively map the viscosity of suspended aerosol particles. Phys Chem Chem Phys 2016; 18:21710-9. [DOI: 10.1039/c6cp03674k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A technique to measure the viscosity of stably levitated single micron-sized aerosol particles.
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Affiliation(s)
- C. Fitzgerald
- Department of Chemistry
- University of Cambridge
- Cambridge
- UK
| | - N. A. Hosny
- Department of Chemistry
- Imperial College London
- London
- UK
| | - H. Tong
- Department of Chemistry
- University of Cambridge
- Cambridge
- UK
| | - P. C. Seville
- School of Pharmacy and Biomedical Sciences
- University of Central Lancashire
- Preston
- UK
| | | | - N. M. Davidson
- School of Geography
- Earth and Environmental Sciences
- University of Birmingham
- Birmingham
- UK
| | | | - S. W. Botchway
- The Science and Technology Facilities Council
- Rutherford Appleton Laboratory
- Research Complex at Harwell
- Oxfordshire
- UK
| | - A. D. Ward
- The Science and Technology Facilities Council
- Rutherford Appleton Laboratory
- Research Complex at Harwell
- Oxfordshire
- UK
| | - M. Kalberer
- Department of Chemistry
- University of Cambridge
- Cambridge
- UK
| | - M. K. Kuimova
- Department of Chemistry
- Imperial College London
- London
- UK
| | - F. D. Pope
- School of Geography
- Earth and Environmental Sciences
- University of Birmingham
- Birmingham
- UK
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28
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Popleteeva M, Haas KT, Stoppa D, Pancheri L, Gasparini L, Kaminski CF, Cassidy LD, Venkitaraman AR, Esposito A. Fast and simple spectral FLIM for biochemical and medical imaging. OPTICS EXPRESS 2015; 23:23511-25. [PMID: 26368450 DOI: 10.1364/oe.23.023511] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Spectrally resolved fluorescence lifetime imaging microscopy (λFLIM) has powerful potential for biochemical and medical imaging applications. However, long acquisition times, low spectral resolution and complexity of λFLIM often narrow its use to specialized laboratories. Therefore, we demonstrate here a simple spectral FLIM based on a solid-state detector array providing in-pixel histrogramming and delivering faster acquisition, larger dynamic range, and higher spectral elements than state-of-the-art λFLIM. We successfully apply this novel microscopy system to biochemical and medical imaging demonstrating that solid-state detectors are a key strategic technology to enable complex assays in biomedical laboratories and the clinic.
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29
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Abstract
Luminescence-based sensing schemes for oxygen have experienced a fast growth and are in the process of replacing the Clark electrode in many fields. Unlike electrodes, sensing is not limited to point measurements via fiber optic microsensors, but includes additional features such as planar sensing, imaging, and intracellular assays using nanosized sensor particles. In this essay, I review and discuss the essentials of (i) common solid-state sensor approaches based on the use of luminescent indicator dyes and host polymers; (ii) fiber optic and planar sensing schemes; (iii) nanoparticle-based intracellular sensing; and (iv) common spectroscopies. Optical sensors are also capable of multiple simultaneous sensing (such as O2 and temperature). Sensors for O2 are produced nowadays in large quantities in industry. Fields of application include sensing of O2 in plant and animal physiology, in clinical chemistry, in marine sciences, in the chemical industry and in process biotechnology.
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Affiliation(s)
- Otto S Wolfbeis
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Regensburg, Germany
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30
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Campos-Delgado DU, Navarro OG, Arce-Santana ER, Jo JA. Extended output phasor representation of multi-spectral fluorescence lifetime imaging microscopy. BIOMEDICAL OPTICS EXPRESS 2015; 6:2088-105. [PMID: 26114031 PMCID: PMC4473746 DOI: 10.1364/boe.6.002088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/01/2015] [Accepted: 05/04/2015] [Indexed: 05/23/2023]
Abstract
In this paper, we investigate novel low-dimensional and model-free representations for multi-spectral fluorescence lifetime imaging microscopy (m-FLIM) data. We depart from the classical definition of the phasor in the complex plane to propose the extended output phasor (EOP) and extended phasor (EP) for multi-spectral information. The frequency domain properties of the EOP and EP are analytically studied based on a multiexponential model for the impulse response of the imaged tissue. For practical implementations, the EOP is more appealing since there is no need to perform deconvolution of the instrument response from the measured m-FLIM data, as in the case of EP. Our synthetic and experimental evaluations with m-FLIM datasets of human coronary atherosclerotic plaques show that low frequency indexes have to be employed for a distinctive representation of the EOP and EP, and to reduce noise distortion. The tissue classification of the m-FLIM datasets by EOP and EP also improves with low frequency indexes, and does not present significant differences by using either phasor.
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Affiliation(s)
| | | | - E. R. Arce-Santana
- Facultad de Ciencias, Universidad Autonoma de San Luis Potosi, SLP,
Mexico
| | - Javier A. Jo
- Department of Biomedical Engineering, Texas A& M University, College Station, TX,
USA
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31
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Abstract
Optical imaging assays, especially fluorescence molecular assays, are minimally invasive if not completely noninvasive, and thus an ideal technique to be applied to live specimens. These fluorescence imaging assays are a powerful tool in biomedical sciences as they allow the study of a wide range of molecular and physiological events occurring in biological systems. Furthermore, optical imaging assays bridge the gap between the in vitro cell-based analysis of subcellular processes and in vivo study of disease mechanisms in small animal models. In particular, the application of Förster resonance energy transfer (FRET) and fluorescence lifetime imaging (FLIM), well-known techniques widely used in microscopy, to the optical imaging assay toolbox, will have a significant impact in the molecular study of protein-protein interactions during cancer progression. This review article describes the application of FLIM-FRET to the field of optical imaging and addresses their various applications, both current and potential, to anti-cancer drug delivery and cancer research.
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Affiliation(s)
- Shilpi Rajoria
- Albany Medical College, The Center for Cardiovascular Sciences, Albany, NY, 12208
| | - Lingling Zhao
- Rensselaer Polytechnic Institute, Biomedical imaging Center and Department of Biomedical Engineering, Troy, NY 12180
| | - Xavier Intes
- Rensselaer Polytechnic Institute, Biomedical imaging Center and Department of Biomedical Engineering, Troy, NY 12180
| | - Margarida Barroso
- Albany Medical College, The Center for Cardiovascular Sciences, Albany, NY, 12208
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32
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Fereidouni F, Bader AN, Colonna A, Gerritsen HC. Phasor analysis of multiphoton spectral images distinguishes autofluorescence components of in vivo human skin. JOURNAL OF BIOPHOTONICS 2014; 7:589-96. [PMID: 23576407 DOI: 10.1002/jbio.201200244] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 02/27/2013] [Accepted: 03/16/2013] [Indexed: 05/25/2023]
Abstract
Skin contains many autofluorescent components that can be studied using spectral imaging. We employed a spectral phasor method to analyse two photon excited autofluorescence and second harmonic generation images of in vivo human skin. This method allows segmentation of images based on spectral features. Various structures in the skin could be distinguished, including Stratum Corneum, epidermal cells and dermis. The spectral phasor analysis allowed investigation of their fluorescence composition and identification of signals from NADH, keratin, FAD, melanin, collagen and elastin. Interestingly, two populations of epidermal cells could be distinguished with different melanin content.
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Affiliation(s)
- Farzad Fereidouni
- Utrecht University, Department of Molecular Biophysics, Utrecht, The Netherlands
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33
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Fereidouni F, Blab GA, Gerritsen HC. Phasor based analysis of FRET images recorded using spectrally resolved lifetime imaging. Methods Appl Fluoresc 2014; 2:035001. [DOI: 10.1088/2050-6120/2/3/035001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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34
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Bücherl CA, Bader A, Westphal AH, Laptenok SP, Borst JW. FRET-FLIM applications in plant systems. PROTOPLASMA 2014; 251:383-394. [PMID: 24390247 DOI: 10.1007/s00709-013-0595-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 12/05/2013] [Indexed: 05/28/2023]
Abstract
A hallmark of cellular processes is the spatio-temporally regulated interplay of biochemical components. Assessing spatial information of molecular interactions within living cells is difficult using traditional biochemical methods. Developments in green fluorescent protein technology in combination with advances in fluorescence microscopy have revolutionised this field of research by providing the genetic tools to investigate the spatio-temporal dynamics of biomolecules in live cells. In particular, fluorescence lifetime imaging microscopy (FLIM) has become an inevitable technique for spatially resolving cellular processes and physical interactions of cellular components in real time based on the detection of Förster resonance energy transfer (FRET). In this review, we provide a theoretical background of FLIM as well as FRET-FLIM analysis. Furthermore, we show two cases in which advanced microscopy applications revealed many new insights of cellular processes in living plant cells as well as in whole plants.
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35
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Biomolecular dynamics and binding studies in the living cell. Phys Life Rev 2014; 11:1-30. [DOI: 10.1016/j.plrev.2013.11.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 11/20/2013] [Indexed: 11/22/2022]
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36
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Kerényi F, Wawer I, Sikorski PJ, Kufel J, Silhavy D. Phosphorylation of the N- and C-terminal UPF1 domains plays a critical role in plant nonsense-mediated mRNA decay. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:836-48. [PMID: 24118551 DOI: 10.1111/tpj.12346] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 09/10/2013] [Accepted: 09/20/2013] [Indexed: 05/11/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is an essential quality control system that degrades aberrant transcripts containing premature termination codons and regulates the expression of several normal transcripts. Targets for NMD are selected during translational termination. If termination is slow, the UPF1 NMD factor binds the eRF3 protein of the termination complex and then recruits UPF2 and UPF3. Consequently, the UPF1-2-3 NMD complex induces SMG7-mediated degradation of the target mRNA. It is unknown how formation of the NMD complex and transcript degradation are linked in plants. Previously we have shown that the N- and C-terminal domains of UPF1 act redundantly and that the N-terminal domain is phosphorylated. To clarify the role of UPF1 phosphorylation in plant NMD, we generated UPF1 mutants and analyzed their phosphorylation status and the NMD competency of the mutants. We show that although several residues in the N-terminal domain of UPF1 are phosphorylated, only three phosphorylated amino acids, S3, S13 and T29, play a role in NMD. Moreover, we found that the C-terminal domain consists of redundant S/TQ-rich segments and that S1076 is involved in NMD. All NMD-relevant phosphorylation sites were in the S/TQ context. Co-localization and fluorescence resonance energy transfer-fluorescence lifetime imaging assays suggest that N-terminal and probably also C-terminal phosphorylated S/TQ residues are the binding platform for SMG7. Our data support the hypothesis that phosphorylation of UPF1 connects NMD complex formation and the SMG7-mediated target transcript degradation steps of NMD. SMG7 binds the phosphorylated S/TQ sites of the UPF1 component of the NMD complex, and then it induces the degradation of the NMD target.
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Affiliation(s)
- Farkas Kerényi
- Agricultural Biotechnology Center, Szent-Györgyi 4, H-2100, Gödöllõ, Hungary
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37
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Warren SC, Margineanu A, Alibhai D, Kelly DJ, Talbot C, Alexandrov Y, Munro I, Katan M, Dunsby C, French PMW. Rapid global fitting of large fluorescence lifetime imaging microscopy datasets. PLoS One 2013; 8:e70687. [PMID: 23940626 PMCID: PMC3734241 DOI: 10.1371/journal.pone.0070687] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 06/20/2013] [Indexed: 12/18/2022] Open
Abstract
Fluorescence lifetime imaging (FLIM) is widely applied to obtain quantitative information from fluorescence signals, particularly using Förster Resonant Energy Transfer (FRET) measurements to map, for example, protein-protein interactions. Extracting FRET efficiencies or population fractions typically entails fitting data to complex fluorescence decay models but such experiments are frequently photon constrained, particularly for live cell or in vivo imaging, and this leads to unacceptable errors when analysing data on a pixel-wise basis. Lifetimes and population fractions may, however, be more robustly extracted using global analysis to simultaneously fit the fluorescence decay data of all pixels in an image or dataset to a multi-exponential model under the assumption that the lifetime components are invariant across the image (dataset). This approach is often considered to be prohibitively slow and/or computationally expensive but we present here a computationally efficient global analysis algorithm for the analysis of time-correlated single photon counting (TCSPC) or time-gated FLIM data based on variable projection. It makes efficient use of both computer processor and memory resources, requiring less than a minute to analyse time series and multiwell plate datasets with hundreds of FLIM images on standard personal computers. This lifetime analysis takes account of repetitive excitation, including fluorescence photons excited by earlier pulses contributing to the fit, and is able to accommodate time-varying backgrounds and instrument response functions. We demonstrate that this global approach allows us to readily fit time-resolved fluorescence data to complex models including a four-exponential model of a FRET system, for which the FRET efficiencies of the two species of a bi-exponential donor are linked, and polarisation-resolved lifetime data, where a fluorescence intensity and bi-exponential anisotropy decay model is applied to the analysis of live cell homo-FRET data. A software package implementing this algorithm, FLIMfit, is available under an open source licence through the Open Microscopy Environment.
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Affiliation(s)
- Sean C Warren
- Department of Chemistry, Institute for Chemical Biology, Imperial College London, London, United Kingdom.
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38
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Leray A, Padilla-Parra S, Roul J, Héliot L, Tramier M. Spatio-Temporal Quantification of FRET in living cells by fast time-domain FLIM: a comparative study of non-fitting methods [corrected]. PLoS One 2013; 8:e69335. [PMID: 23874948 PMCID: PMC3715500 DOI: 10.1371/journal.pone.0069335] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/09/2013] [Indexed: 11/30/2022] Open
Abstract
Förster Resonance Energy Transfer (FRET) measured with Fluorescence Lifetime Imaging Microscopy (FLIM) is a powerful technique to investigate spatio-temporal regulation of protein-protein interactions in living cells. When using standard fitting methods to analyze time domain FLIM, the correct estimation of the FRET parameters requires a high number of photons and therefore long acquisition times which are incompatible with the observation of dynamic protein-protein interactions. Recently, non-fitting strategies have been developed for the analysis of FLIM images: the polar plot or "phasor" and the minimal fraction of interacting donor mfD . We propose here a novel non-fitting strategy based on the calculation of moments. We then compare the performance of these three methods when shortening the acquisition time: either by reducing the number of counted photons N or the number of temporal channels Nch , which is particularly adapted for the original fast-FLIM prototype presented in this work that employs the time gated approach. Based on theoretical calculations, Monte Carlo simulations and experimental data, we determine the domain of validity of each method. We thus demonstrate that the polar approach remains accurate for a large range of conditions (low N, Nch or small fractions of interacting donor fD ). The validity domain of the moments method is more restricted (not applicable when fD <0.25 or when Nch = 4) but it is more precise than the polar approach. We also demonstrate that the mfD is robust in all conditions and it is the most precise strategy; although it does not strictly provide the fraction of interacting donor. We show using the fast-FLIM prototype (with an acquisition rate up to 1 Hz) that these non-fitting strategies are very powerful for on-line analysis on a standard computer and thus for quantifying automatically the spatio-temporal activation of Rac-GTPase in living cells by FRET.
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Affiliation(s)
- Aymeric Leray
- Institut de Recherche Interdisciplinaire, USR 3078 CNRS, Université de Lille-Nord de France, Biophotonique Cellulaire Fonctionnelle, Villeneuve d'Ascq, France.
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39
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Fereidouni F, Reitsma K, Gerritsen HC. High speed multispectral fluorescence lifetime imaging. OPTICS EXPRESS 2013; 21:11769-82. [PMID: 23736399 DOI: 10.1364/oe.21.011769] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We report a spectrally resolved fluorescence lifetime imaging system based on time gated single photon detection with a fixed gate width of 200 ps and 7 spectral channels. Time gated systems can operate at high count rates but usually have large gate widths and sample only part of the fluorescence decay curve. In the system presented in this work, the fluorescence signal is sampled using a high speed transceiver. An error analysis is carried out to characterize the performance of both lifetime and spectral detection. The effect of gate width and spectral channel width on the accuracy of estimated lifetimes and spectral widths is described. The performance of the whole instrument is evaluated at count rates of up to 12 MHz. Accurate fluorescence lifetimes (error < 2%) are recorded at count rates as high as 5 MHz. This is limited by the PMT performance, not by the electronics. Analysis of the large spectral lifetime image sets is challenging and time-consuming. Here, we demonstrate the use of lifetime and spectral phasors for analyzing images of fibroblast cells with 2 different labeled components. The phasor approach provides a fast and intuitive way of analyzing the results of spectrally resolved fluorescence lifetime imaging experiments.
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Affiliation(s)
- Farzad Fereidouni
- Molecular Biophysics, Debye Institute, Utrecht University, Utrecht, The Netherlands
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40
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Leray A, Spriet C, Trinel D, Usson Y, Héliot L. Generalization of the polar representation in time domain fluorescence lifetime imaging microscopy for biological applications: practical implementation. J Microsc 2013; 248:66-76. [PMID: 22971219 DOI: 10.1111/j.1365-2818.2012.03651.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The polar representation or phasor, which provides a fast and visual indication on the number of exponentials present in the intensity decay of the fluorescence lifetime images is increasingly used in time domain fluorescence lifetime imaging microscopy experiments. The calculations of the polar coordinates in time domain fluorescence lifetime imaging microscopy experiments involve several experimental parameters (e.g. instrumental response function, background, angular frequency, number of temporal channels) whose role has not been exhaustively investigated. Here, we study theoretically, computationally and experimentally the influence of each parameter on the polar calculations and suggest parameter optimization for minimizing errors. We identify several sources of mistakes that may occur in the calculations of the polar coordinates and propose adapted corrections to compensate for them. For instance, we demonstrate that the numerical integration method employed for integrals calculations may induce errors when the number of temporal channels is low. We report theoretical generalized expressions to compensate for these deviations and conserve the semicircle integrity, facilitating the comparison between fluorescence lifetime imaging microscopy images acquired with distinct channels number. These theoretical generalized expressions were finally corroborated with both Monte Carlo simulations and experiments.
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Affiliation(s)
- A Leray
- Institut de Recherche Interdisciplinaire, USR 3078 CNRS, Université de Lille-Nord de France, BCF, Parc de la Haute Borne, 59650 Villeneuve d'Ascq, France.
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41
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From FRET Imaging to Practical Methodology for Kinase Activity Sensing in Living Cells. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 113:145-216. [DOI: 10.1016/b978-0-12-386932-6.00005-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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42
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Fereidouni F, Bader AN, Gerritsen HC. Spectral phasor analysis allows rapid and reliable unmixing of fluorescence microscopy spectral images. OPTICS EXPRESS 2012; 20:12729-41. [PMID: 22714302 DOI: 10.1364/oe.20.012729] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A new global analysis algorithm to analyse (hyper-) spectral images is presented. It is based on the phasor representation that has been demonstrated to be very powerful for the analysis of lifetime imaging data. In spectral phasor analysis the fluorescence spectrum of each pixel in the image is Fourier transformed. Next, the real and imaginary components of the first harmonic of the transform are employed as X and Y coordinates in a scatter (spectral phasor) plot. Importantly, the spectral phasor representation allows for rapid (real time) semi-blind spectral unmixing of up to three components in the image. This is demonstrated on slides with fixed cells containing three fluorescent labels. In addition the method is used to analyse autofluorescence of cells in a fresh grass blade. It is shown that the spectral phasor approach is compatible with spectral imaging data recorded with a low number of spectral channels.
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Affiliation(s)
- Farzad Fereidouni
- Department of Molecular Biophysics, Debye Institute, Utrecht University, Utrecht, The Netherlands
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43
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Ishikawa-Ankerhold HC, Ankerhold R, Drummen GPC. Advanced fluorescence microscopy techniques--FRAP, FLIP, FLAP, FRET and FLIM. Molecules 2012; 17:4047-132. [PMID: 22469598 PMCID: PMC6268795 DOI: 10.3390/molecules17044047] [Citation(s) in RCA: 290] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 03/21/2012] [Accepted: 03/21/2012] [Indexed: 12/19/2022] Open
Abstract
Fluorescence microscopy provides an efficient and unique approach to study fixed and living cells because of its versatility, specificity, and high sensitivity. Fluorescence microscopes can both detect the fluorescence emitted from labeled molecules in biological samples as images or photometric data from which intensities and emission spectra can be deduced. By exploiting the characteristics of fluorescence, various techniques have been developed that enable the visualization and analysis of complex dynamic events in cells, organelles, and sub-organelle components within the biological specimen. The techniques described here are fluorescence recovery after photobleaching (FRAP), the related fluorescence loss in photobleaching (FLIP), fluorescence localization after photobleaching (FLAP), Förster or fluorescence resonance energy transfer (FRET) and the different ways how to measure FRET, such as acceptor bleaching, sensitized emission, polarization anisotropy, and fluorescence lifetime imaging microscopy (FLIM). First, a brief introduction into the mechanisms underlying fluorescence as a physical phenomenon and fluorescence, confocal, and multiphoton microscopy is given. Subsequently, these advanced microscopy techniques are introduced in more detail, with a description of how these techniques are performed, what needs to be considered, and what practical advantages they can bring to cell biological research.
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Affiliation(s)
- Hellen C. Ishikawa-Ankerhold
- Ludwig Maximilian University of Munich, Institute of Anatomy and Cell Biology, Schillerstr. 42, 80336 München, Germany
| | - Richard Ankerhold
- Carl Zeiss Microimaging GmbH, Kistlerhofstr. 75, 81379 München, Germany
| | - Gregor P. C. Drummen
- Bionanoscience and Bio-Imaging Program, Cellular Stress and Ageing Program, Bio&Nano-Solutions, Helmutstr. 3A, 40472 Düsseldorf, Germany
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