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George Abraham B, Sarkisyan KS, Mishin AS, Santala V, Tkachenko NV, Karp M. Fluorescent Protein Based FRET Pairs with Improved Dynamic Range for Fluorescence Lifetime Measurements. PLoS One 2015; 10:e0134436. [PMID: 26237400 PMCID: PMC4523203 DOI: 10.1371/journal.pone.0134436] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/09/2015] [Indexed: 11/18/2022] Open
Abstract
Fluorescence Resonance Energy Transfer (FRET) using fluorescent protein variants is widely used to study biochemical processes in living cells. FRET detection by fluorescence lifetime measurements is the most direct and robust method to measure FRET. The traditional cyan-yellow fluorescent protein based FRET pairs are getting replaced by green-red fluorescent protein variants. The green-red pair enables excitation at a longer wavelength which reduces cellular autofluorescence and phototoxicity while monitoring FRET. Despite the advances in FRET based sensors, the low FRET efficiency and dynamic range still complicates their use in cell biology and high throughput screening. In this paper, we utilized the higher lifetime of NowGFP and screened red fluorescent protein variants to develop FRET pairs with high dynamic range and FRET efficiency. The FRET variations were analyzed by proteolytic activity and detected by steady-state and time-resolved measurements. Based on the results, NowGFP-tdTomato and NowGFP-mRuby2 have shown high potentials as FRET pairs with large fluorescence lifetime dynamic range. The in vitro measurements revealed that the NowGFP-tdTomato has the highest Förster radius for any fluorescent protein based FRET pairs yet used in biological studies. The developed FRET pairs will be useful for designing FRET based sensors and studies employing Fluorescence Lifetime Imaging Microscopy (FLIM).
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Affiliation(s)
- Bobin George Abraham
- Department of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, 33101, Tampere, Finland
| | - Karen S. Sarkisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Ville Santala
- Department of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, 33101, Tampere, Finland
| | - Nikolai V. Tkachenko
- Department of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, 33101, Tampere, Finland
| | - Matti Karp
- Department of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, 33101, Tampere, Finland
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De Los Santos C, Chang CW, Mycek MA, Cardullo RA. FRAP, FLIM, and FRET: Detection and analysis of cellular dynamics on a molecular scale using fluorescence microscopy. Mol Reprod Dev 2015; 82:587-604. [PMID: 26010322 PMCID: PMC4515154 DOI: 10.1002/mrd.22501] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 05/01/2015] [Indexed: 01/01/2023]
Abstract
The combination of fluorescent-probe technology plus modern optical microscopes allows investigators to monitor dynamic events in living cells with exquisite temporal and spatial resolution. Fluorescence recovery after photobleaching (FRAP), for example, has long been used to monitor molecular dynamics both within cells and on cellular surfaces. Although bound by the diffraction limit imposed on all optical microscopes, the combination of digital cameras and the application of fluorescence intensity information on large-pixel arrays have allowed such dynamic information to be monitored and quantified. Fluorescence lifetime imaging microscopy (FLIM), on the other hand, utilizes the information from an ensemble of fluorophores to probe changes in the local environment. Using either fluorescence-intensity or lifetime approaches, fluorescence resonance energy transfer (FRET) microscopy provides information about molecular interactions, with Ångstrom resolution. In this review, we summarize the theoretical framework underlying these methods and illustrate their utility in addressing important problems in reproductive and developmental systems.
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Affiliation(s)
- Carla De Los Santos
- Departments of Biology and Bioengineering, University of California, Riverside, Riverside, CA 92501
| | - Ching-Wei Chang
- Department of Bioengineering, University of California, Berkeley 94720
| | - Mary-Ann Mycek
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Richard A. Cardullo
- Departments of Biology and Bioengineering, University of California, Riverside, Riverside, CA 92501
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Chang CW, Kumar S. Vinculin tension distributions of individual stress fibers within cell-matrix adhesions. J Cell Sci 2013; 126:3021-30. [PMID: 23687380 DOI: 10.1242/jcs.119032] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Actomyosin stress fibers (SFs) enable cells to exert traction on planar extracellular matrices (ECMs) by tensing focal adhesions (FAs) at the cell-ECM interface. Although it is widely appreciated that the spatial and temporal distribution of these tensile forces play key roles in polarity, motility, fate choice, and other defining cell behaviors, virtually nothing is known about how an individual SF quantitatively contributes to tensile loads borne by specific molecules within associated FAs. We address this key open question by using femtosecond laser ablation to sever single SFs in cells while tracking tension across vinculin using a molecular optical sensor. We show that disruption of a single SF reduces tension across vinculin in FAs located throughout the cell, with enriched vinculin tension reduction in FAs oriented parallel to the targeted SF. Remarkably, however, some subpopulations of FAs exhibit enhanced vinculin tension upon SF irradiation and undergo dramatic, unexpected transitions between tension-enhanced and tension-reduced states. These changes depend strongly on the location of the severed SF, consistent with our earlier finding that different SF pools are regulated by distinct myosin activators. We critically discuss the extent to which these measurements can be interpreted in terms of whole-FA tension and traction and propose a model that relates SF tension to adhesive loads and cell shape stability. These studies represent the most direct and high-resolution intracellular measurements of SF contributions to tension on specific FA proteins to date and offer a new paradigm for investigating regulation of adhesive complexes by cytoskeletal force.
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Affiliation(s)
- Ching-Wei Chang
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
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Chen LC, Lloyd WR, Chang CW, Sud D, Mycek MA. Fluorescence lifetime imaging microscopy for quantitative biological imaging. Methods Cell Biol 2013; 114:457-88. [PMID: 23931519 DOI: 10.1016/b978-0-12-407761-4.00020-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) is a method for measuring fluorophore lifetimes with microscopic spatial resolution, providing a useful tool for cell biologists to detect, visualize, and investigate structure and function of biological systems. In this chapter, we begin by introducing the basic theory of fluorescence lifetime, including the characteristics of fluorophore decay, followed by a discussion of factors affecting fluorescence lifetimes and the potential advantages of fluorescence lifetime as a source of image contrast. Experimental methods for creating lifetime maps, including both time- and frequency-domain experimental approaches, are then introduced. Then, FLIM data analysis methods are discussed, including rapid lifetime determination, multiexponential fitting, Laguerre polynomial fitting, and phasor plot analysis. After, data analysis methods are introduced that improve lifetime precision of FLIM maps based upon optimal virtual gating and total variation denoising. The chapter concludes by highlighting several recent FLIM applications for quantitative biological imaging, including Förster resonance energy transfer-FLIM, fluorescence correlation spectroscopy-FLIM, multispectral-FLIM, and multiphoton-FLIM.
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Affiliation(s)
- Leng-Chun Chen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA
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Chang CW, Mycek MA. Total variation versus wavelet-based methods for image denoising in fluorescence lifetime imaging microscopy. JOURNAL OF BIOPHOTONICS 2012; 5:449-457. [PMID: 22415891 PMCID: PMC4106132 DOI: 10.1002/jbio.201100137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/10/2012] [Accepted: 02/23/2012] [Indexed: 05/31/2023]
Abstract
We report the first application of wavelet-based denoising (noise removal) methods to time-domain box-car fluorescence lifetime imaging microscopy (FLIM) images and compare the results to novel total variation (TV) denoising methods. Methods were tested first on artificial images and then applied to low-light live-cell images. Relative to undenoised images, TV methods could improve lifetime precision up to 10-fold in artificial images, while preserving the overall accuracy of lifetime and amplitude values of a single-exponential decay model and improving local lifetime fitting in live-cell images. Wavelet-based methods were at least 4-fold faster than TV methods, but could introduce significant inaccuracies in recovered lifetime values. The denoising methods discussed can potentially enhance a variety of FLIM applications, including live-cell, in vivo animal, or endoscopic imaging studies, especially under challenging imaging conditions such as low-light or fast video-rate imaging.
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Affiliation(s)
- Ching-Wei Chang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109-2099
| | - Mary-Ann Mycek
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109-2099
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109-2099
- Applied Physics Program, University of Michigan, Ann Arbor, MI 48109-2099
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Maliwal BP, Raut S, Fudala R, D’Auria S, Marzullo VM, Luini A, Gryczynski I, Gryczynski Z. Extending Förster resonance energy transfer measurements beyond 100 Å using common organic fluorophores: enhanced transfer in the presence of multiple acceptors. JOURNAL OF BIOMEDICAL OPTICS 2012; 17:011006. [PMID: 22352640 PMCID: PMC3379572 DOI: 10.1117/1.jbo.17.1.011006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 08/15/2011] [Accepted: 08/22/2011] [Indexed: 05/22/2023]
Abstract
Using commercially available organic fluorophores, the current applications of Förster (fluorescence) resonance energy transfer (FRET) are limited to about 80 Å. However, many essential activities in cells are spatially and/or temporally dependent on the assembly/disassembly of transient complexes consisting of large-size macromolecules that are frequently separated by distances greater than 100 Å. Expanding the accessible range for FRET to 150 Å would open up many cellular interactions to fluorescence and fluorescence-lifetime imaging. Here, we demonstrate that the use of multiple randomly distributed acceptors on proteins/antibodies, rather than the use of a single localized acceptor, makes it possible to significantly enhance FRET and detect interactions between the donor fluorophore and the acceptor-labeled protein at distances greater than 100 Å. A simple theoretical model for spherical bodies that have been randomly labeled with acceptors has been developed. To test the theoretical predictions of this system, we carried out FRET studies using a 30-mer oligonucleotide-avidin system that was labeled with the acceptors DyLight649 or Dylight750. The opposite 5'-end of the oligonucleotide was labeled with the Alexa568 donor. We observed significantly enhanced energy transfer due to presence of multiple acceptors on the avidin protein. The results and simulation indicate that use of a nanosized body that has been randomly labeled with multiple acceptors allows FRET measurements to be extended to over 150 Å when using commercially available probes and established protein-labeling protocols.
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Affiliation(s)
- Badri P. Maliwal
- University of North Texas Health Science Center, Department of Molecular Biology and Immunology, Center for Commercialization of Fluorescence Technologies, 3500 Camp Bowie Boulevard, Fort Worth, Texas 76106
| | - Sangram Raut
- University of North Texas Health Science Center, Department of Molecular Biology and Immunology, Center for Commercialization of Fluorescence Technologies, 3500 Camp Bowie Boulevard, Fort Worth, Texas 76106
| | - Rafal Fudala
- University of North Texas Health Science Center, Department of Molecular Biology and Immunology, Center for Commercialization of Fluorescence Technologies, 3500 Camp Bowie Boulevard, Fort Worth, Texas 76106
| | - Sabato D’Auria
- Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino, 111 80131 Naples, Italy
| | - Vincenzo M. Marzullo
- Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino, 111 80131 Naples, Italy
- Telethon - Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy
| | - Alberto Luini
- Telethon - Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy
| | - Ignacy Gryczynski
- University of North Texas Health Science Center, Department of Molecular Biology and Immunology, Center for Commercialization of Fluorescence Technologies, 3500 Camp Bowie Boulevard, Fort Worth, Texas 76106
- University of North Texas Health Science Center, Department of Cell Biology and Genetics, 3500 Camp Bowie Boulevard, Fort Worth, Texas 76106
| | - Zygmunt Gryczynski
- University of North Texas Health Science Center, Department of Cell Biology and Genetics, 3500 Camp Bowie Boulevard, Fort Worth, Texas 76106
- Texas Christian University, Department of Physics and Astronomy, TCU Box 298840, Fort Worth, Texas 76129
- Address all correspondence to: Zygmunt Gryczynski, Texas Christian University, Department of Physics and Astronomy, TCU Box 298840, Fort Worth, Texas 76129. Tel: 817 257 4209; E-mail:
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Solomon M, Guo K, Sudlow GP, Berezin MY, Edwards WB, Achilefu S, Akers WJ. Detection of enzyme activity in orthotopic murine breast cancer by fluorescence lifetime imaging using a fluorescence resonance energy transfer-based molecular probe. JOURNAL OF BIOMEDICAL OPTICS 2011; 16:066019. [PMID: 21721820 PMCID: PMC3138800 DOI: 10.1117/1.3594153] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 04/22/2011] [Accepted: 05/04/2011] [Indexed: 05/20/2023]
Abstract
Cancer-related enzyme activity can be detected noninvasively using activatable fluorescent molecular probes. In contrast to "always-on" fluorescent molecular probes, activatable probes are relatively nonfluorescent at the time of administration due to intramolecular fluorescence resonance energy transfer (FRET). Enzyme-mediated hydrolysis of peptide linkers results in reduced FRET and increase of fluorescence yield. Separation of signal from active and inactive probe can be difficult with conventional intensity-based fluorescence imaging. Fluorescence lifetime (FLT) measurement is an alternative method to detect changes in FRET. Thus, we investigate FLT imaging for in vivo detection of FRET-based molecular probe activation in an orthotopic breast cancer model. Indeed, the measured FLT of the enzyme-activatable molecular probe increases from 0.62 ns just after injection to 0.78 ns in tumor tissue after 4 h. A significant increase in FLT is not observed for an always-on targeted molecular probe with the same fluorescent reporter. These results show that FLT contrast is a powerful addition to preclinical imaging because it can report molecular activity in vivo due to changes in FRET. Fluorescence lifetime imaging exploits unique characteristics of fluorescent molecular probes that can be further translated into clinical applications, including noninvasive detection of cancer-related enzyme activity.
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Affiliation(s)
- Metasebya Solomon
- Washington University, Department of Radiology, Optical Radiology Laboratory, 4525 Scott Avenue, St. Louis, Missouri 63110, USA
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Chang CW, Mycek MA. Enhancing precision in time-domain fluorescence lifetime imaging. JOURNAL OF BIOMEDICAL OPTICS 2010; 15:056013. [PMID: 21054107 PMCID: PMC2966491 DOI: 10.1117/1.3494566] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
In biological applications of fluorescence lifetime imaging, low signals from samples can be a challenge, causing poor lifetime precision. We demonstrate how optimal signal gating (a method applied to the temporal dimension of a lifetime image) and novel total variation denoising models (a method applied to the spatial dimension of a lifetime image) can be used in time-domain fluorescence lifetime imaging microscopy (FLIM) to improve lifetime precision. In time-gated FLIM, notable fourfold precision improvements were observed in a low-light example. This approach can be employed to improve FLIM data while minimizing sample light exposure and increasing imaging speed.
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Affiliation(s)
- Ching-Wei Chang
- University of Michigan, Department of Biomedical Engineering, Ann Arbor, Michigan 48109-2099, USA
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Chang CW, Mycek MA. Precise fluorophore lifetime mapping in live-cell, multi-photon excitation microscopy. OPTICS EXPRESS 2010; 18:8688-96. [PMID: 20588712 PMCID: PMC3410727 DOI: 10.1364/oe.18.008688] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Fluorophore excited state lifetime is a useful indicator of micro-environment in cellular optical molecular imaging. For quantitative sensing, precise lifetime determination is important, yet is often difficult to accomplish when using the experimental conditions favored by live cells. Here we report the first application of temporal optimization and spatial denoising methods to two-photon time-correlated single photon counting (TCSPC) fluorescence lifetime imaging microscopy (FLIM) to improve lifetime precision in live-cell images. The results demonstrated a greater than five-fold improvement in lifetime precision. This approach minimizes the adverse effects of excitation light on live cells and should benefit FLIM applications to high content analysis and bioimage informatics.
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Affiliation(s)
- Ching-Wei Chang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2099,
USA
| | - Mary-Ann Mycek
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2099,
USA
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109-2099,
USA
- Applied Physics Program, University of Michigan, Ann Arbor, Michigan 48109-2099,
USA
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