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Hansen-Shearer J, Yan J, Lerendegui M, Huang B, Toulemonde M, Riemer K, Tan Q, Tonko J, Weinberg PD, Dunsby C, Tang MX. Ultrafast 3-D Transcutaneous Super Resolution Ultrasound Using Row-Column Array Specific Coherence-Based Beamforming and Rolling Acoustic Sub-aperture Processing: In Vitro, in Rabbit and in Human Study. Ultrasound Med Biol 2024:S0301-5629(24)00153-4. [PMID: 38702285 DOI: 10.1016/j.ultrasmedbio.2024.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/27/2024] [Accepted: 03/31/2024] [Indexed: 05/06/2024]
Abstract
OBJECTIVE This study aimed to realise 3-D super-resolution ultrasound imaging transcutaneously with a row-column array which has far fewer independent electronic channels and a wider field of view than typical fully addressed 2-D matrix arrays. The in vivo image quality of the row-column array is generally poor, particularly when imaging non-invasively. This study aimed to develop a suite of image formation and post-processing methods to improve image quality and demonstrate the feasibility of ultrasound localisation microscopy using a row-column array, transcutaneously on a rabbit model and in a human. METHODS To achieve this, a processing pipeline was developed which included a new type of rolling window image reconstruction, which integrated a row-column array specific coherence-based beamforming technique with acoustic sub-aperture processing. This and other processing steps reduced the 'secondary' lobe artefacts, and noise and increased the effective frame rate, thereby enabling ultrasound localisation images to be produced. RESULTS Using an in vitro cross tube, it was found that the procedure reduced the percentage of 'false' locations from ∼26% to ∼15% compared to orthogonal plane wave compounding. Additionally, it was found that the noise could be reduced by ∼7 dB and the effective frame rate was increased to over 4000 fps. In vivo, ultrasound localisation microscopy was used to produce images non-invasively of a rabbit kidney and a human thyroid. CONCLUSION It has been demonstrated that the proposed methods using a row-column array can produce large field of view super-resolution microvascular images in vivo and in a human non-invasively.
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Dent LG, Curry N, Sparks H, Bousgouni V, Maioli V, Kumar S, Munro I, Butera F, Jones I, Arias-Garcia M, Rowe-Brown L, Dunsby C, Bakal C. Environmentally dependent and independent control of 3D cell shape. Cell Rep 2024:114016. [PMID: 38636520 DOI: 10.1016/j.celrep.2024.114016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/04/2024] [Accepted: 03/14/2024] [Indexed: 04/20/2024] Open
Abstract
How cancer cells determine their shape in response to three-dimensional (3D) geometric and mechanical cues is unclear. We develop an approach to quantify the 3D cell shape of over 60,000 melanoma cells in collagen hydrogels using high-throughput stage-scanning oblique plane microscopy (ssOPM). We identify stereotypic and environmentally dependent changes in shape and protrusivity depending on whether a cell is proximal to a flat and rigid surface or is embedded in a soft environment. Environmental sensitivity metrics calculated for small molecules and gene knockdowns identify interactions between the environment and cellular factors that are important for morphogenesis. We show that the Rho guanine nucleotide exchange factor (RhoGEF) TIAM2 contributes to shape determination in environmentally independent ways but that non-muscle myosin II, microtubules, and the RhoGEF FARP1 regulate shape in ways dependent on the microenvironment. Thus, changes in cancer cell shape in response to 3D geometric and mechanical cues are modulated in both an environmentally dependent and independent fashion.
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Affiliation(s)
- Lucas G Dent
- Dynamical Cell Systems Group, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Nathan Curry
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK
| | - Hugh Sparks
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK
| | - Vicky Bousgouni
- Dynamical Cell Systems Group, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Vincent Maioli
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK
| | - Ian Munro
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK
| | - Francesca Butera
- Dynamical Cell Systems Group, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Ian Jones
- Dynamical Cell Systems Group, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Mar Arias-Garcia
- Dynamical Cell Systems Group, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Leo Rowe-Brown
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
| | - Chris Bakal
- Dynamical Cell Systems Group, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
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Lerendegui M, Riemer K, Papageorgiou G, Wang B, Arthur L, Chavignon A, Zhang T, Couture O, Huang P, Ashikuzzaman M, Dencks S, Dunsby C, Helfield B, Jensen JA, Lisson T, Lowerison MR, Rivaz H, Samir AE, Schmitz G, Schoen S, Sloun RV, Song P, Stevens T, Yan J, Sboros V, Tang MX. ULTRA-SR Challenge: Assessment of Ultrasound Localization and TRacking Algorithms for Super-Resolution Imaging. IEEE Trans Med Imaging 2024; PP:1-1. [PMID: 38607705 DOI: 10.1109/tmi.2024.3388048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
With the widespread interest and uptake of super-resolution ultrasound (SRUS) through localization and tracking of microbubbles, also known as ultrasound localization microscopy (ULM), many localization and tracking algorithms have been developed. ULM can image many centimeters into tissue in-vivo and track microvascular flow non-invasively with sub-diffraction resolution. In a significant community effort, we organized a challenge, Ultrasound Localization and TRacking Algorithms for Super-Resolution (ULTRA-SR). The aims of this paper are threefold: to describe the challenge organization, data generation, and winning algorithms; to present the metrics and methods for evaluating challenge entrants; and to report results and findings of the evaluation. Realistic ultrasound datasets containing microvascular flow for different clinical ultrasound frequencies were simulated, using vascular flow physics, acoustic field simulation and nonlinear bubble dynamics simulation. Based on these datasets, 38 submissions from 24 research groups were evaluated against ground truth using an evaluation framework with six metrics, three for localization and three for tracking. In-vivo mouse brain and human lymph node data were also provided, and performance assessed by an expert panel. Winning algorithms are described and discussed. The publicly available data with ground truth and the defined metrics for both localization and tracking present a valuable resource for researchers to benchmark algorithms and software, identify optimized methods/software for their data, and provide insight into the current limits of the field. In conclusion, Ultra-SR challenge has provided benchmarking data and tools as well as direct comparison and insights for a number of the state-of-the art localization and tracking algorithms.
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Lightley J, Kumar S, Lim MQ, Garcia E, Görlitz F, Alexandrov Y, Parrado T, Hollick C, Steele E, Roßmann K, Graham J, Broichhagen J, McNeish IA, Roufosse CA, Neil MAA, Dunsby C, French PMW. openFrame: A modular, sustainable, open microscopy platform with single-shot, dual-axis optical autofocus module providing high precision and long range of operation. J Microsc 2023; 292:64-77. [PMID: 37616077 PMCID: PMC10953376 DOI: 10.1111/jmi.13219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/04/2023] [Accepted: 08/21/2023] [Indexed: 08/25/2023]
Abstract
'openFrame' is a modular, low-cost, open-hardware microscopy platform that can be configured or adapted to most light microscopy techniques and is easily upgradeable or expandable to multiple modalities. The ability to freely mix and interchange both open-source and proprietary hardware components or software enables low-cost, yet research-grade instruments to be assembled and maintained. It also enables rapid prototyping of advanced or novel microscope systems. For long-term time-lapse image data acquisition, slide-scanning or high content analysis, we have developed a novel optical autofocus incorporating orthogonal cylindrical optics to provide robust single-shot closed-loop focus lock, which we have demonstrated to accommodate defocus up to ±37 μm with <200 nm accuracy, and a two-step autofocus mode which we have shown can operate with defocus up to ±68 μm. We have used this to implement automated single molecule localisation microscopy (SMLM) in a relatively low-cost openFrame-based instrument using multimode diode lasers for excitation and cooled CMOS cameras.
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Affiliation(s)
- J. Lightley
- Photonics Group, Physics DepartmentImperial College LondonLondonUK
- Francis Crick InstituteLondonUK
| | - S. Kumar
- Photonics Group, Physics DepartmentImperial College LondonLondonUK
- Francis Crick InstituteLondonUK
| | - M. Q. Lim
- Photonics Group, Physics DepartmentImperial College LondonLondonUK
- Department of Surgery and CancerImperial College LondonLondonUK
| | - E. Garcia
- Photonics Group, Physics DepartmentImperial College LondonLondonUK
- Department of Surgery and CancerImperial College LondonLondonUK
| | - F. Görlitz
- Photonics Group, Physics DepartmentImperial College LondonLondonUK
| | - Y. Alexandrov
- Photonics Group, Physics DepartmentImperial College LondonLondonUK
- Francis Crick InstituteLondonUK
| | | | | | - E. Steele
- Cairn Research LtdFavershamKentEngland
| | - K. Roßmann
- Leibniz‐Forschungsinstitut für Molekulare PharmakologieBerlinGermany
| | - J. Graham
- Cairn Research LtdFavershamKentEngland
| | - J. Broichhagen
- Leibniz‐Forschungsinstitut für Molekulare PharmakologieBerlinGermany
| | - I. A. McNeish
- Department of Surgery and CancerImperial College LondonLondonUK
| | - C. A. Roufosse
- Department of Inflammation and ImmunologyImperial College LondonLondonUK
| | - M. A. A. Neil
- Photonics Group, Physics DepartmentImperial College LondonLondonUK
- Francis Crick InstituteLondonUK
| | - C. Dunsby
- Photonics Group, Physics DepartmentImperial College LondonLondonUK
- Francis Crick InstituteLondonUK
| | - P. M. W. French
- Photonics Group, Physics DepartmentImperial College LondonLondonUK
- Francis Crick InstituteLondonUK
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Hong W, Sparks H, Dunsby C. Alignment and characterization of remote-refocusing systems. Appl Opt 2023; 62:7431-7440. [PMID: 37855511 PMCID: PMC10575606 DOI: 10.1364/ao.500281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 10/20/2023]
Abstract
The technique of remote refocusing is used in optical microscopy to provide rapid axial scanning without mechanically perturbing the sample and in techniques such as oblique plane microscopy that build on remote refocusing to image a tilted plane within the sample. The magnification between the pupils of the primary (O1) and secondary (O2) microscope objectives of the remote-refocusing system has been shown previously by Mohanan and Corbett [J. Microsc.288, 95 (2022)JMICAR0022-272010.1111/jmi.12991] to be crucial in obtaining the broadest possible remote-refocusing range. In this work, we performed an initial alignment of a remote-refocusing system and then studied the effect of axial misalignments of O1 and O2, axial misalignment of the primary tube lens (TL1) relative to the secondary tube lens (TL2), lateral misalignments of TL2, and changes in the focal length of TL2. For each instance of the setup, we measured the mean point spread function F W H M xy of 100 nm fluorescent beads and the normalized bead integrated fluorescence signal, and we calculated the axial and lateral distortion of the system; all of these quantities were mapped over the remote-refocusing range and as a function of lateral image position. This allowed us to estimate the volume over which diffraction-limited performance is achieved and how this changes with the alignment of the system.
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Affiliation(s)
- Wenzhi Hong
- Photonics Group, Physics Department, Imperial College London, London, UK
| | - Hugh Sparks
- Photonics Group, Physics Department, Imperial College London, London, UK
| | - Chris Dunsby
- Photonics Group, Physics Department, Imperial College London, London, UK
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Smith MB, Sparks H, Almagro J, Chaigne A, Behrens A, Dunsby C, Salbreux G. Active mesh and neural network pipeline for cell aggregate segmentation. Biophys J 2023; 122:1586-1599. [PMID: 37002604 PMCID: PMC10183373 DOI: 10.1016/j.bpj.2023.03.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/16/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
Segmenting cells within cellular aggregates in 3D is a growing challenge in cell biology due to improvements in capacity and accuracy of microscopy techniques. Here, we describe a pipeline to segment images of cell aggregates in 3D. The pipeline combines neural network segmentations with active meshes. We apply our segmentation method to cultured mouse mammary gland organoids imaged over 24 h with oblique plane microscopy, a high-throughput light-sheet fluorescence microscopy technique. We show that our method can also be applied to images of mouse embryonic stem cells imaged with a spinning disc microscope. We segment individual cells based on nuclei and cell membrane fluorescent markers, and track cells over time. We describe metrics to quantify the quality of the automated segmentation. Our segmentation pipeline involves a Fiji plugin that implements active mesh deformation and allows a user to create training data, automatically obtain segmentation meshes from original image data or neural network prediction, and manually curate segmentation data to identify and correct mistakes. Our active meshes-based approach facilitates segmentation postprocessing, correction, and integration with neural network prediction.
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Affiliation(s)
| | - Hugh Sparks
- Photonics Group, Department of Physics, Imperial College London, London, United Kingdom
| | | | - Agathe Chaigne
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Axel Behrens
- Cancer Stem Cell Team, The Institute of Cancer Research, London, United Kingdom
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, United Kingdom
| | - Guillaume Salbreux
- The Francis Crick Institute, London, United Kingdom; Department of Genetics and Evolution, Geneva, Switzerland.
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7
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Dvinskikh L, Sparks H, Brito L, MacLeod KT, Harding SE, Dunsby C. Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture. Sci Rep 2023; 13:3342. [PMID: 36849727 PMCID: PMC9970973 DOI: 10.1038/s41598-023-29419-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/03/2023] [Indexed: 03/01/2023] Open
Abstract
Improving cardiac function through stem-cell regenerative therapy requires functional and structural integration of the transplanted cells with the host tissue. Visualizing the electromechanical interaction between native and graft cells necessitates 3D imaging with high spatio-temporal resolution and low photo-toxicity. A custom light-sheet fluorescence microscope was used for volumetric imaging of calcium dynamics in co-cultures of adult rat left ventricle cardiomyocytes and human induced pluripotent stem cell-derived cardiomyocytes. Aberration-free remote refocus of the detection plane synchronously to the scanning of the light sheet along the detection axis enabled fast dual-channel 3D imaging at subcellular resolution without mechanical sample disturbance at up to 8 Hz over a ∼300 µm × 40 µm × 50 µm volume. The two cell types were found to undergo electrically stimulated and spontaneous synchronized calcium transients and contraction. Electromechanical coupling improved with co-culture duration, with 50% of adult-CM coupled after 24 h of co-culture, compared to 19% after 4 h (p = 0.0305). Immobilization with para-nitroblebbistatin did not prevent calcium transient synchronization, with 35% and 36% adult-CM coupled in control and treated samples respectively (p = 0.91), indicating that electrical coupling can be maintained independently of mechanotransduction.
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Affiliation(s)
- L Dvinskikh
- Department of Physics, Imperial College London, London, UK. .,National Heart and Lung Institute, Imperial College London, London, UK. .,Department of Chemistry, Imperial College London, London, UK.
| | - H Sparks
- Department of Physics, Imperial College London, London, UK
| | - L Brito
- National Heart and Lung Institute, Imperial College London, London, UK
| | - K T MacLeod
- National Heart and Lung Institute, Imperial College London, London, UK
| | - S E Harding
- National Heart and Lung Institute, Imperial College London, London, UK
| | - C Dunsby
- Department of Physics, Imperial College London, London, UK
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8
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Dvinskikh L, Sparks H, MacLeod KT, Dunsby C. High-speed 2D light-sheet fluorescence microscopy enables quantification of spatially varying calcium dynamics in ventricular cardiomyocytes. Front Physiol 2023; 14:1079727. [PMID: 36866170 PMCID: PMC9971815 DOI: 10.3389/fphys.2023.1079727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/27/2023] [Indexed: 02/16/2023] Open
Abstract
Introduction: Reduced synchrony of calcium release and t-tubule structure organization in individual cardiomyocytes has been linked to loss of contractile strength and arrhythmia. Compared to confocal scanning techniques widely used for imaging calcium dynamics in cardiac muscle cells, light-sheet fluorescence microscopy enables fast acquisition of a 2D plane in the sample with low phototoxicity. Methods: A custom light-sheet fluorescence microscope was used to achieve dual-channel 2D timelapse imaging of calcium and the sarcolemma, enabling calcium sparks and transients in left and right ventricle cardiomyocytes to be correlated with the cell microstructure. Imaging electrically stimulated dual-labelled cardiomyocytes immobilized with para-nitroblebbistatin, a non-phototoxic, low fluorescence contraction uncoupler, with sub-micron resolution at 395 fps over a 38 μm × 170 µm FOV allowed characterization of calcium spark morphology and 2D mapping of the calcium transient time-to-half-maximum across the cell. Results: Blinded analysis of the data revealed sparks with greater amplitude in left ventricle myocytes. The time for the calcium transient to reach half-maximum amplitude in the central part of the cell was found to be, on average, 2 ms shorter than at the cell ends. Sparks co-localized with t-tubules were found to have significantly longer duration, larger area and spark mass than those further away from t-tubules. Conclusion: The high spatiotemporal resolution of the microscope and automated image-analysis enabled detailed 2D mapping and quantification of calcium dynamics of n = 60 myocytes, with the findings demonstrating multi-level spatial variation of calcium dynamics across the cell, supporting the dependence of synchrony and characteristics of calcium release on the underlying t-tubule structure.
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Affiliation(s)
- Liuba Dvinskikh
- Department of Physics, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Department of Chemistry, Imperial College London, London, United Kingdom
| | - Hugh Sparks
- Department of Physics, Imperial College London, London, United Kingdom
| | - Kenneth T. MacLeod
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Chris Dunsby
- Department of Physics, Imperial College London, London, United Kingdom
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Hong W, Dunsby C. Automatic tube lens design from stock optics for microscope remote-refocusing systems. Opt Express 2022; 30:4274-4287. [PMID: 35209667 DOI: 10.1364/oe.450320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
The remote-refocusing approach of Botcherby et al. [Opt. Lett.32, 2007 (2007)10.1364/OL.32.002007] has been applied widely to 2D and 3D fluorescence microscopes to enable rapid refocusing of the optical system without mechanically perturbing the sample. In order for this approach to operate correctly, it requires that the overall magnification of the first two microscope systems matches the ratio of the refractive indices in sample and intermedia image spaces. However, commercially available tube lenses are not always suitable to produce the desired overall magnification. Therefore, a practical approach to produce tube lenses with low expense and diffraction-limited performance is required. Tube lenses can be formed using a pair of stock achromatic doublets, however, selecting appropriate pairs of achromatic doublets from stock optics is a time-consuming process, as many combinations can be considered. In this paper, we present two software packages (Catalogue Generator and Doublet Selector) developed in MATLAB that use the application programming interface (ZOS-API) to the Zemax OpticStudio optical design software to realise an automatic search of stock achromatic doublets to produce microscope tube lenses with a specified focal length, entrance pupil diameter and maximum design field angle. An algorithm to optimise principal plane positions in versions of OpticStudio before 20.2 was also introduced to enable the use of older software versions. To evaluate the performance of Catalogue Generator and Doublet Selector, we used them to generate ten tube lens designs. All of the software-produced tube lenses have a better optical performance than those using manually selected pairs of stock doublets lenses.
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Ramuz M, Diakonov I, Dunsby C, Gorelik J. MultiFRET: A Detailed Protocol for High-Throughput Multiplexed Ratiometric FRET. Methods Mol Biol 2022; 2483:33-59. [PMID: 35286668 DOI: 10.1007/978-1-0716-2245-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The newly generated software plugin MultiFRET allows for real-time measurements of multiplexed fluorescent biosensors in a near high-throughput fashion. Here we describe a detailed protocol for setup and use of this software for any purpose requiring instant feedback during fluorescence measurement experiments. We further describe its non-primary features including beam splitter misalignment correction, custom calculations through input of simple equations typed in a .txt format, customizable Excel output, and offline bulk analysis of image stacks. Finally, we supply a usage example of a cAMP measurement in cultured rat neonatal cardiomyocytes.
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Affiliation(s)
- Masoud Ramuz
- Imperial College London, National Heart and Lung Institute, London, UK
| | - Ivan Diakonov
- Imperial College London, National Heart and Lung Institute, London, UK
| | - Chris Dunsby
- Photonics Group, Department of Physics, and Centre for Pathology, Imperial College London, London, UK
- Department of Medicine, Imperial College London, London, UK
| | - Julia Gorelik
- Imperial College London, National Heart and Lung Institute, London, UK.
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Kalita R, Flanagan W, Lightley J, Kumar S, Alexandrov Y, Garcia E, Hintze M, Barkoulas M, Dunsby C, French PMW. Single-shot phase contrast microscopy using polarisation-resolved differential phase contrast. J Biophotonics 2021; 14:e202100144. [PMID: 34390220 DOI: 10.1002/jbio.202100144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/17/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
We present a robust, low-cost single-shot implementation of differential phase microscopy utilising a polarisation-sensitive camera to simultaneously acquire four images from which phase contrast images can be calculated. This polarisation-resolved differential phase contrast (pDPC) microscopy technique can be easily integrated with fluorescence microscopy.
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Affiliation(s)
- Ranjan Kalita
- Photonics Group, Physics Department, Imperial College London, London, UK
| | - William Flanagan
- Photonics Group, Physics Department, Imperial College London, London, UK
| | - Jonathan Lightley
- Photonics Group, Physics Department, Imperial College London, London, UK
| | - Sunil Kumar
- Photonics Group, Physics Department, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Yuriy Alexandrov
- Photonics Group, Physics Department, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Edwin Garcia
- Photonics Group, Physics Department, Imperial College London, London, UK
| | - Mark Hintze
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Chris Dunsby
- Photonics Group, Physics Department, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Paul M W French
- Photonics Group, Physics Department, Imperial College London, London, UK
- Francis Crick Institute, London, UK
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Wright T, Sparks H, Paterson C, Dunsby C. Video-rate remote refocusing through continuous oscillation of a membrane deformable mirror. JPhys Photonics 2021; 3:045004. [PMID: 34693207 PMCID: PMC8523955 DOI: 10.1088/2515-7647/ac29a2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/27/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023] Open
Abstract
This paper presents the use of a deformable mirror (DM) configured to rapidly refocus a microscope employing a high numerical aperture (NA) objective lens. An Alpao DM97-15 membrane DM was used to refocus a 40×/0.80 NA water-immersion objective through a defocus range of -50-50 μm at 26.3 sweeps s-1. We achieved imaging with a mean Strehl metric of >0.6 over a field of view in the sample of 200 × 200 μm2 over a defocus range of 77 μm. We describe an optimisation procedure where the mirror is swept continuously in order to avoid known problems of hysteresis associated with the membrane DM employed. This work demonstrates that a DM-based refocusing system could in the future be used in light-sheet fluorescence microscopes to achieve video-rate volumetric imaging.
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Affiliation(s)
- Terry Wright
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Hugh Sparks
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Carl Paterson
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
- Centre for Pathology, Department of Medicine, Imperial College London, Du Cane Road, London W12 0NN, United Kingdom
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Cannon TM, Lagarto JL, Dyer BT, Garcia E, Kelly DJ, Peters NS, Lyon AR, French PMW, Dunsby C. Characterization of NADH fluorescence properties under one-photon excitation with respect to temperature, pH, and binding to lactate dehydrogenase. OSA Contin 2021; 4:1610-1625. [PMID: 34458690 PMCID: PMC8367293 DOI: 10.1364/osac.423082] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 05/06/2023]
Abstract
Reduced nicotinamide adenine dinucleotide (NADH) is the principal electron donor in glycolysis and oxidative metabolism and is thus recognized as a key biomarker for probing metabolic state. While the fluorescence characteristics of NADH have been investigated extensively, there are discrepancies in the published data due to diverse experimental conditions, instrumentation and microenvironmental parameters that can affect NADH fluorescence. Using a cuvette-based time-resolved spectrofluorimeter employing one-photon excitation at 375 nm, we characterized the fluorescence intensity, lifetime, spectral response, anisotropy and time-resolved anisotropy of NADH in aqueous solution under varying microenvironmental conditions, namely temperature, pH, and binding to lactate dehydrogenase (LDH). Our results demonstrate how temperature, pH, and binding partners each impact the fluorescence signature of NADH and highlight the complexity of the fluorescence data when different parameters produce competing effects. We hope that the data presented in this study will provide a reference for potential sources of variation in experiments measuring NADH fluorescence.
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Affiliation(s)
- Taylor M. Cannon
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
- These authors contributed equally to this work and are listed in alphabetical order
| | - Joao L. Lagarto
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
- These authors contributed equally to this work and are listed in alphabetical order
| | - Benjamin T. Dyer
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Edwin Garcia
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Douglas J. Kelly
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Nicholas S. Peters
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Alexander R. Lyon
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | | | - Chris Dunsby
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
- Centre for Pathology, Imperial College London, London, W12 0NN, UK
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14
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Jones B, McGlone ER, Fang Z, Pickford P, Corrêa IR, Oishi A, Jockers R, Inoue A, Kumar S, Görlitz F, Dunsby C, French PMW, Rutter GA, Tan T, Tomas A, Bloom SR. Genetic and biased agonist-mediated reductions in β-arrestin recruitment prolong cAMP signaling at glucagon family receptors. J Biol Chem 2020; 296:100133. [PMID: 33268378 PMCID: PMC7948418 DOI: 10.1074/jbc.ra120.016334] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/29/2020] [Accepted: 12/01/2020] [Indexed: 01/20/2023] Open
Abstract
Receptors for the peptide hormones glucagon-like peptide-1 (GLP-1R), glucose-dependent insulinotropic polypeptide (GIPR), and glucagon (GCGR) are important regulators of insulin secretion and energy metabolism. GLP-1R agonists have been successfully deployed for the treatment of type 2 diabetes, but it has been suggested that their efficacy is limited by target receptor desensitization and downregulation due to recruitment of β-arrestins. Indeed, recently described GLP-1R agonists with reduced β-arrestin-2 recruitment have delivered promising results in preclinical and clinical studies. We therefore aimed to determine if the same phenomenon could apply to the closely related GIPR and GCGR. In HEK293 cells depleted of both β-arrestin isoforms the duration of G protein–dependent cAMP/PKA signaling was increased in response to the endogenous ligand for each receptor. Moreover, in wildtype cells, “biased” GLP-1, GCG, and GIP analogs with selective reductions in β-arrestin-2 recruitment led to reduced receptor endocytosis and increased insulin secretion over a prolonged stimulation period, although the latter effect was only seen at high agonist concentrations. Biased GCG analogs increased the duration of cAMP signaling, but this did not lead to increased glucose output from hepatocytes. Our study provides a rationale for the development of GLP-1R, GIPR, and GCGR agonists with reduced β-arrestin recruitment, but further work is needed to maximally exploit this strategy for therapeutic purposes.
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Affiliation(s)
- Ben Jones
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom.
| | - Emma Rose McGlone
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
| | - Zijian Fang
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
| | - Phil Pickford
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
| | | | - Atsuro Oishi
- Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France
| | - Ralf Jockers
- Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Sunil Kumar
- Department of Physics, Imperial College London, London, United Kingdom
| | - Frederik Görlitz
- Department of Physics, Imperial College London, London, United Kingdom
| | - Chris Dunsby
- Department of Physics, Imperial College London, London, United Kingdom
| | - Paul M W French
- Department of Physics, Imperial College London, London, United Kingdom
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Tricia Tan
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
| | - Alejandra Tomas
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom.
| | - Stephen R Bloom
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
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15
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Sparks H, Dent L, Bakal C, Behrens A, Salbreux G, Dunsby C. Dual-view oblique plane microscopy (dOPM). Biomed Opt Express 2020; 11:7204-7220. [PMID: 33408991 PMCID: PMC7747899 DOI: 10.1364/boe.409781] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 05/02/2023]
Abstract
We present a new folded dual-view oblique plane microscopy (OPM) technique termed dOPM that enables two orthogonal views of the sample to be obtained by translating a pair of tilted mirrors in refocussing space. Using a water immersion 40× 1.15 NA primary objective, deconvolved image volumes of 200 nm beads were measured to have full width at half maxima (FWHM) of 0.35 ± 0.04 µm and 0.39 ± 0.02 µm laterally and 0.81 ± 0.07 µm axially. The measured z-sectioning value was 1.33 ± 0.45 µm using light-sheet FWHM in the frames of the two views of 4.99 ± 0.58 µm and 4.89 ± 0.63 µm. To qualitatively demonstrate that the system can reduce shadow artefacts while providing a more isotropic resolution, a multi-cellular spheroid approximately 100 µm in diameter was imaged.
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Affiliation(s)
- Hugh Sparks
- Photonics Group, Department of Physics,
Imperial College London, London, SW7 2AZ, UK
| | - Lucas Dent
- Dynamical Cell Systems Team, The Institute
of Cancer Research, London, SW3 6JB, UK
| | - Chris Bakal
- Dynamical Cell Systems Team, The Institute
of Cancer Research, London, SW3 6JB, UK
| | - Axel Behrens
- Cancer Stem Cell Team, The Institute of
Cancer Research, London, SW3 6JB, UK
| | - Guillaume Salbreux
- The Theoretical Physics of Biology
Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Chris Dunsby
- Photonics Group, Department of Physics,
Imperial College London, London, SW7 2AZ, UK
- Centre for Pathology, Imperial College
London, London, SW7 2AZ, UK
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16
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Sparks H, Dvinskikh L, Firth JM, Francis AJ, Harding SE, Paterson C, MacLeod KT, Dunsby C. Development a flexible light-sheet fluorescence microscope for high-speed 3D imaging of calcium dynamics and 3D imaging of cellular microstructure. J Biophotonics 2020; 13:e201960239. [PMID: 32101366 DOI: 10.1002/jbio.201960239] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/07/2020] [Accepted: 02/22/2020] [Indexed: 06/10/2023]
Abstract
We report a flexible light-sheet fluorescence microscope (LSFM) designed for studying dynamic events in cardiac tissue at high speed in 3D and the correlation of these events to cell microstructure. The system employs two illumination-detection modes: the first uses angle-dithering of a Gaussian light sheet combined with remote refocusing of the detection plane for video-rate volumetric imaging; the second combines digitally-scanned light-sheet illumination with an axially-swept light-sheet waist and stage-scanned acquisition for improved axial resolution compared to the first mode. We present a characterisation of the spatial resolution of the system in both modes. The first illumination-detection mode achieves dual spectral-channel imaging at 25 volumes per second with 1024 × 200 × 50 voxel volumes and is demonstrated by time-lapse imaging of calcium dynamics in a live cardiomyocyte. The second illumination-detection mode is demonstrated through the acquisition of a higher spatial resolution structural map of the t-tubule network in a fixed cardiomyocyte cell.
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Affiliation(s)
- Hugh Sparks
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Liuba Dvinskikh
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, London, UK
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Jahn M Firth
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Alice J Francis
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Sian E Harding
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Carl Paterson
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Ken T MacLeod
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Centre for Pathology, Faculty of Medicine, Imperial College London, London, UK
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17
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Fang Z, Chen S, Pickford P, Broichhagen J, Hodson DJ, Corrêa IR, Kumar S, Görlitz F, Dunsby C, French PMW, Rutter GA, Tan T, Bloom SR, Tomas A, Jones B. The Influence of Peptide Context on Signaling and Trafficking of Glucagon-like Peptide-1 Receptor Biased Agonists. ACS Pharmacol Transl Sci 2020; 3:345-360. [PMID: 32296773 PMCID: PMC7155199 DOI: 10.1021/acsptsci.0c00022] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Indexed: 01/14/2023]
Abstract
Signal bias and membrane trafficking have recently emerged as important considerations in the therapeutic targeting of the glucagon-like peptide-1 receptor (GLP-1R) in type 2 diabetes and obesity. In the present study, we have evaluated a peptide series with varying sequence homology between native GLP-1 and exendin-4, the archetypal ligands on which approved GLP-1R agonists are based. We find notable differences in agonist-mediated cyclic AMP signaling, recruitment of β-arrestins, endocytosis, and recycling, dependent both on the introduction of a His → Phe switch at position 1 and the specific midpeptide helical regions and C-termini of the two agonists. These observations were linked to insulin secretion in a beta cell model and provide insights into how ligand factors influence GLP-1R function at the cellular level.
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Affiliation(s)
- Zijian Fang
- Section
of Endocrinology and Investigative Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Shiqian Chen
- Section
of Endocrinology and Investigative Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Philip Pickford
- Section
of Endocrinology and Investigative Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Johannes Broichhagen
- Department
Chemical Biology, Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Berlin, 13125, Germany
| | - David J. Hodson
- Institute
of Metabolism and Systems Research (IMSR), and Centre of Membrane
Proteins and Receptors (COMPARE), University
of Birmingham, Birmingham, B15 2TT, United Kingdom
- Centre
for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, B15 2TT, United Kingdom
| | - Ivan R. Corrêa
- New
England
Biolabs, Ipswich, Massachusetts 01938, United States
| | - Sunil Kumar
- Department
of Physics, Imperial College London, London, SW7 2BX, United Kingdom
| | - Frederik Görlitz
- Department
of Physics, Imperial College London, London, SW7 2BX, United Kingdom
| | - Chris Dunsby
- Department
of Physics, Imperial College London, London, SW7 2BX, United Kingdom
| | - Paul M. W. French
- Department
of Physics, Imperial College London, London, SW7 2BX, United Kingdom
| | - Guy A. Rutter
- Section
of Cell Biology and Functional Genomics, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Tricia Tan
- Section
of Endocrinology and Investigative Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Stephen R. Bloom
- Section
of Endocrinology and Investigative Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Alejandra Tomas
- Section
of Cell Biology and Functional Genomics, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Ben Jones
- Section
of Endocrinology and Investigative Medicine, Imperial College London, London, W12 0NN, United Kingdom
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18
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Lagarto JL, Nickdel MB, Kelly DJ, Price A, Nanchahal J, Dunsby C, French P, Itoh Y. Autofluorescence Lifetime Reports Cartilage Damage in Osteoarthritis. Sci Rep 2020; 10:2154. [PMID: 32034262 PMCID: PMC7005742 DOI: 10.1038/s41598-020-59219-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/27/2020] [Indexed: 11/09/2022] Open
Abstract
Osteoarthritis (OA) is the most common arthritis and its hallmark is degradation of articular cartilage by proteolytic enzymes leading to loss of joint function. It is challenging to monitor the status of cartilage in vivo and this study explores the use of autofluorescence lifetime (AFL) measurements to provide a label-free optical readout of cartilage degradation that could enable earlier detection and evaluation of potential therapies. We previously reported that treatment of ex vivo porcine cartilage with proteolytic enzymes resulted in decreased AFL. Here we report changes in AFL of ex vivo mouse knee joints, porcine metacarpophalangeal joints, normal human metatarsophalangeal articular tissue and human OA tibial plateau tissues measured with or without treatment using a compact single-point time resolved spectrofluorometer. Our data show that proteolytically damaged areas in porcine metacarpophalangeal joints present a reduced AFL and that inducing aggrecanases in mouse and human joints also significantly reduces AFL. Further, human cartilage from OA patients presents a significantly lower AFL compared to normal human cartilage. Our data suggest that AFL can detect areas of cartilage erosion and may potentially be utilised as a minimally-invasive diagnostic readout for early stage OA in combination with arthroscopy devices.
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Affiliation(s)
- João L Lagarto
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Mohammad B Nickdel
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, UK
| | - Douglas J Kelly
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Andrew Price
- Botner Research Centre, University of Oxford, Oxford, OX3 7LD, UK
| | - Jagdeep Nanchahal
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, UK
| | - Chris Dunsby
- Department of Physics, Imperial College London, London, SW7 2AZ, UK.,Centre for Pathology, Imperial College London, London, SW7 2AZ, UK
| | - Paul French
- Department of Physics, Imperial College London, London, SW7 2AZ, UK.
| | - Yoshifumi Itoh
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, UK.
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19
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Harput S, Christensen-Jeffries K, Ramalli A, Brown J, Zhu J, Zhang G, Leow CH, Toulemonde M, Boni E, Tortoli P, Eckersley RJ, Dunsby C, Tang MX. 3-D Super-Resolution Ultrasound Imaging With a 2-D Sparse Array. IEEE Trans Ultrason Ferroelectr Freq Control 2020; 67:269-277. [PMID: 31562080 PMCID: PMC7614008 DOI: 10.1109/tuffc.2019.2943646] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
High-frame-rate 3-D ultrasound imaging technology combined with super-resolution processing method can visualize 3-D microvascular structures by overcoming the diffraction-limited resolution in every spatial direction. However, 3-D super-resolution ultrasound imaging using a full 2-D array requires a system with a large number of independent channels, the design of which might be impractical due to the high cost, complexity, and volume of data produced. In this study, a 2-D sparse array was designed and fabricated with 512 elements chosen from a density-tapered 2-D spiral layout. High-frame-rate volumetric imaging was performed using two synchronized ULA-OP 256 research scanners. Volumetric images were constructed by coherently compounding nine-angle plane waves acquired at a pulse repetition frequency of 4500 Hz. Localization-based 3-D super-resolution images of two touching subwavelength tubes were generated from 6000 volumes acquired in 12 s. Finally, this work demonstrates the feasibility of 3-D super-resolution imaging and super-resolved velocity mapping using a customized 2-D sparse array transducer.
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Affiliation(s)
- Sevan Harput
- ULIS Group, Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K., and also with the Division of Electrical and Electronic Engineering, London South Bank University, London SE1 0AA, U.K
| | | | - Alessandro Ramalli
- Department of Information Engineering, University of Florence, 50139 Florence, Italy, and also with the Laboratory of Cardiovascular Imaging and Dynamics, Department of Cardiovascular Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Jemma Brown
- Biomedical Engineering Department, Division of Imaging Sciences, King’s College London, London SE1 7EH, U.K
| | - Jiaqi Zhu
- ULIS Group, Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Ge Zhang
- ULIS Group, Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Chee Hau Leow
- ULIS Group, Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Matthieu Toulemonde
- ULIS Group, Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Enrico Boni
- Department of Information Engineering, University of Florence, 50139 Florence, Italy
| | - Piero Tortoli
- Department of Information Engineering, University of Florence, 50139 Florence, Italy
| | - Robert J. Eckersley
- Biomedical Engineering Department, Division of Imaging Sciences, King’s College London, London SE1 7EH, U.K
| | - Chris Dunsby
- Department of Physics and the Centre for Pathology, Imperial College London, London SW7 2AZ, U.K
| | - Meng-Xing Tang
- ULIS Group, Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
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20
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Lagarto JL, Dyer BT, Peters NS, French PMW, Dunsby C, Lyon AR. In vivo label-free optical monitoring of structural and metabolic remodeling of myocardium following infarction. Biomed Opt Express 2019; 10:3506-3521. [PMID: 31360603 PMCID: PMC6640823 DOI: 10.1364/boe.10.003506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/15/2019] [Accepted: 05/29/2019] [Indexed: 05/14/2023]
Abstract
Cardiac remodeling following myocardial infarction (MI) involves structural and functional alterations in the infarcted and remote viable myocardium that can ultimately lead to heart failure. The underlying mechanisms are not fully understood and, following our previous study of the autofluorescence lifetime and diffuse reflectance signatures of the myocardium in vivo at 16 weeks post MI in rats [Biomed. Opt. Express6(2), 324 (2015)], we here present data obtained at 1, 2 and 4 weeks post myocardial infarction that help follow the temporal progression of these changes. Our results demonstrate that both structural and metabolic changes in the heart can be monitored from the earliest time points following MI using label-free optical readouts, not only in the region of infarction but also in the remote non-infarcted myocardium. Changes in the autofluorescence intensity and lifetime parameters associated with collagen type I autofluorescence were indicative of progressive collagen deposition in tissue that was most pronounced at earlier time points and in the region of infarction. In addition to significant collagen deposition in infarcted and non-infarcted myocardium, we also report changes in the autofluorescence parameters associated with reduced nicotinamide adenine (phosphate) dinucleotide (NAD(P)H) and flavin adenine dinucleotide (FAD), which we associate with metabolic alterations throughout the heart. Parallel measurements of the diffuse reflectance spectra indicated an increased contribution of reduced cytochrome c. Our findings suggest that combining time-resolved spectrofluorometry and diffuse reflectance spectroscopy could provide a useful means to monitor cardiac function in vivo at the time of surgery.
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Affiliation(s)
- João L. Lagarto
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, United Kingdom
- Authors contributed equally to this work
| | - Benjamin T. Dyer
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, United Kingdom
- Authors contributed equally to this work
| | - Nicholas S. Peters
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, United Kingdom
- Centre for Cardiac Engineering, Imperial College London, Du Cane Road, London, W12 0NN, United Kingdom
| | - Paul M. W. French
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, United Kingdom
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, United Kingdom
- Centre for Pathology, Imperial College London Du Cane Road, London W12 0NN, United Kingdom
- Authors contributed equally to this work
| | - Alexander R. Lyon
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, United Kingdom
- Authors contributed equally to this work
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21
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Harput S, Christensen-Jeffries K, Brown J, Zhu J, Zhang G, Eckersley RJ, Dunsby C, Tang MX. 3-D Motion Correction for Volumetric Super-Resolution Ultrasound Imaging. IEEE Int Ultrason Symp 2019; 2018. [PMID: 34093969 DOI: 10.1109/ultsym.2018.8580145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Motion during image acquisition can cause image degradation in all medical imaging modalities. This is particularly relevant in 2-D ultrasound imaging, since out-of-plane motion can only be compensated for movements smaller than elevational beamwidth of the transducer. Localization based super-resolution imaging creates even a more challenging motion correction task due to the requirement of a high number of acquisitions to form a single super-resolved frame. In this study, an extension of two-stage motion correction method is proposed for 3-D motion correction. Motion estimation was performed on high volumetric rate ultrasound acquisitions with a handheld probe. The capability of the proposed method was demonstrated with a 3-D microvascular flow simulation to compensate for handheld probe motion. Results showed that two-stage motion correction method reduced the average localization error from 136 to 18 μm.
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Affiliation(s)
- Sevan Harput
- ULIS Group, Department of Bioengineering, Imperial College London, London, SW7 2BP, UK
| | | | - Jemma Brown
- Biomedical Engineering Department, Division of Imaging Sciences, King's College London, SE1 7EH, London, UK
| | - Jiaqi Zhu
- ULIS Group, Department of Bioengineering, Imperial College London, London, SW7 2BP, UK
| | - Ge Zhang
- ULIS Group, Department of Bioengineering, Imperial College London, London, SW7 2BP, UK
| | - Robert J Eckersley
- Biomedical Engineering Department, Division of Imaging Sciences, King's College London, SE1 7EH, London, UK
| | - Chris Dunsby
- Department of Physics and the Centre for Pathology, Imperial College London, London, SW7 2AZ, UK
| | - Meng-Xing Tang
- ULIS Group, Department of Bioengineering, Imperial College London, London, SW7 2BP, UK
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22
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Munro I, García E, Yan M, Guldbrand S, Kumar S, Kwakwa K, Dunsby C, Neil MAA, French PMW. Accelerating single molecule localization microscopy through parallel processing on a high-performance computing cluster. J Microsc 2018; 273:148-160. [PMID: 30508256 PMCID: PMC6378585 DOI: 10.1111/jmi.12772] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/14/2018] [Accepted: 11/18/2018] [Indexed: 12/25/2022]
Abstract
Super‐resolved microscopy techniques have revolutionized the ability to study biological structures below the diffraction limit. Single molecule localization microscopy (SMLM) techniques are widely used because they are relatively straightforward to implement and can be realized at relatively low cost, e.g. compared to laser scanning microscopy techniques. However, while the data analysis can be readily undertaken using open source or other software tools, large SMLM data volumes and the complexity of the algorithms used often lead to long image data processing times that can hinder the iterative optimization of experiments. There is increasing interest in high throughput SMLM, but its further development and application is inhibited by the data processing challenges. We present here a widely applicable approach to accelerating SMLM data processing via a parallelized implementation of ThunderSTORM on a high‐performance computing (HPC) cluster and quantify the speed advantage for a four‐node cluster (with 24 cores and 128 GB RAM per node) compared to a high specification (28 cores, 128 GB RAM, SSD‐enabled) desktop workstation. This data processing speed can be readily scaled by accessing more HPC resources. Our approach is not specific to ThunderSTORM and can be adapted for a wide range of SMLM software. Lay Description Optical microscopy is now able to provide images with a resolution far beyond the diffraction limit thanks to relatively new super‐resolved microscopy (SRM) techniques, which have revolutionized the ability to study biological structures. One approach to SRM is to randomly switch on and off the emission of fluorescent molecules in an otherwise conventional fluorescence microscope. If only a sparse subset of the fluorescent molecules labelling a sample can be switched on at a time, then each emitter will be, on average, spaced further apart than the diffraction‐limited resolution of the conventional microscope and the separate bright spots in the image corresponding to each emitter can be localised to high precision by finding the centre of each feature using a computer program. Thus, a precise map of the emitter positions can be recorded by sequentially mapping the localisation of different subsets of emitters as they are switched on and others switched off. Typically, this approach, described as single molecule localisation microscopy (SMLM), results in large image data sets that can take many minutes to hours to process, depending on the size of the field of view and whether the SMLM analysis employs a computationally‐intensive iterative algorithm. Such a slow workflow makes it difficult to optimise experiments and to analyse large numbers of samples. Faster SMLM experiments would be generally useful and automated high throughput SMLM studies of arrays of samples, such as cells, could be applied to drug discovery and other applications. However, the time required to process the resulting data would be prohibitive on a normal computer. To address this, we have developed a method to run standard SMLM data analysis software tools in parallel on a high‐performance computing cluster (HPC). This can be used to accelerate the analysis of individual SMLM experiments or it can be scaled to analyse high throughput SMLM data by extending it to run on an arbitrary number of HPC processors in parallel. In this paper we outline the design of our parallelised SMLM software for HPC and quantify the speed advantage when implementing it on four HPC nodes compared to a powerful desktop computer.
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Affiliation(s)
- I Munro
- Photonics Group, Physics Department, Imperial College London, London, U.K
| | - E García
- Photonics Group, Physics Department, Imperial College London, London, U.K
| | - M Yan
- Photonics Group, Physics Department, Imperial College London, London, U.K.,Northwest Institute of Nuclear Technology, Xi'an, Shaanxi, P.R. China
| | - S Guldbrand
- Photonics Group, Physics Department, Imperial College London, London, U.K
| | - S Kumar
- Photonics Group, Physics Department, Imperial College London, London, U.K.,The Francis Crick Institute, London, U.K
| | - K Kwakwa
- Photonics Group, Physics Department, Imperial College London, London, U.K
| | - C Dunsby
- Photonics Group, Physics Department, Imperial College London, London, U.K.,Centre for Pathology, Imperial College London, London, U.K
| | - M A A Neil
- Photonics Group, Physics Department, Imperial College London, London, U.K
| | - P M W French
- Photonics Group, Physics Department, Imperial College London, London, U.K
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Lagarto JL, Dyer BT, Talbot CB, Peters NS, French PMW, Lyon AR, Dunsby C. Characterization of NAD(P)H and FAD autofluorescence signatures in a Langendorff isolated-perfused rat heart model. Biomed Opt Express 2018; 9:4961-4978. [PMID: 30319914 PMCID: PMC6179415 DOI: 10.1364/boe.9.004961] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/10/2018] [Accepted: 08/11/2018] [Indexed: 05/22/2023]
Abstract
Autofluorescence spectroscopy is a promising label-free approach to characterize biological samples with demonstrated potential to report structural and biochemical alterations in tissues in a number of clinical applications. We report a characterization of the ex vivo autofluorescence fingerprint of cardiac tissue, exploiting a Langendorff-perfused isolated rat heart model to induce physiological insults to the heart, with a view to understanding how metabolic alterations affect the autofluorescence signals. Changes in the autofluorescence intensity and lifetime signatures associated with reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and flavin adenine dinucleotide (FAD) were characterized during oxygen- or glucose-depletion protocols. Results suggest that both NAD(P)H and FAD autofluorescence intensity and lifetime parameters are sensitive to changes in the metabolic state of the heart owing to oxygen deprivation. We also observed changes in NAD(P)H fluorescence intensity and FAD lifetime parameter on reperfusion of oxygen, which might provide information on reperfusion injury, and permanent tissue damage or changes to the tissue during recovery from oxygen deprivation. We found that changes in the autofluorescence signature following glucose-depletion are, in general, less pronounced, and most clearly visible in NAD(P)H related parameters. Overall, the results reported in this investigation can serve as baseline for future investigations of cardiac tissue involving autofluorescence measurements.
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Affiliation(s)
- João L Lagarto
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2AZ, UK
- Authors contributed equally to this work
| | - Benjamin T Dyer
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London W12 0NN, UK
- Authors contributed equally to this work
| | - Clifford B Talbot
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2AZ, UK
| | - Nicholas S Peters
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2AZ, UK
| | - Alexander R Lyon
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London W12 0NN, UK
- Authors contributed equally to this work
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2AZ, UK
- Centre for Pathology, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Authors contributed equally to this work
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Kim Y, Warren S, Favero F, Stone J, Clegg J, Neil M, Paterson C, Knight J, French P, Dunsby C. Semi-random multicore fibre design for adaptive multiphoton endoscopy. Opt Express 2018; 26:3661-3673. [PMID: 29401893 DOI: 10.1364/oe.26.003661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/24/2018] [Indexed: 06/07/2023]
Abstract
This paper reports the development, modelling and application of a semi-random multicore fibre (MCF) design for adaptive multiphoton endoscopy. The MCF was constructed from 55 sub-units, each comprising 7 single mode cores, in a hexagonally close-packed lattice where each sub-unit had a random angular orientation. The resulting fibre had 385 single mode cores and was double-clad for proximal detection of multiphoton excited fluorescence. The random orientation of each sub-unit in the fibre reduces the symmetry of the positions of the cores in the MCF, reducing the intensity of higher diffracted orders away from the central focal spot formed at the distal tip of the fibre and increasing the maximum size of object that can be imaged. The performance of the MCF was demonstrated by imaging fluorescently labelled beads with both distal and proximal fluorescence detection and pollen grains with distal fluorescence detection. We estimate that the number of independent resolution elements in the final image - measured as the half-maximum area of the two-photon point spread function divided by the area imaged - to be ~3200.
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Sherlock B, Warren SC, Alexandrov Y, Yu F, Stone J, Knight J, Neil MAA, Paterson C, French PMW, Dunsby C. In vivo multiphoton microscopy using a handheld scanner with lateral and axial motion compensation. J Biophotonics 2018; 11:e201700131. [PMID: 28858435 DOI: 10.1002/jbio.201700131] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
This paper reports a handheld multiphoton fluorescence microscope designed for clinical imaging that incorporates axial motion compensation and lateral image stabilization. Spectral domain optical coherence tomography is employed to track the axial position of the skin surface, and lateral motion compensation is realised by imaging the speckle pattern arising from the optical coherence tomography beam illuminating the sample. Our system is able to correct lateral sample velocities of up to approximately 65 μm s-1 . Combined with the use of negative curvature microstructured optical fibre to deliver tunable ultrafast radiation to the handheld multiphoton scanner without the need of a dispersion compensation unit, this instrument has potential for a range of clinical applications. The system is used to compensate for both lateral and axial motion of the sample when imaging human skin in vivo.
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Affiliation(s)
- Ben Sherlock
- Department of Physics, Imperial College London, London, UK
| | - Sean C Warren
- Department of Physics, Imperial College London, London, UK
| | | | - Fei Yu
- Department of Physics, University of Bath, Bath, UK
| | - James Stone
- Department of Physics, University of Bath, Bath, UK
| | | | - Mark A A Neil
- Department of Physics, Imperial College London, London, UK
| | - Carl Paterson
- Department of Physics, Imperial College London, London, UK
| | | | - Chris Dunsby
- Department of Physics, Imperial College London, London, UK
- Centre for Pathology, Imperial College London, London, UK
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26
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Noble E, Kumar S, Görlitz FG, Stain C, Dunsby C, French PMW. In vivo label-free mapping of the effect of a photosystem II inhibiting herbicide in plants using chlorophyll fluorescence lifetime. Plant Methods 2017; 13:48. [PMID: 28638436 PMCID: PMC5472976 DOI: 10.1186/s13007-017-0201-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/08/2017] [Indexed: 06/19/2023]
Abstract
BACKGROUND In order to better understand and improve the mode of action of agrochemicals, it is useful to be able to visualize their uptake and distribution in vivo, non-invasively and, ideally, in the field. Here we explore the potential of plant autofluorescence (specifically chlorophyll fluorescence) to provide a readout of herbicide action across the scales utilising multiphoton-excited fluorescence lifetime imaging, wide-field single-photon excited fluorescence lifetime imaging and single point fluorescence lifetime measurements via a fibre-optic probe. RESULTS Our studies indicate that changes in chlorophyll fluorescence lifetime can be utilised as an indirect readout of a photosystem II inhibiting herbicide activity in living plant leaves at three different scales: cellular (~μm), single point (~1 mm2) and macroscopic (~8 × 6 mm2 of a leaf). Multiphoton excited fluorescence lifetime imaging of Triticum aestivum leaves indicated that there is an increase in the spatially averaged chlorophyll fluorescence lifetime of leaves treated with Flagon EC-a photosystem II inhibiting herbicide. The untreated leaf exhibited an average lifetime of 560 ± 30 ps while the leaf imaged 2 h post treatment exhibited an increased lifetime of 2000 ± 440 ps in different fields of view. The results from in vivo wide-field single-photon excited fluorescence lifetime imaging excited at 440 nm indicated an increase in chlorophyll fluorescence lifetime from 521 ps in an untreated leaf to 1000 ps, just 3 min after treating the same leaf with Flagon EC, and to 2150 ps after 27 min. In vivo single point fluorescence lifetime measurements demonstrated a similar increase in chlorophyll fluorescence lifetime. Untreated leaf presented a fluorescence lifetime of 435 ps in the 440 nm excited chlorophyll channel, CH4 (620-710 nm). In the first 5 min after treatment, mean fluorescence lifetime is observed to have increased to 1 ns and then to 1.3 ns after 60 min. For all these in vivo plant autofluorescence lifetime measurements, the plants were not dark-adapted. CONCLUSIONS We demonstrate that the local impact of a photosystem II herbicide on living plant leaves can be conveniently mapped in space and time via changes in autofluorescence lifetime, which we attribute to changes in chlorophyll fluorescence. Using portable fibre-optic probe instrumentation originally designed for label-free biomedical applications, this capability could be deployed outside the laboratory for monitoring the distribution of herbicides in growing plants.
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Affiliation(s)
- Elizabeth Noble
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ UK
- Department of Chemistry, Imperial College London, London, SW7 2AZ UK
- Institute of Chemical Biology, Imperial College London, London, SW7 2AZ UK
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ UK
| | - Frederik G. Görlitz
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ UK
| | - Chris Stain
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY UK
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ UK
- Centre for Pathology, Imperial College London, London, SW7 2AZ UK
| | - Paul M. W. French
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ UK
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Sikkel MB, Kumar S, Maioli V, Rowlands C, Gordon F, Harding SE, Lyon AR, MacLeod KT, Dunsby C. Erratum: High speed sCMOS-based oblique plane microscopy applied to the study of calcium dynamics in cardiac myocytes: [J. Biophotonics 9, No. 3, 311-323 (2016)]. J Biophotonics 2017; 10:744-745. [PMID: 28498628 PMCID: PMC6885920 DOI: 10.1002/jbio.201700062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In the article by M.B. Sikkel et al. (doi: 10.1002/jbio.201500193), published in J. Biophotonics 9, 311-323 (2016), an error occurred in the computer code that was used to generate Figure 3. This erratum is published to correct Figure 3, the calculated value of tgeom and the experimentally determined value of toptics in the text of the article.
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Sparks H, Görlitz F, Kelly DJ, Warren SC, Kellett PA, Garcia E, Dymoke-Bradshaw AKL, Hares JD, Neil MAA, Dunsby C, French PMW. Characterisation of new gated optical image intensifiers for fluorescence lifetime imaging. Rev Sci Instrum 2017; 88:013707. [PMID: 28147687 DOI: 10.1063/1.4973917] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We report the characterisation of gated optical image intensifiers for fluorescence lifetime imaging, evaluating the performance of several different prototypes that culminate in a new design that provides improved spatial resolution conferred by the addition of a magnetic field to reduce the lateral spread of photoelectrons on their path between the photocathode and microchannel plate, and higher signal to noise ratio conferred by longer time gates. We also present a methodology to compare these systems and their capabilities, including the quantitative readouts of Förster resonant energy transfer.
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Affiliation(s)
- H Sparks
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
| | - F Görlitz
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
| | - D J Kelly
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
| | - S C Warren
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
| | - P A Kellett
- Kentech Instruments Ltd., Howbery Park, Wallingford OX10 8BD, United Kingdom
| | - E Garcia
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
| | | | - J D Hares
- Kentech Instruments Ltd., Howbery Park, Wallingford OX10 8BD, United Kingdom
| | - M A A Neil
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
| | - C Dunsby
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
| | - P M W French
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
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Cortés E, Huidobro PA, Sinclair HG, Guldbrand S, Peveler WJ, Davies T, Parrinello S, Görlitz F, Dunsby C, Neil MAA, Sivan Y, Parkin IP, French PMW, Maier SA. Plasmonic Nanoprobes for Stimulated Emission Depletion Nanoscopy. ACS Nano 2016; 10:10454-10461. [PMID: 27794591 DOI: 10.1021/acsnano.6b06361] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Plasmonic nanoparticles influence the absorption and emission processes of nearby emitters due to local enhancements of the illuminating radiation and the photonic density of states. Here, we use the plasmon resonance of metal nanoparticles in order to enhance the stimulated depletion of excited molecules for super-resolved nanoscopy. We demonstrate stimulated emission depletion (STED) nanoscopy with gold nanorods with a long axis of only 26 nm and a width of 8 nm. These particles provide an enhancement of up to 50% of the resolution compared to fluorescent-only probes without plasmonic components irradiated with the same depletion power. The nanoparticle-assisted STED probes reported here represent a ∼2 × 103 reduction in probe volume compared to previously used nanoparticles. Finally, we demonstrate their application toward plasmon-assisted STED cellular imaging at low-depletion powers, and we also discuss their current limitations.
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Affiliation(s)
| | | | | | | | - William J Peveler
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | | | | | | | | | | | - Yonatan Sivan
- Unit of Electro-optics Engineering, Ben-Gurion University , Beer-Sheba 8410501, Israel
| | - Ivan P Parkin
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
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Warren SC, Kim Y, Stone JM, Mitchell C, Knight JC, Neil MAA, Paterson C, French PMW, Dunsby C. Adaptive multiphoton endomicroscopy through a dynamically deformed multicore optical fiber using proximal detection. Opt Express 2016; 24:21474-84. [PMID: 27661887 DOI: 10.1364/oe.24.021474] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
This paper demonstrates multiphoton excited fluorescence imaging through a polarisation maintaining multicore fiber (PM-MCF) while the fiber is dynamically deformed using all-proximal detection. Single-shot proximal measurement of the relative optical path lengths of all the cores of the PM-MCF in double pass is achieved using a Mach-Zehnder interferometer read out by a scientific CMOS camera operating at 416 Hz. A non-linear least squares fitting procedure is then employed to determine the deformation-induced lateral shift of the excitation spot at the distal tip of the PM-MCF. An experimental validation of this approach is presented that compares the proximally measured deformation-induced lateral shift in focal spot position to an independent distally measured ground truth. The proximal measurement of deformation-induced shift in focal spot position is applied to correct for deformation-induced shifts in focal spot position during raster-scanning multiphoton excited fluorescence imaging.
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Kwakwa K, Savell A, Davies T, Munro I, Parrinello S, Purbhoo MA, Dunsby C, Neil MAA, French PMW. easySTORM: a robust, lower-cost approach to localisation and TIRF microscopy. J Biophotonics 2016; 9:948-957. [PMID: 27592533 DOI: 10.1002/jbio.201500324] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/21/2016] [Accepted: 01/31/2016] [Indexed: 06/06/2023]
Abstract
TIRF and STORM microscopy are super-resolving fluorescence imaging modalities for which current implementations on standard microscopes can present significant complexity and cost. We present a straightforward and low-cost approach to implement STORM and TIRF taking advantage of multimode optical fibres and multimode diode lasers to provide the required excitation light. Combined with open source software and relatively simple protocols to prepare samples for STORM, including the use of Vectashield for non-TIRF imaging, this approach enables TIRF and STORM imaging of cells labelled with appropriate dyes or expressing suitable fluorescent proteins to become widely accessible at low cost.
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Affiliation(s)
- Kwasi Kwakwa
- Photonics Group, Physics Department, Imperial College London, London, SW7 2AZ.
| | - Alexander Savell
- Photonics Group, Physics Department, Imperial College London, London, SW7 2AZ
- Institute of Chemical Biology, Imperial College London, London, SW7 2AZ
| | - Timothy Davies
- MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London, W12 0NN
| | - Ian Munro
- Photonics Group, Physics Department, Imperial College London, London, SW7 2AZ
| | - Simona Parrinello
- MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London, W12 0NN
| | - Marco A Purbhoo
- Section of Hepatology, QEQM Hospital, Imperial College London, London, W2 1PG, UK
| | - Chris Dunsby
- Photonics Group, Physics Department, Imperial College London, London, SW7 2AZ
- Centre for Pathology, Imperial College London, London, W12 0NN
| | - Mark A A Neil
- Photonics Group, Physics Department, Imperial College London, London, SW7 2AZ
| | - Paul M W French
- Photonics Group, Physics Department, Imperial College London, London, SW7 2AZ
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Sherlock B, Yu F, Stone J, Warren S, Paterson C, Neil MAA, French PMW, Knight J, Dunsby C. Tunable fibre-coupled multiphoton microscopy with a negative curvature fibre. J Biophotonics 2016; 9:715-720. [PMID: 26989868 DOI: 10.1002/jbio.201500290] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/20/2016] [Accepted: 01/27/2016] [Indexed: 06/05/2023]
Abstract
Negative curvature fibre (NCF) guides light in its core by inhibiting the coupling of core and cladding modes. In this work, an NCF was designed and fabricated to transmit ultrashort optical pulses for multiphoton microscopy with low group velocity dispersion (GVD) at 800 nm. Its attenuation was measured to be <0.3 dB m(-1) over the range 600-850 nm and the GVD was -180 ± 70 fs(2) m(-1) at 800 nm. Using an average fibre output power of ∼20 mW and pulse repetition rate of 80 MHz, the NCF enabled pulses with a duration of <200 fs to be transmitted through a length of 1.5 m of fibre over a tuning range of 180 nm without the need for dispersion compensation. In a 4 m fibre, temporal and spectral pulse widths were maintained to within 10% of low power values up to the maximum fibre output power achievable with the laser system used of 278 mW at 700 nm, 808 mW at 800 nm and 420 mW at 860 nm. When coupled to a multiphoton microscope, it enabled imaging of ex vivo tissue using excitation wavelengths from 740 nm to 860 nm without any need for adjustments to the set-up.
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Affiliation(s)
- Ben Sherlock
- Department of Physics, Imperial College London, London, SW7 2AZ, UK.
| | - Fei Yu
- Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - Jim Stone
- Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - Sean Warren
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Carl Paterson
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Mark A A Neil
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Paul M W French
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Jonathan Knight
- Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - Chris Dunsby
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
- Centre for Histopathology, Imperial College London, London, SW7 2AZ, UK
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Gore DM, O'Brart DP, French P, Dunsby C, Allan BD. A Comparison of Different Corneal Iontophoresis Protocols for Promoting Transepithelial Riboflavin Penetration. Invest Ophthalmol Vis Sci 2016; 56:7908-14. [PMID: 26670827 DOI: 10.1167/iovs.15-17569] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To measure corneal riboflavin penetration using different transepithelial iontophoresis protocols. METHODS Freshly enucleated rabbit eyes were divided into nine treatment groups of 4 eyes. One group, in which 0.1% wt/vol riboflavin was applied for 30 minutes without iontophoresis after corneal epithelial debridement, acted as a control. The remaining groups were treated with an intact epithelium using different riboflavin formulations and varying iontophoresis current, soak, and rinse times. After riboflavin application, eyes were snap frozen in liquid nitrogen. Corneal cross sections 35 μm thick were then imaged immediately by two-photon fluorescence microscopy, using image processing software to quantify stromal riboflavin concentration at different corneal depths. RESULTS In the epithelium-on iontophoresis treatment groups, greater stromal riboflavin penetration was achieved with higher-concentration riboflavin solutions, greater iontophoresis dosage, and longer solution contact times. A protocol utilizing 0.25% wt/vol riboflavin with benzalkonium chloride (BAC) 0.01% and two cycles of applied current and subsequent soaking (1 mA 5 minutes, soak 5 minutes; 0.5 mA 5 minutes, soak 5 minutes) achieved similar stromal riboflavin penetration to epithelium-off controls. The best-performing non-BAC-containing protocol produced stromal riboflavin penetration approximately 60% that of epithelium-off controls. Riboflavin solutions containing saline resulted in minimal stromal penetration. Riboflavin loading within the epithelium was equivalent to or higher than that in the subjacent stroma, despite rinsing the ocular surface with balanced salt solution. CONCLUSIONS Modified iontophoresis protocols can significantly improve transepithelial riboflavin penetration in experimental corneal collagen cross-linking.
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Affiliation(s)
| | - David P O'Brart
- Keratoconus Research Institute, Department of Ophthalmology, St. Thomas' Hospital, London, United Kingdom
| | - Paul French
- Department of Physics, Imperial College London, South Kensington, London, United Kingdom
| | - Chris Dunsby
- Department of Physics, Imperial College London, South Kensington, London, United Kingdom 4Centre for Histopathology, Imperial College London, London, United Kingdom
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Sikkel MB, Kumar S, Maioli V, Rowlands C, Gordon F, Harding SE, Lyon AR, MacLeod KT, Dunsby C. High speed sCMOS-based oblique plane microscopy applied to the study of calcium dynamics in cardiac myocytes. J Biophotonics 2016; 9:311-23. [PMID: 26488431 PMCID: PMC4874460 DOI: 10.1002/jbio.201500193] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/28/2015] [Accepted: 09/16/2015] [Indexed: 05/18/2023]
Abstract
Oblique plane microscopy (OPM) is a form of light sheet microscopy that uses a single high numerical aperture microscope objective for both fluorescence excitation and collection. In this paper, measurements of the relative collection efficiency of OPM are presented. An OPM system incorporating two sCMOS cameras is then introduced that enables single isolated cardiac myocytes to be studied continuously for 22 seconds in two dimensions at 667 frames per second with 960 × 200 pixels and for 30 seconds with 960 × 200 × 20 voxels at 25 volumes per second. In both cases OPM is able to record in two spectral channels, enabling intracellular calcium to be studied via the probe Fluo-4 AM simultaneously with the sarcolemma and transverse tubule network via the membrane dye Cellmask Orange. The OPM system was then applied to determine the spatial origin of spontaneous calcium waves for the first time and to measure the cell transverse tubule structure at their point of origin. Further results are presented to demonstrate that the OPM system can also be used to study calcium spark parameters depending on their relationship to the transverse tubule structure.
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Affiliation(s)
- Markus B Sikkel
- Myocardial Function Section, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College London, London, United Kingdom
| | - Vincent Maioli
- Photonics Group, Department of Physics, Imperial College London, London, United Kingdom.
| | - Christina Rowlands
- Myocardial Function Section, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Fabiana Gordon
- Statistics Advisory Service, Imperial College London, London, United Kingdom
| | - Sian E Harding
- Myocardial Function Section, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Alexander R Lyon
- Myocardial Function Section, National Heart and Lung Institute, Imperial College, London, United Kingdom
- NIHR Cardiovascular Biomedical Research Unit, Royal Brompton Hospital, London, United Kingdom
| | - Kenneth T MacLeod
- Myocardial Function Section, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, United Kingdom
- Centre for Pathology, Department of Medicine, Imperial College London, United Kingdom
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Gore DM, O'Brart D, French P, Dunsby C, Allan BD. Transepithelial Riboflavin Absorption in an Ex Vivo Rabbit Corneal Model. Invest Ophthalmol Vis Sci 2015; 56:5006-11. [PMID: 26230765 DOI: 10.1167/iovs.15-16903] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To measure depth-specific riboflavin concentrations in corneal stroma using two-photon fluorescence microscopy and compare commercially available transepithelial corneal collagen cross-linking (CXL) protocols. METHODS Transepithelial CXL riboflavin preparations--MedioCross TE, Ribocross TE, Paracel plus VibeX Xtra, and iontophoresis with Ricrolin+--were applied to the corneal surface of fresh postmortem rabbit eyes in accordance with manufacturers' recommendations for clinical use. Riboflavin 0.1% (VibeX Rapid) was applied after corneal epithelial debridement as a positive control. After riboflavin application, eyes were snap frozen in liquid nitrogen. Corneal cross sections 35-μm thick were cut on a cryostat, mounted on a slide, and imaged by two-photon fluorescence microscopy. Mean (SD) concentrations were calculated from five globes tested for each protocol. RESULTS Peak riboflavin concentration of 0.09% (± 0.01) was observed within the most superficial stroma (stromal depth 0-10 μm) in positive controls (epithelium-off). At the same depth, peak stromal riboflavin concentrations for MedioCross TE, Ricrolin+, Paracel/Xtra, and Ribocross TE were 0.054% (± 0.01), 0.031% (0.003), 0.021% (± 0.001), and 0.015% (± 0.004), respectively. At a depth of 300 μm (within the demarcation zone commonly seen after corneal cross-linking), the stromal concentration in epithelium-off positive controls was 0.075% (± 0.006), while at the same depth MedioCross TE and Ricrolin+ achieved 0.018% (± 0.006) and 0.016% (0.002), respectively. None of the remaining transepithelial protocols achieved concentrations above 0.005% at this same 300-μm depth. Overall, MedioCross TE was the best-performing transepithelial formulation. CONCLUSIONS Corneal epithelium is a significant barrier to riboflavin absorption into the stroma. Existing commercial transepithelial CXL protocols achieve relatively low riboflavin concentrations in the anterior corneal stroma when compared to gold standard epithelium-off absorption. Reduced stromal riboflavin concentration may compromise the efficacy of riboflavin/ultraviolet corneal CXL.
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Affiliation(s)
| | - David O'Brart
- Keratoconus Research Institute, Department of Ophthalmology, St. Thomas' Hospital, London, United Kingdom
| | - Paul French
- Department of Physics, Imperial College London, London, United Kingdom
| | - Chris Dunsby
- Department of Physics, Imperial College London, London, United Kingdom 4Centre for Histopathology, London, United Kingdom
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Warren SC, Margineanu A, Katan M, Dunsby C, French PMW. Homo-FRET Based Biosensors and Their Application to Multiplexed Imaging of Signalling Events in Live Cells. Int J Mol Sci 2015; 16:14695-716. [PMID: 26133241 PMCID: PMC4519867 DOI: 10.3390/ijms160714695] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 12/20/2022] Open
Abstract
Multiplexed imaging of Förster Resonance Energy Transfer (FRET)-based biosensors potentially presents a powerful approach to monitoring the spatio-temporal correlation of signalling pathways within a single live cell. Here, we discuss the potential of homo-FRET based biosensors to facilitate multiplexed imaging. We demonstrate that the homo-FRET between pleckstrin homology domains of Akt (Akt-PH) labelled with mCherry may be used to monitor 3'-phosphoinositide accumulation in live cells and show how global analysis of time resolved fluorescence anisotropy measurements can be used to quantify this accumulation. We further present multiplexed imaging readouts of calcium concentration, using fluorescence lifetime measurements of TN-L15-a CFP/YFP based hetero-FRET calcium biosensor-with 3'-phosphoinositide accumulation.
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Affiliation(s)
- Sean C Warren
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
| | - Anca Margineanu
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
| | - Matilda Katan
- Structural and Molecular Biology, University College London, London WC1E 6BT, UK.
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
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Dyer BT, Elder JM, Lagarto J, Harding SE, French PMW, Peters NS, Dunsby C, Lyon AR. 165 Label-free autofluorescence lifetime to assess changes in myocardial fibrosis and metabolism in vivoin a doxorubicin cardiomyopathy heart failure model. Heart 2015. [DOI: 10.1136/heartjnl-2015-308066.165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Sherlock B, Warren S, Stone J, Neil M, Paterson C, Knight J, French P, Dunsby C. Fibre-coupled multiphoton microscope with adaptive motion compensation. Biomed Opt Express 2015; 6:1876-1884. [PMID: 26137387 PMCID: PMC4467716 DOI: 10.1364/boe.6.001876] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/20/2015] [Accepted: 03/20/2015] [Indexed: 06/04/2023]
Abstract
To address the challenge of sample motion during in vivo imaging, we present a fibre-coupled multiphoton microscope with active axial motion compensation. The position of the sample surface is measured using optical coherence tomography and fed back to a piezo actuator that adjusts the axial location of the objective to compensate for sample motion. We characterise the system's performance and demonstrate that it can compensate for axial sample velocities up to 700 µm/s. Finally we illustrate the impact of motion compensation when imaging multiphoton excited autofluorescence in ex vivo mouse skin.
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Affiliation(s)
- Ben Sherlock
- Department of Physics, Imperial College London, London, SW7 2AZ,
UK
| | - Sean Warren
- Department of Physics, Imperial College London, London, SW7 2AZ,
UK
| | - James Stone
- Department of Physics, University of Bath, Bath, BA2 7AY,
UK
| | - Mark Neil
- Department of Physics, Imperial College London, London, SW7 2AZ,
UK
| | - Carl Paterson
- Department of Physics, Imperial College London, London, SW7 2AZ,
UK
| | - Jonathan Knight
- Department of Physics, University of Bath, Bath, BA2 7AY,
UK
| | - Paul French
- Department of Physics, Imperial College London, London, SW7 2AZ,
UK
| | - Chris Dunsby
- Department of Physics, Imperial College London, London, SW7 2AZ,
UK
- Centre for Histopathology, Imperial College London, London, SW7 2AZ,
UK
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Gore DM, French P, O'Brart D, Dunsby C, Allan BD. Two-Photon Fluorescence Microscopy of Corneal Riboflavin Absorption Through an Intact Epithelium. Invest Ophthalmol Vis Sci 2015; 56:1191-2. [DOI: 10.1167/iovs.15-16457] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Lagarto J, Dyer BT, Talbot C, Sikkel MB, Peters NS, French PMW, Lyon AR, Dunsby C. Application of time-resolved autofluorescence to label-free in vivo optical mapping of changes in tissue matrix and metabolism associated with myocardial infarction and heart failure. Biomed Opt Express 2015; 6:324-46. [PMID: 25780727 PMCID: PMC4354591 DOI: 10.1364/boe.6.000324] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/17/2014] [Accepted: 10/21/2014] [Indexed: 05/03/2023]
Abstract
We investigate the potential of an instrument combining time-resolved spectrofluorometry and diffuse reflectance spectroscopy to measure structural and metabolic changes in cardiac tissue in vivo in a 16 week post-myocardial infarction heart failure model in rats. In the scar region, we observed changes in the fluorescence signal that can be explained by increased collagen content, which is in good agreement with histology. In areas remote from the scar tissue, we measured changes in the fluorescence signal (p < 0.001) that cannot be explained by differences in collagen content and we attribute this to altered metabolism within the myocardium. A linear discriminant analysis algorithm was applied to the measurements to predict the tissue disease state. When we combine all measurements, our results reveal high diagnostic accuracy in the infarcted area (100%) and border zone (94.44%) as well as in remote regions from the scar (> 77%). Overall, our results demonstrate the potential of our instrument to characterize structural and metabolic changes in a failing heart in vivo without using exogenous labels.
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Affiliation(s)
- João Lagarto
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ
UK
- Authors contributed equally to this work
| | - Benjamin T. Dyer
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN
UK
- Authors contributed equally to this work
| | - Clifford Talbot
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ
UK
| | - Markus B. Sikkel
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN
UK
| | - Nicholas S. Peters
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN
UK
| | - Paul M. W. French
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN
UK
| | - Alexander R. Lyon
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN
UK
- Authors contributed equally to this work
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ
UK
- Authors contributed equally to this work
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Dyer BT, Lagarto J, French P, Peters NS, Dunsby C, Lyon AR. TIME-RESOLVED AUTOFLUORESCENCE SPECTROSCOPY AS LABEL-FREE METHOD TO CHARACTERISE ACUTE CHANGES IN EX VIVO MODELS OF CARDIAC DISEASE. Heart 2014. [DOI: 10.1136/heartjnl-2014-306916.38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Dyer B, Lagarto J, Sikkel M, French P, Dunsby C, Peters N, Lyon A. 186 The Application of Autofluorescence Lifetime Metrology as a Novel Label-free Technique for the Assessment of Cardiac Disease. Heart 2014. [DOI: 10.1136/heartjnl-2014-306118.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Gore DM, Margineanu A, French P, O'Brart D, Dunsby C, Allan BD. Two-photon fluorescence microscopy of corneal riboflavin absorption. Invest Ophthalmol Vis Sci 2014; 55:2476-81. [PMID: 24644056 DOI: 10.1167/iovs.14-13975] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To correct for attenuation in two-photon fluorescence (TPF) measurements of riboflavin absorption in porcine corneas. METHODS Two-photon fluorescence imaging of riboflavin was performed using excitation at a wavelength of 890 nm, with fluorescence signal detected between 525 and 650 nm. TPF signal attenuation was demonstrated by imaging from either side of a uniformly soaked corneoscleral button. To overcome this attenuation, a reservoir of dextran-free 0.1% wt/vol riboflavin 5'-monophosphate in saline and hydroxypropyl methylcellulose (HPMC) was placed on top of porcine corneas (globe intact-epithelium removed). TPF imaging was performed through this reservoir with image stacks acquired at 10-μm steps through the cornea repeated at regular intervals for up to 60 minutes. A novel correction method was applied to achieve corneal riboflavin concentration measurements in whole eyes (n = 4). RESULTS Significant attenuation of the TPF signal was observed in all eyes, with the signal decreasing approximately linearly with depth in uniformly soaked tissue. Cross-sectional TPF images taken of excised corneal strips confirmed the tissue was uniformly soaked so that the decrease in signal was not due to spatial variations in riboflavin concentration. After correcting for signal attenuation, we observed increased riboflavin concentrations with longer soak duration, with the mean (standard deviation) maximum tissue concentration recorded at 0.094% (± 0.001) wt/vol [1.36 mg/mL]. Uniform riboflavin absorption was achieved after a minimum 50 minutes. Following a standard corneal cross-linking soak of 30 minutes, a mean stromal concentration of 0.086% (± 0.001) wt/vol [1.25 mg/mL] was achieved at a depth of 300 μm. CONCLUSIONS The accuracy of TPF measurements of corneal riboflavin absorption can be increased by applying a correction for depth-related signal attenuation.
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Coda S, Thompson AJ, Kennedy GT, Roche KL, Ayaru L, Bansi DS, Stamp GW, Thillainayagam AV, French PMW, Dunsby C. Fluorescence lifetime spectroscopy of tissue autofluorescence in normal and diseased colon measured ex vivo using a fiber-optic probe. Biomed Opt Express 2014; 5:515-38. [PMID: 24575345 PMCID: PMC3920881 DOI: 10.1364/boe.5.000515] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/11/2013] [Accepted: 11/26/2013] [Indexed: 05/20/2023]
Abstract
We present an ex vivo study of temporally and spectrally resolved autofluorescence in a total of 47 endoscopic excision biopsy/resection specimens from colon, using pulsed excitation laser sources operating at wavelengths of 375 nm and 435 nm. A paired analysis of normal and neoplastic (adenomatous polyp) tissue specimens obtained from the same patient yielded a significant difference in the mean spectrally averaged autofluorescence lifetime -570 ± 740 ps (p = 0.021, n = 12). We also investigated the fluorescence signature of non-neoplastic polyps (n = 6) and inflammatory bowel disease (n = 4) compared to normal tissue in a small number of specimens.
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Affiliation(s)
- Sergio Coda
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
- Endoscopy Unit, Department of Gastroenterology, Charing Cross Hospital, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK
- These authors contributed equally to this work
| | - Alex J. Thompson
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
- These authors contributed equally to this work
| | - Gordon T. Kennedy
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
| | - Kim L. Roche
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
- Endoscopy Unit, Department of Gastroenterology, Charing Cross Hospital, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK
| | - Lakshmana Ayaru
- Endoscopy Unit, Department of Gastroenterology, Charing Cross Hospital, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK
| | - Devinder S. Bansi
- Endoscopy Unit, Department of Gastroenterology, Charing Cross Hospital, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK
| | - Gordon W. Stamp
- Department of Histopathology, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London, WC2A 3LY, UK
| | - Andrew V. Thillainayagam
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
- Endoscopy Unit, Department of Gastroenterology, Charing Cross Hospital, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK
- These authors contributed equally to this work
| | - Paul M. W. French
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
- These authors contributed equally to this work
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
- Department of Histopathology, Imperial College London, Du Cane Road, London, W12 0NN, UK
- These authors contributed equally to this work
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Lenz MO, Sinclair HG, Savell A, Clegg JH, Brown ACN, Davis DM, Dunsby C, Neil MAA, French PMW. 3-D stimulated emission depletion microscopy with programmable aberration correction. J Biophotonics 2014; 7:29-36. [PMID: 23788459 DOI: 10.1002/jbio.201300041] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/03/2013] [Accepted: 06/04/2013] [Indexed: 05/18/2023]
Abstract
We present a stimulated emission depletion (STED) microscope that provides 3-D super resolution by simultaneous depletion using beams with both a helical phase profile for enhanced lateral resolution and an annular phase profile to enhance axial resolution. The 3-D depletion point spread function is realised using a single spatial light modulator that can also be programmed to compensate for aberrations in the microscope and the sample. We apply it to demonstrate the first 3-D super-resolved imaging of an immunological synapse between a Natural Killer cell and its target cell.
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Affiliation(s)
- Martin O Lenz
- Photonics Group, Imperial College London, London SW7 2AZ, UK
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46
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Viessmann OM, Eckersley RJ, Christensen-Jeffries K, Tang MX, Dunsby C. Acoustic super-resolution with ultrasound and microbubbles. Phys Med Biol 2013; 58:6447-58. [DOI: 10.1088/0031-9155/58/18/6447] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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47
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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: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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48
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Alibhai D, Kelly DJ, Warren S, Kumar S, Margineau A, Serwa RA, Thinon E, Alexandrov Y, Murray EJ, Stuhmeier F, Tate EW, Neil MAA, Dunsby C, French PMW. Automated fluorescence lifetime imaging plate reader and its application to Förster resonant energy transfer readout of Gag protein aggregation. J Biophotonics 2013. [PMID: 23184449 DOI: 10.1002/jbio.v6.5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Fluorescence lifetime measurements can provide quantitative readouts of local fluorophore environment and can be applied to biomolecular interactions via Förster resonant energy transfer (FRET). Fluorescence lifetime imaging (FLIM) can therefore provide a high content analysis (HCA) modality to map protein-protein interactions (PPIs) with applications in drug discovery, systems biology and basic research. We present here an automated multiwell plate reader able to perform rapid unsupervised optically sectioned FLIM of fixed and live biological samples and illustrate its potential to assay PPIs through application to Gag protein aggregation during the HIV life cycle. We demonstrate both hetero-FRET and homo-FRET readouts of protein aggregation and report the first quantitative evaluation of a FLIM HCA assay by generating dose response curves through addition of an inhibitor of Gag myristoylation. Z' factors exceeding 0.6 are realised for this FLIM FRET assay.
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Affiliation(s)
- Dominic Alibhai
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, South Kensington Campus, London, UK
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49
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Alibhai D, Kelly DJ, Warren S, Kumar S, Margineau A, Serwa RA, Thinon E, Alexandrov Y, Murray EJ, Stuhmeier F, Tate EW, Neil MAA, Dunsby C, French PMW. Automated fluorescence lifetime imaging plate reader and its application to Förster resonant energy transfer readout of Gag protein aggregation. J Biophotonics 2013; 6:398-408. [PMID: 23184449 PMCID: PMC3660788 DOI: 10.1002/jbio.201200185] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 10/05/2012] [Accepted: 10/14/2012] [Indexed: 05/29/2023]
Abstract
Fluorescence lifetime measurements can provide quantitative readouts of local fluorophore environment and can be applied to biomolecular interactions via Förster resonant energy transfer (FRET). Fluorescence lifetime imaging (FLIM) can therefore provide a high content analysis (HCA) modality to map protein-protein interactions (PPIs) with applications in drug discovery, systems biology and basic research. We present here an automated multiwell plate reader able to perform rapid unsupervised optically sectioned FLIM of fixed and live biological samples and illustrate its potential to assay PPIs through application to Gag protein aggregation during the HIV life cycle. We demonstrate both hetero-FRET and homo-FRET readouts of protein aggregation and report the first quantitative evaluation of a FLIM HCA assay by generating dose response curves through addition of an inhibitor of Gag myristoylation. Z' factors exceeding 0.6 are realised for this FLIM FRET assay.
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Affiliation(s)
- Dominic Alibhai
- Institute of Chemical Biology, Department of Chemistry, Imperial College LondonSouth Kensington Campus, London, SW7 2A, UK
| | - Douglas J Kelly
- Institute of Chemical Biology, Department of Chemistry, Imperial College LondonSouth Kensington Campus, London, SW7 2A, UK
| | - Sean Warren
- Institute of Chemical Biology, Department of Chemistry, Imperial College LondonSouth Kensington Campus, London, SW7 2A, UK
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
| | - Anca Margineau
- Photonics Group, Department of Physics, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
| | - Remigiusz A Serwa
- Department of Chemistry, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
| | - Emmanuelle Thinon
- Department of Chemistry, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
| | - Yuriy Alexandrov
- Photonics Group, Department of Physics, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
| | | | - Frank Stuhmeier
- Pfizer Worldwide Research and DevelopmentPfizer Limited, Sandwich, Kent, CT13 9NJ, UK
| | - Edward W Tate
- Department of Chemistry, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
| | - Mark A A Neil
- Photonics Group, Department of Physics, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
- Centre for Histopathology, Imperial College LondonDu Cane Rd, London, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
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Laine R, Stuckey DW, Manning H, Warren SC, Kennedy G, Carling D, Dunsby C, Sardini A, French PMW. Fluorescence lifetime readouts of Troponin-C-based calcium FRET sensors: a quantitative comparison of CFP and mTFP1 as donor fluorophores. PLoS One 2012; 7:e49200. [PMID: 23152874 PMCID: PMC3494685 DOI: 10.1371/journal.pone.0049200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/08/2012] [Indexed: 11/23/2022] Open
Abstract
We have compared the performance of two Troponin-C-based calcium FRET sensors using fluorescence lifetime read-outs. The first sensor, TN-L15, consists of a Troponin-C fragment inserted between CFP and Citrine while the second sensor, called mTFP-TnC-Cit, was realized by replacing CFP in TN-L15 with monomeric Teal Fluorescent Protein (mTFP1). Using cytosol preparations of transiently transfected mammalian cells, we have measured the fluorescence decay profiles of these sensors at controlled concentrations of calcium using time-correlated single photon counting. These data were fitted to discrete exponential decay models using global analysis to determine the FRET efficiency, fraction of donor molecules undergoing FRET and calcium affinity of these sensors. We have also studied the decay profiles of the donor fluorescent proteins alone and determined the sensitivity of the donor lifetime to temperature and emission wavelength. Live-cell fluorescence lifetime imaging (FLIM) of HEK293T cells expressing each of these sensors was also undertaken. We confirmed that donor fluorescence of mTFP-TnC-Cit fits well to a two-component decay model, while the TN-L15 lifetime data was best fitted to a constrained four-component model, which was supported by phasor analysis of the measured lifetime data. If the constrained global fitting is employed, the TN-L15 sensor can provide a larger dynamic range of lifetime readout than the mTFP-TnC-Cit sensor but the CFP donor is significantly more sensitive to changes in temperature and emission wavelength compared to mTFP and, while the mTFP-TnC-Cit solution phase data broadly agreed with measurements in live cells, this was not the case for the TN-L15 sensor. Our titration experiment also indicates that a similar precision in determination of calcium concentration can be achieved with both FRET biosensors when fitting a single exponential donor fluorescence decay model to the fluorescence decay profiles. We therefore suggest that mTFP-based probes are more suitable for FLIM experiments than CFP-based probes.
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Affiliation(s)
- Romain Laine
- Institute of Chemical Biology (ICB), Imperial College of Science, Technology & Medicine, Institute of Chemical Biology (ICB), London, England
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College of Science, Technology & Medicine, London, England
- * E-mail:
| | - Daniel W. Stuckey
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College of Science, Technology & Medicine, London, England
| | - Hugh Manning
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
| | - Sean C. Warren
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
| | - Gordon Kennedy
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
| | - David Carling
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College of Science, Technology & Medicine, London, England
| | - Chris Dunsby
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
| | - Alessandro Sardini
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College of Science, Technology & Medicine, London, England
| | - Paul M. W. French
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
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