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Prior R, Silva A, Vangansewinkel T, Idkowiak J, Tharkeshwar AK, Hellings TP, Michailidou I, Vreijling J, Loos M, Koopmans B, Vlek N, Agaser C, Kuipers TB, Michiels C, Rossaert E, Verschoren S, Vermeire W, de Laat V, Dehairs J, Eggermont K, van den Biggelaar D, Bademosi AT, Meunier FA, vandeVen M, Van Damme P, Mei H, Swinnen JV, Lambrichts I, Baas F, Fluiter K, Wolfs E, Van Den Bosch L. PMP22 duplication dysregulates lipid homeostasis and plasma membrane organization in developing human Schwann cells. Brain 2024; 147:3113-3130. [PMID: 38743588 PMCID: PMC11370802 DOI: 10.1093/brain/awae158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/08/2024] [Accepted: 04/19/2024] [Indexed: 05/16/2024] Open
Abstract
Charcot-Marie-Tooth disease type 1A (CMT1A) is the most common inherited peripheral neuropathy caused by a 1.5 Mb tandem duplication of chromosome 17 harbouring the PMP22 gene. This dose-dependent overexpression of PMP22 results in disrupted Schwann cell myelination of peripheral nerves. To obtain better insights into the underlying pathogenic mechanisms in CMT1A, we investigated the role of PMP22 duplication in cellular homeostasis in CMT1A mouse models and in patient-derived induced pluripotent stem cells differentiated into Schwann cell precursors (iPSC-SCPs). We performed lipidomic profiling and bulk RNA sequencing (RNA-seq) on sciatic nerves of two developing CMT1A mouse models and on CMT1A patient-derived iPSC-SCPs. For the sciatic nerves of the CMT1A mice, cholesterol and lipid metabolism was downregulated in a dose-dependent manner throughout development. For the CMT1A iPSC-SCPs, transcriptional analysis unveiled a strong suppression of genes related to autophagy and lipid metabolism. Gene ontology enrichment analysis identified disturbances in pathways related to plasma membrane components and cell receptor signalling. Lipidomic analysis confirmed the severe dysregulation in plasma membrane lipids, particularly sphingolipids, in CMT1A iPSC-SCPs. Furthermore, we identified reduced lipid raft dynamics, disturbed plasma membrane fluidity and impaired cholesterol incorporation and storage, all of which could result from altered lipid storage homeostasis in the patient-derived CMT1A iPSC-SCPs. Importantly, this phenotype could be rescued by stimulating autophagy and lipolysis. We conclude that PMP22 duplication disturbs intracellular lipid storage and leads to a more disordered plasma membrane owing to an alteration in the lipid composition, which might ultimately lead to impaired axo-glial interactions. Moreover, targeting lipid handling and metabolism could hold promise for the treatment of patients with CMT1A.
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Affiliation(s)
- Robert Prior
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, Leuven 3000, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium
- Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn 53127, Germany
| | - Alessio Silva
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, Leuven 3000, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium
| | - Tim Vangansewinkel
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium
- UHasselt—Hasselt University, Biomedical Research Institute, Diepenbeek 3590, Belgium
| | - Jakub Idkowiak
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, Leuven 3000, Belgium
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice 532 10, Czech Republic
| | - Arun Kumar Tharkeshwar
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, Leuven 3000, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium
| | - Tom P Hellings
- Department of Clinical Genetics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Iliana Michailidou
- Department of Clinical Genetics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Jeroen Vreijling
- Department of Clinical Genetics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Maarten Loos
- InnoSer Nederland B.V., 2333 CK Leiden, The Netherlands
| | | | - Nina Vlek
- InnoSer Nederland B.V., 2333 CK Leiden, The Netherlands
| | - Cedrick Agaser
- Department of Biomedical Data Sciences, Sequencing Analysis Support Core, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Thomas B Kuipers
- Department of Biomedical Data Sciences, Sequencing Analysis Support Core, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Christine Michiels
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, Leuven 3000, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium
| | - Elisabeth Rossaert
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, Leuven 3000, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium
| | - Stijn Verschoren
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, Leuven 3000, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium
| | - Wendy Vermeire
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, Leuven 3000, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium
| | - Vincent de Laat
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, Leuven 3000, Belgium
| | - Jonas Dehairs
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, Leuven 3000, Belgium
| | - Kristel Eggermont
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, Leuven 3000, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium
| | - Diede van den Biggelaar
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, Leuven 3000, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium
| | - Adekunle T Bademosi
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Frederic A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Martin vandeVen
- UHasselt—Hasselt University, Biomedical Research Institute, Diepenbeek 3590, Belgium
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, Leuven 3000, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven 3000, Belgium
| | - Hailiang Mei
- Department of Biomedical Data Sciences, Sequencing Analysis Support Core, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Johannes V Swinnen
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, Leuven 3000, Belgium
| | - Ivo Lambrichts
- UHasselt—Hasselt University, Biomedical Research Institute, Diepenbeek 3590, Belgium
| | - Frank Baas
- Department of Clinical Genetics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Kees Fluiter
- Department of Clinical Genetics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Esther Wolfs
- UHasselt—Hasselt University, Biomedical Research Institute, Diepenbeek 3590, Belgium
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, Leuven 3000, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium
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2
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Singh D, Singh VK, Kumari N, Ojha H, Tiwari AK. Exploring the Binding Mechanism of 5-HT7 Specific Benzoxazolone alkyl Piperazinium Derivatives: A Comprehensive Analysis Using Spectroscopic and Computational Approaches. J Fluoresc 2024:10.1007/s10895-024-03846-y. [PMID: 39037679 DOI: 10.1007/s10895-024-03846-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024]
Abstract
Recently, the 5-HT7 receptor has achieved greater attention in research fraternity due to the involvement of neurotransmitter serotonin (5-hydroxytryptamine, 5-HT) in several neurological disorders. Targeting this neuroreceptor, we have synthesized six compounds named as butyl-benzoxazolone substituted piperazinium derivatives (BBOP) derivatives, abbreviated as L1-L6. These compounds have been evaluated for their binding interaction with BSA through photophysical and in-silico approaches. The UV absorption of these compounds with BSA at λmax = 280 nm, showed an optical density (O.D.) in the range of 0.5-0.9, i.e., 21%-53% (L1max = 1.4, L5min = 0.7385) at varied concentrations (17 μM-114 μM). For fluorescence studies, the Ksv value varied inversely with temperature, which confirmed the static mechanism of quenching with L1 showing maximum quenching. The parameters (ΔH, ΔS) obtained from the thermodynamic study for interaction between BSA and L1-L6 were correlated with in-silico (molecular docking) data. The in-silico docking study showed hydrophobic and the Van der Waals forces were the most significant forces. Amino acid residues ARG 217 & TRP 213 (Sudlow Site I) and LYS 116 & GLU 125 (Sudlow Site II) of BSA were primarily involved in H-bonding.Furthermore, the catalytic activity of BSA for hydrolyzingdifferent chemical entities have monitored in the presence of L1-L6 through esterase-like assay with p-NPA as a substrate, to get more insight about the interaction with catalytic residues (LYS 414, LYS 413, and TYR 411) in BSA at site II. These findings showed the potential of these 5-HT7 markers as promising ligands with appropriate drug likeliness characteristics.
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Affiliation(s)
- Deepika Singh
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Uttar Pradesh, Lucknow, 226025, India
| | - Vijay Kumar Singh
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Uttar Pradesh, Lucknow, 226025, India
| | - Neelam Kumari
- Division of Radiological, Nuclear and Imaging Sciences, Institute of Nuclear Medicine and Allied Sciences, Brig S K Mazumdar Road, Timarpur, Delhi, 110054, India
- Department of Chemistry, Sri Venkateswara College, University of Delhi, Benito Juarez Marg, New Delhi, 110021, India
| | - Himanshu Ojha
- Division of Radiological, Nuclear and Imaging Sciences, Institute of Nuclear Medicine and Allied Sciences, Brig S K Mazumdar Road, Timarpur, Delhi, 110054, India.
| | - Anjani Kumar Tiwari
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Uttar Pradesh, Lucknow, 226025, India.
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Gómez-Sánchez A, Devos O, Vitale R, Sliwa M, Sakhapov D, Enderlein J, de Juan A, Ruckebusch C. Blind instrument response function identification from fluorescence decays. BIOPHYSICAL REPORTS 2024; 4:100155. [PMID: 38590949 PMCID: PMC11000113 DOI: 10.1016/j.bpr.2024.100155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
Time-resolved fluorescence spectroscopy plays a crucial role when studying dynamic properties of complex photochemical systems. Nevertheless, the analysis of measured time decays and the extraction of exponential lifetimes often requires either the experimental assessment or the modeling of the instrument response function (IRF). However, the intrinsic nature of the IRF in the measurement process, which may vary across measurements due to chemical and instrumental factors, jeopardizes the results obtained by reconvolution approaches. In this paper, we introduce a novel methodology, called blind instrument response function identification (BIRFI), which enables the direct estimation of the IRF from the collected data. It capitalizes on the properties of single exponential signals to transform a deconvolution problem into a well-posed system identification problem. To delve into the specifics, we provide a step-by-step description of the BIRFI method and a protocol for its application to fluorescence decays. The performance of BIRFI is evaluated using simulated and time-correlated single-photon counting data. Our results demonstrate that the BIRFI methodology allows an accurate recovery of the IRF, yielding comparable or even superior results compared with those obtained with experimental IRFs when they are used for reconvolution by parametric model fitting.
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Affiliation(s)
- Adrián Gómez-Sánchez
- Chemometrics Group, Universitat de Barcelona, Barcelona, Spain
- Université Lille, CNRS, UMR 8516, Laboratoire Avancé de Spectroscopie pourles Intéractions la Réactivité et l’Environnement (LASIRE), Lille, France
| | - Olivier Devos
- Université Lille, CNRS, UMR 8516, Laboratoire Avancé de Spectroscopie pourles Intéractions la Réactivité et l’Environnement (LASIRE), Lille, France
| | - Raffaele Vitale
- Université Lille, CNRS, UMR 8516, Laboratoire Avancé de Spectroscopie pourles Intéractions la Réactivité et l’Environnement (LASIRE), Lille, France
| | - Michel Sliwa
- Université Lille, CNRS, UMR 8516, Laboratoire Avancé de Spectroscopie pourles Intéractions la Réactivité et l’Environnement (LASIRE), Lille, France
| | - Damir Sakhapov
- III. Institute of Physics – Biophysics, Georg-August Universität, Göttingen, Germany
| | - Jörg Enderlein
- III. Institute of Physics – Biophysics, Georg-August Universität, Göttingen, Germany
| | - Anna de Juan
- Chemometrics Group, Universitat de Barcelona, Barcelona, Spain
| | - Cyril Ruckebusch
- Université Lille, CNRS, UMR 8516, Laboratoire Avancé de Spectroscopie pourles Intéractions la Réactivité et l’Environnement (LASIRE), Lille, France
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4
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Sánchez-Hernández A, Polleys CM, Georgakoudi I. Formalin fixation and paraffin embedding interfere with the preservation of optical metabolic assessments based on endogenous NAD(P)H and FAD two-photon excited fluorescence. BIOMEDICAL OPTICS EXPRESS 2023; 14:5238-5253. [PMID: 37854574 PMCID: PMC10581792 DOI: 10.1364/boe.498297] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 10/20/2023]
Abstract
Endogenous NAD(P)H and FAD two-photon excited fluorescence (TPEF) images provide functional metabolic information with high spatial resolution for a wide range of living specimens. Preservation of metabolic function optical metrics upon fixation would facilitate studies which assess the impact of metabolic changes in the context of numerous diseases. However, robust assessments of the impact of formalin fixation, paraffin embedding, and sectioning on the preservation of optical metabolic readouts are lacking. Here, we evaluate intensity and lifetime images at excitation/emission settings optimized for NAD(P)H and FAD TPEF detection from freshly excised murine oral epithelia and corresponding bulk and sectioned fixed tissues. We find that fixation impacts the overall intensity as well as the intensity fluctuations of the images acquired. Accordingly, the depth-dependent variations of the optical redox ratio (defined as FAD/(NAD(P)H + FAD)) across squamous epithelia are not preserved following fixation. This is consistent with significant changes in the 755 nm excited spectra, which reveal broadening upon fixation and additional distortions upon paraffin embedding and sectioning. Analysis of fluorescence lifetime images acquired for excitation/emission settings optimized for NAD(P)H TPEF detection indicate that fixation alters the long lifetime of the observed fluorescence and the long lifetime intensity fraction. These parameters as well as the short TPEF lifetime are significantly modified upon embedding and sectioning. Thus, our studies highlight that the autofluorescence products formed during formalin fixation, paraffin embedding and sectioning overlap highly with NAD(P)H and FAD emission and limit the potential to utilize such tissues to assess metabolic activity.
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Affiliation(s)
| | | | - Irene Georgakoudi
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
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5
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Mangiarotti A, Siri M, Tam NW, Zhao Z, Malacrida L, Dimova R. Biomolecular condensates modulate membrane lipid packing and hydration. Nat Commun 2023; 14:6081. [PMID: 37770422 PMCID: PMC10539446 DOI: 10.1038/s41467-023-41709-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023] Open
Abstract
Membrane wetting by biomolecular condensates recently emerged as a key phenomenon in cell biology, playing an important role in a diverse range of processes across different organisms. However, an understanding of the molecular mechanisms behind condensate formation and interaction with lipid membranes is still missing. To study this, we exploited the properties of the dyes ACDAN and LAURDAN as nano-environmental sensors in combination with phasor analysis of hyperspectral and lifetime imaging microscopy. Using glycinin as a model condensate-forming protein and giant vesicles as model membranes, we obtained vital information on the process of condensate formation and membrane wetting. Our results reveal that glycinin condensates display differences in water dynamics when changing the salinity of the medium as a consequence of rearrangements in the secondary structure of the protein. Remarkably, analysis of membrane-condensates interaction with protein as well as polymer condensates indicated a correlation between increased wetting affinity and enhanced lipid packing. This is demonstrated by a decrease in the dipolar relaxation of water across all membrane-condensate systems, suggesting a general mechanism to tune membrane packing by condensate wetting.
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Affiliation(s)
- Agustín Mangiarotti
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476, Potsdam, Germany.
| | - Macarena Siri
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476, Potsdam, Germany
| | - Nicky W Tam
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476, Potsdam, Germany
| | - Ziliang Zhao
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476, Potsdam, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745, Jena, Germany
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 1, 07743, Jena, Germany
| | - Leonel Malacrida
- Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
- Advanced Bioimaging Unit, Institut Pasteur of Montevideo and Universidad de la República, Montevideo, Uruguay.
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476, Potsdam, Germany.
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6
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Sánchez-Hernández A, Polleys CM, Georgakoudi I. Formalin fixation and paraffin embedding interfere with preservation of optical metabolic assessments based on endogenous NAD(P)H and FAD two photon excited fluorescence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545363. [PMID: 37398103 PMCID: PMC10312786 DOI: 10.1101/2023.06.16.545363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Endogenous NAD(P)H and FAD two-photon excited fluorescence (TPEF) images provide functional metabolic information with high spatial resolution for a wide range of living specimens. Preservation of metabolic function optical metrics upon fixation would facilitate studies which assess the impact of metabolic changes in the context of numerous diseases. However, robust assessments of the impact of formalin fixation, paraffin embedding, and sectioning on the preservation of optical metabolic readouts are lacking. Here, we evaluate intensity and lifetime images at excitation/emission settings optimized for NAD(P)H and FAD TPEF detection from freshly excised murine oral epithelia and corresponding bulk and sectioned fixed tissues. We find that fixation impacts the overall intensity as well as the intensity fluctuations of the images acquired. Accordingly, the depth-dependent variations of the optical redox ratio (defined as FAD/(NAD(P)H + FAD)) across squamous epithelia are not preserved following fixation. This is consistent with significant changes in the 755 nm excited spectra, which reveal broadening upon fixation and additional distortions upon paraffin embedding and sectioning. Analysis of fluorescence lifetime images acquired for excitation/emission settings optimized for NAD(P)H TPEF detection indicate that fixation alters the long lifetime of the observed fluorescence and the long lifetime intensity fraction. These parameters as well as the short TPEF lifetime are significantly modified upon embedding and sectioning. Thus, our studies highlight that the autofluorescence products formed during formalin fixation, paraffin embedding and sectioning overlap highly with NAD(P)H and FAD emission and limit the potential to utilize such tissues to assess metabolic activity.
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Affiliation(s)
| | | | - Irene Georgakoudi
- Department of Biomedical Engineering, Tufts University, Medford, MA, US
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7
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Addabbo RM, Hutchinson RB, Allaman HJ, Dalphin MD, Mecha MF, Liu Y, Staikos A, Cavagnero S. Critical Beginnings: Selective Tuning of Solubility and Structural Accuracy of Newly Synthesized Proteins by the Hsp70 Chaperone System. J Phys Chem B 2023; 127:3990-4014. [PMID: 37130318 PMCID: PMC10829761 DOI: 10.1021/acs.jpcb.2c08485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Proteins are particularly prone to aggregation immediately after release from the ribosome, and it is therefore important to elucidate the role of chaperones during these key steps of protein life. The Hsp70 and trigger factor (TF) chaperone systems interact with nascent proteins during biogenesis and immediately post-translationally. It is unclear, however, whether these chaperones can prevent formation of soluble and insoluble aggregates. Here, we address this question by monitoring the solubility and structural accuracy of globin proteins biosynthesized in an Escherichia coli cell-free system containing different concentrations of the bacterial Hsp70 and TF chaperones. We find that Hsp70 concentrations required to grant solubility to newly synthesized proteins are extremely sensitive to client-protein sequence. Importantly, Hsp70 concentrations yielding soluble client proteins are insufficient to prevent formation of soluble aggregates. In fact, for some aggregation-prone protein variants, avoidance of soluble-aggregate formation demands Hsp70 concentrations that exceed cellular levels in E. coli. In all, our data highlight the prominent role of soluble aggregates upon nascent-protein release from the ribosome and show the limitations of the Hsp70 chaperone system in the case of highly aggregation-prone proteins. These results demonstrate the need to devise better strategies to prevent soluble-aggregate formation upon release from the ribosome.
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Affiliation(s)
- Rayna M. Addabbo
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Rachel B. Hutchinson
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Heather J. Allaman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Matthew D. Dalphin
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Miranda F. Mecha
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Yue Liu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Alexios Staikos
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Silvia Cavagnero
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
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8
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Fazel M, Vallmitjana A, Scipioni L, Gratton E, Digman MA, Pressé S. Fluorescence lifetime: Beating the IRF and interpulse window. Biophys J 2023; 122:672-683. [PMID: 36659850 PMCID: PMC9989884 DOI: 10.1016/j.bpj.2023.01.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/29/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
Fluorescence lifetime imaging captures the spatial distribution of chemical species across cellular environments employing pulsed illumination confocal setups. However, quantitative interpretation of lifetime data continues to face critical challenges. For instance, fluorescent species with known in vitro excited-state lifetimes may split into multiple species with unique lifetimes when introduced into complex living environments. What is more, mixtures of species, which may be both endogenous and introduced into the sample, may exhibit 1) very similar lifetimes as well as 2) wide ranges of lifetimes including lifetimes shorter than the instrumental response function or whose duration may be long enough to be comparable to the interpulse window. By contrast, existing methods of analysis are optimized for well-separated and intermediate lifetimes. Here, we broaden the applicability of fluorescence lifetime analysis by simultaneously treating unknown mixtures of arbitrary lifetimes-outside the intermediate, Goldilocks, zone-for data drawn from a single confocal spot leveraging the tools of Bayesian nonparametrics (BNP). We benchmark our algorithm, termed BNP lifetime analysis, using a range of synthetic and experimental data. Moreover, we show that the BNP lifetime analysis method can distinguish and deduce lifetimes using photon counts as small as 500.
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Affiliation(s)
- Mohamadreza Fazel
- Center for Biological Physics, Arizona State University, Tempe, Arizona; Department of Physics, Arizona State University, Tempe, Arizona
| | - Alexander Vallmitjana
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Lorenzo Scipioni
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Michelle A Digman
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, Tempe, Arizona; Department of Physics, Arizona State University, Tempe, Arizona; School of Molecular Science, Arizona State University, Tempe, Arizona.
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9
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Villar SF, Dalla-Rizza J, Möller MN, Ferrer-Sueta G, Malacrida L, Jameson DM, Denicola A. Fluorescence Lifetime Phasor Analysis of the Decamer-Dimer Equilibrium of Human Peroxiredoxin 1. Int J Mol Sci 2022; 23:5260. [PMID: 35563654 PMCID: PMC9100220 DOI: 10.3390/ijms23095260] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/22/2022] Open
Abstract
Protein self-assembly is a common feature in biology and is often required for a myriad of fundamental processes, such as enzyme activity, signal transduction, and transport of solutes across membranes, among others. There are several techniques to find and assess homo-oligomer formation in proteins. Naturally, all these methods have their limitations, meaning that at least two or more different approaches are needed to characterize a case study. Herein, we present a new method to study protein associations using intrinsic fluorescence lifetime with phasors. In this case, the method is applied to determine the equilibrium dissociation constant (KD) of human peroxiredoxin 1 (hPrx1), an efficient cysteine-dependent peroxidase, that has a quaternary structure comprised of five head-to-tail homodimers non-covalently arranged in a decamer. The hPrx1 oligomeric state not only affects its activity but also its association with other proteins. The excited state lifetime of hPrx1 has distinct values at high and low concentrations, suggesting the presence of two different species. Phasor analysis of hPrx1 emission lifetime allowed for the identification and quantification of hPrx1 decamers, dimers, and their mixture at diverse protein concentrations. Using phasor algebra, we calculated the fraction of hPrx1 decamers at different concentrations and obtained KD (1.1 × 10-24 M4) and C0.5 (1.36 μM) values for the decamer-dimer equilibrium. The results were validated and compared with size exclusion chromatography. In addition, spectral phasors provided similar results despite the small differences in emission spectra as a function of hPrx1 concentration. The phasor approach was shown to be a highly sensitive and quantitative method to assess protein oligomerization and an attractive addition to the biophysicist's toolkit.
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Affiliation(s)
- Sebastián F. Villar
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (S.F.V.); (J.D.-R.); (M.N.M.); (G.F.-S.)
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
| | - Joaquín Dalla-Rizza
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (S.F.V.); (J.D.-R.); (M.N.M.); (G.F.-S.)
| | - Matías N. Möller
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (S.F.V.); (J.D.-R.); (M.N.M.); (G.F.-S.)
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
| | - Gerardo Ferrer-Sueta
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (S.F.V.); (J.D.-R.); (M.N.M.); (G.F.-S.)
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
| | - Leonel Malacrida
- Advanced Bioimaging Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay;
- Departamento de Fisiopatología, Hospital de Clínicas, Universidad de la República, Montevideo 11600, Uruguay
| | - David M. Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Ana Denicola
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (S.F.V.); (J.D.-R.); (M.N.M.); (G.F.-S.)
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
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10
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Hart SM, Wang X, Guo J, Bathe M, Schlau-Cohen GS. Tuning Optical Absorption and Emission Using Strongly Coupled Dimers in Programmable DNA Scaffolds. J Phys Chem Lett 2022; 13:1863-1871. [PMID: 35175058 DOI: 10.1021/acs.jpclett.1c03848] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Molecular materials for light harvesting, computing, and fluorescence imaging require nanoscale integration of electronically active subunits. Variation in the optical absorption and emission properties of the subunits has primarily been achieved through modifications to the chemical structure, which is often synthetically challenging. Here, we introduce a facile method for varying optical absorption and emission properties by changing the geometry of a strongly coupled Cy3 dimer on a double-crossover (DX) DNA tile. Leveraging the versatility and programmability of DNA, we tune the length of the complementary strand so that it "pushes" or "pulls" the dimer, inducing dramatic changes in the photophysics including lifetime differences observable at the ensemble and single-molecule level. The separable lifetimes, along with environmental sensitivity also observed in the photophysics, suggest that the Cy3-DX tile constructs could serve as fluorescence probes for multiplexed imaging. More generally, these constructs establish a framework for easily controllable photophysics via geometric changes to coupled chromophores, which could be applied in light-harvesting devices and molecular electronics.
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Affiliation(s)
- Stephanie M Hart
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Xiao Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jiajia Guo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Gabriela S Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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11
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Storti B, Carlotti B, Chiellini G, Ruglioni M, Salvadori T, Scotto M, Elisei F, Diaspro A, Bianchini P, Bizzarri R. An Efficient Aequorea victoria Green Fluorescent Protein for Stimulated Emission Depletion Super-Resolution Microscopy. Int J Mol Sci 2022; 23:ijms23052482. [PMID: 35269626 PMCID: PMC8910729 DOI: 10.3390/ijms23052482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
In spite of their value as genetically encodable reporters for imaging in living systems, fluorescent proteins have been used sporadically for stimulated emission depletion (STED) super-resolution imaging, owing to their moderate photophysical resistance, which does not enable reaching resolutions as high as for synthetic dyes. By a rational approach combining steady-state and ultrafast spectroscopy with gated STED imaging in living and fixed cells, we here demonstrate that F99S/M153T/V163A GFP (c3GFP) represents an efficient genetic reporter for STED, on account of no excited state absorption at depletion wavelengths <600 nm and a long emission lifetime. This makes c3GFP a valuable alternative to more common, but less photostable, EGFP and YFP/Citrine mutants for STED imaging studies targeting the green-yellow region of the optical spectrum.
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Affiliation(s)
- Barbara Storti
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127 Pisa, Italy;
- Correspondence:
| | - Benedetta Carlotti
- Department of Chemistry, Biology and Biotechnology and CEMIN, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy; (B.C.); (F.E.)
| | - Grazia Chiellini
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy; (G.C.); (M.R.); (T.S.)
| | - Martina Ruglioni
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy; (G.C.); (M.R.); (T.S.)
| | - Tiziano Salvadori
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy; (G.C.); (M.R.); (T.S.)
| | - Marco Scotto
- Nanoscopy, CHT, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy; (M.S.); (A.D.); (P.B.)
| | - Fausto Elisei
- Department of Chemistry, Biology and Biotechnology and CEMIN, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy; (B.C.); (F.E.)
| | - Alberto Diaspro
- Nanoscopy, CHT, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy; (M.S.); (A.D.); (P.B.)
- DIFILAB, Dipartimento di Fisica, Università degli Studi di Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - Paolo Bianchini
- Nanoscopy, CHT, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy; (M.S.); (A.D.); (P.B.)
| | - Ranieri Bizzarri
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127 Pisa, Italy;
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy; (G.C.); (M.R.); (T.S.)
- Nanoscopy, CHT, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy; (M.S.); (A.D.); (P.B.)
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12
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Socas LB, Ambroggio EE. Introducing the multi-dimensional spectral phasors: a tool for the analysis of fluorescence excitation-emission matrices. Methods Appl Fluoresc 2022; 10. [PMID: 35139496 DOI: 10.1088/2050-6120/ac5389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 02/09/2022] [Indexed: 11/12/2022]
Abstract
The use of phasors to analyze fluorescence data was first introduced for time-resolved studies for a simpler mathematical analysis of the fluorescence-decay curves. Recently, this approach was extended to steady-state experiments with the introduction of the spectral phasors (SP), derived from the Fourier transform of the fluorescence emission spectrum. In this work, we revise key mathematical aspects that lead to an interpretation of SP as the characteristic function of a probability distribution. This formalism allows us to introduce a new tool, called multi-dimensional spectral phasor (MdSP) that seize, not only the information from the emission spectrum, but from the full excitation-emission matrix (EEM). In addition, we developed a homemade open-source Java software to facilitate the MdSP data processing. Due to this mathematical conceptualization, we settled a mechanism for the use of MdSP as a tool to tackle spectral signal unmixing problems in a more accurate way than SP. As a proof of principle, with the use of MdSP we approach two important biophysical questions: protein conformational changes and protein-ligand interactions. Specifically, we experimentally measure the EEM changes upon denaturation of human serum albumin (HSA) or during its association with the fluorescence dye 1,8-anilinonaphtalene sulphate (ANS) detected via tryptophan-ANS Förster Resonance Energy Transfer (FRET). In this sense, MdSP allows us to obtain information of the system in a simpler and finer way than the traditional SP. Specifically, understanding a protein's EEM as a molecular fingerprint opens new doors for the use of MdSP as a tool to analyze and comprehend protein conformational changes and interactions.
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Affiliation(s)
- Luis Bp Socas
- Química Biológica, Centro de Investigaciones en Química Biológica de Córdoba, Haya de la Torre y Medina Allende s/n, Cordoba, Córdoba, X5000HUA, ARGENTINA
| | - Ernesto Esteban Ambroggio
- Química Biológica, CIQUIBIC Química Biológica, Haya de la Torre y Medina Allende s/n, Cordoba, X5000HUA, ARGENTINA
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13
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Mangiarotti A, Bagatolli LA. Impact of macromolecular crowding on the mesomorphic behavior of lipid self-assemblies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183728. [PMID: 34416246 DOI: 10.1016/j.bbamem.2021.183728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/19/2021] [Accepted: 08/06/2021] [Indexed: 11/26/2022]
Abstract
Using LAURDAN fluorescence we observed that water dynamics measured at the interface of DOPC bilayers can be differentially regulated by the presence of crowded suspensions of different proteins (HSA, IgG, Gelatin) and PEG, under conditions where the polymers are not in direct molecular contact with the lipid interface. Specifically, we found that the decrease in water dipolar relaxation at the membrane interface correlates with an increased fraction of randomly oriented (or random coil) configurations in the polymers, as Gelatin > PEG > IgG > HSA. By using the same experimental strategy, we also demonstrated that structural transitions from globular to extended conformations in proteins can induce transitions between lamellar and non-lamellar phases in mixtures of DOPC and monoolein. Independent experiments using Raman spectroscopy showed that aqueous suspensions of polymers exhibiting high proportions of randomly oriented conformations display increased fractions of tetracoordinated water, a configuration that is dominant in ice. This indicates a greater capacity of this type of structure for polarizing water and consequently reducing its chemical activity. This effect is in line with one of the tenets of the Association Induction Hypothesis, which predicts a long-range dynamic structuring of water molecules via their interactions with proteins (or other polymers) showing extended conformations. Overall, our results suggest a crucial role of water in promoting couplings between structural changes in macromolecules and supramolecular arrangements of lipids. This mechanism may be of relevance to cell structure/function when the crowded nature of the intracellular milieu is considered.
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Affiliation(s)
- Agustín Mangiarotti
- Instituto de Investigación Médica Mercedes y Martín Ferreyra - INIMEC (CONICET) - Universidad Nacional de Córdoba, Friuli 2434, 5016 Córdoba, Argentina
| | - Luis A Bagatolli
- Instituto de Investigación Médica Mercedes y Martín Ferreyra - INIMEC (CONICET) - Universidad Nacional de Córdoba, Friuli 2434, 5016 Córdoba, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
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14
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Zhang S, Wang H, Melick CH, Jeong MH, Curukovic A, Tiwary S, Lama-Sherpa TD, Meng D, Servage KA, James NG, Jewell JL. AKAP13 couples GPCR signaling to mTORC1 inhibition. PLoS Genet 2021; 17:e1009832. [PMID: 34673774 PMCID: PMC8570464 DOI: 10.1371/journal.pgen.1009832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/05/2021] [Accepted: 09/21/2021] [Indexed: 01/14/2023] Open
Abstract
The mammalian target of rapamycin complex 1 (mTORC1) senses multiple stimuli to regulate anabolic and catabolic processes. mTORC1 is typically hyperactivated in multiple human diseases such as cancer and type 2 diabetes. Extensive research has focused on signaling pathways that can activate mTORC1 such as growth factors and amino acids. However, less is known about signaling cues that can directly inhibit mTORC1 activity. Here, we identify A-kinase anchoring protein 13 (AKAP13) as an mTORC1 binding protein, and a crucial regulator of mTORC1 inhibition by G-protein coupled receptor (GPCR) signaling. GPCRs paired to Gαs proteins increase cyclic adenosine 3’5’ monophosphate (cAMP) to activate protein kinase A (PKA). Mechanistically, AKAP13 acts as a scaffold for PKA and mTORC1, where PKA inhibits mTORC1 through the phosphorylation of Raptor on Ser 791. Importantly, AKAP13 mediates mTORC1-induced cell proliferation, cell size, and colony formation. AKAP13 expression correlates with mTORC1 activation and overall lung adenocarcinoma patient survival, as well as lung cancer tumor growth in vivo. Our study identifies AKAP13 as an important player in mTORC1 inhibition by GPCRs, and targeting this pathway may be beneficial for human diseases with hyperactivated mTORC1. The mammalian target of rapamycin complex 1 (mTORC1) can sense multiple upstream stimuli to regulate cell growth and metabolism. Increased mTORC1 activation results in many human diseases such as cancer. Small molecules like rapamycin that target and inhibit mTORC1, are available in the clinic with limited success. Thus, decoding the mechanisms involved in mTORC1 regulation is crucial. Most of the research has focused on stimuli that activate mTORC1. Less is known about signaling pathways that can directly inhibit mTORC1 activity. G-protein coupled receptors (GPCRs) coupled to Gαs proteins signal to and potently inhibit mTORC1. In this study, we have identified AKAP13 to play a crucial role in mTORC1 inhibition by GPCR signaling. Importantly, GPCRs are the largest family of drug targets with many approved FDA compounds. Targeting this signaling pathway may be beneficial for human diseases with hyperactivated mTORC1.
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Affiliation(s)
- Shihai Zhang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Huanyu Wang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Chase H. Melick
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Mi-Hyeon Jeong
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Adna Curukovic
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Shweta Tiwary
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Tshering D. Lama-Sherpa
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Delong Meng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Kelly A. Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nicholas G. James
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Jenna L. Jewell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
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15
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Pham DL, Miller CR, Myers MS, Myers DM, Hansen LA, Nichols MG. Development and characterization of phasor-based analysis for FLIM to evaluate the metabolic and epigenetic impact of HER2 inhibition on squamous cell carcinoma cultures. JOURNAL OF BIOMEDICAL OPTICS 2021; 26:JBO-210187R. [PMID: 34628733 PMCID: PMC8501457 DOI: 10.1117/1.jbo.26.10.106501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
SIGNIFICANCE Deranged metabolism and dysregulated growth factor signaling are closely associated with abnormal levels of proliferation, a recognized hallmark in tumorigenesis. Fluorescence lifetime imaging microscopy (FLIM) of endogenous nicotinamide adenine dinucleotide (NADH), a key metabolic coenzyme, offers a non-invasive, diagnostic indicator of disease progression, and treatment response. The model-independent phasor analysis approach leverages FLIM to rapidly evaluate cancer metabolism in response to targeted therapy. AIM We combined lifetime and phasor FLIM analysis to evaluate the influence of human epidermal growth factor receptor 2 (HER2) inhibition, a prevalent cancer biomarker, on both nuclear and cytoplasmic NAD(P)H of two squamous cell carcinoma (SCC) cultures. While better established, the standard lifetime analysis approach is relatively slow and potentially subject to intrinsic fitting errors and model assumptions. Phasor FLIM analysis offers a rapid, model-independent alternative, but the sensitivity of the bound NAD(P)H fraction to growth factor signaling must also be firmly established. APPROACH Two SCC cultures with low- and high-HER2 expression, were imaged using multiphoton-excited NAD(P)H FLIM, with and without treatment of the HER2 inhibitor AG825. Cells were challenged with mitochondrial inhibition and uncoupling to investigate AG825's impact on the overall metabolic capacity. Phasor FLIM and lifetime fitting analyses were compared within nuclear and cytoplasmic compartments to investigate epigenetic and metabolic impacts of HER2 inhibition. RESULTS NAD(P)H fluorescence lifetime and bound fraction consistently decreased following HER2 inhibition in both cell lines. High-HER2 SCC74B cells displayed a more significant response than low-HER2 SCC74A in both techniques. HER2 inhibition induced greater changes in nuclear than cytoplasmic compartments, leading to an increase in NAD(P)H intensity and concentration. CONCLUSIONS The use of both, complementary FLIM analysis techniques together with quantitative fluorescence intensity revealed consistent, quantitative changes in NAD(P)H metabolism associated with inhibition of growth factor signaling in SCC cell lines. HER2 inhibition promoted increased reliance on oxidative phosphorylation in both cell lines.
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Affiliation(s)
- Dan L. Pham
- Creighton University, Department of Physics, Omaha, Nebraska, United States
| | | | - Molly S. Myers
- Creighton University, Department of Physics, Omaha, Nebraska, United States
| | - Dominick M. Myers
- Creighton University, Department of Biomedical Sciences, Omaha, Nebraska, United States
| | - Laura A. Hansen
- Creighton University, Department of Biomedical Sciences, Omaha, Nebraska, United States
| | - Michael G. Nichols
- Creighton University, Department of Physics, Omaha, Nebraska, United States
- Creighton University, Department of Biomedical Sciences, Omaha, Nebraska, United States
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16
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Liu C, Chisholm A, Fu B, Su CTY, Şencan İ, Sakadžić S, Yaseen MA. Quantitation of cerebral oxygen tension using phasor analysis and phosphorescence lifetime imaging microscopy (PLIM). BIOMEDICAL OPTICS EXPRESS 2021; 12:4192-4206. [PMID: 34457408 PMCID: PMC8367232 DOI: 10.1364/boe.428873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 05/06/2023]
Abstract
Time-domain measurements for fluorescence lifetime imaging microscopy (FLIM) and phosphorescence lifetime imaging microscopy (PLIM) are conventionally computed by nonlinear curve fitting techniques to model the time-resolved profiles as mono- or multi-exponential decays. However, these techniques are computationally intensive and prone to fitting errors. The phasor or "polar plot" analysis method has recently gained attention as a simple method to characterize fluorescence lifetime. Here, we adapted the phasor analysis method for absolute quantitation of phosphorescence lifetimes of oxygen-sensitive phosphors and used the phasor-derived lifetime values to quantify oxygen partial pressure (pO2) in cortical microvessels of awake mice. Our results, both experimental and simulated, demonstrate that oxygen measurements obtained from computationally simpler phasor analysis agree well with traditional curve fitting calculations. To our knowledge, the current study constitutes the first application of the technique for characterizing microsecond-length, time-domain phosphorescence measurements and absolute, in vivo quantitation of a vital physiological parameter. The method shows promise for monitoring cerebral metabolism and pathological changes in preclinical rodent models.
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Affiliation(s)
- Chang Liu
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Amanda Chisholm
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Buyin Fu
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Clover T.-Y. Su
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - İkbal Şencan
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Sava Sakadžić
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Mohammad A. Yaseen
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, Massachusetts 02129, USA
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17
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Malacrida L, Ranjit S, Jameson DM, Gratton E. The Phasor Plot: A Universal Circle to Advance Fluorescence Lifetime Analysis and Interpretation. Annu Rev Biophys 2021; 50:575-593. [PMID: 33957055 DOI: 10.1146/annurev-biophys-062920-063631] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The phasor approach to fluorescence lifetime imaging has become a common method to analyze complicated fluorescence signals from biological samples. The appeal of the phasor representation of complex fluorescence decays in biological systems is that a visual representation of the decay of entire cells or tissues can be used to easily interpret fundamental biological states related to metabolism and oxidative stress. Phenotyping based on autofluorescence provides new avenues for disease characterization and diagnostics. The phasor approach is a transformation of complex fluorescence decays that does not use fits to model decays and therefore has the same information content as the original data. The phasor plot is unique for a given system, is highly reproducible, and provides a robust method to evaluate the existence of molecular interactions such as Förster resonance energy transfer or the response of ion indicators. Recent advances permitquantification of multiple components from phasor plots in fluorescence lifetime imaging microscopy, which is not presently possible using data fitting methods, especially in biological systems.
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Affiliation(s)
- Leonel Malacrida
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA; .,Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay.,Advanced Bioimaging Unit, Institut Pasteur Montevideo and Universidad de la República-Uruguay, 11400 Montevideo, Uruguay
| | - Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA; .,Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA
| | - David M Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, Hawaii 96813, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA;
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18
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Tavakoli M, Jazani S, Sgouralis I, Heo W, Ishii K, Tahara T, Pressé S. Direct Photon-by-Photon Analysis of Time-Resolved Pulsed Excitation Data using Bayesian Nonparametrics. CELL REPORTS. PHYSICAL SCIENCE 2020; 1:100234. [PMID: 34414380 PMCID: PMC8373049 DOI: 10.1016/j.xcrp.2020.100234] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Lifetimes of chemical species are typically estimated by either fitting time-correlated single-photon counting (TCSPC) histograms or phasor analysis from time-resolved photon arrivals. While both methods yield lifetimes in a computationally efficient manner, their performance is limited by choices made on the number of distinct chemical species contributing photons. However, the number of species is encoded in the photon arrival times collected for each illuminated spot and need not be set by hand a priori. Here, we propose a direct photon-by-photon analysis of data drawn from pulsed excitation experiments to infer, simultaneously and self-consistently, the number of species and their associated lifetimes from a few thousand photons. We do so by leveraging new mathematical tools within the Bayesian nonparametric. We benchmark our method for both simulated and experimental data for 1-4 species.
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Affiliation(s)
- Meysam Tavakoli
- Department of Physics, Indiana University-Purdue University, Indianapolis, IN 46202, USA
| | - Sina Jazani
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Ioannis Sgouralis
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wooseok Heo
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Steve Pressé
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Lead Contact
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19
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Vallmitjana A, Torrado B, Dvornikov A, Ranjit S, Gratton E. Blind Resolution of Lifetime Components in Individual Pixels of Fluorescence Lifetime Images Using the Phasor Approach. J Phys Chem B 2020; 124:10126-10137. [PMID: 33140960 PMCID: PMC9272785 DOI: 10.1021/acs.jpcb.0c06946] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The phasor approach is used in fluorescence lifetime imaging microscopy for several purposes, notably to calculate the metabolic index of single cells and tissues. An important feature of the phasor approach is that it is a fit-free method allowing immediate and easy to interpret analysis of images. In a recent paper, we showed that three or four intensity fractions of exponential components can be resolved in each pixel of an image by the phasor approach using simple algebra, provided the component phasors are known. This method only makes use of the rule of linear combination of phasors rather than fits. Without prior knowledge of the components and their single exponential decay times, resolution of components and fractions is much more challenging. Blind decomposition has been carried out only for cuvette experiments wherein the statistics in terms of the number of photons collected is very good. In this paper, we show that using the phasor approach and measurements of the decay at phasor harmonics 2 and 3, available using modern electronics, we could resolve the decay in each pixel of an image in live cells or mice liver tissues with two or more exponential components without prior knowledge of the values of the components. In this paper, blind decomposition is achieved using a graphical method for two components and a minimization method for three components. This specific use of the phasor approach to resolve multicomponents in a pixel enables applications where multiplexing species with different lifetimes and potentially different spectra can provide a different type of super-resolved image content.
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Affiliation(s)
- Alexander Vallmitjana
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Belén Torrado
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Alexander Dvornikov
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Suman Ranjit
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington D.C
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
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20
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Franssen WMJ, Vergeldt FJ, Bader AN, van Amerongen H, Terenzi C. Full-Harmonics Phasor Analysis: Unravelling Multiexponential Trends in Magnetic Resonance Imaging Data. J Phys Chem Lett 2020; 11:9152-9158. [PMID: 33053305 PMCID: PMC7649845 DOI: 10.1021/acs.jpclett.0c02319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Phasor analysis is a robust, nonfitting, method for the study of multiexponential decays in lifetime imaging data, routinely used in Fluorescence Lifetime Imaging Microscopy (FLIM) and only recently validated for Magnetic Resonance Imaging (MRI). In the established phasor approach, typically only the first Fourier harmonic is used to unravel time-domain exponential trends and their intercorrelations across image voxels. Here, we demonstrate the potential of full-harmonics (FH) phasor analysis by using all frequency-domain data points in simulations and quantitative MRI (qMRI) T2 measurements of phantoms with bulk liquids or liquid-filled porous particles and of a human brain. We show that FH analysis, while of limited advantage in FLIM due to the correlated nature of shot noise, in MRI outperforms single-harmonic phasor in unravelling multiple physical environments and partial-volume effects otherwise undiscernible. We foresee application of FH phasor to, e.g., big-data analysis in qMRI of biological or other multiphase systems, where multiparameter fitting is unfeasible.
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Affiliation(s)
- Wouter M. J. Franssen
- Laboratory
of Biophysics, Wageningen University &
Research, Wageningen 6708 WE, The Netherlands
| | - Frank J. Vergeldt
- Laboratory
of Biophysics, Wageningen University &
Research, Wageningen 6708 WE, The Netherlands
| | - Arjen N. Bader
- Laboratory
of Biophysics, Wageningen University &
Research, Wageningen 6708 WE, The Netherlands
- MicroSpectroscopy
Centre, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Herbert van Amerongen
- Laboratory
of Biophysics, Wageningen University &
Research, Wageningen 6708 WE, The Netherlands
- MicroSpectroscopy
Centre, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Camilla Terenzi
- Laboratory
of Biophysics, Wageningen University &
Research, Wageningen 6708 WE, The Netherlands
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21
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Bene L, Damjanovich L. When the Complex Makes It Easy: Phasor Plotting as a Model Independent Representation of Fluorescence Decay in Flow Cytometry. Cytometry A 2020; 97:1211-1216. [PMID: 32876394 DOI: 10.1002/cyto.a.24223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/07/2020] [Accepted: 08/14/2020] [Indexed: 11/07/2022]
Affiliation(s)
- László Bene
- Department of Surgery, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Damjanovich
- Department of Surgery, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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22
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Addabbo RM, Dalphin MD, Mecha MF, Liu Y, Staikos A, Guzman-Luna V, Cavagnero S. Complementary Role of Co- and Post-Translational Events in De Novo Protein Biogenesis. J Phys Chem B 2020; 124:6488-6507. [DOI: 10.1021/acs.jpcb.0c03039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Rayna M. Addabbo
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Matthew D. Dalphin
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Miranda F. Mecha
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Yue Liu
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Alexios Staikos
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Valeria Guzman-Luna
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Silvia Cavagnero
- Biophysics Graduate Degree Program, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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23
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Vallmitjana A, Dvornikov A, Torrado B, Jameson DM, Ranjit S, Gratton E. Resolution of 4 components in the same pixel in FLIM images using the phasor approach. Methods Appl Fluoresc 2020; 8:035001. [PMID: 32235070 DOI: 10.1088/2050-6120/ab8570] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In several cellular systems, the phasor FLIM approach has shown the existence of more than 2 components in the same pixel, a typical example being free and bound NADH. In order to properly quantify the concentrations and the spatial distributions of fluorescence components associated with different molecular species we developed a general method to resolve 3 and 4 components in the same pixel using the phasor approach. The method is based on the law of linear combination of components valid after transformation of the decay curves to phasors for each pixel in the image. In principle, the linear combination rule is valid for an arbitrary number of components. For 3 components we use only the phasor position for the first harmonic, which has a small error, while for 4 components we need the phasor location at higher harmonics that have intrinsically more noise. As a result of the noise in the higher harmonics, caused by limited photon statistics, we are able to use linear algebra to resolve 4 components given the position of the phasors of 4 independent components in mixtures of dyes and 3 components for dyes in cellular systems.
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Affiliation(s)
- Alexander Vallmitjana
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, United States of America
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24
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Figueiras E, Silvestre OF, Ihalainen TO, Nieder JB. Phasor-assisted nanoscopy reveals differences in the spatial organization of major nuclear lamina proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118530. [PMID: 31415840 DOI: 10.1016/j.bbamcr.2019.118530] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/18/2019] [Accepted: 08/05/2019] [Indexed: 11/15/2022]
Abstract
Phasor-assisted Metal Induced Energy Transfer-Fluorescence Lifetime Imaging Microscopy (MIET-FLIM) nanoscopy is introduced as a powerful tool for functional cell biology research. Thin metal substrates can be used to obtain axial super-resolution via nanoscale distance-dependent MIET from fluorescent dyes towards a nearby metal layer, thereby creating fluorescence lifetime contrast between dyes located at different nanoscale distance from the metal. Such data can be used to achieve axially super-resolved microscopy images, a process known as MIET-FLIM nanoscopy. Suitability of the phasor approach in MIET-FLIM nanoscopy is first demonstrated using nanopatterned substrates, and furthermore applied to characterize the distance distribution of the epithelial basal membrane of a biological cell from the gold substrate. The phasor plot of an entire cell can be used to characterize the full Förster resonance energy transfer (FRET) trajectory as a large distance heterogeneity within the sensing range of about 100 nm from the metal surface is present due to the extended shape of cell with curvatures. In contrast, the different proteins of nuclear lamina show strong confinement close to the nuclear envelope in nanoscale. We find the lamin B layer resides in average at shorter distances from the gold surface compared to the lamin A/C layer located in more extended ranges. This and the observed heterogeneity of the protein layer thicknesses suggests that A- and B-type lamins form distinct networks in the nuclear lamina. Our results provide detailed insights for the study of the different roles of lamin proteins in chromatin tethering and nuclear mechanics.
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Affiliation(s)
- Edite Figueiras
- Department of Nanophotonics, Ultrafast Bio- and Nanophotonics Group, INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal
| | - Oscar F Silvestre
- Department of Nanophotonics, Ultrafast Bio- and Nanophotonics Group, INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal
| | - Teemu O Ihalainen
- Faculty of Medicine and Health Technology, BioMediTech, Tampere University, 33014 Tampere, Finland
| | - Jana B Nieder
- Department of Nanophotonics, Ultrafast Bio- and Nanophotonics Group, INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal.
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25
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Nguyen H, Ward WS, James NG. Spatial and temporal resolution of mORC4 fluorescent variants reveals structural requirements for achieving higher order self-association and pronuclei entry. Methods Appl Fluoresc 2019; 7:035002. [PMID: 30865939 PMCID: PMC6636821 DOI: 10.1088/2050-6120/ab0f57] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The Origin Replication Complex (ORC), which is a multi-subunit protein complex composed of six proteins ORC1-6, is essential for initiating licensing at DNA replication origins. We have previously reported that ORC4 has an alternative function wherein it forms a cage surrounding the extruded chromatin in female meiosis and is required for polar body extrusion (PBE). As this is a highly unexpected finding for protein that normally binds DNA, we tested whether ORC4 can actually form larger, higher order structures, which would be necessary to form a cage-like structure. We generated two fluorescent constructs of mouse ORC4, mORC4-EGFP and mORC4-FlAsH, to examine its spatial dynamics during oocyte activation in live cells. We show that both constructs were primarily monomeric throughout the embryo but self-association into larger units was detected with both probes. However, mORC4-FlAsH clearly showed higher order self-association and unique spatial distribution while mORC4-EGFP failed to form large structures during Anaphase II. Interestingly, both variants were found in the pronuclei suggesting that its role in DNA licensing is still functional. Our results with both constructs support the prediction that ORC4 can form higher order structures in the cytoplasm, suggesting that it is possible to form a cage-like structure. The finding that FlAsH labeled ORC4 formed demonstrably larger higher order structures than ORC4-GFP suggests that ORC4 oligomerization is sensitive to the bulky addition of GFP at its carboxy terminus.
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Affiliation(s)
- Hieu Nguyen
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, 1960 East-West Rd., University of Hawaii, Honolulu, HI 96822, United States of America
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26
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Peltier C, Winckler P, Dujourdy L, Bechoua S, Perrier-Cornet JM. Analysis of multivariate images in fluorescence microscopy. Methods Appl Fluoresc 2019; 7:035004. [PMID: 30974420 DOI: 10.1088/2050-6120/ab1886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A multivariate image is an image stack in which each pixel contains several variables. Such images are common in many fields (medicine, imaging microscopy, satellite imaging...) and their analysis requires adapted multivariate statistical methods. In fluorescence imaging microscopy, different probes or different measurements such as intensity, fluorescence lifetime or spectral information can be observed from one view. However, this is not yet analysed as multivariate images. Here, we are presenting a full approach of multivariate analysis of fluorescence microscopy images and we are proposing a free R package (multifluo) to conduct it.
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Affiliation(s)
- Caroline Peltier
- Univ. Bourgogne Franche-Comte, Agrosup Dijon, PAM UMR A 02.102, F21000 Dijon, France
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27
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Kolenc OI, Quinn KP. Evaluating Cell Metabolism Through Autofluorescence Imaging of NAD(P)H and FAD. Antioxid Redox Signal 2019; 30:875-889. [PMID: 29268621 PMCID: PMC6352511 DOI: 10.1089/ars.2017.7451] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
SIGNIFICANCE Optical imaging using the endogenous fluorescence of metabolic cofactors has enabled nondestructive examination of dynamic changes in cell and tissue function both in vitro and in vivo. Quantifying NAD(P)H and FAD fluorescence through an optical redox ratio and fluorescence lifetime imaging (FLIM) provides sensitivity to the relative balance between oxidative phosphorylation and glucose catabolism. Since its introduction decades ago, the use of NAD(P)H imaging has expanded to include applications involving almost every major tissue type and a variety of pathologies. Recent Advances: This review focuses on the use of two-photon excited fluorescence and NAD(P)H fluorescence lifetime techniques in cancer, neuroscience, tissue engineering, and other biomedical applications over the last 5 years. In a variety of cancer models, NAD(P)H fluorescence intensity and lifetime measurements demonstrate a sensitivity to the Warburg effect, suggesting potential for early detection or high-throughput drug screening. The sensitivity to the biosynthetic demands of stem cell differentiation and tissue repair processes indicates the range of applications for this imaging technology may be broad. CRITICAL ISSUES As the number of applications for these fluorescence imaging techniques expand, identifying and characterizing additional intrinsic fluorophores and chromophores present in vivo will be vital to accurately measure and interpret metabolic outcomes. Understanding the full capabilities and limitations of FLIM will also be key to future advances. FUTURE DIRECTIONS Future work is needed to evaluate whether a combination of different biochemical and structural outcomes using these imaging techniques can provide complementary information regarding the utilization of specific metabolic pathways.
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Affiliation(s)
- Olivia I Kolenc
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas
| | - Kyle P Quinn
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas
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28
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Sugár IP, Bonanno AP, Chong PLG. Gramicidin Lateral Distribution in Phospholipid Membranes: Fluorescence Phasor Plots and Statistical Mechanical Model. Int J Mol Sci 2018; 19:E3690. [PMID: 30469389 PMCID: PMC6274966 DOI: 10.3390/ijms19113690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 11/16/2022] Open
Abstract
When using small mole fraction increments to study gramicidins in phospholipid membranes, we found that the phasor dots of intrinsic fluorescence of gramicidin D and gramicidin A in dimyristoyl-sn-glycero-3-phosphocholine (DMPC) unilamellar and multilamellar vesicles exhibit a biphasic change with peptide content at 0.143 gramicidin mole fraction. To understand this phenomenon, we developed a statistical mechanical model of gramicidin/DMPC mixtures. Our model assumes a sludge-like mixture of fluid phase and aggregates of rigid clusters. In the fluid phase, gramicidin monomers are randomly distributed. A rigid cluster is formed by a gramicidin dimer and DMPC molecules that are condensed to the dimer, following particular stoichiometries (critical gramicidin mole fractions, Xcr including 0.143). Rigid clusters form aggregates in which gramicidin dimers are regularly distributed, in some cases, even to superlattices. At Xcr, the size of cluster aggregates and regular distributions reach a local maximum. Before a similar model was developed for cholesterol/DMPC mixtures (Sugar and Chong (2012) J. Am. Chem. Soc. 134, 1164⁻1171) and here the similarities and differences are discussed between these two models.
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Affiliation(s)
- István P Sugár
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Alexander P Bonanno
- Department of Medical Genetics and Molecular Biochemistry, The Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA.
| | - Parkson Lee-Gau Chong
- Department of Medical Genetics and Molecular Biochemistry, The Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA.
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29
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30
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Ranjit S, Malacrida L, Gratton E. Differences between FLIM phasor analyses for data collected with the Becker and Hickl SPC830 card and with the FLIMbox card. Microsc Res Tech 2018; 81:980-989. [PMID: 30295346 PMCID: PMC6240382 DOI: 10.1002/jemt.23061] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/13/2018] [Indexed: 01/31/2023]
Abstract
The phasor approach to FLIM (Fluorescence Lifetime Imaging Microscopy) is becoming popular due to the powerful fit free analysis and the visualization of the decay at each point in images of cells and tissues. However, although several implementation of the method are offered by manufactures of FLIM accessories for microscopes, the details of the conversion of the decay to phasors at each point in an image requires some consideration. Here, we show that if the decay is not properly acquired, the apparently simple phasor transformation can provide incorrect phasor plots and the results may be misinterpreted. In particular, we show the disagreement in experimental data acquired on the same samples using the two cards (FLIMbox, frequency domain and Becker & Hickl BH 830, time domain) and the effect produced by using the BH 830 card with different settings. This difference in data acquisition translates to the assignment of phasor components calculated using different acquisition parameters. This effect is already present in the original data that are not acquired with the proper parameters for the phasor conversion. We also show that the difference in the resolution of components already exists in the data acquired in the time domain when used with settings that do not allow acquisition of the fluorescence decay on a sufficient large time scale. RESEARCH HIGHLIGHTS: This paper is intended to made researchers aware of some simple requirements for the conversion of time-domain data (typically TCSPC) to phasors. The use of phasors for FLIM analysis has seen a surge of popularity. Since the phasor approach is a fit free method and has a powerful visualization of the data, it appears very simple to use. This paper shows that when the original data in the time domain is not acquired with the proper time range to cover the lifetimes in a sample, the conversion to phasors can produce very erroneous results. These results are appearing more frequently in the literature since many of the manufacturers of FLIM accessories for microscopes are now offering the phasor analysis in their software. Here, we show that the phasor transformation per se cannot correct for the problems with data acquisition and that one is misled to think that the "phasor approach" is a universal fix for the lack of the proper time range for data acquisition.
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Affiliation(s)
- Suman Ranjit
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, California
| | - Leonel Malacrida
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, California
- Departamento de Fisiopatología, Hospital de Clínicas, Universidad de la República, Montevideo, Uruguay
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, California
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31
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Characterization of esterase activity from an Acetomicrobium hydrogeniformans enzyme with high structural stability in extreme conditions. Extremophiles 2018; 22:781-793. [DOI: 10.1007/s00792-018-1038-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/09/2018] [Indexed: 01/06/2023]
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32
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Günther G, Herlax V, Lillo MP, Sandoval-Altamirano C, Belmar LN, Sánchez SA. Study of rabbit erythrocytes membrane solubilization by sucrose monomyristate using laurdan and phasor analysis. Colloids Surf B Biointerfaces 2018; 161:375-385. [DOI: 10.1016/j.colsurfb.2017.10.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 10/06/2017] [Accepted: 10/30/2017] [Indexed: 12/13/2022]
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33
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Osseiran S, Roider EM, Wang H, Suita Y, Murphy M, Fisher DE, Evans CL. Non-Euclidean phasor analysis for quantification of oxidative stress in ex vivo human skin exposed to sun filters using fluorescence lifetime imaging microscopy. JOURNAL OF BIOMEDICAL OPTICS 2017; 22:1-10. [PMID: 29222855 PMCID: PMC5722918 DOI: 10.1117/1.jbo.22.12.125004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/20/2017] [Indexed: 05/08/2023]
Abstract
Chemical sun filters are commonly used as active ingredients in sunscreens due to their efficient absorption of ultraviolet (UV) radiation. Yet, it is known that these compounds can photochemically react with UV light and generate reactive oxygen species and oxidative stress in vitro, though this has yet to be validated in vivo. One label-free approach to probe oxidative stress is to measure and compare the relative endogenous fluorescence generated by cellular coenzymes nicotinamide adenine dinucleotides and flavin adenine dinucleotides. However, chemical sun filters are fluorescent, with emissive properties that contaminate endogenous fluorescent signals. To accurately distinguish the source of fluorescence in ex vivo skin samples treated with chemical sun filters, fluorescence lifetime imaging microscopy data were processed on a pixel-by-pixel basis using a non-Euclidean separation algorithm based on Mahalanobis distance and validated on simulated data. Applying this method, ex vivo samples exhibited a small oxidative shift when exposed to sun filters alone, though this shift was much smaller than that imparted by UV irradiation. Given the need for investigative tools to further study the clinical impact of chemical sun filters in patients, the reported methodology may be applied to visualize chemical sun filters and measure oxidative stress in patients' skin.
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Affiliation(s)
- Sam Osseiran
- Harvard Medical School, Massachusetts General Hospital, Wellman Center for Photomedicine, Charlestown, Massachusetts, United States
- Massachusetts Institute of Technology, Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, United States
| | - Elisabeth M. Roider
- Harvard Medical School, Massachusetts General Hospital, Cutaneous Biology Research Center, Charlestown, Massachusetts, United States
| | - Hequn Wang
- Harvard Medical School, Massachusetts General Hospital, Wellman Center for Photomedicine, Charlestown, Massachusetts, United States
| | - Yusuke Suita
- Harvard Medical School, Massachusetts General Hospital, Cutaneous Biology Research Center, Charlestown, Massachusetts, United States
| | - Michael Murphy
- Harvard Medical School, Massachusetts General Hospital, Wellman Center for Photomedicine, Charlestown, Massachusetts, United States
| | - David E. Fisher
- Harvard Medical School, Massachusetts General Hospital, Cutaneous Biology Research Center, Charlestown, Massachusetts, United States
| | - Conor L. Evans
- Harvard Medical School, Massachusetts General Hospital, Wellman Center for Photomedicine, Charlestown, Massachusetts, United States
- Address all correspondence to: Conor L. Evans, E-mail:
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34
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Checcucci G, Storti B, Ghetti F, Signore G, Bizzarri R. Fluorescence lifetime microscopy reveals the biologically-related photophysical heterogeneity of oxyblepharismin in light-adapted (blue) Blepharisma japonicum cells. Photochem Photobiol Sci 2017. [PMID: 28636018 DOI: 10.1039/c7pp00072c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The step-up photophobic response of the heterotrich ciliate Blepharisma japonicum is mediated by a hypericinic pigment, blepharismin, which is not present in any of the known six families of photoreceptors, namely rhodopsins, phytochromes, xanthopsins, cryptochromes, phototropins, and BLUF proteins. Upon irradiation, native cells become light-adapted (blue) by converting blepharismin into the photochemically stable oxyblepharismin (OxyBP). So far, OxyBP has been investigated mainly from a photophysical point of view in vitro, either alone or complexed with proteins. In this work, we exploit the vivid fluorescence of OxyBP to characterize its lifetime emission in blue B. Japonicum cells, on account of the recognized role of the fluorescence lifetime to provide physicochemical insights into the fluorophore environment at the nanoscale. In a biological context, OxyBP modifies its emission lifetime as compared to isotropic media. The phasor approach to fluorescence lifetime microscopy in confocal mode highlights that fluorescence originates from two excited states, whose relative balance changes throughout the cell body. Additionally, Cilia and kinetids, i.e., the organelles involved in photomovement, display lifetime asymmetry between the anterior and posterior part of the cell. From these data, some hypotheses on the phototransduction mechanism are proposed.
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Affiliation(s)
- G Checcucci
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, I-56127 Pisa, Italy.
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35
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Fereidouni F, Gorpas D, Ma D, Fatakdawala H, Marcu L. Rapid fluorescence lifetime estimation with modified phasor approach and Laguerre deconvolution: a comparative study. Methods Appl Fluoresc 2017; 5:035003. [PMID: 28644150 PMCID: PMC6043162 DOI: 10.1088/2050-6120/aa7b62] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fluorescence lifetime imaging has been shown to serve as a valuable tool for interrogating and diagnosis of biological tissue at a mesoscopic level. The ability to analyze fluorescence decay curves to extract lifetime values in real-time is crucial for clinical translation and applications such as tumor margin delineation or intracoronary imaging of atherosclerotic plaques. In this work, we compare the performance of two popular non-parametric (fit-free) methods for determining lifetime values from fluorescence decays in real-time-the Phasor approach and Laguerre deconvolution. We demonstrate results from simulated and experimental data to compare the accuracy and speed of both methods and their dependence on noise and model parameters.
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Affiliation(s)
- Farzad Fereidouni
- Department of Pathology and Laboratory Medicine, 4400 V Street, CA 95817, United States of America
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36
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Malacrida L, Jameson DM, Gratton E. A multidimensional phasor approach reveals LAURDAN photophysics in NIH-3T3 cell membranes. Sci Rep 2017; 7:9215. [PMID: 28835608 PMCID: PMC5569084 DOI: 10.1038/s41598-017-08564-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/11/2017] [Indexed: 11/13/2022] Open
Abstract
Mammalian cell membranes have different phospholipid composition and cholesterol content, displaying a profile of fluidity that depends on their intracellular location. Among the dyes used in membrane studies, LAURDAN has the advantage to be sensitive to the lipid composition as well as to membrane fluidity. The LAURDAN spectrum is sensitive to the lipid composition and dipolar relaxation arising from water penetration, but disentangling lipid composition from membrane fluidity can be obtained if time resolved spectra could be measured at each cell location. Here we describe a method in which spectral and lifetime information obtained in different measurements at the same plane in a cell are used in the phasor plot providing a solution to analyze multiple lifetime or spectral data through a common visualization approach. We exploit a property of phasor plots based on the reciprocal role of the phasor plot and the image. In the phasor analysis each pixel of the image is associated with a phasor and each phasor maps to pixels and features in the image. In this paper the lifetime and spectral fluorescence data are used simultaneously to determine the contribution of polarity and dipolar relaxations of LAURDAN in each pixel of an image.
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Affiliation(s)
- Leonel Malacrida
- Laboratory for Fluorescence Dynamics, Biomedical Engineering Department, University of California at Irvine, Irvine, California, USA
- Área de Investigación Respiratoria, Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur of Montevideo, Montevideo, Uruguay
| | - David M Jameson
- Department Cell and Molecular Biology, University of Hawai'i at Manoa, John A. Burns School of Medicine, Honolulu, HI, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Biomedical Engineering Department, University of California at Irvine, Irvine, California, USA.
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37
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Lakner PH, Monaghan MG, Möller Y, Olayioye MA, Schenke-Layland K. Applying phasor approach analysis of multiphoton FLIM measurements to probe the metabolic activity of three-dimensional in vitro cell culture models. Sci Rep 2017; 7:42730. [PMID: 28211922 PMCID: PMC5304149 DOI: 10.1038/srep42730] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/13/2017] [Indexed: 01/25/2023] Open
Abstract
Fluorescence lifetime imaging microscopy (FLIM) can measure and discriminate endogenous fluorophores present in biological samples. This study seeks to identify FLIM as a suitable method to non-invasively detect a shift in cellular metabolic activity towards glycolysis or oxidative phosphorylation in 3D Caco-2 models of colorectal carcinoma. These models were treated with potassium cyanide or hydrogen peroxide as controls, and epidermal growth factor (EGF) as a physiologically-relevant influencer of cell metabolic behaviour. Autofluorescence, attributed to nicotinamide adenine dinucleotide (NADH), was induced by two-photon laser excitation and its lifetime decay was analysed using a standard multi-exponential decay approach and also a novel custom-written code for phasor-based analysis. While both methods enabled detection of a statistically significant shift of metabolic activity towards glycolysis using potassium cyanide, and oxidative phosphorylation using hydrogen peroxide, employing the phasor approach required fewer initial assumptions to quantify the lifetimes of contributing fluorophores. 3D Caco-2 models treated with EGF had increased glucose consumption, production of lactate, and presence of ATP. FLIM analyses of these cultures revealed a significant shift in the contribution of protein-bound NADH towards free NADH, indicating increased glycolysis-mediated metabolic activity. This data demonstrate that FLIM is suitable to interpret metabolic changes in 3D in vitro models.
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Affiliation(s)
- Pirmin H Lakner
- Department of Women's Health, Research Institute for Women's Health, University Hospital of the Eberhard Karls University Tübingen, Tübingen, Germany
| | - Michael G Monaghan
- Department of Women's Health, Research Institute for Women's Health, University Hospital of the Eberhard Karls University Tübingen, Tübingen, Germany
- Trinity Centre for Bioengineering, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- Department of Mechanical and Manufacturing Engineering, School of Engineering, Trinity College Dublin, Dublin, Ireland
- Department of Cell and Tissue Engineering, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
| | - Yvonne Möller
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
- Center for Personalised Medicine (ZPM), University Hospital of the Eberhard Karls University Tübingen, Tübingen, Germany
| | - Monilola A Olayioye
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
- Stuttgart Research Center Systems Biology, University of Stuttgart, Stuttgart, Germany
| | - Katja Schenke-Layland
- Department of Women's Health, Research Institute for Women's Health, University Hospital of the Eberhard Karls University Tübingen, Tübingen, Germany
- Department of Cell and Tissue Engineering, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
- Department of Medicine/Cardiology, University of California Los Angeles (UCLA), Los Angeles/CA, USA
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38
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Ranjit S, Dvornikov A, Levi M, Furgeson S, Gratton E. Characterizing fibrosis in UUO mice model using multiparametric analysis of phasor distribution from FLIM images. BIOMEDICAL OPTICS EXPRESS 2016; 7:3519-3530. [PMID: 27699117 PMCID: PMC5030029 DOI: 10.1364/boe.7.003519] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/09/2016] [Accepted: 08/12/2016] [Indexed: 05/22/2023]
Abstract
Phasor approach to fluorescence lifetime microscopy is used to study development of fibrosis in the unilateral ureteral obstruction model (UUO) of kidney in mice. Traditional phasor analysis has been modified to create a multiparametric analysis scheme that splits the phasor points in four equidistance segments based on the height of peak of the phasor distribution and calculates six parameters including average phasor positions, the shape of each segment, the angle of the distribution and the number of points in each segment. These parameters are used to create a spectrum of twenty four points specific to the phasor distribution of each sample. Comparisons of spectra from diseased and healthy tissues result in quantitative separation and calculation of statistical parameters including AUC values, positive prediction values and sensitivity. This is a new method in the evolving field of analyzing phasor distribution of FLIM data and provides further insights. Additionally, the progression of fibrosis with time is detected using this multiparametric approach to phasor analysis.
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Affiliation(s)
- Suman Ranjit
- Laboratory Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA
| | - Alexander Dvornikov
- Laboratory Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA
| | - Moshe Levi
- Departments of Medicine, University of Colorado-Anschutz Medical Campus, Aurora, Colorado, USA
| | - Seth Furgeson
- Departments of Medicine, University of Colorado-Anschutz Medical Campus, Aurora, Colorado, USA
| | - Enrico Gratton
- Laboratory Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA
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39
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Ranjit S, Dobrinskikh E, Montford J, Dvornikov A, Lehman A, Orlicky DJ, Nemenoff R, Gratton E, Levi M, Furgeson S. Label-free fluorescence lifetime and second harmonic generation imaging microscopy improves quantification of experimental renal fibrosis. Kidney Int 2016; 90:1123-1128. [PMID: 27555119 DOI: 10.1016/j.kint.2016.06.030] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 06/07/2016] [Accepted: 06/23/2016] [Indexed: 01/13/2023]
Abstract
All forms of progressive renal diseases develop a final pathway of tubulointerstitial fibrosis and glomerulosclerosis. Renal fibrosis is usually quantified using histological staining, a process that is time-consuming and pathologist dependent. Here we develop a fast and operator-independent method to measure fibrosis utilizing the murine unilateral ureteral obstruction model which manifests a time-dependent fibrotic increase in obstructed kidneys while the contralateral kidneys are used as controls. After ureteral obstruction, kidneys were analyzed at 7, 14, and 21 days. Fibrosis was quantified using fluorescence lifetime imaging (FLIM) and second harmonic generation (SHG) in a Deep Imaging via Enhanced photon Recovery deep tissue imaging microscope. This microscope was developed for deep tissue along with second and third harmonic generation imaging and has extraordinary sensitivity toward harmonic generation. SHG data suggest the presence of more fibrillar collagen in the obstructed kidneys. The combination of short-wavelength FLIM and SHG analysis results in a robust assessment procedure independent of observer interpretation and let us create criteria to quantify the extent of fibrosis directly from the image. Thus, the FLIM-SHG technique shows remarkable improvement in quantification of renal fibrosis compared to standard histological techniques.
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Affiliation(s)
- Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, USA
| | - Evgenia Dobrinskikh
- Department of Medicine, University of Colorado-Anschutz Medical Campus, Aurora, Colorado, USA
| | - John Montford
- Department of Medicine, University of Colorado-Anschutz Medical Campus, Aurora, Colorado, USA
| | - Alexander Dvornikov
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, USA
| | - Allison Lehman
- Department of Medicine, University of Colorado-Anschutz Medical Campus, Aurora, Colorado, USA
| | - David J Orlicky
- Department of Pathology, University of Colorado-Anschutz Medical Campus, Aurora, Colorado, USA
| | - Raphael Nemenoff
- Department of Medicine, University of Colorado-Anschutz Medical Campus, Aurora, Colorado, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, USA.
| | - Moshe Levi
- Department of Medicine, University of Colorado-Anschutz Medical Campus, Aurora, Colorado, USA.
| | - Seth Furgeson
- Department of Medicine, University of Colorado-Anschutz Medical Campus, Aurora, Colorado, USA
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40
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Lopes JLS, Yoneda JS, Martins JM, DeMarco R, Jameson DM, Castro AM, Bossolan NRS, Wallace BA, Araujo APU. Environmental Factors Modulating the Stability and Enzymatic Activity of the Petrotoga mobilis Esterase (PmEst). PLoS One 2016; 11:e0158146. [PMID: 27351338 PMCID: PMC4924860 DOI: 10.1371/journal.pone.0158146] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/11/2016] [Indexed: 01/20/2023] Open
Abstract
Enzymes isolated from thermophilic organisms found in oil reservoirs can find applications in many fields, including the oleochemical, pharmaceutical, bioenergy, and food/dairy industries. In this study, in silico identification and recombinant production of an esterase from the extremophile bacteria Petrotoga mobilis (designated PmEst) were performed. Then biochemical, bioinformatics and structural characterizations were undertaken using a combination of synchrotron radiation circular dichroism (SRCD) and fluorescence spectroscopies to correlate PmEst stability and hydrolytic activity on different substrates. The enzyme presented a high Michaelis-Menten constant (KM 0.16 mM) and optimum activity at ~55°C for p-nitrophenyl butyrate. The secondary structure of PmEst was preserved at acid pH, but not under alkaline conditions. PmEst was unfolded at high concentrations of urea or guanidine through apparently different mechanisms. The esterase activity of PmEst was preserved in the presence of ethanol or propanol and its melting temperature increased ~8°C in the presence of these organic solvents. PmEst is a mesophilic esterase with substrate preference towards short-to medium-length acyl chains. The SRCD data of PmEst is in agreement with the prediction of an α/β protein, which leads us to assume that it displays a typical fold of esterases from this family. The increased enzyme stability in organic solvents may enable novel applications for its use in synthetic biology. Taken together, our results demonstrate features of the PmEst enzyme that indicate it may be suitable for applications in industrial processes, particularly, when the use of polar organic solvents is required.
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Affiliation(s)
- Jose L. S. Lopes
- Instituto de Física, Universidade de São Paulo, São Paulo, Brazil
| | - Juliana S. Yoneda
- Instituto de Física, Universidade de São Paulo, São Paulo, Brazil
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Julia M. Martins
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Ricardo DeMarco
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - David M. Jameson
- Department of Cell and Molecular Biology, University of Hawai’i at Manoa, Hawaii, United States of America
| | - Aline M. Castro
- Biotechnology Division, Research and Development Center, Petrobras, Brazil
| | - Nelma R. S. Bossolan
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - B. A. Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Ana P. U. Araujo
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
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41
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Chen W, Avezov E, Schlachter SC, Gielen F, Laine RF, Harding HP, Hollfelder F, Ron D, Kaminski CF. A method to quantify FRET stoichiometry with phasor plot analysis and acceptor lifetime ingrowth. Biophys J 2016; 108:999-1002. [PMID: 25762312 PMCID: PMC4375440 DOI: 10.1016/j.bpj.2015.01.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 11/23/2014] [Accepted: 01/09/2015] [Indexed: 11/26/2022] Open
Abstract
FRET is widely used for the study of protein-protein interactions in biological samples. However, it is difficult to quantify both the FRET efficiency (E) and the affinity (Kd) of the molecular interaction from intermolecular FRET signals in samples of unknown stoichiometry. Here, we present a method for the simultaneous quantification of the complete set of interaction parameters, including fractions of bound donors and acceptors, local protein concentrations, and dissociation constants, in each image pixel. The method makes use of fluorescence lifetime information from both donor and acceptor molecules and takes advantage of the linear properties of the phasor plot approach. We demonstrate the capability of our method in vitro in a microfluidic device and also in cells, via the determination of the binding affinity between tagged versions of glutathione and glutathione S-transferase, and via the determination of competitor concentration. The potential of the method is explored with simulations.
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Affiliation(s)
- WeiYue Chen
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Edward Avezov
- The Wellcome Trust Medical Research Council Institute of Metabolic Science and National Institute for Health Research, Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Simon C Schlachter
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Fabrice Gielen
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Romain F Laine
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Heather P Harding
- The Wellcome Trust Medical Research Council Institute of Metabolic Science and National Institute for Health Research, Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - David Ron
- The Wellcome Trust Medical Research Council Institute of Metabolic Science and National Institute for Health Research, Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom.
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42
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Ferri G, Nucara L, Biver T, Battisti A, Signore G, Bizzarri R. Organization of inner cellular components as reported by a viscosity-sensitive fluorescent Bodipy probe suitable for phasor approach to FLIM. Biophys Chem 2016; 208:17-25. [DOI: 10.1016/j.bpc.2015.06.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 06/18/2015] [Accepted: 06/18/2015] [Indexed: 10/23/2022]
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43
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Malacrida L, Gratton E, Jameson DM. Model-free methods to study membrane environmental probes: a comparison of the spectral phasor and generalized polarization approaches. Methods Appl Fluoresc 2015; 3:047001. [PMID: 27182438 PMCID: PMC4862737 DOI: 10.1088/2050-6120/3/4/047001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this note, we present a discussion of the advantages and scope of model-free analysis methods applied to the popular solvatochromic probe LAURDAN, which is widely used as an environmental probe to study dynamics and structure in membranes. In particular, we compare and contrast the generalized polarization approach with the spectral phasor approach. To illustrate our points we utilize several model membrane systems containing pure lipid phases and, in some cases, cholesterol or surfactants. We demonstrate that the spectral phasor method offers definitive advantages in the case of complex systems.
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Affiliation(s)
- Leonel Malacrida
- Área de Investigación Respiratoria, Departamento de Fisiopatología, Hospital de Medicina-Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Biochemistry and Proteomic Analytical Unit, Institut Pasteur of Montevideo, Montevideo, Uruguay
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Biomedical Engineering Department, University of California at Irvine, Irvine, CA 92697, USA
| | - David M Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, 651 Halo St., BSB222, Honolulu, HI 96813, USA
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44
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Martelo L, Fedorov A, Berberan-Santos MN. Phasor Representation of Monomer–Excimer Kinetics: General Results and Application to Pyrene. J Phys Chem B 2015; 119:15023-9. [DOI: 10.1021/acs.jpcb.5b08875] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Liliana Martelo
- CQFM - Centro de Química-Física
Molecular and IN - Institute of Nanoscience and Nanotechnology, Instituto
Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Alexander Fedorov
- CQFM - Centro de Química-Física
Molecular and IN - Institute of Nanoscience and Nanotechnology, Instituto
Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Mário N. Berberan-Santos
- CQFM - Centro de Química-Física
Molecular and IN - Institute of Nanoscience and Nanotechnology, Instituto
Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
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45
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Imaging Fibrosis and Separating Collagens using Second Harmonic Generation and Phasor Approach to Fluorescence Lifetime Imaging. Sci Rep 2015; 5:13378. [PMID: 26293987 PMCID: PMC4543938 DOI: 10.1038/srep13378] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/24/2015] [Indexed: 01/13/2023] Open
Abstract
In this paper we have used second harmonic generation (SHG) and phasor approach to auto fluorescence lifetime imaging (FLIM) to obtain fingerprints of different collagens and then used these fingerprints to observe bone marrow fibrosis in the mouse femur. This is a label free approach towards fast automatable detection of fibrosis in tissue samples. FLIM has previously been used as a method of contrast in different tissues and in this paper phasor approach to FLIM is used to separate collagen I from collagen III, the markers of fibrosis, the largest groups of disorders that are often without any effective therapy. Often characterized by an increase in collagen content of the corresponding tissue, the samples are usually visualized by histochemical staining, which is pathologist dependent and cannot be automated.
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46
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Martelo L, Fedorov A, Berberan-Santos MN. Fluorescence Phasor Plots Using Time Domain Data: Effect of the Instrument Response Function. J Phys Chem B 2015; 119:10267-74. [PMID: 26182386 DOI: 10.1021/acs.jpcb.5b00261] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phasor plots of the fluorescence intensity decay (plots of the Fourier sine transform vs the Fourier cosine transform, for one or several angular frequencies) are being increasingly used, namely, in fluorescence lifetime imaging microscopy (FLIM) of cells, tissues, and surfaces, but are also relevant for the characterization of homogeneous (e.g., solution) systems. In this work, the construction of the phasor plot using time domain data is discussed, including the effect of the instrument response function (IRF). A deconvolution method in the Fourier space is described. The results obtained are applied to fluorescence decays of aqueous fluorescein (basic form) in the presence of concentrated potassium iodide. The effect of the impulse is clearly shown, in accordance with model predictions. Deconvolution in the Fourier space works well for lifetimes at least 1 order of magnitude higher than the IRF time width.
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Affiliation(s)
- Liliana Martelo
- CQFM - Centro de Química-Física Molecular and IN - Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Alexander Fedorov
- CQFM - Centro de Química-Física Molecular and IN - Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Mário N Berberan-Santos
- CQFM - Centro de Química-Física Molecular and IN - Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
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47
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Campos-Delgado DU, Navarro OG, Arce-Santana ER, Jo JA. Extended output phasor representation of multi-spectral fluorescence lifetime imaging microscopy. BIOMEDICAL OPTICS EXPRESS 2015; 6:2088-105. [PMID: 26114031 PMCID: PMC4473746 DOI: 10.1364/boe.6.002088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/01/2015] [Accepted: 05/04/2015] [Indexed: 05/23/2023]
Abstract
In this paper, we investigate novel low-dimensional and model-free representations for multi-spectral fluorescence lifetime imaging microscopy (m-FLIM) data. We depart from the classical definition of the phasor in the complex plane to propose the extended output phasor (EOP) and extended phasor (EP) for multi-spectral information. The frequency domain properties of the EOP and EP are analytically studied based on a multiexponential model for the impulse response of the imaged tissue. For practical implementations, the EOP is more appealing since there is no need to perform deconvolution of the instrument response from the measured m-FLIM data, as in the case of EP. Our synthetic and experimental evaluations with m-FLIM datasets of human coronary atherosclerotic plaques show that low frequency indexes have to be employed for a distinctive representation of the EOP and EP, and to reduce noise distortion. The tissue classification of the m-FLIM datasets by EOP and EP also improves with low frequency indexes, and does not present significant differences by using either phasor.
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Affiliation(s)
| | | | - E. R. Arce-Santana
- Facultad de Ciencias, Universidad Autonoma de San Luis Potosi, SLP,
Mexico
| | - Javier A. Jo
- Department of Biomedical Engineering, Texas A& M University, College Station, TX,
USA
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48
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Lopes JLS, Araujo APU, Jameson DM. Investigation of the conformational flexibility of DGAT1 peptides using tryptophan fluorescence. Methods Appl Fluoresc 2015; 3:025003. [PMID: 29148488 DOI: 10.1088/2050-6120/3/2/025003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The conformational behavior of synthetic peptides corresponding to the putative binding sites of the diacylglycerol acyltransferase 1 enzyme (a polytopic integral membrane protein) was investigated using steady-state and time-resolved fluorescence spectroscopies. Three small linear peptides with 13, 15 and 22 amino acid residues, containing one, two and three Trp residues, respectively, were studied in aqueous solution, in the absence and presence of model membranes. The high flexibility and unordered conformation of the peptides in solution were confirmed by the low Trp polarization values, the high accessibility to water-soluble quencher, and the fast rotational correlation times of the Trp residues. However, upon binding to the lipid systems, the Trp residues were incorporated within the acyl hydrophobic core and their lifetimes and rotational correlation times increased. Phasor plots were employed to analyze intensity decay of peptide-lipid binding and provided a trajectory, in phasor space, that lies along a line connecting the points of the free and bound peptide. This trajectory was analyzed to determine the association constant of the peptide to the model membrane.
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Affiliation(s)
- Jose L S Lopes
- Institute of Physics of Sao Carlos, University of Sao Paulo, Sao Carlos, SP, Brazil. Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI, USA
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Bonaventura G, Barcellona ML, Golfetto O, Nourse JL, Flanagan LA, Gratton E. Laurdan monitors different lipids content in eukaryotic membrane during embryonic neural development. Cell Biochem Biophys 2014; 70:785-94. [PMID: 24839062 PMCID: PMC4228983 DOI: 10.1007/s12013-014-9982-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We describe a method based on fluorescence-lifetime imaging microscopy (FLIM) to assess the fluidity of various membranes in neuronal cells at different stages of development [day 12 (E12) and day 16 (E16) of gestation]. For the FLIM measurements, we use the Laurdan probe which is commonly used to assess membrane water penetration in model and in biological membranes using spectral information. Using the FLIM approach, we build a fluidity scale based on calibration with model systems of different lipid compositions. In neuronal cells, we found a marked difference in fluidity between the internal membranes and the plasma membrane, being the plasma membrane the less fluid. However, we found no significant differences between the two cell groups, E12 and E16. Comparison with NIH3T3 cells shows that the plasma membranes of E12 and E16 cells are significantly more fluid than the plasma membrane of the cancer cells.
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Affiliation(s)
- Gabriele Bonaventura
- Department of Drug Science, Section of Biochemistry, University of Catania, Catania, Italy,
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