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Wohland T, Sim SR, Demoustier M, Pandey S, Kulkarni R, Aik D. FCS videos: Fluorescence correlation spectroscopy in space and time. Biochim Biophys Acta Gen Subj 2024; 1868:130716. [PMID: 39349260 DOI: 10.1016/j.bbagen.2024.130716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 09/20/2024] [Accepted: 09/23/2024] [Indexed: 10/02/2024]
Abstract
Fluorescence Correlation Spectroscopy (FCS), invented more than 50 years ago is a widely used tool providing information on molecular processes in a variety of samples from materials to life sciences. In the last two decades FCS was multiplexed and ultimately made into an imaging technique that provided maps of molecular parameters over whole sample cross-section. However, it was still limited by a measurement time on the order of minutes. With the improvement of FCS time resolution to seconds using deep learning, we extend here FCS to so-called FCS videos that can provide information how the molecular parameters determined by Imaging FCS change in space and time. This opens up new possibilities for the investigation of molecular processes. Here, we demonstrate the feasibility of the approach and show FCS video applications to lipid bilayers and cell membranes.
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Affiliation(s)
- Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, 117543 Singapore, Singapore; Centre for BioImaging Sciences, National University of Singapore, 117557 Singapore, Singapore; Institute of Digital Molecular Analytics and Science, 117557 Singapore, Singapore; Department of Chemistry, National University of Singapore, 117543 Singapore, Singapore.
| | - Shao Ren Sim
- Department of Biological Sciences, National University of Singapore, 117543 Singapore, Singapore; Centre for BioImaging Sciences, National University of Singapore, 117557 Singapore, Singapore; Institute of Digital Molecular Analytics and Science, 117557 Singapore, Singapore
| | - Marc Demoustier
- Department of Biological Sciences, National University of Singapore, 117543 Singapore, Singapore; Centre for BioImaging Sciences, National University of Singapore, 117557 Singapore, Singapore; Institute of Digital Molecular Analytics and Science, 117557 Singapore, Singapore
| | - Shambhavi Pandey
- Department of Biological Sciences, National University of Singapore, 117543 Singapore, Singapore; Centre for BioImaging Sciences, National University of Singapore, 117557 Singapore, Singapore
| | - Rutuparna Kulkarni
- Department of Biological Sciences, National University of Singapore, 117543 Singapore, Singapore; Centre for BioImaging Sciences, National University of Singapore, 117557 Singapore, Singapore
| | - Daniel Aik
- Centre for BioImaging Sciences, National University of Singapore, 117557 Singapore, Singapore; Institute of Digital Molecular Analytics and Science, 117557 Singapore, Singapore; Department of Chemistry, National University of Singapore, 117543 Singapore, Singapore
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2
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Caranfil A, Le Cunff Y, Kervrann C. BayesTICS: Local temporal image correlation spectroscopy and Bayesian simulation technique for sparse estimation of diffusion in fluorescence imaging. BIOLOGICAL IMAGING 2023; 3:e5. [PMID: 38487689 PMCID: PMC10936362 DOI: 10.1017/s2633903x23000041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 10/29/2022] [Accepted: 01/28/2023] [Indexed: 03/17/2024]
Abstract
The dynamics and fusion of vesicles during the last steps of exocytosis are not well established yet in cell biology. An open issue is the characterization of the diffusion process at the plasma membrane. Total internal reflection fluorescence microscopy (TIRFM) has been successfully used to analyze the coordination of proteins involved in this mechanism. It enables to capture dynamics of proteins with high frame rate and reasonable signal-to-noise values. Nevertheless, methodological approaches that can analyze and estimate diffusion in local small areas at the scale of a single diffusing spot within cells, are still lacking. To address this issue, we propose a novel correlation-based method for local diffusion estimation. As a starting point, we consider Fick's second law of diffusion that relates the diffusive flux to the gradient of the concentration. Then, we derive an explicit parametric model which is further fitted to time-correlation signals computed from regions of interest (ROI) containing individual spots. Our modeling and Bayesian estimation framework are well appropriate to represent isolated diffusion events and are robust to noise, ROI sizes, and localization of spots in ROIs. The performance of BayesTICS is shown on both synthetic and real TIRFM images depicting Transferrin Receptor proteins.
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Affiliation(s)
- Anca Caranfil
- SERPICO Project-Team, INRIA Rennes, UMR144 CNRS Institut Curie, PSL Research, Sorbonne Université, Campus universitaire de Beaulieu, Rennes, France
- CeDRE Team, GDR UMR6290-CNRS, Faculty of Medicine, University of Rennes 1, Rennes, France
| | - Yann Le Cunff
- CeDRE Team, GDR UMR6290-CNRS, Faculty of Medicine, University of Rennes 1, Rennes, France
- Dyliss Team, Univ Rennes, CNRS, Inria, IRISA, UMR 6074, Campus de Beaulieu, Rennes, France
| | - Charles Kervrann
- SERPICO Project-Team, INRIA Rennes, UMR144 CNRS Institut Curie, PSL Research, Sorbonne Université, Campus universitaire de Beaulieu, Rennes, France
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3
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Andersen C, Zulueta Díaz YDLM, Kure JL, Hessellund Eriksen M, Lovatt AL, Lagerholm C, Morales S, Sehayek S, Sheard TMD, Wiseman PW, Arnspang EC. Angiotensin II Treatment Induces Reorganization and Changes in the Lateral Dynamics of Angiotensin II Type 1 Receptor in the Plasma Membrane Elucidated by Photoactivated Localization Microscopy Combined with Image Spatial Correlation Analysis. Anal Chem 2023; 95:730-738. [PMID: 36574961 DOI: 10.1021/acs.analchem.2c02720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The mechanisms by which angiotensin II type 1 receptor is distributed and the diffusional pattern in the plasma membrane (PM) remain unclear, despite their crucial role in cardiovascular homeostasis. In this work, we obtained quantitative information of angiotensin II type 1 receptor (AT1R) lateral dynamics as well as changes in the diffusion properties after stimulation with ligands in living cells using photoactivated localization microscopy (PALM) combined with image spatial-temporal correlation analysis. To study the organization of the receptor at the nanoscale, expansion microscopy (ExM) combined with PALM was performed. This study revealed that AT1R lateral diffusion increased after binding to angiotensin II (Ang II) and the receptor diffusion was transiently confined in the PM. In addition, ExM revealed that AT1R formed nanoclusters at the PM and the cluster size significantly decreased after Ang II treatment. Taking these results together suggest that Ang II binding and activation cause reorganization and changes in the dynamics of AT1R at the PM.
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Affiliation(s)
- Camilla Andersen
- SDU Biotechnology, Department of Green Technology, University of Southern Denmark, Odense M5230, Denmark
| | | | - Jakob L Kure
- SDU Biotechnology, Department of Green Technology, University of Southern Denmark, Odense M5230, Denmark
| | - Mathias Hessellund Eriksen
- SDU Biotechnology, Department of Green Technology, University of Southern Denmark, Odense M5230, Denmark
| | - Adam Leslie Lovatt
- SDU Biotechnology, Department of Green Technology, University of Southern Denmark, Odense M5230, Denmark
| | | | - Sebastian Morales
- Department of Physics and Department of Chemistry, McGill University, MontrealH3A 0B8, Canada
| | - Simon Sehayek
- Department of Physics and Department of Chemistry, McGill University, MontrealH3A 0B8, Canada
| | - Thomas M D Sheard
- School of Biosciences, University of Sheffield, SheffieldS10 2TN, U.K
| | - Paul W Wiseman
- Department of Physics and Department of Chemistry, McGill University, MontrealH3A 0B8, Canada
| | - Eva C Arnspang
- SDU Biotechnology, Department of Green Technology, University of Southern Denmark, Odense M5230, Denmark
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Abu-Arish A, Pandžić E, Luo Y, Sato Y, Turner MJ, Wiseman PW, Hanrahan JW. Lipid-driven CFTR clustering is impaired in CF and restored by corrector drugs. J Cell Sci 2022; 135:274066. [PMID: 35060604 PMCID: PMC8976878 DOI: 10.1242/jcs.259002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/08/2022] [Indexed: 11/20/2022] Open
Abstract
Membrane proteins often cluster in nanoscale membrane domains (lipid rafts) that coalesce into ceramide-rich platforms during cell stress, however the clustering mechanisms remain uncertain. The cystic fibrosis transmembrane conductance regulator (CFTR), which is mutated in cystic fibrosis (CF), forms clusters that are cholesterol-dependent and become incorporated into long-lived platforms during hormonal stimulation. We report here that clustering does not involve known tethering interactions of CFTR with PDZ domain proteins, filamin A or the actin cytoskeleton. It also does not require CFTR palmitoylation but is critically dependent on membrane lipid order and is induced by detergents that increase the phase separation of membrane lipids. Clustering and integration of CFTR into ceramide-rich platforms are abolished by the disease mutations F508del and S13F and rescued by the CFTR modulators elexacaftor+tezacaftor. These results indicate CF therapeutics that correct mutant protein folding restore both trafficking and normal lipid interactions in the plasma membrane.
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Affiliation(s)
- Asmahan Abu-Arish
- Department of Physiology, McGill University, Montréal QC H3G 1Y6, Canada
- Cystic Fibrosis Translational Research centre, McGill University, Canada
| | - Elvis Pandžić
- UNSW Australia, Biomedical Imaging Facility, Mark Wainwright Analytical Center, Sydney, Australia
| | - Yishan Luo
- Department of Physiology, McGill University, Montréal QC H3G 1Y6, Canada
- Cystic Fibrosis Translational Research centre, McGill University, Canada
| | - Yukiko Sato
- Department of Physiology, McGill University, Montréal QC H3G 1Y6, Canada
- Cystic Fibrosis Translational Research centre, McGill University, Canada
| | - Mark J. Turner
- Department of Physiology, McGill University, Montréal QC H3G 1Y6, Canada
- Cystic Fibrosis Translational Research centre, McGill University, Canada
| | - Paul W. Wiseman
- Department of Chemistry and Department of Physics, McGill University, Montréal, QC, Canada
| | - John W. Hanrahan
- Department of Physiology, McGill University, Montréal QC H3G 1Y6, Canada
- Cystic Fibrosis Translational Research centre, McGill University, Canada
- Research Institute of the McGill University Health Centre, Canada
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Rapid ensemble measurement of protein diffusion and probe blinking dynamics in cells. BIOPHYSICAL REPORTS 2021; 1:100015. [PMID: 36425455 PMCID: PMC9680803 DOI: 10.1016/j.bpr.2021.100015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/30/2021] [Indexed: 12/25/2022]
Abstract
We present a fluorescence fluctuation image correlation analysis method that can rapidly and simultaneously measure the diffusion coefficient, photoblinking rates, and fraction of diffusing particles of fluorescent molecules in cells. Unlike other image correlation techniques, we demonstrated that our method could be applied irrespective of a nonuniformly distributed, immobile blinking fluorophore population. This allows us to measure blinking and transport dynamics in complex cell morphologies, a benefit for a range of super-resolution fluorescence imaging approaches that rely on probe emission blinking. Furthermore, we showed that our technique could be applied without directly accounting for photobleaching. We successfully employed our technique on several simulations with realistic EMCCD noise and photobleaching models, as well as on Dronpa-C12-labeled β-actin in living NIH/3T3 and HeLa cells. We found that the diffusion coefficients measured using our method were consistent with previous literature values. We further found that photoblinking rates measured in the live HeLa cells varied as expected with changing excitation power.
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Using kICS to Reveal Changed Membrane Diffusion of AQP-9 Treated with Drugs. MEMBRANES 2021; 11:membranes11080568. [PMID: 34436330 PMCID: PMC8399444 DOI: 10.3390/membranes11080568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 11/18/2022]
Abstract
The formation of nanodomains in the plasma membrane are thought to be part of membrane proteins regulation and signaling. Plasma membrane proteins are often investigated by analyzing the lateral mobility. k-space ICS (kICS) is a powerful image correlation spectroscopy (ICS) technique and a valuable supplement to fluorescence correlation spectroscopy (FCS). Here, we study the diffusion of aquaporin-9 (AQP9) in the plasma membrane, and the effect of different membrane and cytoskeleton affecting drugs, and therefore nanodomain perturbing, using kICS. We measured the diffusion coefficient of AQP9 after addition of these drugs using live cell Total Internal Reflection Fluorescence imaging on HEK-293 cells. The actin polymerization inhibitors Cytochalasin D and Latrunculin A do not affect the diffusion coefficient of AQP9. Methyl-β-Cyclodextrin decreases GFP-AQP9 diffusion coefficient in the plasma membrane. Human epidermal growth factor led to an increase in the diffusion coefficient of AQP9. These findings led to the conclusion that kICS can be used to measure diffusion AQP9, and suggests that the AQP9 is not part of nanodomains.
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Revealing Plasma Membrane Nano-Domains with Diffusion Analysis Methods. MEMBRANES 2020; 10:membranes10110314. [PMID: 33138102 PMCID: PMC7693849 DOI: 10.3390/membranes10110314] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022]
Abstract
Nano-domains are sub-light-diffraction-sized heterogeneous areas in the plasma membrane of cells, which are involved in cell signalling and membrane trafficking. Throughout the last thirty years, these nano-domains have been researched extensively and have been the subject of multiple theories and models: the lipid raft theory, the fence model, and the protein oligomerization theory. Strong evidence exists for all of these, and consequently they were combined into a hierarchal model. Measurements of protein and lipid diffusion coefficients and patterns have been instrumental in plasma membrane research and by extension in nano-domain research. This has led to the development of multiple methodologies that can measure diffusion and confinement parameters including single particle tracking, fluorescence correlation spectroscopy, image correlation spectroscopy and fluorescence recovery after photobleaching. Here we review the performance and strengths of these methods in the context of their use in identification and characterization of plasma membrane nano-domains.
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Abu-Arish A, Pandžić E, Kim D, Tseng HW, Wiseman PW, Hanrahan JW. Agonists that stimulate secretion promote the recruitment of CFTR into membrane lipid microdomains. J Gen Physiol 2019; 151:834-849. [PMID: 31048413 PMCID: PMC6572005 DOI: 10.1085/jgp.201812143] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 04/05/2019] [Indexed: 01/20/2023] Open
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is a tightly regulated anion channel that mediates secretion by epithelia and is mutated in the disease cystic fibrosis. CFTR forms macromolecular complexes with many proteins; however, little is known regarding its associations with membrane lipids or the regulation of its distribution and mobility at the cell surface. We report here that secretagogues (agonists that stimulate secretion) such as the peptide hormone vasoactive intestinal peptide (VIP) and muscarinic agonist carbachol increase CFTR aggregation into cholesterol-dependent clusters, reduce CFTR lateral mobility within and between membrane microdomains, and trigger the fusion of clusters into large (3.0 µm2) ceramide-rich platforms. CFTR clusters are closely associated with motile cilia and with the enzyme acid sphingomyelinase (ASMase) that is constitutively bound on the cell surface. Platform induction is prevented by pretreating cells with cholesterol oxidase to disrupt lipid rafts or by exposure to the ASMase functional inhibitor amitriptyline or the membrane-impermeant reducing agent 2-mercaptoethanesulfonate. Platforms are reversible, and their induction does not lead to an increase in apoptosis; however, blocking platform formation does prevent the increase in CFTR surface expression that normally occurs during VIP stimulation. These results demonstrate that CFTR is colocalized with motile cilia and reveal surprisingly robust regulation of CFTR distribution and lateral mobility, most likely through autocrine redox activation of extracellular ASMase. Formation of ceramide-rich platforms containing CFTR enhances transepithelial secretion and likely has other functions related to inflammation and mucosal immunity.
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Affiliation(s)
- Asmahan Abu-Arish
- Department of Physiology, McGill University, Montréal, Canada
- Department of Physics, McGill University, Montréal, Canada
- Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada
| | - Elvis Pandžić
- Department of Physics, McGill University, Montréal, Canada
| | - Dusik Kim
- Department of Physiology, McGill University, Montréal, Canada
- Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada
| | - Hsin Wei Tseng
- Department of Physiology, McGill University, Montréal, Canada
| | - Paul W Wiseman
- Department of Physics, McGill University, Montréal, Canada
- Department of Chemistry, McGill University, Montréal, Canada
- Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada
| | - John W Hanrahan
- Department of Physiology, McGill University, Montréal, Canada
- Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada
- McGill University Health Centre Research Institute, Montréal, Canada
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9
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De Mets R, Wang I, Balland M, Oddou C, Moreau P, Fourcade B, Albiges-Rizo C, Delon A, Destaing O. Cellular tension encodes local Src-dependent differential β 1 and β 3 integrin mobility. Mol Biol Cell 2018; 30:181-190. [PMID: 30462575 PMCID: PMC6589565 DOI: 10.1091/mbc.e18-04-0253] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Integrins are transmembrane receptors that have a pivotal role in mechanotransduction processes by connecting the extracellular matrix to the cytoskeleton. Although it is well established that integrin activation/inhibition cycles are due to highly dynamic interactions, whether integrin mobility depends on local tension and cytoskeletal organization remains surprisingly unclear. Using an original approach combining micropatterning on glass substrates to induce standardized local mechanical constraints within a single cell with temporal image correlation spectroscopy, we measured the mechanosensitive response of integrin mobility at the whole cell level and in adhesion sites under different mechanical constraints. Contrary to β1 integrins, high tension increases β3 integrin residence time in adhesive regions. Chimeric integrins and structure–function studies revealed that the ability of β3 integrins to specifically sense local tensional organization is mostly encoded by its cytoplasmic domain and is regulated by tuning the affinity of its NPXY domains through phosphorylation by Src family kinases.
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Affiliation(s)
- Richard De Mets
- Laboratoire interdisciplinaire de Physique, Université Grenoble Alpes et CNRS, 38402 Grenoble, Cedex, France
| | - Irene Wang
- Laboratoire interdisciplinaire de Physique, Université Grenoble Alpes et CNRS, 38402 Grenoble, Cedex, France
| | - Martial Balland
- Laboratoire interdisciplinaire de Physique, Université Grenoble Alpes et CNRS, 38402 Grenoble, Cedex, France
| | - Christiane Oddou
- Institut Albert Bonniot, Université Joseph Fourier, INSERM U823, CNRS ERL 5284, Grenoble Alpessite Santé, F38042 Grenoble Cedex 09, France
| | - Philippe Moreau
- Laboratoire interdisciplinaire de Physique, Université Grenoble Alpes et CNRS, 38402 Grenoble, Cedex, France
| | - Bertrand Fourcade
- Laboratoire interdisciplinaire de Physique, Université Grenoble Alpes et CNRS, 38402 Grenoble, Cedex, France
| | - Corinne Albiges-Rizo
- Institut Albert Bonniot, Université Joseph Fourier, INSERM U823, CNRS ERL 5284, Grenoble Alpessite Santé, F38042 Grenoble Cedex 09, France
| | - Antoine Delon
- Laboratoire interdisciplinaire de Physique, Université Grenoble Alpes et CNRS, 38402 Grenoble, Cedex, France
| | - Olivier Destaing
- Institut Albert Bonniot, Université Joseph Fourier, INSERM U823, CNRS ERL 5284, Grenoble Alpessite Santé, F38042 Grenoble Cedex 09, France
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10
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Collini M, Bouzin M, Chirico G. Out of the Randomness: Correlating Noise in Biological Systems. Biophys J 2018; 114:2298-2307. [PMID: 29477335 PMCID: PMC6129560 DOI: 10.1016/j.bpj.2018.01.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/23/2018] [Accepted: 01/29/2018] [Indexed: 11/23/2022] Open
Abstract
The study of the dynamics of biological systems requires one to follow relaxation processes in time with micron-size spatial resolution. This need has led to the development of different fluorescence correlation techniques with high spatial resolution and a tremendous (from nanoseconds to seconds) temporal dynamic range. Spatiotemporal information can be obtained even on complex dynamic processes whose time evolution is not forecast by simple Brownian diffusion. Our discussion of the most recent applications of image correlation spectroscopy to the study of anomalous sub- or superdiffusion suggests that this field still requires the development of multidimensional image analyses based on analytical models or numerical simulations. We focus in particular on the framework of spatiotemporal image correlation spectroscopy and examine the critical steps in getting information on anomalous diffusive processes from the correlation maps. We point out how a dual space-time correlative analysis, in both the direct and the Fourier space, can provide quantitative information on superdiffusional processes when these are analyzed through an empirical model based on intermittent active dynamics. We believe that this dual space-time analysis, potentially amenable to mathematical treatment and to the exact fit of experimental data, could be extended to include the rich phenomenology of subdiffusive processes, thereby quantifying relevant parameters for the various motivating biological problems of interest.
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Affiliation(s)
- Maddalena Collini
- Dipartimento di Fisica e Centro di Nanomedicina, Università degli Studi di Milano-Bicocca, Milan, Italy; CNR-ISASI, Center for Complex Systems, Pozzuoli, Italy
| | - Margaux Bouzin
- Dipartimento di Fisica e Centro di Nanomedicina, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Giuseppe Chirico
- Dipartimento di Fisica e Centro di Nanomedicina, Università degli Studi di Milano-Bicocca, Milan, Italy; CNR-ISASI, Center for Complex Systems, Pozzuoli, Italy.
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11
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Pandžić E, Abu-Arish A, Whan RM, Hanrahan JW, Wiseman PW. Velocity landscape correlation resolves multiple flowing protein populations from fluorescence image time series. Methods 2018; 140-141:126-139. [DOI: 10.1016/j.ymeth.2018.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/06/2017] [Accepted: 02/12/2018] [Indexed: 11/16/2022] Open
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Schrimpf W, Barth A, Hendrix J, Lamb DC. PAM: A Framework for Integrated Analysis of Imaging, Single-Molecule, and Ensemble Fluorescence Data. Biophys J 2018; 114:1518-1528. [PMID: 29642023 PMCID: PMC5954487 DOI: 10.1016/j.bpj.2018.02.035] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/15/2018] [Accepted: 02/12/2018] [Indexed: 11/24/2022] Open
Abstract
Fluorescence microscopy and spectroscopy data hold a wealth of information on the investigated molecules, structures, or organisms. Nowadays, the same fluorescence data set can be analyzed in many ways to extract different properties of the measured sample. Yet, doing so remains slow and cumbersome, often requiring incompatible software packages. Here, we present PAM (pulsed interleaved excitation analysis with MATLAB), an open-source software package written in MATLAB that offers a simple and efficient workflow through its graphical user interface. PAM is a framework for integrated and robust analysis of fluorescence ensemble, single-molecule, and imaging data. Although it was originally developed for the analysis of pulsed interleaved excitation experiments, PAM has since been extended to support most types of data collection modalities. It combines a multitude of powerful analysis algorithms, ranging from time- and space-correlation analysis, over single-molecule burst analysis, to lifetime imaging microscopy, while offering intrinsic support for multicolor experiments. We illustrate the key concepts and workflow of the software by discussing data handling and sorting and provide step-by-step descriptions for the individual usage cases.
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Affiliation(s)
- Waldemar Schrimpf
- Department of Physical Chemistry, Center for Integrated Protein Science Munich (CIPSM), Nanosystems Initiative Munich (NIM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Anders Barth
- Department of Physical Chemistry, Center for Integrated Protein Science Munich (CIPSM), Nanosystems Initiative Munich (NIM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Biomedical Research Institute (BIOMED), Advanced Optical Microscopy Centre, Faculty of Medicine and Life Sciences, Hasselt University, Diepenbeek, Belgium; Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics Division, KU Leuven, Heverlee, Belgium
| | - Don C Lamb
- Department of Physical Chemistry, Center for Integrated Protein Science Munich (CIPSM), Nanosystems Initiative Munich (NIM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany.
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13
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Malacrida L, Rao E, Gratton E. Comparison between iMSD and 2D-pCF analysis for molecular motion studies on in vivo cells: The case of the epidermal growth factor receptor. Methods 2018; 140-141:74-84. [PMID: 29501424 DOI: 10.1016/j.ymeth.2018.01.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 01/16/2018] [Accepted: 01/22/2018] [Indexed: 11/20/2022] Open
Abstract
Image correlation analysis has evolved to become a valuable method of analysis of the diffusional motion of molecules in every points of a live cell. Here we compare the iMSD and the 2D-pCF approaches that provide complementary information. The iMSD method provides the law of diffusion and it requires spatial averaging over a small region of the cell. The 2D-pCF does not require spatial averaging and it gives information about obstacles for diffusion at pixel resolution. We show the analysis of the same set of data by the two methods to emphasize that both methods could be needed to have a comprehensive understanding of the molecular diffusional flow in a live cell.
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Affiliation(s)
- Leonel Malacrida
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, USA; Área de Investigación Respiratoria, Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Uruguay
| | - Estella Rao
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, USA; Dipartimento di Fisica e Chimica, Università di Palermo, Italy
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, USA.
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14
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Malacrida L, Hedde PN, Ranjit S, Cardarelli F, Gratton E. Visualization of barriers and obstacles to molecular diffusion in live cells by spatial pair-cross-correlation in two dimensions. BIOMEDICAL OPTICS EXPRESS 2018; 9:303-321. [PMID: 29359105 PMCID: PMC5772584 DOI: 10.1364/boe.9.000303] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/09/2017] [Accepted: 12/11/2017] [Indexed: 05/09/2023]
Abstract
Despite recent advances in optical super-resolution, we lack a method that can visualize the path followed by diffusing molecules in the cytoplasm or in the nucleus of cells. Fluorescence correlation spectroscopy (FCS) provides molecular dynamics at the single molecule level by averaging the behavior of many molecules over time at a single spot, thus achieving very good statistics but at only one point in the cell. Earlier image-based methods including raster-scan and spatiotemporal image correlation need spatial averaging over relatively large areas, thus compromising spatial resolution. Here, we use spatial pair-cross-correlation in two dimensions (2D-pCF) to obtain relatively high resolution images of molecular diffusion dynamics and transport in live cells. The 2D-pCF method measures the time for a particle to go from one location to another by cross-correlating the intensity fluctuations at specific points in an image. Hence, a visual map of the average path followed by molecules is created.
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Affiliation(s)
- Leonel Malacrida
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, USA
- Área de Investigación Respiratoria, Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Uruguay
- LM and PNH contributed equally to this work
| | - Per Niklas Hedde
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, USA
- LM and PNH contributed equally to this work
| | - Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, USA
| | - Francesco Cardarelli
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, USA
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15
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Toplak T, Palmieri B, Juanes-García A, Vicente-Manzanares M, Grant M, Wiseman PW. Wavelet Imaging on Multiple Scales (WIMS) reveals focal adhesion distributions, dynamics and coupling between actomyosin bundle stability. PLoS One 2017; 12:e0186058. [PMID: 29049414 PMCID: PMC5648137 DOI: 10.1371/journal.pone.0186058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 09/25/2017] [Indexed: 11/22/2022] Open
Abstract
We introduce and use Wavelet Imaging on Multiple Scales (WIMS) as an improvement to fluorescence correlation spectroscopy to measure physical processes and features that occur across multiple length scales. In this study, wavelet transforms of cell images are used to characterize molecular dynamics at the cellular and subcellular levels (i.e. focal adhesions). We show the usefulness of the technique by applying WIMS to an image time series of a migrating osteosarcoma cell expressing fluorescently labelled adhesion proteins, which allows us to characterize different components of the cell ranging from optical resolution scale through to focal adhesion and whole cell size scales. Using WIMS we measured focal adhesion numbers, orientation and cell boundary velocities for retraction and protrusion. We also determine the internal dynamics of individual focal adhesions undergoing assembly, disassembly or elongation. Thus confirming as previously shown, WIMS reveals that the number of adhesions and the area of the protruding region of the cell are strongly correlated, establishing a correlation between protrusion size and adhesion dynamics. We also apply this technique to characterize the behavior of adhesions, actin and myosin in Chinese hamster ovary cells expressing a mutant form of myosin IIB (1935D) that displays decreased filament stability and impairs front-back cell polarity. We find separate populations of actin and myosin at each adhesion pole for both the mutant and wild type form. However, we find these populations move rapidly inwards toward one another in the mutant case in contrast to the cells that express wild type myosin IIB where those populations remain stationary. Results obtained with these two systems demonstrate how WIMS has the potential to reveal novel correlations between chosen parameters that belong to different scales.
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Affiliation(s)
- Tim Toplak
- Department of Physics, McGill University, Montréal, Québec, Canada
| | - Benoit Palmieri
- Department of Physics, McGill University, Montréal, Québec, Canada
| | - Alba Juanes-García
- Universidad Autonoma de Madrid School of Medicine/IIS-Princesa Diego de Leon, Madrid, Spain
| | | | - Martin Grant
- Department of Physics, McGill University, Montréal, Québec, Canada
| | - Paul W. Wiseman
- Department of Physics, McGill University, Montréal, Québec, Canada
- Department of Chemistry, McGill University, Montréal, Québec, Canada
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16
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Hendrix J, Dekens T, Schrimpf W, Lamb DC. Arbitrary-Region Raster Image Correlation Spectroscopy. Biophys J 2017; 111:1785-1796. [PMID: 27760364 PMCID: PMC5073057 DOI: 10.1016/j.bpj.2016.09.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/04/2016] [Accepted: 09/12/2016] [Indexed: 11/23/2022] Open
Abstract
Combining imaging with correlation spectroscopy, as in raster image correlation spectroscopy (RICS), makes it possible to extract molecular translational diffusion constants and absolute concentrations, and determine intermolecular interactions from single-channel or multicolor confocal laser-scanning microscopy (CLSM) images. Region-specific RICS analysis remains very challenging because correlations are always calculated in a square region-of-interest (ROI). In this study, we describe a generalized image correlation spectroscopy algorithm that accepts arbitrarily shaped ROIs. We show that an image series can be cleaned up before arbitrary-region RICS (ARICS) analysis. We demonstrate the power of ARICS by simultaneously measuring molecular mobility in the cell membrane and the cytosol. Mobility near dynamic subcellular structures can be investigated with ARICS by generating a dynamic ROI. Finally, we derive diffusion and concentration pseudo-maps using the ARICS method. ARICS is a powerful expansion of image correlation spectroscopy with the potential of becoming the new standard for extracting biophysical parameters from confocal fluorescence images.
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Affiliation(s)
- Jelle Hendrix
- Laboratory for Photochemistry and Spectroscopy, Division of Molecular Imaging and Photonics, KU Leuven, Leuven, Belgium.
| | - Tomas Dekens
- Department of ETRO, Vrije Universiteit Brussel, Brussels, Belgium; iMinds vzw, Zwijnaarde, Belgium
| | - Waldemar Schrimpf
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Don C Lamb
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
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17
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Rowland DJ, Tuson HH, Biteen JS. Resolving Fast, Confined Diffusion in Bacteria with Image Correlation Spectroscopy. Biophys J 2017; 110:2241-51. [PMID: 27224489 DOI: 10.1016/j.bpj.2016.04.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 04/14/2016] [Accepted: 04/18/2016] [Indexed: 01/30/2023] Open
Abstract
By following single fluorescent molecules in a microscope, single-particle tracking (SPT) can measure diffusion and binding on the nanometer and millisecond scales. Still, although SPT can at its limits characterize the fastest biomolecules as they interact with subcellular environments, this measurement may require advanced illumination techniques such as stroboscopic illumination. Here, we address the challenge of measuring fast subcellular motion by instead analyzing single-molecule data with spatiotemporal image correlation spectroscopy (STICS) with a focus on measurements of confined motion. Our SPT and STICS analysis of simulations of the fast diffusion of confined molecules shows that image blur affects both STICS and SPT, and we find biased diffusion rate measurements for STICS analysis in the limits of fast diffusion and tight confinement due to fitting STICS correlation functions to a Gaussian approximation. However, we determine that with STICS, it is possible to correctly interpret the motion that blurs single-molecule images without advanced illumination techniques or fast cameras. In particular, we present a method to overcome the bias due to image blur by properly estimating the width of the correlation function by directly calculating the correlation function variance instead of using the typical Gaussian fitting procedure. Our simulation results are validated by applying the STICS method to experimental measurements of fast, confined motion: we measure the diffusion of cytosolic mMaple3 in living Escherichia coli cells at 25 frames/s under continuous illumination to illustrate the utility of STICS in an experimental parameter regime for which in-frame motion prevents SPT and tight confinement of fast diffusion precludes stroboscopic illumination. Overall, our application of STICS to freely diffusing cytosolic protein in small cells extends the utility of single-molecule experiments to the regime of fast confined diffusion without requiring advanced microscopy techniques.
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Affiliation(s)
- David J Rowland
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Hannah H Tuson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Julie S Biteen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan.
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18
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Rowland DJ, Biteen JS. Measuring molecular motions inside single cells with improved analysis of single-particle trajectories. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Lagerholm BC, Andrade DM, Clausen MP, Eggeling C. Convergence of lateral dynamic measurements in the plasma membrane of live cells from single particle tracking and STED-FCS. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2017; 50:063001. [PMID: 28458397 PMCID: PMC5390782 DOI: 10.1088/1361-6463/aa519e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 11/15/2016] [Accepted: 12/05/2016] [Indexed: 05/06/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) in combination with the super-resolution imaging method STED (STED-FCS), and single-particle tracking (SPT) are able to directly probe the lateral dynamics of lipids and proteins in the plasma membrane of live cells at spatial scales much below the diffraction limit of conventional microscopy. However, a major disparity in interpretation of data from SPT and STED-FCS remains, namely the proposed existence of a very fast (unhindered) lateral diffusion coefficient, ⩾5 µm2 s-1, in the plasma membrane of live cells at very short length scales, ≈⩽ 100 nm, and time scales, ≈1-10 ms. This fast diffusion coefficient has been advocated in several high-speed SPT studies, for lipids and membrane proteins alike, but the equivalent has not been detected in STED-FCS measurements. Resolving this ambiguity is important because the assessment of membrane dynamics currently relies heavily on SPT for the determination of heterogeneous diffusion. A possible systematic error in this approach would thus have vast implications in this field. To address this, we have re-visited the analysis procedure for SPT data with an emphasis on the measurement errors and the effect that these errors have on the measurement outputs. We subsequently demonstrate that STED-FCS and SPT data, following careful consideration of the experimental errors of the SPT data, converge to a common interpretation which for the case of a diffusing phospholipid analogue in the plasma membrane of live mouse embryo fibroblasts results in an unhindered, intra-compartment, diffusion coefficient of ≈0.7-1.0 µm2 s-1, and a compartment size of about 100-150 nm.
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Affiliation(s)
- B Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Débora M Andrade
- Centre for Neural Circuits and Behaviour, University of Oxford, Mansfield Road, Oxford OX1 3SR, UK
| | - Mathias P Clausen
- MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Campusvej 55, Odense M DK-5230, Denmark
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Christian Eggeling
- Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
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20
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Arnspang EC, Login FH, Koffman JS, Sengupta P, Nejsum LN. AQP2 Plasma Membrane Diffusion Is Altered by the Degree of AQP2-S256 Phosphorylation. Int J Mol Sci 2016; 17:ijms17111804. [PMID: 27801846 PMCID: PMC5133805 DOI: 10.3390/ijms17111804] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/15/2016] [Accepted: 09/22/2016] [Indexed: 01/21/2023] Open
Abstract
Fine tuning of urine concentration occurs in the renal collecting duct in response to circulating levels of arginine vasopressin (AVP). AVP stimulates intracellular cAMP production, which mediates exocytosis of sub-apical vesicles containing the water channel aquaporin-2 (AQP2). Protein Kinase A (PKA) phosphorylates AQP2 on serine-256 (S256), which triggers plasma membrane accumulation of AQP2. This mediates insertion of AQP2 into the apical plasma membrane, increasing water permeability of the collecting duct. AQP2 is a homo-tetramer. When S256 on all four monomers is changed to the phosphomimic aspartic acid (S256D), AQP2-S256D localizes to the plasma membrane and internalization is decreased. In contrast, when S256 is mutated to alanine (S256A) to mimic non-phosphorylated AQP2, AQP2-S256A localizes to intracellular vesicles as well as the plasma membrane, with increased internalization from the plasma membrane. S256 phosphorylation is not necessary for exocytosis and dephosphorylation is not necessary for endocytosis, however, the degree of S256 phosphorylation is hypothesized to regulate the kinetics of AQP2 endocytosis and thus, retention time in the plasma membrane. Using k-space Image Correlation Spectroscopy (kICS), we determined how the number of phosphorylated to non-phosphorylated S256 monomers in the AQP2 tetramer affects diffusion speed of AQP2 in the plasma membrane. When all four monomers mimicked constitutive phosphorylation (AQP2-S256D), diffusion was faster than when all four were non-phosphorylated (AQP2-S256A). AQP2-WT diffused at a speed similar to that of AQP2-S256D. When an average of two or three monomers in the tetramer were constitutively phosphorylated, the average diffusion coefficients were not significantly different to that of AQP2-S256D. However, when only one monomer was phosphorylated, diffusion was slower and similar to AQP2-S256A. Thus, AQP2 with two to four phosphorylated monomers has faster plasma membrane kinetics, than the tetramer which contains just one or no phosphorylated monomers. This difference in diffusion rate may reflect behavior of AQP2 tetramers destined for either plasma membrane retention or endocytosis.
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Affiliation(s)
- Eva C Arnspang
- Department of Clinical Medicine, Aarhus University, DK-8000 Aarhus C, Denmark.
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Frédéric H Login
- Department of Clinical Medicine, Aarhus University, DK-8000 Aarhus C, Denmark.
| | - Jennifer S Koffman
- Department of Interdisciplinary Nanoscience Center, Aarhus University, DK-8000 Aarhus C, Denmark.
| | - Prabuddha Sengupta
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Lene N Nejsum
- Department of Clinical Medicine, Aarhus University, DK-8000 Aarhus C, Denmark.
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21
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An Intermittent Model for Intracellular Motions of Gold Nanostars by k-Space Scattering Image Correlation. Biophys J 2016; 109:2246-58. [PMID: 26636936 DOI: 10.1016/j.bpj.2015.10.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/09/2015] [Accepted: 10/21/2015] [Indexed: 11/20/2022] Open
Abstract
Anisotropic metallic nanoparticles have been devised as powerful potential tools for in vivo imaging, photothermal therapy, and drug delivery thanks to plasmon-enhanced absorption and scattering cross sections, ease in synthesis and functionalization, and controlled cytotoxicity. The rational design of all these applications requires the characterization of the nanoparticles intracellular trafficking pathways. In this work, we exploit live-cell time-lapse confocal reflectance microscopy and image correlation in both direct and reciprocal space to investigate the intracellular transport of branched gold nanostars (GNSs). Different transport mechanisms, spanning from pure Brownian diffusion to (sub-)ballistic superdiffusion, are revealed by temporal and spatio-temporal image correlation spectroscopy on the tens-of-seconds timescale. According to these findings, combined with numerical simulations and with a Bayesian (hidden Markov model-based) analysis of single particle tracking data, we ascribe the superdiffusive, subballistic behavior characterizing the GNSs dynamics to a two-state switching between Brownian diffusion in the cytoplasm and molecular motor-mediated active transport. For the investigation of intermittent-type transport phenomena, we derive an analytical theoretical framework for Fourier-space image correlation spectroscopy (kICS). At first, we evaluate the influence of all the dynamic and kinetic parameters (the diffusion coefficient, the drift velocity, and the transition rates between the diffusive and the active transport regimes) on simulated kICS correlation functions. Then we outline a protocol for data analysis and employ it to derive whole-cell maps for each parameter underlying the GNSs intracellular dynamics. Capable of identifying even simpler transport phenomena, whether purely diffusive or ballistic, our intermittent kICS approach allows an exhaustive investigation of the dynamics of GNSs and biological macromolecules.
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22
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Wulstein DM, Regan KE, Robertson-Anderson RM, McGorty R. Light-sheet microscopy with digital Fourier analysis measures transport properties over large field-of-view. OPTICS EXPRESS 2016; 24:20881-94. [PMID: 27607692 PMCID: PMC5946909 DOI: 10.1364/oe.24.020881] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Using light-sheet microscopy combined with digital Fourier methods we probe the dynamics of colloidal samples and DNA molecules. This combination, referred to as selective-plane illumination differential dynamic microscopy (SPIDDM), has the benefit of optical sectioning to study, with minimal photobleaching, thick samples allowing us to measure the diffusivity of colloidal particles at high volume fractions. Further, SPIDDM exploits the inherent spatially-varying thickness of Gaussian light-sheets. Where the excitation sheet is most focused, we capture high spatial frequency dynamics as the signal-to-background is high. In thicker regions, we capture the slower dynamics as diffusion out of the sheet takes longer.
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23
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Gaus K. Biologists Wanted: New Fluorescence Fluctuation Tools for Cell Biology. Biophys J 2016; 111:677-678. [PMID: 27558711 DOI: 10.1016/j.bpj.2016.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 07/07/2016] [Accepted: 07/11/2016] [Indexed: 11/28/2022] Open
Affiliation(s)
- Katharina Gaus
- European Molecular Biology Laboratory Australia Node in Single Molecule Science, School of Medical Sciences, Sydney, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia.
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24
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Get your kICS by measuring membrane protein dynamics. Biophys J 2016; 109:1-2. [PMID: 26153695 DOI: 10.1016/j.bpj.2015.05.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 05/22/2015] [Accepted: 05/28/2015] [Indexed: 01/17/2023] Open
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25
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Abu-Arish A, Pandzic E, Goepp J, Matthes E, Hanrahan JW, Wiseman PW. Cholesterol modulates CFTR confinement in the plasma membrane of primary epithelial cells. Biophys J 2016; 109:85-94. [PMID: 26153705 DOI: 10.1016/j.bpj.2015.04.042] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 04/23/2015] [Indexed: 01/01/2023] Open
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is a plasma-membrane anion channel that, when mutated, causes the disease cystic fibrosis. Although CFTR has been detected in a detergent-resistant membrane fraction prepared from airway epithelial cells, suggesting that it may partition into cholesterol-rich membrane microdomains (lipid rafts), its compartmentalization has not been demonstrated in intact cells and the influence of microdomains on CFTR lateral mobility is unknown. We used live-cell imaging, spatial image correlation spectroscopy, and k-space image correlation spectroscopy to examine the aggregation state of CFTR and its dynamics both within and outside microdomains in the plasma membrane of primary human bronchial epithelial cells. These studies were also performed during treatments that augment or deplete membrane cholesterol. We found two populations of CFTR molecules that were distinguishable based on their dynamics at the cell surface. One population showed confinement and had slow dynamics that were highly cholesterol dependent. The other, more abundant population was less confined and diffused more rapidly. Treatments that deplete the membrane of cholesterol caused the confined fraction and average number of CFTR molecules per cluster to decrease. Elevating cholesterol had the opposite effect, increasing channel aggregation and the fraction of channels displaying confinement, consistent with CFTR recruitment into cholesterol-rich microdomains with dimensions below the optical resolution limit. Viral infection caused the nanoscale microdomains to fuse into large platforms and reduced CFTR mobility. To our knowledge, these results provide the first biophysical evidence for multiple CFTR populations and have implications for regulation of their surface expression and channel function.
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Affiliation(s)
| | - Elvis Pandzic
- Physics, McGill University, Montreal, Quebec, Canada
| | - Julie Goepp
- Physiology, McGill University, Montreal, Quebec, Canada
| | | | | | - Paul W Wiseman
- Chemistry & Physics, McGill University, Montreal, Quebec, Canada.
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26
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Shaikh SR, Boyle S, Edidin M. A high fat diet containing saturated but not unsaturated fatty acids enhances T cell receptor clustering on the nanoscale. Prostaglandins Leukot Essent Fatty Acids 2015; 100:1-4. [PMID: 26143085 PMCID: PMC4554807 DOI: 10.1016/j.plefa.2015.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 05/07/2015] [Indexed: 01/16/2023]
Abstract
Cell culture studies show that the nanoscale lateral organization of surface receptors, their clustering or dispersion, can be altered by changing the lipid composition of the membrane bilayer. However, little is known about similar changes in vivo, which can be effected by changing dietary lipids. We describe the use of a newly developed method, k-space image correlation spectroscopy, kICS, for analysis of quantum dot fluorescence to show that a high fat diet can alter the nanometer-scale clustering of the murine T cell receptor, TCR, on the surface of naive CD4(+) T cells. We found that diets enriched primarily in saturated fatty acids increased TCR nanoscale clustering to a level usually seen only on activated cells. Diets enriched in monounsaturated or n-3 polyunsaturated fatty acids had no effect on TCR clustering. Also none of the high fat diets affected TCR clustering on the micrometer scale. Furthermore, the effect of the diets was similar in young and middle aged mice. Our data establish proof-of-principle that TCR nanoscale clustering is sensitive to the composition of dietary fat.
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MESH Headings
- Animals
- CD4-Positive T-Lymphocytes/metabolism
- Diet, High-Fat
- Fatty Acids/metabolism
- Fatty Acids, Monounsaturated/metabolism
- Fatty Acids, Omega-3/metabolism
- Mice
- Mice, Transgenic
- Protein Multimerization
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Spectrum Analysis/methods
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Affiliation(s)
- Saame Raza Shaikh
- Department of Biochemistry & Molecular Biology, East Carolina Diabetes & Obesity Institute, East Carolina University, 600 Moye Blvd, Greenville, NC 27834, USA.
| | - Sarah Boyle
- Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Michael Edidin
- Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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27
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Koffman JS, Arnspang EC, Marlar S, Nejsum LN. Opposing Effects of cAMP and T259 Phosphorylation on Plasma Membrane Diffusion of the Water Channel Aquaporin-5 in Madin-Darby Canine Kidney Cells. PLoS One 2015. [PMID: 26218429 PMCID: PMC4517861 DOI: 10.1371/journal.pone.0133324] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Aquaporin-5 (AQP5) facilitates passive water transport in glandular epithelia in response to secretory stimuli via intracellular pathways involving calcium release, cAMP and protein kinase A (PKA). In epithelial plasma membranes, AQP5 may be acutely regulated to facilitate water transport in response to physiological stimuli by changes in protein modifications, interactions with proteins and lipids, nanoscale membrane domain organization, and turnover rates. Such regulatory mechanisms could potentially be associated with alteration of diffusion behavior, possibly resulting in a change in the plasma membrane diffusion coefficient of AQP5. We aimed to test the short-term regulatory effects of the above pathways, by measuring lateral diffusion of AQP5 and an AQP5 phospho-mutant, T259A, using k-space Image Correlation Spectroscopy of quantum dot- and EGFP-labeled AQP5. Elevated cAMP and PKA inhibition significantly decreased lateral diffusion of AQP5, whereas T259A mutation showed opposing effects; slowing diffusion without stimulation and increasing diffusion to basal levels after cAMP elevation. Thus, lateral diffusion of AQP5 is significantly regulated by cAMP, PKA, and T259 phosphorylation, which could be important for regulating water flow in glandular secretions.
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Affiliation(s)
- Jennifer S. Koffman
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Eva C. Arnspang
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Saw Marlar
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Lene N. Nejsum
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
- * E-mail:
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28
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Wiseman PW. Image correlation spectroscopy: principles and applications. Cold Spring Harb Protoc 2015; 2015:336-48. [PMID: 25834267 DOI: 10.1101/pdb.top086124] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Image correlation spectroscopy (ICS) was developed as the imaging analog of fluorescence correlation spectroscopy. Using standard fluorescence microscopy image series as input, different versions of ICS can be used to extract parameters on the molecular transport properties (diffusion and flow) and oligomerization state for fluorescently labeled species in cells. This review introduces the various forms of spatial and temporal ICS and discusses application of these methods to reveal properties of the biomolecules that can be measured from standard fluorescence image time series sampled from cells and neurons.
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29
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Pandžić E, Rossy J, Gaus K. Tracking molecular dynamics without tracking: image correlation of photo-activation microscopy. Methods Appl Fluoresc 2015; 3:014006. [PMID: 29148482 DOI: 10.1088/2050-6120/3/1/014006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Measuring protein dynamics in the plasma membrane can provide insights into the mechanisms of receptor signaling and other cellular functions. To quantify protein dynamics on the single molecule level over the entire cell surface, sophisticated approaches such as single particle tracking (SPT), photo-activation localization microscopy (PALM) and fluctuation-based analysis have been developed. However, analyzing molecular dynamics of fluorescent particles with intermittent excitation and low signal-to-noise ratio present at high densities has remained a challenge. We overcame this problem by applying spatio-temporal image correlation spectroscopy (STICS) analysis to photo-activated (PA) microscopy time series. In order to determine under which imaging conditions this approach is valid, we simulated PA images of diffusing particles in a homogeneous environment and varied photo-activation, reversible blinking and irreversible photo-bleaching rates. Further, we simulated data with high particle densities that populated mobile objects (such as adhesions and vesicles) that often interfere with STICS and fluctuation-based analysis. We demonstrated in experimental measurements that the diffusion coefficient of the epidermal growth factor receptor (EGFR) fused to PAGFP in live COS-7 cells can be determined in the plasma membrane and revealed differences in the time-dependent diffusion maps between wild-type and mutant Lck in activated T cells. In summary, we have developed a new analysis approach for live cell photo-activation microscopy data based on image correlation spectroscopy to quantify the spatio-temporal dynamics of single proteins.
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Affiliation(s)
- Elvis Pandžić
- ARC Centre for Advanced Molecular Imaging, Australian Centre for NanoMedicine University of New South Wales Australia, Sydney, NSW, Australia
| | - Jérémie Rossy
- ARC Centre for Advanced Molecular Imaging, Australian Centre for NanoMedicine University of New South Wales Australia, Sydney, NSW, Australia
| | - Katharina Gaus
- ARC Centre for Advanced Molecular Imaging, Australian Centre for NanoMedicine University of New South Wales Australia, Sydney, NSW, Australia
- Lowy Cancer Research Centre, Centre for Vascular Research Level 3, Kensington, NSW, Australia
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30
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Abstract
Systems biology has recently achieved significant success in the understanding of complex interconnected phenomena such as cell polarity and migration. In this context, the definition of systems biology has come to encompass the integration of quantitative measurements with sophisticated modeling approaches. This article will review recent progress in live cell imaging technologies that have expanded the possibilities of quantitative in vivo measurements, particularly in regards to molecule counting and quantitative measurements of protein concentration and dynamics. These methods have gained and continue to gain popularity with the biological community. In general, we will discuss three broad categories: protein interactions, protein quantitation, and protein dynamics.
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Affiliation(s)
- Sarah E Smith
- a Stowers Institute for Medical Research ; Kansas City , MO USA
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Marlar S, Arnspang EC, Pedersen GA, Koffman JS, Nejsum LN. Measuring localization and diffusion coefficients of basolateral proteins in lateral versus basal membranes using functionalized substrates and kICS analysis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2404-11. [DOI: 10.1016/j.bbamem.2014.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 06/03/2014] [Accepted: 06/09/2014] [Indexed: 11/17/2022]
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Arnspang EC, Koffman JS, Marlar S, Wiseman PW, Nejsum LN. Easy measurement of diffusion coefficients of EGFP-tagged plasma membrane proteins using k-Space Image Correlation Spectroscopy. J Vis Exp 2014. [PMID: 24893770 DOI: 10.3791/51074] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Lateral diffusion and compartmentalization of plasma membrane proteins are tightly regulated in cells and thus, studying these processes will reveal new insights to plasma membrane protein function and regulation. Recently, k-Space Image Correlation Spectroscopy (kICS)(1) was developed to enable routine measurements of diffusion coefficients directly from images of fluorescently tagged plasma membrane proteins, that avoided systematic biases introduced by probe photophysics. Although the theoretical basis for the analysis is complex, the method can be implemented by nonexperts using a freely available code to measure diffusion coefficients of proteins. kICS calculates a time correlation function from a fluorescence microscopy image stack after Fourier transformation of each image to reciprocal (k-) space. Subsequently, circular averaging, natural logarithm transform and linear fits to the correlation function yields the diffusion coefficient. This paper provides a step-by-step guide to the image analysis and measurement of diffusion coefficients via kICS. First, a high frame rate image sequence of a fluorescently labeled plasma membrane protein is acquired using a fluorescence microscope. Then, a region of interest (ROI) avoiding intracellular organelles, moving vesicles or protruding membrane regions is selected. The ROI stack is imported into a freely available code and several defined parameters (see Method section) are set for kICS analysis. The program then generates a "slope of slopes" plot from the k-space time correlation functions, and the diffusion coefficient is calculated from the slope of the plot. Below is a step-by-step kICS procedure to measure the diffusion coefficient of a membrane protein using the renal water channel aquaporin-3 tagged with EGFP as a canonical example.
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Affiliation(s)
- Eva C Arnspang
- Institute of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center, Aarhus University;
| | - Jennifer S Koffman
- Institute of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center, Aarhus University
| | - Saw Marlar
- Institute of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center, Aarhus University
| | | | - Lene N Nejsum
- Institute of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center, Aarhus University;
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Rinehart M, Grab S, Rohan L, Katz D, Wax A. Analysis of vaginal microbicide film hydration kinetics by quantitative imaging refractometry. PLoS One 2014; 9:e95005. [PMID: 24736376 PMCID: PMC3988224 DOI: 10.1371/journal.pone.0095005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 03/22/2014] [Indexed: 11/21/2022] Open
Abstract
We have developed a quantitative imaging refractometry technique, based on holographic phase microscopy, as a tool for investigating microscopic structural changes in water-soluble polymeric materials. Here we apply the approach to analyze the structural degradation of vaginal topical microbicide films due to water uptake. We implemented transmission imaging of 1-mm diameter film samples loaded into a flow chamber with a 1.5×2 mm field of view. After water was flooded into the chamber, interference images were captured and analyzed to obtain high resolution maps of the local refractive index and subsequently the volume fraction and mass density of film material at each spatial location. Here, we compare the hydration dynamics of a panel of films with varying thicknesses and polymer compositions, demonstrating that quantitative imaging refractometry can be an effective tool for evaluating and characterizing the performance of candidate microbicide film designs for anti-HIV drug delivery.
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Affiliation(s)
- Matthew Rinehart
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- * E-mail:
| | - Sheila Grab
- University of Pittsburgh, School of Pharmacy, Magee Womens Research Institute, Pittsburgh, Pennsylvania, United States of America
| | - Lisa Rohan
- University of Pittsburgh, School of Pharmacy, Magee Womens Research Institute, Pittsburgh, Pennsylvania, United States of America
| | - David Katz
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- Department of Obstetrics and Gynecology, Duke University, Durham, North Carolina, United States of America
| | - Adam Wax
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
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Brandão HB, Sangji H, Pandžić E, Bechstedt S, Brouhard GJ, Wiseman PW. Measuring ligand–receptor binding kinetics and dynamics using k-space image correlation spectroscopy. Methods 2014; 66:273-82. [DOI: 10.1016/j.ymeth.2013.07.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 07/25/2013] [Accepted: 07/27/2013] [Indexed: 10/26/2022] Open
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Marlar S, Arnspang EC, Koffman JS, Løcke EM, Christensen BM, Nejsum LN. Elevated cAMP increases aquaporin-3 plasma membrane diffusion. Am J Physiol Cell Physiol 2014; 306:C598-606. [PMID: 24452376 DOI: 10.1152/ajpcell.00132.2013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Regulated urine concentration takes place in the renal collecting duct upon arginine vasopressin (AVP) stimulation, where subapical vesicles containing aquaporin-2 (AQP2) are inserted into the apical membrane instantly increasing water reabsorption and urine concentration. The reabsorped water exits via basolateral AQP3 and AQP4. Upon long-term stimulation with AVP or during thirst, expression levels of both AQP2 and AQP3 are increased; however, there is so far no evidence for short-term AVP regulation of AQP3 or AQP4. To facilitate the increase in transepithelial water transport, AQP3 may be short-term regulated via changes in protein-protein interactions, incorporation into lipid rafts, and/or changes in steady-state turnover, which could result in changes in the diffusion behavior of AQP3. Thus we measured AQP3 diffusion coefficients upon stimulation with the AVP mimic forskolin to reveal if AQP3 could be short-term regulated by AVP. k-Space image correlation spectroscopy (kICS) analysis of time-lapse image sequences of basolateral enhanced green fluorescent protein-tagged AQP3 (AQP3-EGFP) revealed that the forskolin-mediated elevation of cAMP increased the diffusion coefficient by 58% from 0.0147 ± 0.0082 μm(2)/s (control) to 0.0232 ± 0.0085 μm(2)/s (forskolin, P < 0.05). Quantum dot-conjugated antibody labeling also revealed a significant increase in AQP3 diffusion upon forskolin treatment by 44% [0.0104 ± 0.0040 μm(2)/s (control) vs. 0.0150 ± 0.0016 μm(2)/s (forskolin, P < 0.05)]. Immunoelectron microscopy showed no obvious difference in AQP3-EGFP expression levels or localization in the plasma membrane upon forskolin stimulation. Thus AQP3-EGFP diffusion is altered upon increased cAMP, which may correspond to basolateral adaptations in response to the increased apical water readsorption.
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Affiliation(s)
- Saw Marlar
- Institute of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark; and
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36
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Bag N, Wohland T. Imaging fluorescence fluctuation spectroscopy: new tools for quantitative bioimaging. Annu Rev Phys Chem 2013; 65:225-48. [PMID: 24328446 DOI: 10.1146/annurev-physchem-040513-103641] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fluorescence fluctuation spectroscopy (FFS) techniques provide information at the single-molecule level with excellent time resolution. Usually applied at a single spot in a sample, they have been recently extended into imaging formats, referred to as imaging FFS. They provide spatial information at the optical diffraction limit and temporal information in the microsecond to millisecond range. This review provides an overview of the different modalities in which imaging FFS techniques have been implemented and discusses present imaging FFS capabilities and limitations. A combination of imaging FFS and nanoscopy would allow one to record information with the detailed spatial information of nanoscopy, which is ∼20 nm and limited only by fluorophore size and labeling density, and the time resolution of imaging FFS, limited by the fluorescence lifetime. This combination would provide new insights into biological events by providing spatiotemporal resolution at unprecedented levels.
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Affiliation(s)
- Nirmalya Bag
- Departments of Biological Sciences and Chemistry, and NUS Center for Bio-Imaging Sciences (CBIS), National University of Singapore, 117557 Singapore; ,
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37
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Arnspang EC, Schwartzentruber J, Clausen MP, Wiseman PW, Lagerholm BC. Bridging the gap between single molecule and ensemble methods for measuring lateral dynamics in the plasma membrane. PLoS One 2013; 8:e78096. [PMID: 24324577 PMCID: PMC3850922 DOI: 10.1371/journal.pone.0078096] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 09/17/2013] [Indexed: 11/22/2022] Open
Abstract
The lateral dynamics of proteins and lipids in the mammalian plasma membrane are heterogeneous likely reflecting both a complex molecular organization and interactions with other macromolecules that reside outside the plane of the membrane. Several methods are commonly used for characterizing the lateral dynamics of lipids and proteins. These experimental and data analysis methods differ in equipment requirements, labeling complexities, and further oftentimes give different results. It would therefore be very convenient to have a single method that is flexible in the choice of fluorescent label and labeling densities from single molecules to ensemble measurements, that can be performed on a conventional wide-field microscope, and that is suitable for fast and accurate analysis. In this work we show that k-space image correlation spectroscopy (kICS) analysis, a technique which was originally developed for analyzing lateral dynamics in samples that are labeled at high densities, can also be used for fast and accurate analysis of single molecule density data of lipids and proteins labeled with quantum dots (QDs). We have further used kICS to investigate the effect of the label size and by comparing the results for a biotinylated lipid labeled at high densities with Atto647N-strepatvidin (sAv) or sparse densities with sAv-QDs. In this latter case, we see that the recovered diffusion rate is two-fold greater for the same lipid and in the same cell-type when labeled with Atto647N-sAv as compared to sAv-QDs. This data demonstrates that kICS can be used for analysis of single molecule data and furthermore can bridge between samples with a labeling densities ranging from single molecule to ensemble level measurements.
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Affiliation(s)
- Eva C. Arnspang
- Department of Physics, Chemistry and Pharmacy, MEMPHYS-Center for Biomembrane Physics & DaMBIC – Danish Molecular Biomedical Imaging Center, University of Southern Denmark, Odense, Denmark
| | | | - Mathias P. Clausen
- Department of Physics, Chemistry and Pharmacy, MEMPHYS-Center for Biomembrane Physics & DaMBIC – Danish Molecular Biomedical Imaging Center, University of Southern Denmark, Odense, Denmark
| | - Paul W. Wiseman
- Department of Physics and Department of Chemistry, McGill University, Montreal, Canada
| | - B. Christoffer Lagerholm
- Department of Physics, Chemistry and Pharmacy, MEMPHYS-Center for Biomembrane Physics & DaMBIC – Danish Molecular Biomedical Imaging Center, University of Southern Denmark, Odense, Denmark
- * E-mail:
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Potvin-Trottier L, Chen L, Horwitz AR, Wiseman PW. A nu-space for ICS: characterization and application to measure protein transport in live cells. NEW JOURNAL OF PHYSICS 2013; 15:10.1088/1367-2630/15/8/085006. [PMID: 24223019 PMCID: PMC3821402 DOI: 10.1088/1367-2630/15/8/085006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We introduce a new generalized theoretical framework for image correlation spectroscopy (ICS). Using this framework, we extend the ICS method in time-frequency (ν, nu) space to map molecular flow of fluorescently tagged proteins in individual living cells. Even in the presence of a dominant immobile population of fluorescent molecules, nu-space ICS (nICS) provides an unbiased velocity measurement, as well as the diffusion coefficient of the flow, without requiring filtering. We also develop and characterize a tunable frequency-filter for STICS that allows quantification of the density, the diffusion coefficient and the velocity of biased diffusion. We show that the techniques are accurate over a wide range of parameter space in computer simulation. We then characterize the retrograde flow of adhesion proteins (α6- and αLβ2-GFP integrins and mCherry-paxillin) in CHO.B2 cells plated on laminin and ICAM ligands respectively. STICS with a tunable frequency filter, in conjunction with nICS, measures two new transport parameters, the density and transport bias coefficient (a measure of the diffusive character of a flow/biased diffusion), showing that molecular flow in this cell system has a significant diffusive component. Our results suggest that the integrinligand interaction, along with the internal myosin-motor generated force, varies for different integrin-ligand pairs, consistent with previous results.
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39
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Perica K, Bieler JG, Edidin M, Schneck J. Modulation of MHC binding by lateral association of TCR and coreceptor. Biophys J 2013. [PMID: 23199917 DOI: 10.1016/j.bpj.2012.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The structure of a T cell receptor (TCR) and its affinity for cognate antigen are fixed, but T cells regulate binding sensitivity through changes in lateral membrane organization. TCR microclusters formed upon antigen engagement participate in downstream signaling. Microclusters are also found 3-4 days after activation, leading to enhanced antigen binding upon rechallenge. However, others have found an almost complete loss of antigen binding four days after T cell activation, when TCR clusters are present. To resolve these contradictory results, we compared binding of soluble MHC-Ig dimers by transgenic T cells stimulated with a high (100 μM) or low (100 fM) dose of cognate antigen. Cells activated by a high dose of peptide bound sixfold lower amounts of CD8-dependent ligand K(b)-SIY than cells activated by a low dose of MHC/peptide. In contrast, both cell populations bound a CD8-independent ligand L(d)-QL9 equally well. Consistent with the differences between binding of CD8-dependent and CD8-independent peptide/MHC, Förster resonance energy transfer (FRET) measurements of molecular proximity reported little nanoscale association of TCR with CD8 (16 FRET units) compared to their association on cells stimulated by low antigen dose (62 FRET units). Loss of binding induced by changes in lateral organization of TCR and CD8 may serve as a regulatory mechanism to avoid excessive inflammation and immunopathology in response to aggressive infection.
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Affiliation(s)
- Karlo Perica
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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40
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Michalet X, Colyer RA, Scalia G, Ingargiola A, Lin R, Millaud JE, Weiss S, Siegmund OHW, Tremsin AS, Vallerga JV, Cheng A, Levi M, Aharoni D, Arisaka K, Villa F, Guerrieri F, Panzeri F, Rech I, Gulinatti A, Zappa F, Ghioni M, Cova S. Development of new photon-counting detectors for single-molecule fluorescence microscopy. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120035. [PMID: 23267185 PMCID: PMC3538434 DOI: 10.1098/rstb.2012.0035] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Two optical configurations are commonly used in single-molecule fluorescence microscopy: point-like excitation and detection to study freely diffusing molecules, and wide field illumination and detection to study surface immobilized or slowly diffusing molecules. Both approaches have common features, but also differ in significant aspects. In particular, they use different detectors, which share some requirements but also have major technical differences. Currently, two types of detectors best fulfil the needs of each approach: single-photon-counting avalanche diodes (SPADs) for point-like detection, and electron-multiplying charge-coupled devices (EMCCDs) for wide field detection. However, there is room for improvements in both cases. The first configuration suffers from low throughput owing to the analysis of data from a single location. The second, on the other hand, is limited to relatively low frame rates and loses the benefit of single-photon-counting approaches. During the past few years, new developments in point-like and wide field detectors have started addressing some of these issues. Here, we describe our recent progresses towards increasing the throughput of single-molecule fluorescence spectroscopy in solution using parallel arrays of SPADs. We also discuss our development of large area photon-counting cameras achieving subnanosecond resolution for fluorescence lifetime imaging applications at the single-molecule level.
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Affiliation(s)
- X Michalet
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095-1547, USA.
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41
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Wiseman PW. Image correlation spectroscopy: mapping correlations in space, time, and reciprocal space. Methods Enzymol 2013; 518:245-67. [PMID: 23276542 DOI: 10.1016/b978-0-12-388422-0.00010-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This chapter presents an overview of two recent implementations of image correlation spectroscopy (ICS). The background theory is presented for spatiotemporal image correlation spectroscopy and image cross-correlation spectroscopy (STICS and STICCS, respectively) as well as k-(reciprocal) space image correlation spectroscopy (kICS). An introduction to the background theory is followed by sections outlining procedural aspects for properly implementing STICS, STICCS, and kICS. These include microscopy image collection, sampling in space and time, sample and fluorescent probe requirements, signal to noise, and background considerations that are all required to properly implement the ICS methods. Finally, procedural steps for immobile population removal and actual implementation of the ICS analysis programs to fluorescence microscopy image time stacks are described.
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Affiliation(s)
- Paul W Wiseman
- Department of Physics, McGill University, Montreal, Quebec, Canada.
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43
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Toplak T, Pandzic E, Chen L, Vicente-Manzanares M, Horwitz AR, Wiseman PW. STICCS reveals matrix-dependent adhesion slipping and gripping in migrating cells. Biophys J 2012; 103:1672-82. [PMID: 23083710 DOI: 10.1016/j.bpj.2012.08.060] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 08/16/2012] [Accepted: 08/28/2012] [Indexed: 12/16/2022] Open
Abstract
Two-color spatio-temporal image cross-correlation spectroscopy (STICCS) is a new, to our knowledge, image analysis method that calculates space-time autocorrelation and cross-correlation functions from fluorescence intensity fluctuations. STICCS generates cellular flow and diffusion maps that reveal interactions and cotransport of two distinct molecular species labeled with different fluorophores. Here we use computer simulations to map the capabilities and limitations of STICCS for measurements in complex heterogeneous environments containing micro- and macrostructures. We then use STICCS to analyze the co-flux of adhesion components in migrating cells imaged using total internal reflection fluorescence microscopy. The data reveal a robust, time-dependent co-fluxing of certain integrins and paxillin in adhesions in protrusions when they pause, and in adhesions that are sliding and disassembling, demonstrating that the molecules in these adhesions move as a complex. In these regions, both α6β1- or αLβ2-integrins, expressed in CHO.B2 cells, co-flux with paxillin; an analogous cotransport was seen for α6β1-integrin and α-actinin in U2OS. This contrasts with the behavior of the α5β1-integrin and paxillin, which do not co-flux. Our results clearly show that integrins can move in complexes with adhesion proteins in protrusions that are retracting.
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Affiliation(s)
- Tim Toplak
- Department of Physics, McGill University, Montréal, Québec, Canada
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44
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Honerkamp-Smith AR, Machta BB, Keller SL. Experimental observations of dynamic critical phenomena in a lipid membrane. PHYSICAL REVIEW LETTERS 2012; 108:265702. [PMID: 23004996 PMCID: PMC3722069 DOI: 10.1103/physrevlett.108.265702] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Indexed: 05/04/2023]
Abstract
Near a critical point, the time scale of thermally induced fluctuations diverges in a manner determined by the dynamic universality class. Experiments have verified predicted three-dimensional dynamic critical exponents in many systems, but similar experiments in two dimensions have been lacking for the case of conserved order parameter. Here we analyze the time-dependent correlation functions of a quasi-two-dimensional lipid bilayer in water to show that its critical dynamics agree with a recently predicted universality class. In particular, the effective dynamic exponent z(eff) crosses over from ~2 to ~3 as the correlation length of fluctuations exceeds a hydrodynamic length set by the membrane and bulk viscosities.
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Affiliation(s)
| | | | - Sarah L. Keller
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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45
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Boyle S, Kolin DL, Bieler JG, Schneck JP, Wiseman PW, Edidin M. Quantum dot fluorescence characterizes the nanoscale organization of T cell receptors for antigen. Biophys J 2012; 101:L57-9. [PMID: 22261075 DOI: 10.1016/j.bpj.2011.10.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 09/19/2011] [Accepted: 10/13/2011] [Indexed: 11/20/2022] Open
Abstract
Changes in the clustering of surface receptors modulate cell responses to ligands. Hence, global measures of receptor clustering can be useful for characterizing cell states. Using T cell receptor for antigen as an example, we show that k-space image correlation spectroscopy of quantum dots blinking detects T cell receptor clusters on a scale of tens of nanometers and reports changes in clustering after T cell activation. Our results offer a general approach to the global analysis of lateral organization and receptor clustering in single cells, and can thus be applied when the cell type of interest is rare.
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Affiliation(s)
- Sarah Boyle
- Biology Department, The Johns Hopkins University, Baltimore, Maryland, USA
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46
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Zhou C, Slaughter BD, Unruh JR, Eldakak A, Rubinstein B, Li R. Motility and segregation of Hsp104-associated protein aggregates in budding yeast. Cell 2012; 147:1186-96. [PMID: 22118470 DOI: 10.1016/j.cell.2011.11.002] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 08/03/2011] [Accepted: 11/03/2011] [Indexed: 12/12/2022]
Abstract
During yeast cell division, aggregates of damaged proteins are segregated asymmetrically between the bud and the mother. It is thought that protein aggregates are cleared from the bud via actin cable-based retrograde transport toward the mother and that Bni1p formin regulates this transport. Here, we examined the dynamics of Hsp104-associated protein aggregates by video microscopy, particle tracking, and image correlation analysis. We show that protein aggregates undergo random walk without directional bias. Clearance of heat-induced aggregates from the bud does not depend on formin proteins but occurs mostly through dissolution via Hsp104p chaperon. Aggregates formed naturally in aged cells also exhibit random walk but do not dissolve during observation. Although our data do not disagree with a role for actin or cell polarity in aggregate segregation, modeling suggests that their asymmetric inheritance can be a predictable outcome of aggregates' slow diffusion and the geometry of yeast cells.
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Affiliation(s)
- Chuankai Zhou
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
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47
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Elson EL. Fluorescence correlation spectroscopy: past, present, future. Biophys J 2011; 101:2855-70. [PMID: 22208184 PMCID: PMC3244056 DOI: 10.1016/j.bpj.2011.11.012] [Citation(s) in RCA: 284] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 11/09/2011] [Accepted: 11/10/2011] [Indexed: 11/17/2022] Open
Abstract
In recent years fluorescence correlation spectroscopy (FCS) has become a routine method for determining diffusion coefficients, chemical rate constants, molecular concentrations, fluorescence brightness, triplet state lifetimes, and other molecular parameters. FCS measures the spatial and temporal correlation of individual molecules with themselves and so provides a bridge between classical ensemble and contemporary single-molecule measurements. It also provides information on concentration and molecular number fluctuations for nonlinear reaction systems that complement single-molecule measurements. Typically implemented on a fluorescence microscope, FCS samples femtoliter volumes and so is especially useful for characterizing small dynamic systems such as biological cells. In addition to its practical utility, however, FCS provides a window on mesoscopic systems in which fluctuations from steady states not only provide the basis for the measurement but also can have important consequences for the behavior and evolution of the system. For example, a new and potentially interesting field for FCS studies could be the study of nonequilibrium steady states, especially in living cells.
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Affiliation(s)
- Elliot L Elson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA.
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48
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Abstract
Molecular diffusion and transport processes are fundamental in physical, chemical, and biological systems. Current approaches to measuring molecular transport in cells and tissues based on perturbation methods, e.g., fluorescence recovery after photobleaching, are invasive; single-point fluctuation correlation methods are local; and single-particle tracking requires the observation of isolated particles for relatively long periods of time. We discuss here the detection of molecular transport by exploiting spatiotemporal correlations measured among points at large distances (>1 μm). We illustrate the evolution of the conceptual framework that started with single-point fluorescence fluctuation analysis based on the transit of fluorescent molecules through a small volume of illumination. This idea has evolved to include the measurement of fluctuations at many locations in the sample using microscopy imaging methods. Image fluctuation analysis has become a rich and powerful technique that can be used to extract information about the spatial distribution of molecular concentration and transport in cells and tissues.
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Affiliation(s)
- Michelle A Digman
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA
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49
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Gröner N, Capoulade J, Cremer C, Wachsmuth M. Measuring and imaging diffusion with multiple scan speed image correlation spectroscopy. OPTICS EXPRESS 2010; 18:21225-37. [PMID: 20941019 DOI: 10.1364/oe.18.021225] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The intracellular mobility of biomolecules is determined by transport and diffusion as well as molecular interactions and is crucial for many processes in living cells. Methods of fluorescence microscopy like confocal laser scanning microscopy (CLSM) can be used to characterize the intracellular distribution of fluorescently labeled biomolecules. Fluorescence correlation spectroscopy (FCS) is used to describe diffusion, transport and photo-physical processes quantitatively. As an alternative to FCS, spatially resolved measurements of mobilities can be implemented using a CLSM by utilizing the spatio-temporal information inscribed into the image by the scan process, referred to as raster image correlation spectroscopy (RICS). Here we present and discuss an extended approach, multiple scan speed image correlation spectroscopy (msICS), which benefits from the advantages of RICS, i.e. the use of widely available instrumentation and the extraction of spatially resolved mobility information, without the need of a priori knowledge of diffusion properties. In addition, msICS covers a broad dynamic range, generates correlation data comparable to FCS measurements, and allows to derive two-dimensional maps of diffusion coefficients. We show the applicability of msICS to fluorophores in solution and to free EGFP in living cells.
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Affiliation(s)
- Nadine Gröner
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
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50
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Nanoscale Techniques for Biomarker Quantification. Biomarkers 2010. [DOI: 10.1002/9780470918562.ch18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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