1
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Nguyen TD, Chen YI, Nguyen AT, Chen LH, Yonas S, Litvinov M, He Y, Kuo YA, Hong S, Rylander HG, Yeh HC. Multiplexed imaging in live cells using pulsed interleaved excitation spectral FLIM. OPTICS EXPRESS 2024; 32:3290-3307. [PMID: 38297554 PMCID: PMC11018333 DOI: 10.1364/oe.505667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/30/2023] [Accepted: 12/30/2023] [Indexed: 02/02/2024]
Abstract
Multiplexed fluorescence detection has become increasingly important in the fields of biosensing and bioimaging. Although a variety of excitation/detection optical designs and fluorescence unmixing schemes have been proposed to allow for multiplexed imaging, rapid and reliable differentiation and quantification of multiple fluorescent species at each imaging pixel is still challenging. Here we present a pulsed interleaved excitation spectral fluorescence lifetime microscopic (PIE-sFLIM) system that can simultaneously image six fluorescent tags in live cells in a single hyperspectral snapshot. Using an alternating pulsed laser excitation scheme at two different wavelengths and a synchronized 16-channel time-resolved spectral detector, our PIE-sFLIM system can effectively excite multiple fluorophores and collect their emission over a broad spectrum for analysis. Combining our system with the advanced live-cell labeling techniques and the lifetime/spectral phasor analysis, our PIE-sFLIM approach can well unmix the fluorescence of six fluorophores acquired in a single measurement, thus improving the imaging speed in live-specimen investigation.
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Affiliation(s)
- Trung Duc Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Yuan-I Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Anh-Thu Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Limin H. Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Siem Yonas
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Mitchell Litvinov
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Yujie He
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Yu-An Kuo
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Soonwoo Hong
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - H. Grady Rylander
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
- Texas Materials Institute, University of Texas at Austin, Austin, TX, USA
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2
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Coucke Q, Parveen N, Fernández GS, Qian C, Hofkens J, Debyser Z, Hendrix J. Particle-based phasor-FLIM-FRET resolves protein-protein interactions inside single viral particles. BIOPHYSICAL REPORTS 2023; 3:100122. [PMID: 37649577 PMCID: PMC10463199 DOI: 10.1016/j.bpr.2023.100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/07/2023] [Indexed: 09/01/2023]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) is a popular modality to create additional contrast in fluorescence images. By carefully analyzing pixel-based nanosecond lifetime patterns, FLIM allows studying complex molecular populations. At the single-molecule or single-particle level, however, image series often suffer from low signal intensities per pixel, rendering it difficult to quantitatively disentangle different lifetime species, such as during Förster resonance energy transfer (FRET) analysis in the presence of a significant donor-only fraction. In this article we investigate whether an object localization strategy and the phasor approach to FLIM have beneficial effects when carrying out FRET analyses of single particles. Using simulations, we first showed that an average of ∼300 photons, spread over the different pixels encompassing single fluorescing particles and without background, is enough to determine a correct phasor signature (SD < 5% for a 4-ns lifetime). For immobilized single- or double-labeled dsDNA molecules, we next validated that particle-based phasor-FLIM-FRET readily allows estimating fluorescence lifetimes and FRET from single molecules. Thirdly, we applied particle-based phasor-FLIM-FRET to investigate protein-protein interactions in subdiffraction HIV-1 viral particles. To do this, we first quantitatively compared the fluorescence brightness, lifetime, and photostability of different popular fluorescent protein-based FRET probes when genetically fused to the HIV-1 integrase enzyme in viral particles, and conclude that eGFP, mTurquoise2, and mScarlet perform best. Finally, for viral particles coexpressing FRET-donor/acceptor-labeled IN, we determined the absolute FRET efficiency of IN oligomers. Available in a convenient open-source graphical user interface, we believe that particle-based phasor-FLIM-FRET is a promising tool to provide detailed insights in samples suffering from low overall signal intensities.
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Affiliation(s)
- Quinten Coucke
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Nagma Parveen
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Guillermo Solís Fernández
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- UFIEC, National Institute of Health Carlos III, Madrid, Spain
| | - Chen Qian
- Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science Munich (CIPSM), and Nanosystems Initiative Munich (NIM), Ludwig Maximilians-Universität München, Munich, Germany
| | - Johan Hofkens
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jelle Hendrix
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute, Hasselt University, Hasselt, Belgium
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3
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Dynamics of HIV-1 Gag Processing as Revealed by Fluorescence Lifetime Imaging Microscopy and Single Virus Tracking. Viruses 2022; 14:v14020340. [PMID: 35215933 PMCID: PMC8874525 DOI: 10.3390/v14020340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/04/2022] [Accepted: 02/06/2022] [Indexed: 12/04/2022] Open
Abstract
The viral polyprotein Gag plays a central role for HIV-1 assembly, release and maturation. Proteolytic processing of Gag by the viral protease is essential for the structural rearrangements that mark the transition from immature to mature, infectious viruses. The timing and kinetics of Gag processing are not fully understood. Here, fluorescence lifetime imaging microscopy and single virus tracking are used to follow Gag processing in nascent HIV-1 particles in situ. Using a Gag polyprotein labelled internally with eCFP, we show that proteolytic release of the fluorophore from Gag is accompanied by an increase in its fluorescence lifetime. By tracking nascent virus particles in situ and analyzing the intensity and fluorescence lifetime of individual traces, we detect proteolytic cleavage of eCFP from Gag in a subset (6.5%) of viral particles. This suggests that for the majority of VLPs, Gag processing occurs with a delay after particle assembly.
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4
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Dunsing V, Petrich A, Chiantia S. Multicolor fluorescence fluctuation spectroscopy in living cells via spectral detection. eLife 2021; 10:e69687. [PMID: 34494547 PMCID: PMC8545396 DOI: 10.7554/elife.69687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/07/2021] [Indexed: 01/20/2023] Open
Abstract
Signaling pathways in biological systems rely on specific interactions between multiple biomolecules. Fluorescence fluctuation spectroscopy provides a powerful toolbox to quantify such interactions directly in living cells. Cross-correlation analysis of spectrally separated fluctuations provides information about intermolecular interactions but is usually limited to two fluorophore species. Here, we present scanning fluorescence spectral correlation spectroscopy (SFSCS), a versatile approach that can be implemented on commercial confocal microscopes, allowing the investigation of interactions between multiple protein species at the plasma membrane. We demonstrate that SFSCS enables cross-talk-free cross-correlation, diffusion, and oligomerization analysis of up to four protein species labeled with strongly overlapping fluorophores. As an example, we investigate the interactions of influenza A virus (IAV) matrix protein 2 with two cellular host factors simultaneously. We furthermore apply raster spectral image correlation spectroscopy for the simultaneous analysis of up to four species and determine the stoichiometry of ternary IAV polymerase complexes in the cell nucleus.
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Affiliation(s)
- Valentin Dunsing
- Universität Potsdam, Institute of Biochemistry and BiologyPotsdamGermany
| | - Annett Petrich
- Universität Potsdam, Institute of Biochemistry and BiologyPotsdamGermany
| | - Salvatore Chiantia
- Universität Potsdam, Institute of Biochemistry and BiologyPotsdamGermany
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5
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Fukushima R, Yamamoto J, Kinjo M. Empirical Bayes method using surrounding pixel information for number and brightness analysis. Biophys J 2021; 120:2156-2171. [PMID: 33812845 PMCID: PMC8390835 DOI: 10.1016/j.bpj.2021.03.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 03/13/2021] [Accepted: 03/23/2021] [Indexed: 11/26/2022] Open
Abstract
Number and brightness (N&B) analysis is useful for monitoring the spatial distribution of the concentration and oligomeric state of fluorescently labeled proteins in cells. N&B analysis is based on the statistical analysis of fluorescence images by using the method of moments (MoM). Furthermore, N&B analysis can determine the particle number and particle brightness, which indicate the concentration and oligomeric state, respectively. However, the statistical accuracy and precision are limited in actual experiments with fluorescent proteins, owing to low excitation and the limited number of images. In this study, we applied maximum likelihood (ML) estimation and maximum a posteriori (MAP) estimation coupled with the empirical Bayes (EB) method (referred to as EB-MAP). In EB-MAP, we constructed a simple prior distribution for a pixel to utilize the information of the surrounding pixels. To evaluate the accuracy and precision of our method, we conducted simulations and experiments and compared the results of MoM, ML, and EB-MAP. The results showed that MoM estimated the particle number with many outliers. The outliers hampered the visibility of the spatial distribution and cellular structure. In contrast, EB-MAP suppressed the number of outliers and improved the visibility notably. The precision of EB-MAP was better by an order of magnitude in terms of particle number and 1.5 times better in terms of particle brightness compared with those of MoM. The proposed method (EB-MAP-N&B) is applicable to studies on fluorescence imaging and would aid in accurately recognizing changes in the concentration and oligomeric state in cells. Our results hold significant importance because quantifying the concentration and oligomeric state would contribute to the understanding of dynamic processes in molecular mechanism in cells.
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Affiliation(s)
- Ryosuke Fukushima
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Johtaro Yamamoto
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan; Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.
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6
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DE Mets R, Delon A, Balland M, Destaing O, Wang I. Dynamic range and background filtering in raster image correlation spectroscopy. J Microsc 2020; 279:123-138. [PMID: 32441342 DOI: 10.1111/jmi.12925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 05/04/2020] [Accepted: 05/18/2020] [Indexed: 11/28/2022]
Abstract
Raster-scan image correlation spectroscopy (RICS) enables researchers to measure molecular translational diffusion constants and concentrations from standard confocal laser scanning microscope images and is suitable for measuring a wide range of mobility, especially fast-diffusing molecules. However, as RICS analysis is based on the spatial autocorrelation function of fluorescence images, it is sensitive to the presence of fluorescent structures within the image. In this study, we investigate methods to filter out immobile or slow moving background structures and their impact on RICS results. Both the conventional moving-average subtraction-based method and cross-correlation subtraction-based method are rationalized and quantified. Simulated data and experimental measurements in living cells stress the importance of optimizing the temporal resolution of background filtering for reliable RICS measurements. Finally, the capacity of RICS analysis to separate two species is studied.
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Affiliation(s)
- R DE Mets
- Université Grenoble Alpes, CNRS, LIPhy, Grenoble, France.,Mechanobiology Institute, National University of Singapore, Singapore
| | - A Delon
- Université Grenoble Alpes, CNRS, LIPhy, Grenoble, France
| | - M Balland
- Université Grenoble Alpes, CNRS, LIPhy, Grenoble, France
| | - O Destaing
- Institute for Advanced Biosciences, Université Grenoble Alpes, Grenoble, France
| | - I Wang
- Université Grenoble Alpes, CNRS, LIPhy, Grenoble, France
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7
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Reissaus CA, Day KH, Mirmira RG, Dunn KW, Pavalko FM, Day RN. PIE-FLIM Measurements of Two Different FRET-Based Biosensor Activities in the Same Living Cells. Biophys J 2020; 118:1820-1829. [PMID: 32191861 DOI: 10.1016/j.bpj.2020.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/27/2020] [Accepted: 03/02/2020] [Indexed: 12/14/2022] Open
Abstract
We report the use of pulsed interleaved excitation (PIE)-fluorescence lifetime imaging microscopy (FLIM) to measure the activities of two different biosensor probes simultaneously in single living cells. Many genetically encoded biosensors rely on the measurement of Förster resonance energy transfer (FRET) to detect changes in biosensor conformation that accompany the targeted cell signaling event. One of the most robust ways of quantifying FRET is to measure changes in the fluorescence lifetime of the donor fluorophore using FLIM. The study of complex signaling networks in living cells demands the ability to track more than one of these cellular events at the same time. Here, we demonstrate how PIE-FLIM can separate and quantify the signals from different FRET-based biosensors to simultaneously measure changes in the activity of two cell signaling pathways in the same living cells in tissues. The imaging system described here uses selectable laser wavelengths and synchronized detection gating that can be tailored and optimized for each FRET pair. Proof-of-principle studies showing simultaneous measurement of cytosolic calcium and protein kinase A activity are shown, but the PIE-FLIM approach is broadly applicable to other signaling pathways.
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Affiliation(s)
- Christopher A Reissaus
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana; The Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kathleen H Day
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Raghavendra G Mirmira
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana; The Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kenneth W Dunn
- The Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana; Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Fredrick M Pavalko
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, Indiana; The Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, Indiana
| | - Richard N Day
- The Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana; Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, Indiana.
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8
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Longfils M, Smisdom N, Ameloot M, Rudemo M, Lemmens V, Fernández GS, Röding M, Lorén N, Hendrix J, Särkkä A. Raster Image Correlation Spectroscopy Performance Evaluation. Biophys J 2019; 117:1900-1914. [PMID: 31668746 PMCID: PMC7018992 DOI: 10.1016/j.bpj.2019.09.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/28/2019] [Accepted: 09/30/2019] [Indexed: 01/02/2023] Open
Abstract
Raster image correlation spectroscopy (RICS) is a fluorescence image analysis method for extracting the mobility, concentration, and stoichiometry of diffusing fluorescent molecules from confocal image stacks. The method works by calculating a spatial correlation function for each image and analyzing the average of those by model fitting. Rules of thumb exist for RICS image acquisitioning, yet a rigorous theoretical approach to predict the accuracy and precision of the recovered parameters has been lacking. We outline explicit expressions to reveal the dependence of RICS results on experimental parameters. In terms of imaging settings, we observed that a twofold decrease of the pixel size, e.g., from 100 to 50 nm, decreases the error on the translational diffusion constant (D) between three- and fivefold. For D = 1 μm2 s-1, a typical value for intracellular measurements, ∼25-fold lower mean-squared relative error was obtained when the optimal scan speed was used, although more drastic improvements were observed for other values of D. We proposed a slightly modified RICS calculation that allows correcting for the significant bias of the autocorrelation function at small (≪50 × 50 pixels) sizes of the region of interest. In terms of sample properties, at molecular brightness E = 100 kHz and higher, RICS data quality was sufficient using as little as 20 images, whereas the optimal number of frames for lower E scaled pro rata. RICS data quality was constant over the nM-μM concentration range. We developed a bootstrap-based confidence interval of D that outperformed the classical least-squares approach in terms of coverage probability of the true value of D. We validated the theory via in vitro experiments of enhanced green fluorescent protein at different buffer viscosities. Finally, we outline robust practical guidelines and provide free software to simulate the parameter effects on recovery of the diffusion coefficient.
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Affiliation(s)
- Marco Longfils
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.
| | - Nick Smisdom
- Stadius Centre for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, Leuven, Belgium; Advanced Optical Microscopy Centre, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Marcel Ameloot
- Advanced Optical Microscopy Centre, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Mats Rudemo
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Veerle Lemmens
- Advanced Optical Microscopy Centre, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium; Dynamic Bioimaging Lab, Hasselt University, Diepenbeek, Belgium; Molecular Imaging and Photonics, Chemistry Department, KU Leuven, Heverlee, Belgium
| | | | | | - Niklas Lorén
- RISE Bioscience and Materials, Gothenburg, Sweden; Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Jelle Hendrix
- Advanced Optical Microscopy Centre, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium; Dynamic Bioimaging Lab, Hasselt University, Diepenbeek, Belgium.
| | - Aila Särkkä
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
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9
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Connolly BM, Aragones-Anglada M, Gandara-Loe J, Danaf NA, Lamb DC, Mehta JP, Vulpe D, Wuttke S, Silvestre-Albero J, Moghadam PZ, Wheatley AEH, Fairen-Jimenez D. Tuning porosity in macroscopic monolithic metal-organic frameworks for exceptional natural gas storage. Nat Commun 2019; 10:2345. [PMID: 31138802 PMCID: PMC6538620 DOI: 10.1038/s41467-019-10185-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/15/2019] [Indexed: 12/23/2022] Open
Abstract
Widespread access to greener energy is required in order to mitigate the effects of climate change. A significant barrier to cleaner natural gas usage lies in the safety/efficiency limitations of storage technology. Despite highly porous metal-organic frameworks (MOFs) demonstrating record-breaking gas-storage capacities, their conventionally powdered morphology renders them non-viable. Traditional powder shaping utilising high pressure or chemical binders collapses porosity or creates low-density structures with reduced volumetric adsorption capacity. Here, we report the engineering of one of the most stable MOFs, Zr-UiO-66, without applying pressure or binders. The process yields centimetre-sized monoliths, displaying high microporosity and bulk density. We report the inclusion of variable, narrow mesopore volumes to the monoliths’ macrostructure and use this to optimise the pore-size distribution for gas uptake. The optimised mixed meso/microporous monoliths demonstrate Type II adsorption isotherms to achieve benchmark volumetric working capacities for methane and carbon dioxide. This represents a critical advance in the design of air-stable, conformed MOFs for commercial gas storage. While metal–organic frameworks exhibit record-breaking gas storage capacities, their typically powdered form hinders their industrial applicability. Here, the authors engineer UiO-66 into centimetre-sized monoliths with optimal pore-size distributions, achieving benchmark volumetric working capacities for both CH4 and CO2.
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Affiliation(s)
- B M Connolly
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Adsorption & Advanced Materials (AAM) Laboratory, Department of Chemical Engineering & Biotechnology, University of Cambridge, Philippa Fawcett Dr, Cambridge, CB3 0AS, UK
| | - M Aragones-Anglada
- Adsorption & Advanced Materials (AAM) Laboratory, Department of Chemical Engineering & Biotechnology, University of Cambridge, Philippa Fawcett Dr, Cambridge, CB3 0AS, UK
| | - J Gandara-Loe
- Laboratorio de Materiales Avanzados, Departamento de Química Inorgánica-Instituto Universitario de Materiales, Universidad de Alicante, Ctra. San Vicente-Alicante s/n, E-03690, San Vicente del Raspeig, Spain
| | - N A Danaf
- Department of Chemistry, Center for NanoScience (CeNS), Nanosystems Initiative Munich, Center for Integrated Protein Science Munich, Ludwig-Maximilians-Univerität, München (LMU), Butenandtstrasse 11, 81377, Munich, Germany
| | - D C Lamb
- Department of Chemistry, Center for NanoScience (CeNS), Nanosystems Initiative Munich, Center for Integrated Protein Science Munich, Ludwig-Maximilians-Univerität, München (LMU), Butenandtstrasse 11, 81377, Munich, Germany
| | - J P Mehta
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Adsorption & Advanced Materials (AAM) Laboratory, Department of Chemical Engineering & Biotechnology, University of Cambridge, Philippa Fawcett Dr, Cambridge, CB3 0AS, UK
| | - D Vulpe
- Adsorption & Advanced Materials (AAM) Laboratory, Department of Chemical Engineering & Biotechnology, University of Cambridge, Philippa Fawcett Dr, Cambridge, CB3 0AS, UK
| | - S Wuttke
- Department of Chemistry, Center for NanoScience (CeNS), Nanosystems Initiative Munich, Center for Integrated Protein Science Munich, Ludwig-Maximilians-Univerität, München (LMU), Butenandtstrasse 11, 81377, Munich, Germany.,School of Chemistry, College of Science, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK
| | - J Silvestre-Albero
- Laboratorio de Materiales Avanzados, Departamento de Química Inorgánica-Instituto Universitario de Materiales, Universidad de Alicante, Ctra. San Vicente-Alicante s/n, E-03690, San Vicente del Raspeig, Spain
| | - P Z Moghadam
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - A E H Wheatley
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - D Fairen-Jimenez
- Adsorption & Advanced Materials (AAM) Laboratory, Department of Chemical Engineering & Biotechnology, University of Cambridge, Philippa Fawcett Dr, Cambridge, CB3 0AS, UK.
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10
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Gegenfurtner FA, Zisis T, Al Danaf N, Schrimpf W, Kliesmete Z, Ziegenhain C, Enard W, Kazmaier U, Lamb DC, Vollmar AM, Zahler S. Transcriptional effects of actin-binding compounds: the cytoplasm sets the tone. Cell Mol Life Sci 2018; 75:4539-4555. [PMID: 30206640 PMCID: PMC11105542 DOI: 10.1007/s00018-018-2919-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/19/2018] [Accepted: 08/14/2018] [Indexed: 12/23/2022]
Abstract
Actin has emerged as a versatile regulator of gene transcription. Cytoplasmatic actin regulates mechanosensitive-signaling pathways such as MRTF-SRF and Hippo-YAP/TAZ. In the nucleus, both polymerized and monomeric actin directly interfere with transcription-associated molecular machineries. Natural actin-binding compounds are frequently used tools to study actin-related processes in cell biology. However, their influence on transcriptional regulation and intranuclear actin polymerization is poorly understood to date. Here, we analyze the effects of two representative actin-binding compounds, Miuraenamide A (polymerizing properties) and Latrunculin B (depolymerizing properties), on transcriptional regulation in primary cells. We find that actin stabilizing and destabilizing compounds inversely shift nuclear actin levels without a direct influence on polymerization state and intranuclear aspects of transcriptional regulation. Furthermore, we identify Miuraenamide A as a potent inducer of G-actin-dependent SRF target gene expression. In contrast, the F-actin-regulated Hippo-YAP/TAZ axis remains largely unaffected by compound-induced actin aggregation. This is due to the inability of AMOTp130 to bind to the amorphous actin aggregates resulting from treatment with miuraenamide. We conclude that actin-binding compounds predominantly regulate transcription via their influence on cytoplasmatic G-actin levels, while transcriptional processes relying on intranuclear actin polymerization or functional F-actin networks are not targeted by these compounds at tolerable doses.
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Affiliation(s)
- Florian A Gegenfurtner
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-University Munich, 81377, Munich, Germany
| | - Themistoklis Zisis
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-University Munich, 81377, Munich, Germany
| | - Nader Al Danaf
- Department of Chemistry, Munich Center for Integrated Protein Science, Nanosystems Initiative Munich and Centre for Nanoscience, Ludwig-Maximilians-University Munich, 81377, Munich, Germany
| | - Waldemar Schrimpf
- Department of Chemistry, Munich Center for Integrated Protein Science, Nanosystems Initiative Munich and Centre for Nanoscience, Ludwig-Maximilians-University Munich, 81377, Munich, Germany
| | - Zane Kliesmete
- Department Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany
| | - Christoph Ziegenhain
- Department Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany
| | - Wolfgang Enard
- Department Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany
| | - Uli Kazmaier
- Institute of Organic Chemistry, Saarland University, 66041, Saarbrücken, Germany
| | - Don C Lamb
- Department of Chemistry, Munich Center for Integrated Protein Science, Nanosystems Initiative Munich and Centre for Nanoscience, Ludwig-Maximilians-University Munich, 81377, Munich, Germany
| | - Angelika M Vollmar
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-University Munich, 81377, Munich, Germany
| | - Stefan Zahler
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-University Munich, 81377, Munich, Germany.
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11
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Gao X, Gao P, Prunsche B, Nienhaus K, Nienhaus GU. Pulsed interleaved excitation-based line-scanning spatial correlation spectroscopy (PIE-lsSCS). Sci Rep 2018; 8:16722. [PMID: 30425308 PMCID: PMC6233157 DOI: 10.1038/s41598-018-35146-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/31/2018] [Indexed: 11/09/2022] Open
Abstract
We report pulsed interleaved excitation (PIE) based line-scanning spatial correlation spectroscopy (PIE-lsSCS), a quantitative fluorescence microscopy method for the study of dynamics in free-standing lipid bilayer membranes. Using a confocal microscope, we scan multiple lines perpendicularly through the membrane, each one laterally displaced from the previous one by several ten nanometers. Scanning through the membrane enables us to eliminate intensity fluctuations due to membrane displacements with respect to the observation volume. The diffusion of fluorescent molecules within the membrane is quantified by spatial correlation analysis, based on the fixed lag times between successive line scans. PIE affords dual-color excitation within a single line scan and avoids channel crosstalk. PIE-lsSCS data are acquired from a larger membrane region so that sampling is more efficient. Moreover, the local photon flux is reduced compared with single-point experiments, resulting in a smaller fraction of photobleached molecules for identical exposure times. This is helpful for precise measurements on live cells and tissues. We have evaluated the method with experiments on fluorescently labeled giant unilamellar vesicles (GUVs) and membrane-stained live cells.
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Affiliation(s)
- Xiang Gao
- Institute of Applied Physics, Karlsruhe Institute of Technology, 76128, Karlsruhe, Germany
| | - Peng Gao
- Institute of Applied Physics, Karlsruhe Institute of Technology, 76128, Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76344, Eggenstein-Leopoldshafen, Germany
| | - Benedikt Prunsche
- Institute of Applied Physics, Karlsruhe Institute of Technology, 76128, Karlsruhe, Germany
| | - Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, 76128, Karlsruhe, Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, 76128, Karlsruhe, Germany.
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76344, Eggenstein-Leopoldshafen, Germany.
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76344, Eggenstein-Leopoldshafen, Germany.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA.
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12
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Parveen N, Borrenberghs D, Rocha S, Hendrix J. Single Viruses on the Fluorescence Microscope: Imaging Molecular Mobility, Interactions and Structure Sheds New Light on Viral Replication. Viruses 2018; 10:E250. [PMID: 29748498 PMCID: PMC5977243 DOI: 10.3390/v10050250] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/24/2018] [Accepted: 05/04/2018] [Indexed: 12/13/2022] Open
Abstract
Viruses are simple agents exhibiting complex reproductive mechanisms. Decades of research have provided crucial basic insights, antiviral medication and moderately successful gene therapy trials. The most infectious viral particle is, however, not always the most abundant one in a population, questioning the utility of classic ensemble-averaging virology. Indeed, viral replication is often not particularly efficient, prone to errors or containing parallel routes. Here, we review different single-molecule sensitive fluorescence methods that we employ routinely to investigate viruses. We provide a brief overview of the microscopy hardware needed and discuss the different methods and their application. In particular, we review how we applied (i) single-molecule Förster resonance energy transfer (smFRET) to probe the subviral human immunodeficiency virus (HIV-1) integrase (IN) quaternary structure; (ii) single particle tracking to study interactions of the simian virus 40 with membranes; (iii) 3D confocal microscopy and smFRET to quantify the HIV-1 pre-integration complex content and quaternary structure; (iv) image correlation spectroscopy to quantify the cytosolic HIV-1 Gag assembly, and finally; (v) super-resolution microscopy to characterize the interaction of HIV-1 with tetherin during assembly. We hope this review is an incentive for setting up and applying similar single-virus imaging studies in daily virology practice.
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Affiliation(s)
- Nagma Parveen
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics Division, Chemistry Department, KU Leuven, B-3001 Leuven, Belgium.
| | - Doortje Borrenberghs
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics Division, Chemistry Department, KU Leuven, B-3001 Leuven, Belgium.
| | - Susana Rocha
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics Division, Chemistry Department, KU Leuven, B-3001 Leuven, Belgium.
| | - Jelle Hendrix
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics Division, Chemistry Department, KU Leuven, B-3001 Leuven, Belgium.
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt University, B-3590 Diepenbeek, Belgium.
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13
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Schrimpf W, Lemmens V, Smisdom N, Ameloot M, Lamb DC, Hendrix J. Crosstalk-free multicolor RICS using spectral weighting. Methods 2018; 140-141:97-111. [DOI: 10.1016/j.ymeth.2018.01.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/15/2018] [Accepted: 01/30/2018] [Indexed: 11/16/2022] Open
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14
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Chemical diversity in a metal-organic framework revealed by fluorescence lifetime imaging. Nat Commun 2018; 9:1647. [PMID: 29695805 PMCID: PMC5916894 DOI: 10.1038/s41467-018-04050-w] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/29/2018] [Indexed: 01/01/2023] Open
Abstract
The presence and variation of chemical functionality and defects in crystalline materials, such as metal-organic frameworks (MOFs), have tremendous impact on their properties. Finding a means of identifying and characterizing this chemical diversity is an important ongoing challenge. This task is complicated by the characteristic problem of bulk measurements only giving a statistical average over an entire sample, leaving uncharacterized any diversity that might exist between crystallites or even within individual crystals. Here, we show that by using fluorescence imaging and lifetime analysis, both the spatial arrangement of functionalities and the level of defects within a multivariable MOF crystal can be determined for the bulk as well as for the individual constituent crystals. We apply these methods to UiO-67 to study the incorporation of functional groups and their consequences on the structural features. We believe that the potential of the techniques presented here in uncovering chemical diversity in what is generally assumed to be homogeneous systems can provide a new level of understanding of materials properties.
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15
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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: 85] [Impact Index Per Article: 14.2] [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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16
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Fukushima R, Yamamoto J, Ishikawa H, Kinjo M. Two-detector number and brightness analysis reveals spatio-temporal oligomerization of proteins in living cells. Methods 2018; 140-141:161-171. [PMID: 29572069 DOI: 10.1016/j.ymeth.2018.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 03/06/2018] [Accepted: 03/16/2018] [Indexed: 01/10/2023] Open
Abstract
Number and brightness analysis (N&B) is a useful tool for the simultaneous visualization of protein oligomers and their localization, with single-molecule sensitivity. N&B determines particle brightness (fluorescence intensity per particle) and maps the spatial distribution of fluorescently labeled proteins by performing statistical analyses of the image series obtained using laser scanning microscopy. The brightness map reveals presence of the oligomers of the targeted protein and their distribution in living cells. However, even when corrections are applied, conventional N&B is affected by afterpulsing, shot noise, thermal noise, dead time, and overestimation of particle brightness when the concentration of the fluorescent particles changes during measurement. The drawbacks of conventional N&B can be circumvented by using two detectors, a novel approach that we henceforth call two-detector number and brightness analysis (TD-N&B), and introducing a linear regression of fluorescence intensity. This statistically eliminates the effect of noise from the detectors, and ensures that the correct particle brightness is obtained. Our method was theoretically assessed by numerical simulations and experimentally validated using a dilution series of purified enhanced green fluorescent protein (EGFP), EGFP tandem oligomers in cell lysate, and EGFP tandem oligomers in living cells. Furthermore, this method was used to characterize the complex process of ligand-induced glucocorticoid receptor dimerization and their translocation to the cell nucleus in live cells. Our method can be applied to other oligomer-forming proteins in cell signaling, or to aggregations of proteins such as those that cause neurodegenerative diseases.
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Affiliation(s)
- Ryosuke Fukushima
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Johtaro Yamamoto
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Hideto Ishikawa
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.
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17
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Vandenberk N, Barth A, Borrenberghs D, Hofkens J, Hendrix J. Evaluation of Blue and Far-Red Dye Pairs in Single-Molecule Förster Resonance Energy Transfer Experiments. J Phys Chem B 2018. [DOI: 10.1021/acs.jpcb.8b00108] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Niels Vandenberk
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Anders Barth
- Physical Chemistry, Department of Chemistry, Munich Center for Integrated Protein Science, Nanosystems Initiative Munich and Centre for Nanoscience, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Doortje Borrenberghs
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Jelle Hendrix
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute, Hasselt University, Agoralaan C (BIOMED), Diepenbeek, B-3590, Belgium
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18
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Nolan R, Iliopoulou M, Alvarez L, Padilla-Parra S. Detecting protein aggregation and interaction in live cells: A guide to number and brightness. Methods 2017; 140-141:172-177. [PMID: 29221925 DOI: 10.1016/j.ymeth.2017.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/01/2017] [Accepted: 12/03/2017] [Indexed: 12/31/2022] Open
Abstract
The possibility to detect and quantify protein-protein interactions with good spatial and temporal resolutions in live cells is crucial in biology. Number and brightness is a powerful approach to detect both protein aggregation/desegregation dynamics and stoichiometry in live cells. Importantly, this technique can be applied in commercial set ups: both camera based and laser scanning microscopes. It provides pixel-by-pixel information on protein oligomeric states. If performed with two colours, the technique can retrieve the stoichiometry of the reaction under study. In this review, we discuss the strengths and weaknesses of the technique, stressing which are the correct acquisition parameters for a given microscope, the main challenges in analysis, and the limitations of the technique.
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Affiliation(s)
- Rory Nolan
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Maro Iliopoulou
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Luis Alvarez
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Sergi Padilla-Parra
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK.
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19
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Lanzanò L, Scipioni L, Di Bona M, Bianchini P, Bizzarri R, Cardarelli F, Diaspro A, Vicidomini G. Measurement of nanoscale three-dimensional diffusion in the interior of living cells by STED-FCS. Nat Commun 2017; 8:65. [PMID: 28684735 PMCID: PMC5500520 DOI: 10.1038/s41467-017-00117-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 06/01/2017] [Indexed: 01/12/2023] Open
Abstract
The observation of molecular diffusion at different spatial scales, and in particular below the optical diffraction limit (<200 nm), can reveal details of the subcellular topology and its functional organization. Stimulated-emission depletion microscopy (STED) has been previously combined with fluorescence correlation spectroscopy (FCS) to investigate nanoscale diffusion (STED-FCS). However, stimulated-emission depletion fluorescence correlation spectroscopy has only been used successfully to reveal functional organization in two-dimensional space, such as the plasma membrane, while, an efficient implementation for measurements in three-dimensional space, such as the cellular interior, is still lacking. Here we integrate the STED-FCS method with two analytical approaches, the recent separation of photons by lifetime tuning and the fluorescence lifetime correlation spectroscopy, to simultaneously probe diffusion in three dimensions at different sub-diffraction scales. We demonstrate that this method efficiently provides measurement of the diffusion of EGFP at spatial scales tunable from the diffraction size down to ∼80 nm in the cytoplasm of living cells. The measurement of molecular diffusion at sub-diffraction scales has been achieved in 2D space using STED-FCS, but an implementation for 3D diffusion is lacking. Here the authors present an analytical approach to probe diffusion in 3D space using STED-FCS and measure the diffusion of EGFP at different spatial scales.
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Affiliation(s)
- Luca Lanzanò
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy.
| | - Lorenzo Scipioni
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy.,Department of Computer Science, Bioengineering, Robotics and Systems Engineering, University of Genoa, Genoa, 16145, Italy
| | - Melody Di Bona
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy.,Department of Physics, University of Genoa, via Dodecaneso 33, Genoa, 16146, Italy
| | - Paolo Bianchini
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy.,Nikon Imaging Center, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy
| | - Ranieri Bizzarri
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy.,NEST, Scuola Normale Superiore and Istituto Nanoscienze, CNR (NANO-CNR) piazza San Silvestro 12, Pisa, 56127, Italy
| | - Francesco Cardarelli
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, piazza San Silvestro 12, Pisa, 56127, Italy.,NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa, 56127, Italy
| | - Alberto Diaspro
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy. .,Department of Physics, University of Genoa, via Dodecaneso 33, Genoa, 16146, Italy. .,Nikon Imaging Center, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy.
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy.
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20
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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: 4.3] [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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21
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Monitoring integrity and localization of modified single-stranded RNA oligonucleotides using ultrasensitive fluorescence methods. PLoS One 2017; 12:e0173401. [PMID: 28278199 PMCID: PMC5344492 DOI: 10.1371/journal.pone.0173401] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/20/2017] [Indexed: 12/20/2022] Open
Abstract
Short single-stranded oligonucleotides represent a class of promising therapeutics with diverse application areas. Antisense oligonucleotides, for example, can interfere with various processes involved in mRNA processing through complementary base pairing. Also RNA interference can be regulated by antagomirs, single-stranded siRNA and single-stranded microRNA mimics. The increased susceptibility to nucleolytic degradation of unpaired RNAs can be counteracted by chemical modification of the sugar phosphate backbone. In order to understand the dynamics of such single-stranded RNAs, we investigated their fate after exposure to cellular environment by several fluorescence spectroscopy techniques. First, we elucidated the degradation of four differently modified, dual-dye labeled short RNA oligonucleotides in HeLa cell extracts by fluorescence correlation spectroscopy, fluorescence cross-correlation spectroscopy and Förster resonance energy transfer. We observed that the integrity of the oligonucleotide sequence correlates with the extent of chemical modifications. Furthermore, the data showed that nucleolytic degradation can only be distinguished from unspecific effects like aggregation, association with cellular proteins, or intramolecular dynamics when considering multiple measurement and analysis approaches. We also investigated the localization and integrity of the four modified oligonucleotides in cultured HeLa cells using fluorescence lifetime imaging microscopy. No intracellular accumulation could be observed for unmodified oligonucleotides, while completely stabilized oligonucleotides showed strong accumulation within HeLa cells with no changes in fluorescence lifetime over 24 h. The integrity and accumulation of partly modified oligonucleotides was in accordance with their extent of modification. In highly fluorescent cells, the oligonucleotides were transported to the nucleus. The lifetime of the RNA in the cells could be explained by a balance between release of the oligonucleotides from endosomes, degradation by RNases and subsequent depletion from the cells.
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22
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Galilee M, Britan-Rosich E, Griner SL, Uysal S, Baumgärtel V, Lamb DC, Kossiakoff AA, Kotler M, Stroud RM, Marx A, Alian A. The Preserved HTH-Docking Cleft of HIV-1 Integrase Is Functionally Critical. Structure 2016; 24:1936-1946. [PMID: 27692964 DOI: 10.1016/j.str.2016.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/19/2016] [Accepted: 08/19/2016] [Indexed: 02/06/2023]
Abstract
HIV-1 integrase (IN) catalyzes viral DNA integration into the host genome and facilitates multifunctional steps including virus particle maturation. Competency of IN to form multimeric assemblies is functionally critical, presenting an approach for anti-HIV strategies. Multimerization of IN depends on interactions between the distinct subunit domains and among the flanking protomers. Here, we elucidate an overlooked docking cleft of IN core domain that anchors the N-terminal helix-turn-helix (HTH) motif in a highly preserved and functionally critical configuration. Crystallographic structure of IN core domain in complex with Fab specifically targeting this cleft reveals a steric overlap that would inhibit HTH-docking, C-terminal domain contacts, DNA binding, and subsequent multimerization. While Fab inhibits in vitro IN integration activity, in vivo it abolishes virus particle production by specifically associating with preprocessed IN within Gag-Pol and interfering with early cytosolic Gag/Gag-Pol assemblies. The HTH-docking cleft may offer a fresh hotspot for future anti-HIV intervention strategies.
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Affiliation(s)
- Meytal Galilee
- Department of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Elena Britan-Rosich
- Department of Immunology and Pathology, The Lautenberg Center for General and Tumor Immunology, The Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
| | - Sarah L Griner
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Serdar Uysal
- Department of Biophysics, Bezmialem Vakif University, Istanbul 34093, Turkey
| | - Viola Baumgärtel
- Physical Chemistry, Department of Chemistry, Nanosystem Initiative Munich (NIM), Center for Integrated Protein Science Munich (CiPSM), Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Nanosystem Initiative Munich (NIM), Center for Integrated Protein Science Munich (CiPSM), Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Moshe Kotler
- Department of Immunology and Pathology, The Lautenberg Center for General and Tumor Immunology, The Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ailie Marx
- Department of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Akram Alian
- Department of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel.
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23
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Oura M, Yamamoto J, Ishikawa H, Mikuni S, Fukushima R, Kinjo M. Polarization-dependent fluorescence correlation spectroscopy for studying structural properties of proteins in living cell. Sci Rep 2016; 6:31091. [PMID: 27489044 PMCID: PMC4973283 DOI: 10.1038/srep31091] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/14/2016] [Indexed: 11/10/2022] Open
Abstract
Rotational diffusion measurement is predicted as an important method in cell biology because the rotational properties directly reflect molecular interactions and environment in the cell. To prove this concept, polarization-dependent fluorescence correlation spectroscopy (pol-FCS) measurements of purified fluorescent proteins were conducted in viscous solution. With the comparison between the translational and rotational diffusion coefficients obtained from pol-FCS measurements, the hydrodynamic radius of an enhanced green fluorescent protein (EGFP) was estimated as a control measurement. The orientation of oligomer EGFP in living cells was also estimated by pol-FCS and compared with Monte Carlo simulations. The results of this pol-FCS experiment indicate that this method allows an estimation of the molecular orientation using the characteristics of rotational diffusion. Further, it can be applied to analyze the degree of molecular orientation and multimerization or detection of tiny aggregation of aggregate-prone proteins.
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Affiliation(s)
- Makoto Oura
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Johtaro Yamamoto
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Hideto Ishikawa
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Shintaro Mikuni
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Ryousuke Fukushima
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
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24
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Ghosh S, Nandi S, Ghosh C, Bhattacharyya K. Fluorescence Dynamics in the Endoplasmic Reticulum of a Live Cell: Time-Resolved Confocal Microscopy. Chemphyschem 2016; 17:2818-23. [PMID: 27245117 DOI: 10.1002/cphc.201600425] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Indexed: 11/11/2022]
Abstract
Fluorescence dynamics in the endoplasmic reticulum (ER) of a live non-cancer lung cell (WI38) and a lung cancer cell (A549) are studied by using time-resolved confocal microscopy. To selectively study the organelle, ER, we have used an ER-Tracker dye. From the emission maximum (λmaxem) of the ER-Tracker dye, polarity (i.e. dielectric constant, ϵ) in the ER region of the cells (≈500 nm in WI38 and ≈510 nm in A549) is estimated to be similar to that of chloroform (λmaxem =506 nm, ϵ≈5). The red shift by 10 nm in λmaxem in the cancer cell (A549) suggests a slightly higher polarity compared to the non-cancer cell (WI38). The fluorescence intensity of the ER-Tracker dye exhibits prolonged intermittent oscillations on a timescale of 2-6 seconds for the cancer cell (A549). For the non-cancer cell (WI38), such fluorescence oscillations are much less prominent. The marked fluorescence intensity oscillations in the cancer cell are attributed to enhanced calcium oscillations. The average solvent relaxation time (<τs >) of the ER region in the lung cancer cell (A549, 250±50 ps) is about four times faster than that in the non-cancer cell (WI38, 1000±50 ps).
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Affiliation(s)
- Shirsendu Ghosh
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India), Fax: (91)-33-2473-2805
| | - Somen Nandi
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India), Fax: (91)-33-2473-2805
| | - Catherine Ghosh
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India), Fax: (91)-33-2473-2805
| | - Kankan Bhattacharyya
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India), Fax: (91)-33-2473-2805.
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25
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Schrimpf W, Ossato G, Hirschle P, Wuttke S, Lamb DC. Investigation of the Co-Dependence of Morphology and Fluorescence Lifetime in a Metal-Organic Framework. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:3651-3657. [PMID: 27171620 DOI: 10.1002/smll.201600619] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/30/2016] [Indexed: 06/05/2023]
Abstract
Porous materials, due to their large surface-to-volume ratio, are important for a broad range of applications and are the subject of intense research. Most studies investigate the bulk properties of these materials, which are not sensitive to the effect of heterogeneities within the sample. Herein, a new strategy based on correlative fluorescence lifetime imaging and scanning electron microscopy is presented that allows the detection and localization of those heterogeneities, and connects them to morphological and structural features of the material. By applying this method to a dye-modified metal-organic framework (MOF), two independent fluorescence quenching mechanisms in the MOF scaffold are identified and quantified. The first mechanism is based on quenching via amino groups, while the second mechanism is influenced by morphology. Furthermore, a similar correlation between the inherent luminescence lifetime and the morphology of the unmodified MOF structure is demonstrated.
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Affiliation(s)
- Waldemar Schrimpf
- Department of Chemistry and Center for NanoScience (CeNS), University of Munich (LMU), Butenandtstraße 11, 81377, München, Germany
| | - Giulia Ossato
- Department of Chemistry and Center for NanoScience (CeNS), University of Munich (LMU), Butenandtstraße 11, 81377, München, Germany
| | - Patrick Hirschle
- Department of Chemistry and Center for NanoScience (CeNS), University of Munich (LMU), Butenandtstraße 11, 81377, München, Germany
| | - Stefan Wuttke
- Department of Chemistry and Center for NanoScience (CeNS), University of Munich (LMU), Butenandtstraße 11, 81377, München, Germany
| | - Don C Lamb
- Department of Chemistry and Center for NanoScience (CeNS), University of Munich (LMU), Butenandtstraße 11, 81377, München, Germany
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26
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Hendrix J, Baumgärtel V, Schrimpf W, Ivanchenko S, Digman MA, Gratton E, Kräusslich HG, Müller B, Lamb DC. Live-cell observation of cytosolic HIV-1 assembly onset reveals RNA-interacting Gag oligomers. J Cell Biol 2015; 210:629-46. [PMID: 26283800 PMCID: PMC4539982 DOI: 10.1083/jcb.201504006] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Analysis of the cytosolic HIV-1 Gag fraction in live cells via advanced fluctuation imaging methods reveals potential nucleation steps before membrane-assisted Gag assembly. Assembly of the Gag polyprotein into new viral particles in infected cells is a crucial step in the retroviral replication cycle. Currently, little is known about the onset of assembly in the cytosol. In this paper, we analyzed the cytosolic HIV-1 Gag fraction in real time in live cells using advanced fluctuation imaging methods and thereby provide detailed insights into the complex relationship between cytosolic Gag mobility, stoichiometry, and interactions. We show that Gag diffuses as a monomer on the subsecond timescale with severely reduced mobility. Reduction of mobility is associated with basic residues in its nucleocapsid (NC) domain, whereas capsid (CA) and matrix (MA) domains do not contribute significantly. Strikingly, another diffusive Gag species was observed on the seconds timescale that oligomerized in a concentration-dependent manner. Both NC- and CA-mediated interactions strongly assist this process. Our results reveal potential nucleation steps of cytosolic Gag fractions before membrane-assisted Gag assembly.
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Affiliation(s)
- Jelle Hendrix
- Physical Chemistry, Department of Chemistry, Ludwig Maximilian University of Munich, D-81377 Munich, Germany NanoSystems Initiative Munich (NIM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Munich Center for Integrated Protein Science (CiPSM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Center for Nanoscience (CeNS), Ludwig Maximilian University of Munich, D-81377 Munich, Germany
| | - Viola Baumgärtel
- Physical Chemistry, Department of Chemistry, Ludwig Maximilian University of Munich, D-81377 Munich, Germany NanoSystems Initiative Munich (NIM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Munich Center for Integrated Protein Science (CiPSM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Center for Nanoscience (CeNS), Ludwig Maximilian University of Munich, D-81377 Munich, Germany
| | - Waldemar Schrimpf
- Physical Chemistry, Department of Chemistry, Ludwig Maximilian University of Munich, D-81377 Munich, Germany NanoSystems Initiative Munich (NIM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Munich Center for Integrated Protein Science (CiPSM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Center for Nanoscience (CeNS), Ludwig Maximilian University of Munich, D-81377 Munich, Germany
| | - Sergey Ivanchenko
- Physical Chemistry, Department of Chemistry, Ludwig Maximilian University of Munich, D-81377 Munich, Germany NanoSystems Initiative Munich (NIM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Munich Center for Integrated Protein Science (CiPSM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Center for Nanoscience (CeNS), Ludwig Maximilian University of Munich, D-81377 Munich, Germany
| | - Michelle A Digman
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697 Development Biology Center Optical Biology Core Facility, University of California, Irvine, Irvine, CA 92697
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697 Development Biology Center Optical Biology Core Facility, University of California, Irvine, Irvine, CA 92697
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, D-69120 Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, D-69120 Heidelberg, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Ludwig Maximilian University of Munich, D-81377 Munich, Germany NanoSystems Initiative Munich (NIM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Munich Center for Integrated Protein Science (CiPSM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Center for Nanoscience (CeNS), Ludwig Maximilian University of Munich, D-81377 Munich, Germany
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Weidemann T, Mücksch J, Schwille P. Fluorescence fluctuation microscopy: a diversified arsenal of methods to investigate molecular dynamics inside cells. Curr Opin Struct Biol 2014; 28:69-76. [DOI: 10.1016/j.sbi.2014.07.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/11/2014] [Indexed: 11/26/2022]
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Ozgen H, Schrimpf W, Hendrix J, de Jonge JC, Lamb DC, Hoekstra D, Kahya N, Baron W. The lateral membrane organization and dynamics of myelin proteins PLP and MBP are dictated by distinct galactolipids and the extracellular matrix. PLoS One 2014; 9:e101834. [PMID: 25003183 PMCID: PMC4086962 DOI: 10.1371/journal.pone.0101834] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 06/12/2014] [Indexed: 01/03/2023] Open
Abstract
In the central nervous system, lipid-protein interactions are pivotal for myelin maintenance, as these interactions regulate protein transport to the myelin membrane as well as the molecular organization within the sheath. To improve our understanding of the fundamental properties of myelin, we focused here on the lateral membrane organization and dynamics of peripheral membrane protein 18.5-kDa myelin basic protein (MBP) and transmembrane protein proteolipid protein (PLP) as a function of the typical myelin lipids galactosylceramide (GalC), and sulfatide, and exogenous factors such as the extracellular matrix proteins laminin-2 and fibronectin, employing an oligodendrocyte cell line, selectively expressing the desired galactolipids. The dynamics of MBP were monitored by z-scan point fluorescence correlation spectroscopy (FCS) and raster image correlation spectroscopy (RICS), while PLP dynamics in living cells were investigated by circular scanning FCS. The data revealed that on an inert substrate the diffusion rate of 18.5-kDa MBP increased in GalC-expressing cells, while the diffusion coefficient of PLP was decreased in sulfatide-containing cells. Similarly, when cells were grown on myelination-promoting laminin-2, the lateral diffusion coefficient of PLP was decreased in sulfatide-containing cells. In contrast, PLP's diffusion rate increased substantially when these cells were grown on myelination-inhibiting fibronectin. Additional biochemical analyses revealed that the observed differences in lateral diffusion coefficients of both proteins can be explained by differences in their biophysical, i.e., galactolipid environment, specifically with regard to their association with lipid rafts. Given the persistence of pathological fibronectin aggregates in multiple sclerosis lesions, this fundamental insight into the nature and dynamics of lipid-protein interactions will be instrumental in developing myelin regenerative strategies.
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Affiliation(s)
- Hande Ozgen
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Waldemar Schrimpf
- Physical Chemistry, Department of Chemistry, Munich Center for Integrated Protein Science (CiPSM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Jelle Hendrix
- Physical Chemistry, Department of Chemistry, Munich Center for Integrated Protein Science (CiPSM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Jenny C. de Jonge
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Don C. Lamb
- Physical Chemistry, Department of Chemistry, Munich Center for Integrated Protein Science (CiPSM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Dick Hoekstra
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nicoletta Kahya
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- * E-mail: (NK) (WB)
| | - Wia Baron
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- * E-mail: (NK) (WB)
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29
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Statistical filtering in fluorescence microscopy and fluorescence correlation spectroscopy. Anal Bioanal Chem 2014; 406:4797-813. [DOI: 10.1007/s00216-014-7892-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 05/07/2014] [Accepted: 05/13/2014] [Indexed: 01/21/2023]
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30
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Singh AP, Wohland T. Applications of imaging fluorescence correlation spectroscopy. Curr Opin Chem Biol 2014; 20:29-35. [DOI: 10.1016/j.cbpa.2014.04.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 11/16/2022]
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31
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Borrenberghs D, Thys W, Rocha S, Demeulemeester J, Weydert C, Dedecker P, Hofkens J, Debyser Z, Hendrix J. HIV virions as nanoscopic test tubes for probing oligomerization of the integrase enzyme. ACS NANO 2014; 8:3531-45. [PMID: 24654558 PMCID: PMC4004294 DOI: 10.1021/nn406615v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Employing viruses as nanoscopic lipid-enveloped test tubes allows the miniaturization of protein-protein interaction (PPI) assays while preserving the physiological environment necessary for particular biological processes. Applied to the study of the human immunodeficiency virus type 1 (HIV-1), viral biology and pathology can also be investigated in novel ways, both in vitro as well as in infected cells. In this work we report on an experimental strategy that makes use of engineered HIV-1 viral particles, to allow for probing PPIs of the HIV-1 integrase (IN) inside viruses with single-molecule Förster resonance energy transfer (FRET) using fluorescent proteins (FP). We show that infectious fluorescently labeled viruses can be obtained and that the quantity of labels can be accurately measured and controlled inside individual viral particles. We demonstrate, with proper control experiments, the formation of IN oligomers in single viral particles and inside viral complexes in infected cells. Finally, we show a clear effect on IN oligomerization of small molecule inhibitors of interactions of IN with its natural human cofactor LEDGF/p75, corroborating that IN oligomer enhancing drugs are active already at the level of the virus and strongly suggesting the presence of a dynamic, enhanceable equilibrium between the IN dimer and tetramer in viral particles. Although applied to the HIV-1 IN enzyme, our methodology for utilizing HIV virions as nanoscopic test tubes for probing PPIs is generic, i.e., other PPIs targeted into the HIV-1, or PPIs targeted into other viruses, can potentially be studied with a similar strategy.
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Affiliation(s)
- Doortje Borrenberghs
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Flanders, Belgium
| | - Wannes Thys
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, 3000 Leuven, Flanders, Belgium
| | - Susana Rocha
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Flanders, Belgium
| | - Jonas Demeulemeester
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, 3000 Leuven, Flanders, Belgium
| | - Caroline Weydert
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, 3000 Leuven, Flanders, Belgium
| | - Peter Dedecker
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Flanders, Belgium
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Flanders, Belgium
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, 3000 Leuven, Flanders, Belgium
| | - Jelle Hendrix
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Flanders, Belgium
- Address correspondence to
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32
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Recent applications of fluorescence correlation spectroscopy in live systems. FEBS Lett 2014; 588:3571-84. [PMID: 24726724 DOI: 10.1016/j.febslet.2014.03.056] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 03/29/2014] [Accepted: 03/31/2014] [Indexed: 11/20/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a widely used technique in biophysics and has helped address many questions in the life sciences. It provides important advantages compared to other fluorescence and biophysical methods. Its single molecule sensitivity allows measuring proteins within biological samples at physiological concentrations without the need of overexpression. It provides quantitative data on concentrations, diffusion coefficients, molecular transport and interactions even in live organisms. And its reliance on simple fluorescence intensity and its fluctuations makes it widely applicable. In this review we focus on applications of FCS in live samples, with an emphasis on work in the last 5 years, in the hope to provide an overview of the present capabilities of FCS to address biologically relevant questions.
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33
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Hendrix J, van Heertum B, Vanstreels E, Daelemans D, De Rijck J. Dynamics of the ternary complex formed by c-Myc interactor JPO2, transcriptional co-activator LEDGF/p75, and chromatin. J Biol Chem 2014; 289:12494-506. [PMID: 24634210 DOI: 10.1074/jbc.m113.525964] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Lens epithelium-derived growth factor (LEDGF/p75) is a transcriptional co-activator involved in targeting human immunodeficiency virus (HIV) integration and the development of MLL fusion-mediated acute leukemia. A previous study revealed that LEDGF/p75 dynamically scans the chromatin, and upon interaction with HIV-1 integrase, their complex is locked on chromatin. At present, it is not known whether LEDGF/p75-mediated chromatin locking is typical for interacting proteins. Here, we employed continuous photobleaching and fluorescence correlation and cross-correlation spectroscopy to investigate in vivo chromatin binding of JPO2, a LEDGF/p75- and c-Myc-interacting protein involved in transcriptional regulation. In the absence of LEDGF/p75, JPO2 performs chromatin scanning inherent to transcription factors. However, whereas the dynamics of JPO2 chromatin binding are decelerated upon interaction with LEDGF/p75, very strong locking of their complex onto chromatin is absent. Similar results were obtained with the domesticated transposase PogZ, another cellular interaction partner of LEDGF/p75. We furthermore show that diffusive JPO2 can oligomerize; that JPO2 and LEDGF/p75 interact directly and specifically in vivo through the specific interaction domain of JPO2 and the C-terminal domain of LEDGF/p75, comprising the integrase-binding domain; and that modulation of JPO2 dynamics requires a functional PWWP domain in LEDGF/p75. Our results suggest that the dynamics of the LEDGF/p75-chromatin interaction depend on the specific partner and that strong chromatin locking is not a property of all LEDGF/p75-binding proteins.
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Affiliation(s)
- Jelle Hendrix
- From the Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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MFD-PIE and PIE-FI: Ways to Extract More Information with TCSPC. SPRINGER SERIES ON FLUORESCENCE 2014. [DOI: 10.1007/4243_2014_66] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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35
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Hendrix J, Lamb DC. Implementation and application of pulsed interleaved excitation for dual-color FCS and RICS. Methods Mol Biol 2014; 1076:653-682. [PMID: 24108649 DOI: 10.1007/978-1-62703-649-8_30] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Pulsed interleaved excitation (PIE) employs pulsed laser sources that are interleaved such that differentially colored fluorophores can be measured or imaged quasi-simultaneously in the absence of spectral crosstalk. PIE improves the robustness and reduces data analysis complexity of many fluorescence techniques, such as fluorescence cross-correlation spectroscopy (FCCS) and raster image cross-correlation spectroscopy (ccRICS), two methods used for quantitative investigation of molecular interactions in vitro and in living cells. However, as PIE is most often used for fluorescence fluctuation spectroscopy and burst analysis experiments and utilizes time-correlated single-photon counting detection and advanced optoelectronics, it has remained a technique that is mostly used by specialized single-molecule research groups. This protocols chapter provides an accessible overview of PIE for anyone considering implementing the method on a homebuilt or commercial microscope. We give details on the instrumentation, data collection and analysis software, on how to properly set up and align a PIE microscope, and finally, on how to perform proper dual-color FCS and RICS experiments.
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Affiliation(s)
- Jelle Hendrix
- Physical Chemistry, Department of Chemistry, Munich Center for Integrated Protein Science (CiPSM) and Center for Nanoscience (CeNS), Ludwig-Maximilian-Universität München, Munich, Germany
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36
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Wiseman P. Fluctuation Imaging Spiced Up with a Piece of PIE. Biophys J 2013; 105:831. [DOI: 10.1016/j.bpj.2013.05.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 05/22/2013] [Indexed: 11/17/2022] Open
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