1
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Smith AW. Recent applications of fluorescence correlation spectroscopy in live cells. Curr Opin Chem Biol 2024; 81:102480. [PMID: 38905722 DOI: 10.1016/j.cbpa.2024.102480] [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: 01/31/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
As a time-domain analogue of fluorescence imaging, FCS offers valuable insights into molecular dynamics, interactions, and concentrations within living cells. The primary insight generated by FCS is molecular mobility and concentration, which makes it useful for investigating molecular-scale details without the need for enrichment or separation. A specific strength of FCS is the ability to probe protein-protein interactions in live cells and several recent applications in this area are summarized. FCS is also used to investigate plasma membrane protein organization, with many applications to cell surface receptors and the mechanisms of drug binding. Finally, FCS is undergoing continual methodological innovations, such as imaging FCS, SPIM-FCS PIE-FCCS, STED-FCS, three-color FCS, and massively parallel FCS, which extend the capabilities to investigate molecular dynamics at different spatial and temporal scales. These innovations enable detailed examinations of cellular processes, including cellular transport and the spatial organization of membrane proteins.
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Affiliation(s)
- Adam W Smith
- Texas Tech University, Department of Chemistry & Biochemistry, Lubbock, TX, USA.
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2
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Tripathy A, Priyadarsinee S, Bag N. Evaluation of functional transbilayer coupling in live cells by controlled lipid exchange and imaging fluorescence correlation spectroscopy. Methods Enzymol 2024; 700:1-32. [PMID: 38971596 DOI: 10.1016/bs.mie.2024.04.001] [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] [Indexed: 07/08/2024]
Abstract
Biophysical coupling between the inner and outer leaflets, known as inter-leaflet or transbilayer coupling, is a fundamental organizational principle in the plasma membranes of live mammalian cells. Lipid-based interactions between the two leaflets are proposed to be a primary mechanism underlying transbilayer coupling. However, there are only a few experimental evidence supporting the existence of such interactions in live cells. This is seemingly due to the lack of experimental strategies to perturb the lipid composition in one leaflet and quantitative techniques to evaluate the biophysical properties of the opposite leaflet. The existing strategies often dependent on immobilization and clustering a component in one of the leaflets and technically demanding biophysical tools to evaluate the effects on the opposing leaflet. In the recent years, the London group developed a simple but elegant method, namely methyl-alpha-cyclodextrin catalyzed lipid exchange (LEX), to efficiently exchange outer leaflet lipids with an exogenous lipid of choice. Here, we adopted this method to perturb outer leaflet lipid composition. The corresponding changes in the inner leaflet is evaluated by comparing the diffusion of lipid probes localized in this leaflet in unperturbed and perturbed conditions. We employed highly multiplexed imaging fluorescence correlation spectroscopy (ImFCS), realized in a commercially available or home-built total internal reflection fluorescence microsocope equipped with a fast and sensitive camera, to determine diffusion coefficient of the lipid probes. Using the combination of LEX and ImFCS, we directly demonstrate lipid-based transbilayer coupling that does not require immobilization of membrane components in live mast cells in resting conditions. Overall, we present a relatively straightforward experimental strategy to evaluate transbilayer coupling quantitively in live cells.
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Affiliation(s)
- Arpita Tripathy
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Sudipti Priyadarsinee
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Nirmalya Bag
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India.
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3
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Filan C, Green M, Diering A, Cicerone MT, Cheung LS, Kostka JE, Robles FE. Label-free functional analysis of root-associated microbes with dynamic quantitative oblique back-illumination microscopy. Sci Rep 2024; 14:5812. [PMID: 38461279 PMCID: PMC10925023 DOI: 10.1038/s41598-024-56443-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/06/2024] [Indexed: 03/11/2024] Open
Abstract
The increasing global demand for food, coupled with concerns about the environmental impact of synthetic fertilizers, underscores the urgency of developing sustainable agricultural practices. Nitrogen-fixing bacteria, known as diazotrophs, offer a potential solution by converting atmospheric nitrogen into bioavailable forms, reducing the reliance on synthetic fertilizers. However, a deeper understanding of their interactions with plants and other microbes is needed. In this study, we introduce a recently developed label-free 3D quantitative phase imaging technology called dynamic quantitative oblique back-illumination microscopy (DqOBM) to assess the functional dynamic activity of diazotrophs in vitro and in situ. Our experiments involved three different diazotrophs (Sinorhizobium meliloti, Azotobacter vinelandii, and Rahnella aquatilis) cultured on media with amendments of carbon and nitrogen sources. Over 5 days, we observed increased dynamics in nutrient-amended media. These results suggest that the observed bacterial dynamics correlate with their metabolic activity. Furthermore, we applied qOBM to visualize microbial dynamics within the root cap and elongation zone of Arabidopsis thaliana primary roots. This allowed us to identify distinct areas of microbial infiltration in plant roots without the need for fluorescent markers. Our findings demonstrate that DqOBM can effectively characterize microbial dynamics and provide insights into plant-microbe interactions in situ, offering a valuable tool for advancing our understanding of sustainable agriculture.
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Affiliation(s)
- Caroline Filan
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30318, USA
| | - Madison Green
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30318, USA
| | - Abigail Diering
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Marcus T Cicerone
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Lily S Cheung
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30318, USA
| | - Francisco E Robles
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30318, USA.
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4
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Sankaran J, Rice SA, Wohland T. Single Microcolony Diffusion Analysis in Pseudomonas aeruginosa Biofilms. Methods Mol Biol 2024; 2721:153-168. [PMID: 37819521 DOI: 10.1007/978-1-0716-3473-8_11] [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] [Indexed: 10/13/2023]
Abstract
Diffusion phenomena play an important role during various stages of biofilm development. Hence, quantification of the diffusion coefficient of molecules provides important information necessary to understand the variability in diffusion profiles at different biofilm stages. Imaging fluorescence correlation spectroscopy (FCS) enables the visualization of 3D diffusion profiles of biofilms. In this protocol, we explain how to grow biofilms for investigation using imaging FCS and how to acquire and analyze the data.
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Affiliation(s)
| | - Scott A Rice
- Singapore Centre for Environmental Life Science and Engineering, Singapore, Singapore
- University of Technology Sydney, Ultimo, NSW, Australia
- CSIRO, Agriculture and Food, Microbiomes for One Systems Health, Coopers Plains, QLD, Australia
| | - Thorsten Wohland
- Departments of Biological Sciences and Chemistry, National University of Singapore, Singapore, Singapore.
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5
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Erstling JA, Bag N, Gardinier TC, Kohle FFE, DomNwachukwu N, Butler SD, Kao T, Ma K, Turker MZ, Feuer GB, Lee R, Naguib N, Tallman JF, Malarkey HF, Tsaur L, Moore WL, Chapman DV, Aubert T, Mehta S, Cerione RA, Weiss RS, Baird BA, Wiesner UB. Overcoming Barriers Associated with Oral Delivery of Differently Sized Fluorescent Core-Shell Silica Nanoparticles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2305937. [PMID: 37689973 DOI: 10.1002/adma.202305937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/07/2023] [Indexed: 09/11/2023]
Abstract
Oral delivery, while a highly desirable form of nanoparticle-drug administration, is limited by challenges associated with overcoming several biological barriers. Here, the authors study how fluorescent and poly(ethylene glycol)-coated (PEGylated) core-shell silica nanoparticles sized 5 to 50 nm interact with major barriers including intestinal mucus, intestinal epithelium, and stomach acid. From imaging fluorescence correlation spectroscopy studies using quasi-total internal reflection fluorescence microscopy, diffusion of nanoparticles through highly scattering mucus is progressively hindered above a critical hydrodynamic size around 20 nm. By studying Caco-2 cell monolayers mimicking the intestinal epithelia, it is observed that ultrasmall nanoparticles below 10 nm diameter (Cornell prime dots, [C' dots]) show permeabilities correlated with high absorption in humans from primarily enhanced passive passage through tight junctions. Particles above 20 nm diameter exclusively show active transport through cells. After establishing C' dot stability in artificial gastric juice, in vivo oral gavage experiments in mice demonstrate successful passage through the body followed by renal clearance without protein corona formation. Results suggest C' dots as viable candidates for oral administration to patients with a proven pathway towards clinical translation and may generate renewed interest in examining silica as a food additive and its effects on nutrition and health.
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Affiliation(s)
- Jacob A Erstling
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Nirmalya Bag
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Thomas C Gardinier
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Ferdinand F E Kohle
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Naedum DomNwachukwu
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Scott D Butler
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Teresa Kao
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Kai Ma
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Melik Z Turker
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Grant B Feuer
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Rachel Lee
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Nada Naguib
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - James F Tallman
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Henry F Malarkey
- Department of Applied and Engineering Physics, Cornell University, Ithaca, NY, 14853, USA
| | - Lieihn Tsaur
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - William L Moore
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Dana V Chapman
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Tangi Aubert
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Saurabh Mehta
- Center for Precision Nutrition and Health, Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Richard A Cerione
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Robert S Weiss
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Barbara A Baird
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ulrich B Wiesner
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, 14853, USA
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6
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Filan C, Green M, Diering A, Cicerone MT, Cheung LS, Kostka JE, Robles FE. Label-Free Functional Analysis of Root-Associated Microbes with Dynamic Quantitative Oblique Back-illumination Microscopy. RESEARCH SQUARE 2023:rs.3.rs-3517586. [PMID: 37961396 PMCID: PMC10635382 DOI: 10.21203/rs.3.rs-3517586/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The increasing global demand for food, coupled with concerns about the environmental impact of synthetic fertilizers, underscores the urgency of developing sustainable agricultural practices. Nitrogen-fixing bacteria, known as diazotrophs, offer a potential solution by converting atmospheric nitrogen into bioavailable forms, reducing the reliance on synthetic fertilizers. However, a deeper understanding of their interactions with plants and other microbes is needed. In this study, we introduce a recently developed label-free 3D quantitative phase imaging technology called dynamic quantitative oblique back-illumination microscopy (DqOBM) to assess the dynamic activity of diazotrophs in vitro and in situ. Our experiments involved three different diazotrophs (Sinorhizobium meliloti, Azotobacter vinelandii, and Rahnella aquatilis) cultured on media with amendments of carbon and nitrogen sources. Over five days, we observed increased dynamic activity in nutrient-amended media. These results suggest that the observed bacterial dynamics correlate with their metabolic activity. Furthermore, we applied qOBM to visualize bacterial activity within the root cap and elongation zone of Arabidopsis thaliana primary roots. This allowed us to identify distinct areas of microbial infiltration in plant roots without the need for fluorescent markers. Our findings demonstrate that DqOBM can effectively characterize microbial activity and provide insights into plant-microbe interactions in situ, offering a valuable tool for advancing our understanding of sustainable agriculture.
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Affiliation(s)
- Caroline Filan
- Georgia Institute of Technology, George W. Woodruff School of Mechanical Engineering, Atlanta, GA, 30318, USA
| | - Madison Green
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30318, USA
| | - Abigail Diering
- Georgia Institute of Technology, School of Chemistry and Biochemistry, Atlanta, GA, 30332, USA
| | - Marcus T. Cicerone
- Georgia Institute of Technology, School of Chemistry and Biochemistry, Atlanta, GA, 30332, USA
| | - Lily S. Cheung
- Georgia Institute of Technology, School of Chemical and Biomolecular Engineering, Atlanta, GA, 30332, USA
| | - Joel E. Kostka
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30318, USA
| | - Francisco E. Robles
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, GA, 30318, USA
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7
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Nikolić S, Oasa S, Krmpot AJ, Terenius L, Belić MR, Rigler R, Vukojević V. Mapping the Direction of Nucleocytoplasmic Transport of Glucocorticoid Receptor (GR) in Live Cells Using Two-Foci Cross-Correlation in Massively Parallel Fluorescence Correlation Spectroscopy (mpFCS). Anal Chem 2023; 95:15171-15179. [PMID: 37782779 PMCID: PMC10585663 DOI: 10.1021/acs.analchem.3c01427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 09/15/2023] [Indexed: 10/04/2023]
Abstract
Nucleocytoplasmic transport of transcription factors is vital for normal cellular function, and its breakdown is a major contributing factor in many diseases. The glucocorticoid receptor (GR) is an evolutionarily conserved, ligand-dependent transcription factor that regulates homeostasis and response to stress and is an important target for therapeutics in inflammation and cancer. In unstimulated cells, the GR resides in the cytoplasm bound to other molecules in a large multiprotein complex. Upon stimulation with endogenous or synthetic ligands, GR translocation to the cell nucleus occurs, where the GR regulates the transcription of numerous genes by direct binding to glucocorticoid response elements or by physically associating with other transcription factors. While much is known about molecular mechanisms underlying GR function, the spatial organization of directionality of GR nucleocytoplasmic transport remains less well characterized, and it is not well understood how the bidirectional nucleocytoplasmic flow of GR is coordinated in stimulated cells. Here, we use two-foci cross-correlation in a massively parallel fluorescence correlation spectroscopy (mpFCS) system to map in live cells the directionality of GR translocation at different positions along the nuclear envelope. We show theoretically and experimentally that cross-correlation of signals from two nearby observation volume elements (OVEs) in an mpFCS setup presents a sharp peak when the OVEs are positioned along the trajectory of molecular motion and that the time position of the peak corresponds to the average time of flight of the molecule between the two OVEs. Hence, the direction and velocity of nucleocytoplasmic transport can be determined simultaneously at several locations along the nuclear envelope. We reveal that under ligand-induced GR translocation, nucleocytoplasmic import/export of GR proceeds simultaneously but at different locations in the cell nucleus. Our data show that mpFCS can characterize in detail the heterogeneity of directional nucleocytoplasmic transport in a live cell and may be invaluable for studies aiming to understand how the bidirectional flow of macromolecules through the nuclear pore complex (NPC) is coordinated to avoid intranuclear transcription factor accretion/abatement.
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Affiliation(s)
- Stanko
N. Nikolić
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
- Institute
of Physics Belgrade, University of Belgrade, 11080 Belgrade, Serbia
- Division
of Arts and Sciences, Texas A&M University
at Qatar, Doha, Qatar
| | - Sho Oasa
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
| | - Aleksandar J. Krmpot
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
- Institute
of Physics Belgrade, University of Belgrade, 11080 Belgrade, Serbia
- Division
of Arts and Sciences, Texas A&M University
at Qatar, Doha, Qatar
| | - Lars Terenius
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
| | - Milivoj R. Belić
- Division
of Arts and Sciences, Texas A&M University
at Qatar, Doha, Qatar
| | - Rudolf Rigler
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
| | - Vladana Vukojević
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
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8
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Sankaran J, Wohland T. Current capabilities and future perspectives of FCS: super-resolution microscopy, machine learning, and in vivo applications. Commun Biol 2023; 6:699. [PMID: 37419967 PMCID: PMC10328937 DOI: 10.1038/s42003-023-05069-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
Fluorescence correlation spectroscopy (FCS) is a single molecule sensitive tool for the quantitative measurement of biomolecular dynamics and interactions. Improvements in biology, computation, and detection technology enable real-time FCS experiments with multiplexed detection even in vivo. These new imaging modalities of FCS generate data at the rate of hundreds of MB/s requiring efficient data processing tools to extract information. Here, we briefly review FCS's capabilities and limitations before discussing recent directions that address these limitations with a focus on imaging modalities of FCS, their combinations with super-resolution microscopy, new evaluation strategies, especially machine learning, and applications in vivo.
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Affiliation(s)
- Jagadish Sankaran
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138632, Singapore.
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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9
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Latreille PL, Rabanel JM, Le Goas M, Salimi S, Arlt J, Patten SA, Ramassamy C, Hildgen P, Martinez VA, Banquy X. In Situ Characterization of the Protein Corona of Nanoparticles In Vitro and In Vivo. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2203354. [PMID: 35901787 DOI: 10.1002/adma.202203354] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/23/2022] [Indexed: 06/15/2023]
Abstract
A new theoretical framework that enables the use of differential dynamic microscopy (DDM) in fluorescence imaging mode to quantify in situ protein adsorption onto nanoparticles (NP) while simultaneously monitoring for NP aggregation is proposed. This methodology is used to elucidate the thermodynamic and kinetic properties of the protein corona (PC) in vitro and in vivo. The results show that protein adsorption triggers particle aggregation over a wide concentration range and that the formed aggregate structures can be quantified using the proposed methodology. Protein affinity for polystyrene (PS) NPs is observed to be dependent on particle concentration. For complex protein mixtures, this methodology identifies that the PC composition changes with the dilution of serum proteins, demonstrating a Vroman effect never quantitatively assessed in situ on NPs. Finally, DDM allows monitoring of the evolution of the PC in vivo. This results show that the PC composition evolves significantly over time in zebrafish larvae, confirming the inherently dynamic nature of the PC. The performance of the developed methodology allows to obtain quantitative insights into nano-bio interactions in a vast array of physiologically relevant conditions that will serve to further improve the design of nanomedicine.
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Affiliation(s)
- Pierre-Luc Latreille
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Jean-Michel Rabanel
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, Québec, H3C 3J7, Canada
- INRS, Centre Armand Frappier Santé Biotechnologie, 531 Boul des Prairies, Laval, Québec, H7V 1B7, Canada
| | - Marine Le Goas
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Sina Salimi
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Jochen Arlt
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - Shunmoogum A Patten
- INRS, Centre Armand Frappier Santé Biotechnologie, 531 Boul des Prairies, Laval, Québec, H7V 1B7, Canada
| | - Charles Ramassamy
- INRS, Centre Armand Frappier Santé Biotechnologie, 531 Boul des Prairies, Laval, Québec, H7V 1B7, Canada
| | - Patrice Hildgen
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Vincent A Martinez
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - Xavier Banquy
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, Québec, H3C 3J7, Canada
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10
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Casteleiro Costa P, Wang B, Filan C, Bowles-Welch A, Yeago C, Roy K, Robles FE. Functional imaging with dynamic quantitative oblique back-illumination microscopy. JOURNAL OF BIOMEDICAL OPTICS 2022; 27:066502. [PMID: 35773755 PMCID: PMC9243522 DOI: 10.1117/1.jbo.27.6.066502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
SIGNIFICANCE Quantitative oblique back-illumination microscopy (qOBM) is a recently developed label-free imaging technique that enables 3D quantitative phase imaging of thick scattering samples with epi-illumination. Here, we propose dynamic qOBM to achieve functional imaging based on subcellular dynamics, potentially indicative of metabolic activity. We show the potential utility of this novel technique by imaging adherent mesenchymal stromal cells (MSCs) grown in bioreactors, which can help address important unmet needs in cell manufacturing for therapeutics. AIM We aim to develop dynamic qOBM and demonstrate its potential for functional imaging based on cellular and subcellular dynamics. APPROACH To obtain functional images with dynamic qOBM, a sample is imaged over a period of time and its temporal signals are analyzed. The dynamic signals display an exponential frequency response that can be analyzed with phasor analysis. Functional images of the dynamic signatures are obtained by mapping the frequency dynamic response to phasor space and color-coding clustered signals. RESULTS Functional imaging with dynamic qOBM provides unique information related to subcellular activity. The functional qOBM images of MSCs not only improve conspicuity of cells in complex environments (e.g., porous micro-carriers) but also reveal two distinct cell populations with different dynamic behavior. CONCLUSIONS In this work we present a label-free, fast, and scalable functional imaging approach to study and intuitively display cellular and subcellular dynamics. We further show the potential utility of this novel technique to help monitor adherent MSCs grown in bioreactors, which can help achieve quality-by-design of cell products, a significant unmet need in the field of cell therapeutics. This approach also has great potential for dynamic studies of other thick samples, such as organoids.
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Affiliation(s)
- Paloma Casteleiro Costa
- Georgia Institute of Technology, School of Electrical and Computer Engineering, Atlanta, Georgia, United States
| | - Bryan Wang
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
- Georgia Institute of Technology, Marcus Center for Therapeutic Cell Characterization and Manufacturing, Atlanta, Georgia, United States
| | - Caroline Filan
- Georgia Institute of Technology, Nuclear & Radiological Engineering and Medical Physics Program, Atlanta, Georgia, United States
| | - Annie Bowles-Welch
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
- Georgia Institute of Technology, Marcus Center for Therapeutic Cell Characterization and Manufacturing, Atlanta, Georgia, United States
| | - Carolyn Yeago
- Georgia Institute of Technology, Marcus Center for Therapeutic Cell Characterization and Manufacturing, Atlanta, Georgia, United States
| | - Krishnendu Roy
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
- Georgia Institute of Technology, Marcus Center for Therapeutic Cell Characterization and Manufacturing, Atlanta, Georgia, United States
| | - Francisco E. Robles
- Georgia Institute of Technology, School of Electrical and Computer Engineering, Atlanta, Georgia, United States
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
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11
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Bag N, London E, Holowka DA, Baird BA. Transbilayer Coupling of Lipids in Cells Investigated by Imaging Fluorescence Correlation Spectroscopy. J Phys Chem B 2022; 126:2325-2336. [PMID: 35294838 DOI: 10.1021/acs.jpcb.2c00117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plasma membranes host numerous receptors, sensors, and ion channels involved in cellular signaling. Phase separation within the plasma membrane has emerged as a key biophysical regulator of signaling reactions in multiple physiological and pathological contexts. There is much evidence that plasma membrane composition supports the coexistence of liquid-ordered (Lo) and liquid-disordered (Ld) phases or domains at physiological conditions. However, this phase/domain separation is nanoscopic and transient in live cells. It has been recently proposed that transbilayer coupling between the inner and outer leaflets of the plasma membrane is driven by their asymmetric lipid distribution and by dynamic cytoskeleton-lipid composites that contribute to the formation and transience of Lo/Ld phase separation in live cells. In this Perspective, we highlight new approaches to investigate how transbilayer coupling may influence phase separation. For quantitative evaluation of the impact of these interactions, we introduce an experimental strategy centered around Imaging Fluorescence Correlation Spectroscopy (ImFCS), which measures membrane diffusion with very high precision. To demonstrate this strategy, we choose two well-established model systems for transbilayer interactions: cross-linking by multivalent antigen of immunoglobulin E bound to receptor FcεRI and cross-linking by cholera toxin B of GM1 gangliosides. We discuss emerging methods to systematically perturb membrane lipid composition, particularly exchange of outer leaflet lipids with exogenous lipids using methyl alpha cyclodextrin. These selective perturbations may be quantitatively evaluated with ImFCS and other high-resolution biophysical tools to discover novel principles of lipid-mediated phase separation in live cells in the context of their pathophysiological relevance.
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Affiliation(s)
- Nirmalya Bag
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Erwin London
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - David A Holowka
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Barbara A Baird
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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12
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Lyu X, Wang J, Wang J, Yin YS, Zhu Y, Li LL, Huang S, Peng S, Xue B, Liao R, Wang SQ, Long M, Wohland T, Chua BT, Sun Y, Li P, Chen XW, Xu L, Chen FJ, Li P. A gel-like condensation of Cidec generates lipid-permeable plates for lipid droplet fusion. Dev Cell 2021; 56:2592-2606.e7. [PMID: 34508658 DOI: 10.1016/j.devcel.2021.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 05/02/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Membrane contact between intracellular organelles is important in mediating organelle communication. However, the assembly of molecular machinery at membrane contact site and its internal organization correlating with its functional activity remain unclear. Here, we demonstrate that a gel-like condensation of Cidec, a crucial protein for obesity development by facilitating lipid droplet (LD) fusion, occurs at the LD-LD contact site (LDCS) through phase separation. The homomeric interaction between the multivalent N terminus of Cidec is sufficient to promote its phase separation both in vivo and in vitro. Interestingly, Cidec condensation at LDCSs generates highly plastic and lipid-permeable fusion plates that are geometrically constrained by donor LDs. In addition, Cidec condensates are distributed unevenly in the fusion plate generating stochastic sub-compartments that may represent unique lipid passageways during LD fusion. We have thus uncovered the organization and functional significance of geometry-constrained Cidec phase separation in mediating LD fusion and lipid homeostasis.
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Affiliation(s)
- Xuchao Lyu
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jia Wang
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianqin Wang
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ye-Sheng Yin
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yun Zhu
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Lin-Lin Li
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Shuangru Huang
- Departments of Biological Sciences and Chemistry and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
| | - Shuang Peng
- Institute of Mechanics, Chinese Academy of Sciences, No.15 Beisihuanxi Road, Beijing 100190, China
| | - Boxin Xue
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Rongyu Liao
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shi-Qiang Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Mian Long
- Institute of Mechanics, Chinese Academy of Sciences, No.15 Beisihuanxi Road, Beijing 100190, China
| | - Thorsten Wohland
- Departments of Biological Sciences and Chemistry and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
| | - Boon Tin Chua
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yujie Sun
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiao-Wei Chen
- State Key Laboratory of Membrane Biology, Center for Life Sciences and Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100101, China
| | - Li Xu
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Shanghai Qi Zhi Institute, Shanghai 200030, China
| | - Feng-Jung Chen
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Shanghai Qi Zhi Institute, Shanghai 200030, China.
| | - Peng Li
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Shanghai Qi Zhi Institute, Shanghai 200030, China.
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13
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Živanović V, Milewska A, Leosson K, Kneipp J. Molecular Structure and Interactions of Lipids in the Outer Membrane of Living Cells Based on Surface-Enhanced Raman Scattering and Liposome Models. Anal Chem 2021; 93:10106-10113. [PMID: 34264630 DOI: 10.1021/acs.analchem.1c00964] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The distribution and interaction of lipids determine the structure and function of the cellular membrane. Surface-enhanced Raman scattering (SERS) is used for selective molecular probing of the cell membrane of living fibroblast cells grown adherently on gold nanoisland substrates across their whole contact areas with the substrate, enabling mapping of the membrane's composition and interaction. From the SERS data, the localization and distribution of different lipids and their interactions, together with proteins in the outer cell membrane, are inferred. Interpretation of the spectra is mainly supported by comparison with the spectra of model liposomes composed of phosphatidylcholine, sphingomyelin, and cholesterol obtained on the same gold substrate. The interaction of the liposomes with the substrate differs from that with gold nanoparticles. The SERS maps indicate colocalization of ordered lipid domains with cholesterol in the living cells. They support the observation of ordered membrane regions of micrometer dimensions in the outer leaflet of the cell membrane that are rich in sphingomyelin. Moreover, the spectra of the living cells contain bands from the groups of the lipid heads, phosphate, choline, and ethanolamine, combined with those from membrane proteins, as indicated by signals assigned to prenyl attachment. Elucidating the composition and structure of lipid membranes in living cells can find application in many fields of research.
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Affiliation(s)
- Vesna Živanović
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, Berlin 12489, Germany
| | - Adrianna Milewska
- Innovation Center Iceland, Árleynir 2-8, Reykjavík 112, Iceland.,The Blood Bank, Landspitali University Hospital, Snorrabraut 60, Reykjavík 105, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Sæmundargötu 2, Reykjavík 101, Iceland
| | - Kristjan Leosson
- Innovation Center Iceland, Árleynir 2-8, Reykjavík 112, Iceland.,Science Institute, University of Iceland, Dunhaga 3, Reykjavík 107, Iceland
| | - Janina Kneipp
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, Berlin 12489, Germany
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14
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Wang J, He Y, Wu Y, Tang P, Wang Y, Tang Z. Cytomembrane visualization using Stokes parameter confocal microscopy. APPLIED OPTICS 2021; 60:5081-5086. [PMID: 34143073 DOI: 10.1364/ao.420892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
A new, to the best of our knowledge, method for Stokes vector imaging is proposed to achieve imaging and dynamic monitoring of a non-labeled cytomembrane. In this work, a polarization state vector is described by a Stokes vector and expressed in chrominance space. A physical quantity called polarization chromaticity value (PCV) corresponding to a Stokes vector is used as the imaging parameter to perform Stokes vector imaging. By using the PCV imaging technique, the Stokes vector can be expressed in three-dimensional real space rather than in a Poincare sphere. Furthermore, a four-way Stokes parameter confocal microscopy system is designed to measure four Stokes parameters simultaneously and obtain micro-imaging. Label-free living onion cell membranes and their plasmolysis process are selected as the representative micro-anisotropy experimental analysis. It is proved that PCV imaging can perform visualization of cytomembranes, and further, microscopic orientation is demonstrated. The prospect of universal measurement of anisotropy details for analysis and diagnosis is provided.
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15
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Dhasmana D, Veerapathiran S, Azbazdar Y, Nelanuthala AVS, Teh C, Ozhan G, Wohland T. Wnt3 Is Lipidated at Conserved Cysteine and Serine Residues in Zebrafish Neural Tissue. Front Cell Dev Biol 2021; 9:671218. [PMID: 34124053 PMCID: PMC8189181 DOI: 10.3389/fcell.2021.671218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/28/2021] [Indexed: 12/22/2022] Open
Abstract
Wnt proteins are a family of hydrophobic cysteine-rich secreted glycoproteins that regulate a gamut of physiological processes involved in embryonic development and tissue homeostasis. Wnt ligands are post-translationally lipidated in the endoplasmic reticulum (ER), a step essential for its membrane targeting, association with lipid domains, secretion and interaction with receptors. However, at which residue(s) Wnts are lipidated remains an open question. Initially it was proposed that Wnts are lipid-modified at their conserved cysteine and serine residues (C77 and S209 in mWnt3a), and mutations in either residue impedes its secretion and activity. Conversely, some studies suggested that serine is the only lipidated residue in Wnts, and substitution of serine with alanine leads to retention of Wnts in the ER. In this work, we investigate whether in zebrafish neural tissues Wnt3 is lipidated at one or both conserved residues. To this end, we substitute the homologous cysteine and serine residues of zebrafish Wnt3 with alanine (C80A and S212A) and investigate their influence on Wnt3 membrane organization, secretion, interaction and signaling activity. Collectively, our results indicate that Wnt3 is lipid modified at its C80 and S212 residues. Further, we find that lipid addition at either C80 or S212 is sufficient for its secretion and membrane organization, while the lipid modification at S212 is indispensable for receptor interaction and signaling.
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Affiliation(s)
- Divya Dhasmana
- Department of Biological Sciences and Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Sapthaswaran Veerapathiran
- Department of Biological Sciences and Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Yagmur Azbazdar
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Izmir, Turkey
| | | | - Cathleen Teh
- Department of Biological Sciences and Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Gunes Ozhan
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Izmir, Turkey
| | - Thorsten Wohland
- Department of Biological Sciences and Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
- Department of Chemistry, National University of Singapore, Singapore, Singapore
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16
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Sankaran J, Balasubramanian H, Tang WH, Ng XW, Röllin A, Wohland T. Simultaneous spatiotemporal super-resolution and multi-parametric fluorescence microscopy. Nat Commun 2021; 12:1748. [PMID: 33741958 PMCID: PMC7979808 DOI: 10.1038/s41467-021-22002-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 02/15/2021] [Indexed: 11/29/2022] Open
Abstract
Super-resolution microscopy and single molecule fluorescence spectroscopy require mutually exclusive experimental strategies optimizing either temporal or spatial resolution. To achieve both, we implement a GPU-supported, camera-based measurement strategy that highly resolves spatial structures (~100 nm), temporal dynamics (~2 ms), and molecular brightness from the exact same data set. Simultaneous super-resolution of spatial and temporal details leads to an improved precision in estimating the diffusion coefficient of the actin binding polypeptide Lifeact and corrects structural artefacts. Multi-parametric analysis of epidermal growth factor receptor (EGFR) and Lifeact suggests that the domain partitioning of EGFR is primarily determined by EGFR-membrane interactions, possibly sub-resolution clustering and inter-EGFR interactions but is largely independent of EGFR-actin interactions. These results demonstrate that pixel-wise cross-correlation of parameters obtained from different techniques on the same data set enables robust physicochemical parameter estimation and provides biological knowledge that cannot be obtained from sequential measurements.
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Affiliation(s)
- Jagadish Sankaran
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Harikrushnan Balasubramanian
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Wai Hoh Tang
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Xue Wen Ng
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Adrian Röllin
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore.
- Department of Chemistry, National University of Singapore, Singapore, Singapore.
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17
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Sankaran J, Wohland T. Fluorescence strategies for mapping cell membrane dynamics and structures. APL Bioeng 2020; 4:020901. [PMID: 32478279 PMCID: PMC7228782 DOI: 10.1063/1.5143945] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 04/17/2020] [Indexed: 12/20/2022] Open
Abstract
Fluorescence spectroscopy has been a cornerstone of research in membrane dynamics and organization. Technological advances in fluorescence spectroscopy went hand in hand with discovery of various physicochemical properties of membranes at nanometric spatial and microsecond timescales. In this perspective, we discuss the various challenges associated with quantification of physicochemical properties of membranes and how various modes of fluorescence spectroscopy have overcome these challenges to shed light on the structure and organization of membranes. Finally, we discuss newer measurement strategies and data analysis tools to investigate the structure, dynamics, and organization of membranes.
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18
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Schneider F, Hernandez-Varas P, Christoffer Lagerholm B, Shrestha D, Sezgin E, Julia Roberti M, Ossato G, Hecht F, Eggeling C, Urbančič I. High photon count rates improve the quality of super-resolution fluorescence fluctuation spectroscopy. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2020; 53:164003. [PMID: 33191951 PMCID: PMC7655148 DOI: 10.1088/1361-6463/ab6cca] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/19/2019] [Accepted: 01/16/2020] [Indexed: 05/15/2023]
Abstract
Probing the diffusion of molecules has become a routine measurement across the life sciences, chemistry and physics. It provides valuable insights into reaction dynamics, oligomerisation, molecular (re-)organisation or cellular heterogeneities. Fluorescence correlation spectroscopy (FCS) is one of the widely applied techniques to determine diffusion dynamics in two and three dimensions. This technique relies on the temporal autocorrelation of intensity fluctuations but recording these fluctuations has thus far been limited by the detection electronics, which could not efficiently and accurately time-tag photons at high count rates. This has until now restricted the range of measurable dye concentrations, as well as the data quality of the FCS recordings, especially in combination with super-resolution stimulated emission depletion (STED) nanoscopy. Here, we investigate the applicability and reliability of (STED-)FCS at high photon count rates (average intensities of more than 1 MHz) using novel detection equipment, namely hybrid detectors and real-time gigahertz sampling of the photon streams implemented on a commercial microscope. By measuring the diffusion of fluorophores in solution and cytoplasm of live cells, as well as in model and cellular membranes, we show that accurate diffusion and concentration measurements are possible in these previously inaccessible high photon count regimes. Specifically, it offers much greater flexibility of experiments with biological samples with highly variable intensity, e.g. due to a wide range of expression levels of fluorescent proteins. In this context, we highlight the independence of diffusion properties of cytosolic GFP in a concentration range of approx. 0.01-1 µm. We further show that higher photon count rates also allow for much shorter acquisition times, and improved data quality. Finally, this approach also pronouncedly increases the robustness of challenging live cell STED-FCS measurements of nanoscale diffusion dynamics, which we testify by confirming a free diffusion pattern for a fluorescent lipid analogue on the apical membrane of adherent cells.
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Affiliation(s)
- Falk Schneider
- MRC Human Immunology Unit and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Pablo Hernandez-Varas
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
- Core Facility for Integrated Microscopy, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - B Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Dilip Shrestha
- MRC Human Immunology Unit and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Erdinc Sezgin
- MRC Human Immunology Unit and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - M Julia Roberti
- Leica Microsystems CMS GmbH, Am Friedensplatz 3, 68163 Mannheim, Germany
| | - Giulia Ossato
- Leica Microsystems CMS GmbH, Am Friedensplatz 3, 68163 Mannheim, Germany
| | - Frank Hecht
- Leica Microsystems CMS GmbH, Am Friedensplatz 3, 68163 Mannheim, Germany
| | - Christian Eggeling
- MRC Human Immunology Unit and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Iztok Urbančič
- MRC Human Immunology Unit and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
- Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
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19
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Togo S, Sato K, Kawamura R, Kobayashi N, Noiri M, Nakabayashi S, Teramura Y, Yoshikawa HY. Quantitative evaluation of the impact of artificial cell adhesion via DNA hybridization on E-cadherin-mediated cell adhesion. APL Bioeng 2020; 4:016103. [PMID: 32002498 PMCID: PMC6984976 DOI: 10.1063/1.5123749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/12/2019] [Indexed: 01/10/2023] Open
Abstract
Programmable cell adhesion with DNA hybridization is a promising approach for fabricating various tissue architectures without sophisticated instrumentation. However, little is known about how this artificial interaction influences the binding of cell adhesion proteins, E-cadherin. In this work, we designed a planar and fluid lipid membrane displaying E-cadherin and/or single-strand DNA with well-defined densities. Visualization of cells on membranes by fluorescence and interference microscopy revealed cell adhesion to be a two-step process: artificial adhesion by DNA hybridization within a few minutes followed by biological adhesion via cadherin-cadherin binding within hours. Furthermore, we discovered that DNA hybridization can substantially facilitate E-cadherin-mediated cell adhesion. The promotive effect is probably due to the enforced binding between E-cadherin molecules in geometrical confinement between two membranes. Our in vitro model of cell adhesion can potentially be used to design functional synthetic molecules that can regulate cell adhesion via cell adhesion proteins for tissue engineering.
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Affiliation(s)
- Shodai Togo
- Department of Chemistry, Saitama University, 338-8570 Saitama, Japan
| | - Ken Sato
- Department of Chemistry, Saitama University, 338-8570 Saitama, Japan
| | | | - Naritaka Kobayashi
- Division of Strategic Research and Development, Saitama University, 338-8570 Saitama, Japan
| | - Makoto Noiri
- Department of Bioengineering, The University of Tokyo, 113-8656 Tokyo, Japan
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20
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Visualizing Biological Membrane Organization and Dynamics. J Mol Biol 2019; 431:1889-1919. [DOI: 10.1016/j.jmb.2019.02.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/02/2019] [Accepted: 02/13/2019] [Indexed: 11/22/2022]
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21
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Gupta A, Sankaran J, Wohland T. Fluorescence correlation spectroscopy: The technique and its applications in soft matter. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2017-0104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Abstract
Fluorescence correlation spectroscopy (FCS) is a well-established single-molecule method used for the quantitative spatiotemporal analysis of dynamic processes in a wide range of samples. It possesses single-molecule sensitivity but provides ensemble averaged molecular parameters such as mobility, concentration, chemical reaction kinetics, photophysical properties and interaction properties. These parameters have been utilized to characterize a variety of soft matter systems. This review provides an overview of the basic principles of various FCS modalities, their instrumentation, data analysis, and the applications of FCS to soft matter systems.
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22
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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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23
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Unsay JD, Murad F, Hermann E, Ries J, García-Sáez AJ. Scanning Fluorescence Correlation Spectroscopy for Quantification of the Dynamics and Interactions in Tube Organelles of Living Cells. Chemphyschem 2018; 19:3273-3278. [PMID: 30335213 DOI: 10.1002/cphc.201800705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Indexed: 01/03/2023]
Abstract
Single-molecule spectroscopic quantification of protein-protein interactions directly in the organelles of living cells is highly desirable but remains challenging. Bulk methods, such as Förster resonance energy transfer (FRET), currently only give a relative quantification of the strength of protein-protein interactions. Here, we introduce tube scanning fluorescence cross-correlation spectroscopy (tubeSFCCS) for the absolute quantification of diffusion and complex formation of fluorescently labeled molecules in the mitochondrial compartments. We determined the extent of association between the apoptosis regulators Bcl-xL and tBid at the mitochondrial outer membrane of living cells and discovered that practically all mitochondria-bound Bcl-xL and tBid are associated with each other, in contrast to undetectable association in the cytosol. Furthermore, we show further applicability of our method to other mitochondrial proteins, as well as to proteins in the endoplasmic reticulum (ER) membrane.
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Affiliation(s)
- Joseph D Unsay
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076, Tübingen, Germany
- Max Planck Insitute for Intteligen Systems, Heisenbergstrasse 3, 70569, Stuttgart, Germany
- German Cancer Research Center, Im Neuenheimer Feld 280, 62120, Heidelberg, Germany
| | - Fabronia Murad
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076, Tübingen, Germany
| | - Eduard Hermann
- Max Planck Insitute for Intteligen Systems, Heisenbergstrasse 3, 70569, Stuttgart, Germany
| | - Jonas Ries
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Ana J García-Sáez
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076, Tübingen, Germany
- Max Planck Insitute for Intteligen Systems, Heisenbergstrasse 3, 70569, Stuttgart, Germany
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24
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Protein oligomerization and mobility within the nuclear envelope evaluated by the time-shifted mean-segmented Q factor. Methods 2018; 157:28-41. [PMID: 30268407 DOI: 10.1016/j.ymeth.2018.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/14/2018] [Accepted: 09/25/2018] [Indexed: 11/21/2022] Open
Abstract
Analysis of fluorescence fluctuation experiments by the mean-segmented Q (MSQ) method was recently used to successfully characterize the oligomeric state and mobility of proteins within the nuclear envelope (NE) of living cells. However, two significant shortcomings of MSQ were recognized. Non-ideal detector behavior due to dead-time and afterpulsing as well as the lack of error analysis currently limit the potential of MSQ. This paper presents time-shifted MSQ (tsMSQ), a new formulation of MSQ that is robust with respect to dead-time and afterpulsing. In addition, a protocol for performing error analysis on tsMSQ data is introduced to assess the quality of fit models and estimate the uncertainties of fit parameters. Together, these developments significantly simplify and improve the analysis of fluorescence fluctuation data taken within the NE. To demonstrate these new developments, tsMSQ was used to characterize the oligomeric state and mobility of the luminal domains of two inner nuclear membrane SUN proteins. The results for the luminal domain of SUN2 obtained through tsMSQ without correction for non-ideal detector effects agree with a recent study that was conducted using the original MSQ formulation. Finally, tsMSQ was applied to characterize the oligomeric state and mobility of the luminal domain of the germline-restricted SUN3.
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Schneider F, Waithe D, Lagerholm BC, Shrestha D, Sezgin E, Eggeling C, Fritzsche M. Statistical Analysis of Scanning Fluorescence Correlation Spectroscopy Data Differentiates Free from Hindered Diffusion. ACS NANO 2018; 12:8540-8546. [PMID: 30028588 PMCID: PMC6117752 DOI: 10.1021/acsnano.8b04080] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/20/2018] [Indexed: 05/28/2023]
Abstract
Cells rely on versatile diffusion dynamics in their plasma membrane. Quantification of this often heterogeneous diffusion is essential to the understanding of cell regulation and function. Yet such measurements remain a major challenge in cell biology, usually due to low sampling throughput, a necessity for dedicated equipment, sophisticated fluorescent label strategies, and limited sensitivity. Here, we introduce a robust, broadly applicable statistical analysis pipeline for large scanning fluorescence correlation spectroscopy data sets, which uncovers the nanoscale heterogeneity of the plasma membrane in living cells by differentiating free from hindered diffusion modes of fluorescent lipid and protein analogues.
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Affiliation(s)
- Falk Schneider
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Dominic Waithe
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - B. Christoffer Lagerholm
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Dilip Shrestha
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Erdinc Sezgin
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Christian Eggeling
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
- Institute of Applied
Optics, Friedrich-Schiller-University and
Leibniz Institute of Photonic Technology, Helmholtzweg 4, 07743 Jena, Germany
| | - Marco Fritzsche
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
- Kennedy
Institute for Rheumatology, University of
Oxford, Roosevelt Drive, Oxford OX3 7LF, United Kingdom
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26
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Lyman E, Hsieh CL, Eggeling C. From Dynamics to Membrane Organization: Experimental Breakthroughs Occasion a "Modeling Manifesto". Biophys J 2018; 115:595-604. [PMID: 30075850 PMCID: PMC6103736 DOI: 10.1016/j.bpj.2018.07.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/29/2018] [Accepted: 07/16/2018] [Indexed: 11/19/2022] Open
Abstract
New experimental techniques, especially in the context of observing molecular dynamics, reveal the plasma membrane to be heterogeneous and "scale rich," from nanometers to microns and from microseconds to seconds. This is critical information, which shows that scale-dependent transport governs the molecular encounters that underlie cellular signaling. The data are rich and reaffirm the importance of the cortical cytoskeleton, protein aggregates, and lipidomic complexity on the statistics of molecular encounters. Moreover, the data demand simulation approaches with a particular set of features, hence the "manifesto." Together with the experimental data, simulations that satisfy these requirements hold the promise of a deeper understanding of membrane spatiotemporal organization. Several experimental breakthroughs in measuring molecular membrane dynamics are reviewed, the constraints that they place on simulations are discussed, and the status of simulation approaches that aim to meet them are detailed.
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Affiliation(s)
- Edward Lyman
- Department of Physics and Astrophysics, University of Delaware, Newark, Delaware; Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware.
| | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taiwan
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Institute of Applied Optics, Friedrich-Schiller-University Jena, Jena, Germany; Leibniz Institute of Photonic Technology, Jena, Germany
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27
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Waithe D, Schneider F, Chojnacki J, Clausen MP, Shrestha D, de la Serna JB, Eggeling C. Optimized processing and analysis of conventional confocal microscopy generated scanning FCS data. Methods 2018; 140-141:62-73. [PMID: 28963070 PMCID: PMC6026296 DOI: 10.1016/j.ymeth.2017.09.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/09/2017] [Accepted: 09/24/2017] [Indexed: 01/18/2023] Open
Abstract
Scanning Fluorescence Correlation Spectroscopy (scanning FCS) is a variant of conventional point FCS that allows molecular diffusion at multiple locations to be measured simultaneously. It enables disclosure of potential spatial heterogeneity in molecular diffusion dynamics and also the acquisition of a large amount of FCS data at the same time, providing large statistical accuracy. Here, we optimize the processing and analysis of these large-scale acquired sets of FCS data. On one hand we present FoCuS-scan, scanning FCS software that provides an end-to-end solution for processing and analysing scanning data acquired on commercial turnkey confocal systems. On the other hand, we provide a thorough characterisation of large-scale scanning FCS data over its intended time-scales and applications and propose a unique solution for the bias and variance observed when studying slowly diffusing species. Our manuscript enables researchers to straightforwardly utilise scanning FCS as a powerful technique for measuring diffusion across a broad range of physiologically relevant length scales without specialised hardware or expensive software.
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Affiliation(s)
- Dominic Waithe
- Wolfson Imaging Centre, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Falk Schneider
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jakub Chojnacki
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mathias P Clausen
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Dilip Shrestha
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jorge Bernardino de la Serna
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Department of Physics, King's College London, London WC2R 2LS, UK
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Wolfson Imaging Centre, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
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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: 1.5] [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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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: 15] [Impact Index Per Article: 2.5] [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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30
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Veerapathiran S, Wohland T. The imaging FCS diffusion law in the presence of multiple diffusive modes. Methods 2017; 140-141:140-150. [PMID: 29203404 DOI: 10.1016/j.ymeth.2017.11.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/24/2017] [Accepted: 11/28/2017] [Indexed: 01/21/2023] Open
Abstract
The cellular plasma membrane is the barrier over which cells exchange materials and communicate with their surroundings, and thus plays the central role in cellular sensing and metabolism. Therefore, the investigation of plasma membrane organization and dynamics is required for understanding of cellular functions. The plasma membrane is a heterogeneous matrix. The presence of structures such as lipid and protein domains and the cytoskeleton meshwork poses a hindrance to the free diffusion of membrane associated biomolecules. However, these domains and the cytoskeleton meshwork barriers are below the optical diffraction limit with potentially short lifetimes and are not easily detected even in super-resolution microscopy. Therefore, dynamic measurements are often used to indirectly prove the existence of domains and barriers by analyzing the mode of diffusion of probe molecules. One of these tools is the Fluorescence Correlation Spectroscopy (FCS) diffusion law. The FCS diffusion law is a plot of diffusion time (τd) versus observation area. For at least three different diffusive modes - free, domain confined, and meshwork hindered hop diffusion - the expected plots have been characterized, typically by its y-intercept (τ0) when fit with a linear model, and have been verified in many cases. However, a description of τ0 has only been given for pure diffusive modes. But in many experimental cases it is not evident that a protein will undergo only one kind of diffusion, and thus the interpretation of the τ0 value is problematic. Here, we therefore address the question about the absolute value of τ0 in the case of complex diffusive modes, i.e. when either one molecule is domain confined and cytoskeleton hindered or when two molecules exhibit different diffusive behavior at the same position in a sample. In addition, we investigate how τ0 changes when the diffusive mode of a probe alters upon disruption of domains or the cytoskeleton by drug treatments. By a combination of experimental studies and simulations, we show that τ0 is not influenced equally by the different diffusive modes as typically found in cellular environments, and that it is the relative change of τ0 rather than its absolute value that provides information on the mode of diffusion.
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Affiliation(s)
- Sapthaswaran Veerapathiran
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore, Singapore; Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore, Singapore.
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31
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Tian X, Zheng H, Mirsaidov U. Aggregation dynamics of nanoparticles at solid-liquid interfaces. NANOSCALE 2017; 9:10044-10050. [PMID: 28685791 DOI: 10.1039/c7nr01985h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The dynamics of molecules or nanoparticles (NPs) at solid-liquid interfaces plays an important role in many natural and industrial processes. However, the effects of a solid-liquid interface on NP motion and on the interactions between these NPs is still not well understood. Here, using in situ liquid cell transmission electron microscopy (TEM), we directly observed the movement of gold NPs and their aggregation dynamics at solid-liquid interfaces. We found that the solid surfaces transiently pin the NPs during their aggregation, dampening their translational and rotational movements. This surface pinning reduces both the movement of NPs and their aggregation rate as the aggregates grow by attachment. However, the pinning of the NP aggregates affects their translational and rotational motions differently. Initially, with increasing aggregate size, the aggregate's translational motion dampens more than its rotational motion. Consequently, the initial aggregation stages are driven by both the translational and rotational motions, whereas the rotational motion dominates the later aggregation stages. Our results provide insight into the movements of NPs and their aggregates at solid-liquid interfaces, which may assist in the future design and control of NP assemblies at interfaces.
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Affiliation(s)
- Xuezeng Tian
- Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, 117557, Singapore
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32
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Yavas S, Macháň R, Wohland T. The Epidermal Growth Factor Receptor Forms Location-Dependent Complexes in Resting Cells. Biophys J 2017; 111:2241-2254. [PMID: 27851946 DOI: 10.1016/j.bpj.2016.09.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 07/25/2016] [Accepted: 09/26/2016] [Indexed: 10/20/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is a prototypical receptor tyrosine kinase involved in cell growth and proliferation and associated with various cancers. It is commonly assumed that after activation by binding of epidermal growth factor to the extracellular domain it dimerizes, followed by autophosphorylation of tyrosine residues at the intracellular domain. However, its oligomerization state before activation is controversial. In the absence of ligands, EGFR has been found in various, inconsistent amounts of monomeric, inactive dimeric, and oligomeric forms. In addition, evidence suggests that the active conformation is not a simple dimer but contains higher oligomers. As experiments in the past have been conducted at different conditions, we investigate here the influence of cell lines (HEK293, COS-7, and CHO-K1), temperature (room temperature and 37°C), and membrane localization on the quantitation of preformed dimers using SW-FCCS, DC-FCCS, quasi PIE-FCCS, and imaging FCCS. While measurement modality, temperature, and localization on upper or lower membranes have only a limited influence on the dimerization amount observed, the cell line and location to periphery versus center of the cell can change dimerization results significantly. The observed dimerization amount is strongly dependent on the expression level of endogenous EGFR in a cell line and shows a strong cell-to-cell variability even within the same cell line. In addition, using imaging FCCS, we find that dimers have a tendency to be found at the periphery of cells compared to central positions.
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Affiliation(s)
- Sibel Yavas
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Radek Macháň
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Thorsten Wohland
- Department of Chemistry, National University of Singapore, Singapore, Singapore; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, Singapore.
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33
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Macháň R, Foo YH, Wohland T. On the Equivalence of FCS and FRAP: Simultaneous Lipid Membrane Measurements. Biophys J 2017; 111:152-61. [PMID: 27410743 DOI: 10.1016/j.bpj.2016.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 06/02/2016] [Accepted: 06/02/2016] [Indexed: 10/21/2022] Open
Abstract
Fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP) are widely used methods to determine diffusion coefficients. However, they often do not yield the same results. With the advent of camera-based imaging FCS, which measures the diffusion coefficient in each pixel of an image, and proper bleaching corrections, it is now possible to measure the diffusion coefficient by FRAP and FCS in the exact same images. We thus performed simultaneous FCS and FRAP measurements on supported lipid bilayers and live cell membranes to test how far the two methods differ in their results and whether the methodological differences, in particular the high bleach intensity in FRAP, the bleach corrections, and the fitting procedures in the two methods explain observed differences. Overall, we find that the FRAP bleach intensity does not measurably influence the diffusion in the samples, but that bleach correction and fitting introduce large uncertainties in FRAP. We confirm our results by simulations.
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Affiliation(s)
- Radek Macháň
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Yong Hwee Foo
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore; Department of Chemistry, National University of Singapore, Singapore.
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Huang S, Lim SY, Gupta A, Bag N, Wohland T. Plasma membrane organization and dynamics is probe and cell line dependent. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:1483-1492. [PMID: 27998689 DOI: 10.1016/j.bbamem.2016.12.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/03/2016] [Accepted: 12/08/2016] [Indexed: 01/01/2023]
Abstract
The action and interaction of membrane receptor proteins take place within the plasma membrane. The plasma membrane, however, is not a passive matrix. It rather takes an active role and regulates receptor distribution and function by its composition and the interaction of its lipid components with embedded and surrounding proteins. Furthermore, it is not a homogenous fluid but contains lipid and protein domains of various sizes and characteristic lifetimes which are important in regulating receptor function and signaling. The precise lateral organization of the plasma membrane, the differences between the inner and outer leaflet, and the influence of the cytoskeleton are still debated. Furthermore, there is a lack of comparisons of the organization and dynamics of the plasma membrane of different cell types. Therefore, we used four different specific membrane markers to test the lateral organization, the differences between the inner and outer membrane leaflet, and the influence of the cytoskeleton of up to five different cell lines, including Chinese hamster ovary (CHO-K1), Human cervical carcinoma (HeLa), neuroblastoma (SH-SY5Y), fibroblast (WI-38) and rat basophilic leukemia (RBL-2H3) cells by Imaging Total Internal Reflection (ITIR)-Fluorescence Correlation Spectroscopy (FCS). We measure diffusion in the temperature range of 298-310K to measure the Arrhenius activation energy (EArr) of diffusion and apply the FCS diffusion law to obtain information on the spatial organization of the probe molecules on the various cell membranes. Our results show clear differences of the FCS diffusion law and EArr for the different probes in dependence of their localization. These differences are similar in the outer and inner leaflet of the membrane. However, these values can differ significantly between different cell lines raising the question how molecular plasma membrane events measured in different cell lines can be compared. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova.
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Affiliation(s)
- Shuangru Huang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore; NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore
| | - Shi Ying Lim
- NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore; Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore
| | - Anjali Gupta
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore; NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore
| | - Nirmalya Bag
- NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore; Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore; NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore; Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore.
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35
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Di Rienzo C, Cardarelli F, Di Luca M, Beltram F, Gratton E. Diffusion Tensor Analysis by Two-Dimensional Pair Correlation of Fluorescence Fluctuations in Cells. Biophys J 2016; 111:841-851. [PMID: 27558727 PMCID: PMC5002073 DOI: 10.1016/j.bpj.2016.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 07/08/2016] [Accepted: 07/08/2016] [Indexed: 11/22/2022] Open
Abstract
In a living cell, the movement of biomolecules is highly regulated by the cellular organization into subcompartments that impose barriers to diffusion, can locally break the spatial isotropy, and ultimately guide these molecules to their targets. Despite the pivotal role of these processes, experimental tools to fully probe the complex connectivity (and accessibility) of the cell interior with adequate spatiotemporal resolution are still lacking. Here, we show how the heterogeneity of molecular dynamics and the location of barriers to molecular motion can be mapped in live cells by exploiting a two-dimensional (2D) extension of the pair correlation function (pCF) analysis. Starting from a time series of images collected for the same field of view, the resulting 2D pCF is calculated in the proximity of each point for each time delay and allows us to probe the spatial distribution of the molecules that started from a given pixel. This 2D pCF yields an accurate description of the preferential diffusive routes. Furthermore, we combine this analysis with the image-derived mean-square displacement approach and gain information on the average nanoscopic molecular displacements in different directions. Through these quantities, we build a fluorescence-fluctuation-based diffusion tensor that contains information on speed and directionality of the local dynamical processes. Contrary to classical fluorescence correlation spectroscopy and related methods, this combined approach can distinguish between isotropic and anisotropic local diffusion. We argue that the measurement of this iMSD tensor will contribute to advance our understanding of the role played by the intracellular environment in the regulation of molecular diffusion at the nanoscale.
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Affiliation(s)
- Carmine Di Rienzo
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro, Pisa, Italy; Center for Nanotechnology Innovation @NEST, Istituto Italiano di Technologia, Piazza San Silvestro, Pisa, Italy.
| | - Francesco Cardarelli
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Technologia, Piazza San Silvestro, Pisa, Italy
| | - Mariagrazia Di Luca
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro, Pisa, Italy
| | - Fabio Beltram
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro, Pisa, Italy; Center for Nanotechnology Innovation @NEST, Istituto Italiano di Technologia, Piazza San Silvestro, Pisa, Italy
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California.
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Bag N, Ng XW, Sankaran J, Wohland T. Spatiotemporal mapping of diffusion dynamics and organization in plasma membranes. Methods Appl Fluoresc 2016; 4:034003. [PMID: 28355150 DOI: 10.1088/2050-6120/4/3/034003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Imaging fluorescence correlation spectroscopy (FCS) and the related FCS diffusion law have been applied in recent years to investigate the diffusion modes of lipids and proteins in membranes. These efforts have provided new insights into the membrane structure below the optical diffraction limit, new information on the existence of lipid domains, and on the influence of the cytoskeleton on membrane dynamics. However, there has been no systematic study to evaluate how domain size, domain density, and the probe partition coefficient affect the resulting imaging FCS diffusion law parameters. Here, we characterize the effects of these factors on the FCS diffusion law through simulations and experiments on lipid bilayers and live cells. By segmenting images into smaller 7 × 7 pixel areas, we can evaluate the FCS diffusion law on areas smaller than 2 µm and thus provide detailed maps of information on the membrane structure and heterogeneity at this length scale. We support and extend this analysis by deriving a mathematical expression to calculate the mean squared displacement (MSDACF) from the autocorrelation function of imaging FCS, and demonstrate that the MSDACF plots depend on the existence of nanoscopic domains. Based on the results, we derive limits for the detection of domains depending on their size, density, and relative viscosity in comparison to the surroundings. Finally, we apply these measurements to bilayers and live cells using imaging total internal reflection FCS and single plane illumination microscopy FCS.
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Affiliation(s)
- Nirmalya Bag
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore. NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
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Marquezin CA, Ceffa NG, Cotelli F, Collini M, Sironi L, Chirico G. Image Cross-Correlation Analysis of Time Varying Flows. Anal Chem 2016; 88:7115-22. [PMID: 27348197 DOI: 10.1021/acs.analchem.6b01143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In vivo studies of blood circulation pathologies have great medical relevance and need methods for the characterization of time varying flows at high spatial and time resolution in small animal models. We test here the efficacy of the combination of image correlation techniques and single plane illumination microscopy (SPIM) in characterizing time varying flows in vitro and in vivo. As indicated by numerical simulations and by in vitro experiments on straight capillaries, the complex analytical form of the cross-correlation function for SPIM detection can be simplified, in conditions of interest for hemodynamics, to a superposition of Gaussian components, easily amenable to the analysis of variable flows. The possibility to select a wide field of view with a good spatial resolution along the collection optical axis and to compute the cross-correlation between regions of interest at varying distances on a single time stack of images allows one to single out periodic flow components from spurious peaks on the cross-correlation functions and to infer the duration of each flow component. We apply this cross-correlation analysis to the blood flow in Zebrafish embryos at 4 days after fertilization, measuring the average speed and the duration of the systolic and diastolic phases.
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Affiliation(s)
- Cassia A Marquezin
- Dipartimento di Fisica e Centro di Nanomedicina, Università di Milano-Bicocca , Piazza della Scienza 3, 20126, Milano, Italy.,Instituto de Física, Universidade Federal de Goiás , Goiânia, Goiás 74.690-900, Brasil
| | - Nicolò G Ceffa
- Dipartimento di Fisica e Centro di Nanomedicina, Università di Milano-Bicocca , Piazza della Scienza 3, 20126, Milano, Italy
| | - Franco Cotelli
- Dipartimento di Bioscienze, Università di Milano , Via Celoria 26, I-20133, Milano, Italy
| | - Maddalena Collini
- Dipartimento di Fisica e Centro di Nanomedicina, Università di Milano-Bicocca , Piazza della Scienza 3, 20126, Milano, Italy
| | - Laura Sironi
- Dipartimento di Fisica e Centro di Nanomedicina, Università di Milano-Bicocca , Piazza della Scienza 3, 20126, Milano, Italy
| | - Giuseppe Chirico
- Dipartimento di Fisica e Centro di Nanomedicina, Università di Milano-Bicocca , Piazza della Scienza 3, 20126, Milano, Italy
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Imaging fluorescence (cross-) correlation spectroscopy in live cells and organisms. Nat Protoc 2015; 10:1948-74. [DOI: 10.1038/nprot.2015.100] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Aβ1-25-Derived Sphingolipid-Domain Tracer Peptide SBD Interacts with Membrane Ganglioside Clusters via a Coil-Helix-Coil Motif. Int J Mol Sci 2015; 16:26318-32. [PMID: 26540054 PMCID: PMC4661814 DOI: 10.3390/ijms161125955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/19/2015] [Accepted: 10/22/2015] [Indexed: 12/30/2022] Open
Abstract
The Amyloid-β (Aβ)-derived, sphingolipid binding domain (SBD) peptide is a fluorescently tagged probe used to trace the diffusion behavior of sphingolipid-containing microdomains in cell membranes through binding to a constellation of glycosphingolipids, sphingomyelin, and cholesterol. However, the molecular details of the binding mechanism between SBD and plasma membrane domains remain unclear. Here, to investigate how the peptide recognizes the lipid surface at an atomically detailed level, SBD peptides in the environment of raft-like bilayers were examined in micro-seconds-long molecular dynamics simulations. We found that SBD adopted a coil-helix-coil structural motif, which binds to multiple GT1b gangliosides via salt bridges and CH–π interactions. Our simulation results demonstrate that the CH–π and electrostatic forces between SBD monomers and GT1b gangliosides clusters are the main driving forces in the binding process. The presence of the fluorescent dye and linker molecules do not change the binding mechanism of SBD probes with gangliosides, which involves the helix-turn-helix structural motif that was suggested to constitute a glycolipid binding domain common to some sphingolipid interacting proteins, including HIV gp120, prion, and Aβ.
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Wu B, Buxbaum AR, Katz ZB, Yoon YJ, Singer RH. Quantifying Protein-mRNA Interactions in Single Live Cells. Cell 2015; 162:211-20. [PMID: 26140598 DOI: 10.1016/j.cell.2015.05.054] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 05/04/2015] [Accepted: 05/19/2015] [Indexed: 11/17/2022]
Abstract
Specific binding proteins are crucial for the correct spatiotemporal expression of mRNA. To understand this process, a method is required to characterize RNA-protein interactions in single living cells with subcellular resolution. We combined endogenous single RNA and protein detection with two-photon fluorescence fluctuation analysis to measure the average number of proteins bound to mRNA at specific locations within live cells. We applied this to quantify the known binding of zipcode binding protein 1 (ZBP1) and ribosomes to β-actin mRNA within subcellular compartments of primary fibroblasts and neurons. ZBP1-mRNA binding did not occur in nuclei, contrary to previous conclusions. ZBP1 interaction with β-actin mRNA was enhanced perinuclearly in neurons compared to fibroblasts. Cytoplasmic ZBP1 and ribosome binding to the mRNA were anti-correlated depending on their location in the cell. These measurements support a mechanism whereby ZBP1 inhibits translation of localizing mRNA until its release from the mRNA peripherally, allowing ribosome binding.
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Affiliation(s)
- Bin Wu
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Adina R Buxbaum
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Zachary B Katz
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Young J Yoon
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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Paramelle D, Nieves D, Brun B, Kraut RS, Fernig DG. Targeting Cell Membrane Lipid Rafts by Stoichiometric Functionalization of Gold Nanoparticles With a Sphingolipid-Binding Domain Peptide. Adv Healthc Mater 2015; 4:911-7. [PMID: 25650337 DOI: 10.1002/adhm.201400730] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/14/2015] [Indexed: 01/15/2023]
Abstract
A non-membrane protein-based nanoparticle agent for the tracking of lipid rafts on live cells is produced by stoichiometric functionalization of gold nanoparticles with a previously characterized sphingolipid- and cell membrane microdomain-binding domain peptide (SBD). The SBD peptide is inserted in a self-assembled monolayer of peptidol and alkane thiol ethylene glycol, on gold nanoparticles surface. The stoichiometric functionalization of nanoparticles with the SBD peptide, essential for single molecule tracking, is achieved by means of non-affinity nanoparticle purification. The SBD-nanoparticles have remarkable long-term resistance to electrolyte-induced aggregation and ligand-exchange and have no detectable non-specific binding to live cells. Binding and diffusion of SBD-nanoparticles bound to the membrane of live cells is measured by real-time photothermal microscopy and shows the dynamics of sphingolipid-enriched microdomains on cells membrane, with evidence for clustering, splitting, and diffusion over time of the SBD-nanoparticle labeled membrane domains. The monofunctionalized SBD-nanoparticle is a promising targeting agent for the tracking of lipid rafts independently of their protein composition and the labelling requires no prior modification of the cells. This approach has potential for further functionalization of the particles to manipulate the organization of, or targeting to microdomains that control signaling events and thereby lead to novel diagnostics and therapeutics.
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Affiliation(s)
- David Paramelle
- Institute of Materials Research and Engineering; A*STAR (Agency for Science Technology and Research); 3 Research Link 117602 Singapore
| | - Daniel Nieves
- Department of Biochemistry; Institute of Integrative Biology; University of Liverpool; Liverpool L69 7ZB UK
| | - Benjamin Brun
- Institute of Materials Research and Engineering; A*STAR (Agency for Science Technology and Research); 3 Research Link 117602 Singapore
| | - Rachel S. Kraut
- School of Biological Sciences; Nanyang Technological University; 50 Nanyang Ave 639798 Singapore
| | - David G. Fernig
- Department of Biochemistry; Institute of Integrative Biology; University of Liverpool; Liverpool L69 7ZB UK
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Pernuš A, Langowski J. Imaging Fos-Jun transcription factor mobility and interaction in live cells by single plane illumination-fluorescence cross correlation spectroscopy. PLoS One 2015; 10:e0123070. [PMID: 25875593 PMCID: PMC4397054 DOI: 10.1371/journal.pone.0123070] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 02/27/2015] [Indexed: 11/20/2022] Open
Abstract
We collected mobility and interaction maps of c-Fos-eGFP and c-Jun-mRFP1 transcription factors within living cell nuclei. c-Fos dimerizes with c-Jun to form the transcription activator protein-1 (AP-1) which binds to the specific recognition site. To monitor this process, we used fluorescence cross-correlation spectroscopy on a single plane illumination microscope (SPIM-FCCS), which provides diffusion coefficient and protein-protein interaction data in the whole image plane simultaneously, instead of just one point on conventional confocal FCS. We find a strong correlation between diffusional mobility and interaction: regions of strong interaction show slow mobility. Controls containing either an eGFP-mRFP dimer, separately expressing eGFP and mRPF, or c-Fos-eGFP and c-Jun-mRFP1 mutants lacking dimerization and DNA-binding domains, showed no such correlation. These results extend our earlier findings from confocal FCCS to include spatial information.
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Affiliation(s)
- Agata Pernuš
- Division Biophysics of Macromolecules, DKFZ, Heidelberg, Germany
| | - Jörg Langowski
- Division Biophysics of Macromolecules, DKFZ, Heidelberg, Germany
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Aigal S, Claudinon J, Römer W. Plasma membrane reorganization: A glycolipid gateway for microbes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:858-71. [PMID: 25450969 DOI: 10.1016/j.bbamcr.2014.11.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/27/2014] [Accepted: 11/11/2014] [Indexed: 02/08/2023]
Abstract
Ligand-receptor interactions, which represent the core for cell signaling and internalization processes are largely affected by the spatial configuration of host cell receptors. There is a growing piece of evidence that receptors are not homogeneously distributed within the plasma membrane, but are rather pre-clustered in nanodomains, or clusters are formed upon ligand binding. Pathogens have evolved many strategies to evade the host immune system and to ensure their survival by hijacking plasma membrane receptors that are most often associated with lipid rafts. In this review, we discuss the early stage molecular and physiological events that occur following ligand binding to host cell glycolipids. The ability of various biological ligands (e.g. toxins, lectins, viruses or bacteria) that bind to glycolipids to induce their own uptake into mammalian cells by creating negative membrane curvature and membrane invaginations is explored. We highlight recent trends in understanding nanoscale plasma membrane (re-)organization and present the benefits of using synthetic membrane systems. This article is part of a Special Issue entitled: Nanoscale membrane organisation and signalling.
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Affiliation(s)
- Sahaja Aigal
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Schänzlestraβe 18, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.
| | - Julie Claudinon
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Schänzlestraβe 18, 79104 Freiburg, Germany
| | - Winfried Römer
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Schänzlestraβe 18, 79104 Freiburg, Germany.
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TrackArt: the user friendly interface for single molecule tracking data analysis and simulation applied to complex diffusion in mica supported lipid bilayers. BMC Res Notes 2014; 7:274. [PMID: 24885944 PMCID: PMC4021860 DOI: 10.1186/1756-0500-7-274] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 04/23/2014] [Indexed: 01/22/2023] Open
Abstract
Background Single molecule tracking (SMT) analysis of fluorescently tagged lipid and protein probes is an attractive alternative to ensemble averaged methods such as fluorescence correlation spectroscopy (FCS) or fluorescence recovery after photobleaching (FRAP) for measuring diffusion in artificial and plasma membranes. The meaningful estimation of diffusion coefficients and their errors is however not straightforward, and is heavily dependent on sample type, acquisition method, and equipment used. Many approaches require advanced computing and programming skills for their implementation. Findings Here we present TrackArt software, an accessible graphic interface for simulation and complex analysis of multiple particle paths. Imported trajectories can be filtered to eliminate spurious or corrupted tracks, and are then analyzed using several previously described methodologies, to yield single or multiple diffusion coefficients, their population fractions, and estimated errors. We use TrackArt to analyze the single-molecule diffusion behavior of a sphingolipid analog SM-Atto647N, in mica supported DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) bilayers. Fitting with a two-component diffusion model confirms the existence of two separate populations of diffusing particles in these bilayers on mica. As a demonstration of the TrackArt workflow, we characterize and discuss the effective activation energies required to increase the diffusion rates of these populations, obtained from Arrhenius plots of temperature-dependent diffusion. Finally, TrackArt provides a simulation module, allowing the user to generate models with multiple particle trajectories, diffusing with different characteristics. Maps of domains, acting as impermeable or permeable obstacles for particles diffusing with given rate constants and diffusion coefficients, can be simulated or imported from an image. Importantly, this allows one to use simulated data with a known diffusion behavior as a comparison for results acquired using particular algorithms on actual, “natural” samples whose diffusion behavior is to be extracted. It can also serve as a tool for demonstrating diffusion principles. Conclusions TrackArt is an open source, platform-independent, Matlab-based graphical user interface, and is easy to use even for those unfamiliar with the Matlab programming environment. TrackArt can be used for accurate simulation and analysis of complex diffusion data, such as diffusion in lipid bilayers, providing publication-quality formatted results.
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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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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: 0.6] [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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Bag N, Yap DHX, Wohland T. Temperature dependence of diffusion in model and live cell membranes characterized by imaging fluorescence correlation spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014. [DOI: 10.1016/j.bbamem.2013.10.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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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: 3.4] [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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Singh AP, Krieger JW, Buchholz J, Charbon E, Langowski J, Wohland T. The performance of 2D array detectors for light sheet based fluorescence correlation spectroscopy. OPTICS EXPRESS 2013; 21:8652-68. [PMID: 23571955 DOI: 10.1364/oe.21.008652] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Single plane illumination microscopy based fluorescence correlation spectroscopy (SPIM-FCS) is a new method for imaging FCS in 3D samples, providing diffusion coefficients, transport, flow velocities and concentrations in an imaging mode. SPIM-FCS records correlation functions over a whole plane in a sample, which requires array detectors for recording the fluorescence signal. Several types of image sensors are suitable for FCS. They differ in properties such as effective area per pixel, quantum efficiency, noise level and read-out speed. Here we compare the performance of several low light array detectors based on three different technologies: (1) Single-photon avalanche diode (SPAD) arrays, (2) passive-pixel electron multiplying charge coupled device (EMCCD) and (3) active-pixel scientific-grade complementary metal oxide semiconductor cameras (sCMOS). We discuss the influence of the detector characteristics on the effective FCS observation volume, and demonstrate that light sheet based SPIM-FCS provides absolute diffusion coefficients. This is verified by parallel measurements with confocal FCS, single particle tracking (SPT), and the determination of concentration gradients in space and time. While EMCCD cameras have a temporal resolution in the millisecond range, sCMOS cameras and SPAD arrays can extend the time resolution of SPIM-FCS down to 10 μs or lower.
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Affiliation(s)
- Anand Pratap Singh
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, 117557, Singapore
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