1
|
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] [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.
Collapse
Affiliation(s)
- Adam W Smith
- Texas Tech University, Department of Chemistry & Biochemistry, Lubbock, TX, USA.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Tang WH, Sim SR, Aik DYK, Nelanuthala AVS, Athilingam T, Röllin A, Wohland T. Deep learning reduces data requirements and allows real-time measurements in imaging FCS. Biophys J 2024; 123:655-666. [PMID: 38050354 PMCID: PMC10995408 DOI: 10.1016/j.bpj.2023.11.3403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/18/2023] [Accepted: 11/30/2023] [Indexed: 12/06/2023] Open
Abstract
Imaging fluorescence correlation spectroscopy (FCS) is a powerful tool to extract information on molecular mobilities, actions, and interactions in live cells, tissues, and organisms. Nevertheless, several limitations restrict its applicability. First, FCS is data hungry, requiring 50,000 frames at 1-ms time resolution to obtain accurate parameter estimates. Second, the data size makes evaluation slow. Third, as FCS evaluation is model dependent, data evaluation is significantly slowed unless analytic models are available. Here, we introduce two convolutional neural networks-FCSNet and ImFCSNet-for correlation and intensity trace analysis, respectively. FCSNet robustly predicts parameters in 2D and 3D live samples. ImFCSNet reduces the amount of data required for accurate parameter retrieval by at least one order of magnitude and makes correct estimates even in moderately defocused samples. Both convolutional neural networks are trained on simulated data, are model agnostic, and allow autonomous, real-time evaluation of imaging FCS measurements.
Collapse
Affiliation(s)
- Wai Hoh Tang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore; Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore; Institute of Digital Molecular Analytics and Science, National University of Singapore, Singapore, Singapore
| | - Shao Ren Sim
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Daniel Ying Kia Aik
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore; Institute of Digital Molecular Analytics and Science, National University of Singapore, Singapore, Singapore; Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Ashwin Venkata Subba Nelanuthala
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | | | - Adrian Röllin
- Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore; Institute of Digital Molecular Analytics and Science, National University of Singapore, Singapore, Singapore; Department of Chemistry, National University of Singapore, Singapore, Singapore.
| |
Collapse
|
4
|
Fang Q, Tomar A, Dunn AK. Wide-field intensity fluctuation imaging. BIOMEDICAL OPTICS EXPRESS 2024; 15:1004-1020. [PMID: 38404351 PMCID: PMC10890890 DOI: 10.1364/boe.506870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/27/2024]
Abstract
The temporal intensity fluctuations contain important information about the light source and light-medium interaction and are typically characterized by the intensity autocorrelation function, g2(τ). The measurement of g2(τ) is a central topic in many optical sensing applications, ranging from stellar intensity interferometer in astrophysics, to fluorescence correlation spectroscopy in biomedical sciences and blood flow measurement with dynamic light scattering. Currently, g2(τ) at a single point is readily accessible through high-frequency sampling of the intensity signal. However, two-dimensional wide-field imaging of g2(τ) is still limited by the cameras' frame rate. We propose and demonstrate a 2-pulse within-exposure modulation approach to break through the camera frame rate limit and obtain the quasi g2(τ) map in wide field with cameras of only ordinary frame rates.
Collapse
Affiliation(s)
- Qingwei Fang
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, USA
| | - Alankrit Tomar
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Andrew K Dunn
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, USA
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Fessl T, Majellaro M, Bondar A. Microscopy and spectroscopy approaches to study GPCR structure and function. Br J Pharmacol 2023. [PMID: 38087925 DOI: 10.1111/bph.16297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/03/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
The GPCR signalling cascade is a key pathway responsible for the signal transduction of a multitude of physical and chemical stimuli, including light, odorants, neurotransmitters and hormones. Understanding the structural and functional properties of the GPCR cascade requires direct observation of signalling processes in high spatial and temporal resolution, with minimal perturbation to endogenous systems. Optical microscopy and spectroscopy techniques are uniquely suited to this purpose because they excel at multiple spatial and temporal scales and can be used in living objects. Here, we review recent developments in microscopy and spectroscopy technologies which enable new insights into GPCR signalling. We focus on advanced techniques with high spatial and temporal resolution, single-molecule methods, labelling strategies and approaches suitable for endogenous systems and large living objects. This review aims to assist researchers in choosing appropriate microscopy and spectroscopy approaches for a variety of applications in the study of cellular signalling.
Collapse
Affiliation(s)
- Tomáš Fessl
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | | | - Alexey Bondar
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Laboratory of Microscopy and Histology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Solano A, Lou J, Scipioni L, Gratton E, Hinde E. Radial pair correlation of molecular brightness fluctuations maps protein diffusion as a function of oligomeric state within live-cell nuclear architecture. Biophys J 2022; 121:2152-2167. [PMID: 35490296 PMCID: PMC9247470 DOI: 10.1016/j.bpj.2022.04.030] [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: 06/08/2021] [Revised: 11/16/2021] [Accepted: 04/26/2022] [Indexed: 11/22/2022] Open
Abstract
Nuclear proteins can modulate their DNA binding activity and the exploration volume available during DNA target search by self-associating into higher-order oligomers. Directly tracking this process in the nucleoplasm of a living cell is, however, a complex task. Thus, here we present a microscopy method based on radial pair correlation of molecular brightness fluctuations (radial pCOMB) that can extract the mobility of a fluorescently tagged nuclear protein as a function of its oligomeric state and spatiotemporally map the anisotropy of this parameter with respect to nuclear architecture. By simply performing a rapid frame scan acquisition, radial pCOMB has the capacity to detect, within each pixel, protein oligomer formation and the size-dependent obstruction nuclear architecture imparts on this complex's transport across sub-micrometer distances. From application of radial pCOMB to an oligomeric transcription factor and DNA repair protein, we demonstrate that homo-oligomer formation differentially regulates chromatin accessibility and interaction with the DNA template.
Collapse
Affiliation(s)
- Ashleigh Solano
- School of Physics, University of Melbourne; Department of Biochemistry and Pharmacology, University of Melbourne
| | - Jieqiong Lou
- School of Physics, University of Melbourne; Department of Biochemistry and Pharmacology, University of Melbourne
| | - Lorenzo Scipioni
- Department of Biomedical Engineering, University of California, Irvine
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine.
| | - Elizabeth Hinde
- School of Physics, University of Melbourne; Department of Biochemistry and Pharmacology, University of Melbourne.
| |
Collapse
|
10
|
Hobson CM, Falvo MR, Superfine R. A survey of physical methods for studying nuclear mechanics and mechanobiology. APL Bioeng 2021; 5:041508. [PMID: 34849443 PMCID: PMC8604565 DOI: 10.1063/5.0068126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/20/2021] [Indexed: 12/23/2022] Open
Abstract
It is increasingly appreciated that the cell nucleus is not only a home for DNA but also a complex material that resists physical deformations and dynamically responds to external mechanical cues. The molecules that confer mechanical properties to nuclei certainly contribute to laminopathies and possibly contribute to cellular mechanotransduction and physical processes in cancer such as metastasis. Studying nuclear mechanics and the downstream biochemical consequences or their modulation requires a suite of complex assays for applying, measuring, and visualizing mechanical forces across diverse length, time, and force scales. Here, we review the current methods in nuclear mechanics and mechanobiology, placing specific emphasis on each of their unique advantages and limitations. Furthermore, we explore important considerations in selecting a new methodology as are demonstrated by recent examples from the literature. We conclude by providing an outlook on the development of new methods and the judicious use of the current techniques for continued exploration into the role of nuclear mechanobiology.
Collapse
Affiliation(s)
| | - Michael R. Falvo
- Department of Physics and Astronomy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Richard Superfine
- Department of Applied Physical Science, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| |
Collapse
|
11
|
Oasa S, Krmpot AJ, Nikolić SN, Clayton AHA, Tsigelny IF, Changeux JP, Terenius L, Rigler R, Vukojević V. Dynamic Cellular Cartography: Mapping the Local Determinants of Oligodendrocyte Transcription Factor 2 (OLIG2) Function in Live Cells Using Massively Parallel Fluorescence Correlation Spectroscopy Integrated with Fluorescence Lifetime Imaging Microscopy (mpFCS/FLIM). Anal Chem 2021; 93:12011-12021. [PMID: 34428029 PMCID: PMC8427561 DOI: 10.1021/acs.analchem.1c02144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Compartmentalization
and integration of molecular
processes through diffusion are basic mechanisms through which cells
perform biological functions. To characterize these mechanisms in
live cells, quantitative and ultrasensitive analytical methods with
high spatial and temporal resolution are needed. Here, we present
quantitative scanning-free confocal microscopy with single-molecule
sensitivity, high temporal resolution (∼10 μs/frame),
and fluorescence lifetime imaging capacity, developed by integrating
massively parallel fluorescence correlation spectroscopy with fluorescence
lifetime imaging microscopy (mpFCS/FLIM); we validate the method,
use it to map in live cell location-specific variations in the concentration,
diffusion, homodimerization, DNA binding, and local environment of
the oligodendrocyte transcription factor 2 fused with the enhanced
Green Fluorescent Protein (OLIG2-eGFP), and characterize the effects
of an allosteric inhibitor of OLIG2 dimerization on these determinants
of OLIG2 function. In particular, we show that cytoplasmic OLIG2-eGFP
is largely monomeric and freely diffusing, with the fraction of freely
diffusing OLIG2-eGFP molecules being fD,freecyt = (0.75
± 0.10) and the diffusion time τD,freecyt = (0.5 ± 0.3) ms. In contrast,
OLIG2-eGFP homodimers are abundant in the cell nucleus, constituting
∼25% of the nuclear pool, some fD,boundnuc = (0.65
± 0.10) of nuclear OLIG2-eGFP is bound to chromatin DNA, whereas
freely moving OLIG2-eGFP molecules diffuse at the same rate as those
in the cytoplasm, as evident from the lateral diffusion times τD,freenuc = τD,freecyt = (0.5
± 0.3) ms. OLIG2-eGFP interactions with chromatin DNA, revealed
through their influence on the apparent diffusion behavior of OLIG2-eGFP,
τD,boundnuc (850 ± 500) ms, are characterized by an apparent dissociation
constant Kd,appOLIG2-DNA = (45 ± 30) nM. The apparent
dissociation constant of OLIG2-eGFP homodimers was estimated to be Kd,app(OLIG2-eGFP)2 ≈ 560 nM. The allosteric inhibitor of OLIG2 dimerization,
compound NSC 50467, neither affects OLIG2-eGFP properties in the cytoplasm
nor does it alter the overall cytoplasmic environment. In contrast,
it significantly impedes OLIG2-eGFP homodimerization in the cell nucleus,
increasing five-fold the apparent dissociation constant, Kd,app,NSC50467(OLIG2-eGFP)2 ≈ 3 μM, thus reducing homodimer levels to below 7%
and effectively abolishing OLIG2-eGFP specific binding to chromatin
DNA. The mpFCS/FLIM methodology has a myriad of applications in biomedical
research and pharmaceutical industry. For example, it is indispensable
for understanding how biological functions emerge through the dynamic
integration of location-specific molecular processes and invaluable
for drug development, as it allows us to quantitatively characterize
the interactions of drugs with drug targets in live cells.
Collapse
Affiliation(s)
- Sho Oasa
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden
| | - Aleksandar J Krmpot
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden.,Institute of Physics Belgrade, University of Belgrade, 11080 Belgrade, Serbia
| | - Stanko N Nikolić
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden.,Institute of Physics Belgrade, University of Belgrade, 11080 Belgrade, Serbia
| | - Andrew H A Clayton
- Optical Sciences Centre, Department of Physics and Astronomy, School of Science, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Igor F Tsigelny
- Department of Neurosciences, University of California San Diego, La Jolla, California 92093-0819, United States
| | - Jean-Pierre Changeux
- Department of Neuroscience, Unité Neurobiologie Intégrative des Systèmes Cholinergiques, Institut Pasteur, F-75724 Paris 15, France
| | - Lars Terenius
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden
| | - Rudolf Rigler
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden.,Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, 17177 Stockholm, Sweden
| | - Vladana Vukojević
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Yoshida S, Schmid W, Vo N, Calabrase W, Kisley L. Computationally-efficient spatiotemporal correlation analysis super-resolves anomalous diffusion. OPTICS EXPRESS 2021; 29:7616-7629. [PMID: 33726259 DOI: 10.1364/oe.416465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
Anomalous diffusion dynamics in confined nanoenvironments govern the macroscale properties and interactions of many biophysical and material systems. Currently, it is difficult to quantitatively link the nanoscale structure of porous media to anomalous diffusion within them. Fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) has been shown to extract nanoscale structure and Brownian diffusion dynamics within gels, liquid crystals, and polymers, but has limitations which hinder its wider application to more diverse, biophysically-relevant datasets. Here, we parallelize the least-squares curve fitting step on a GPU improving computation times by up to a factor of 40, implement anomalous diffusion and two-component Brownian diffusion models, and make fcsSOFI more accessible by packaging it in a user-friendly GUI. We apply fcsSOFI to simulations of the protein fibrinogen diffusing in polyacrylamide of varying matrix densities and super-resolve locations where slower, anomalous diffusion occurs within smaller, confined pores. The improvements to fcsSOFI in speed, scope, and usability will allow for the wider adoption of super-resolution correlation analysis to diverse research topics.
Collapse
|
15
|
Schneider F, Colin-York H, Fritzsche M. Quantitative Bio-Imaging Tools to Dissect the Interplay of Membrane and Cytoskeletal Actin Dynamics in Immune Cells. Front Immunol 2021; 11:612542. [PMID: 33505401 PMCID: PMC7829180 DOI: 10.3389/fimmu.2020.612542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Cellular function is reliant on the dynamic interplay between the plasma membrane and the actin cytoskeleton. This critical relationship is of particular importance in immune cells, where both the cytoskeleton and the plasma membrane work in concert to organize and potentiate immune signaling events. Despite their importance, there remains a critical gap in understanding how these respective dynamics are coupled, and how this coupling in turn may influence immune cell function from the bottom up. In this review, we highlight recent optical technologies that could provide strategies to investigate the simultaneous dynamics of both the cytoskeleton and membrane as well as their interplay, focusing on current and future applications in immune cells. We provide a guide of the spatio-temporal scale of each technique as well as highlighting novel probes and labels that have the potential to provide insights into membrane and cytoskeletal dynamics. The quantitative biophysical tools presented here provide a new and exciting route to uncover the relationship between plasma membrane and cytoskeletal dynamics that underlies immune cell function.
Collapse
Affiliation(s)
- Falk Schneider
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Huw Colin-York
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Marco Fritzsche
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
- Rosalind Franklin Institute, Harwell Campus, Didcot, United Kingdom
| |
Collapse
|
16
|
Auer JMT, Stoddart JJ, Christodoulou I, Lima A, Skouloudaki K, Hall HN, Vukojević V, Papadopoulos DK. Of numbers and movement - understanding transcription factor pathogenesis by advanced microscopy. Dis Model Mech 2020; 13:dmm046516. [PMID: 33433399 PMCID: PMC7790199 DOI: 10.1242/dmm.046516] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Transcription factors (TFs) are life-sustaining and, therefore, the subject of intensive research. By regulating gene expression, TFs control a plethora of developmental and physiological processes, and their abnormal function commonly leads to various developmental defects and diseases in humans. Normal TF function often depends on gene dosage, which can be altered by copy-number variation or loss-of-function mutations. This explains why TF haploinsufficiency (HI) can lead to disease. Since aberrant TF numbers frequently result in pathogenic abnormalities of gene expression, quantitative analyses of TFs are a priority in the field. In vitro single-molecule methodologies have significantly aided the identification of links between TF gene dosage and transcriptional outcomes. Additionally, advances in quantitative microscopy have contributed mechanistic insights into normal and aberrant TF function. However, to understand TF biology, TF-chromatin interactions must be characterised in vivo, in a tissue-specific manner and in the context of both normal and altered TF numbers. Here, we summarise the advanced microscopy methodologies most frequently used to link TF abundance to function and dissect the molecular mechanisms underlying TF HIs. Increased application of advanced single-molecule and super-resolution microscopy modalities will improve our understanding of how TF HIs drive disease.
Collapse
Affiliation(s)
- Julia M T Auer
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | - Jack J Stoddart
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | | | - Ana Lima
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | | | - Hildegard N Hall
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | - Vladana Vukojević
- Center for Molecular Medicine (CMM), Department of Clinical Neuroscience, Karolinska Institutet, 17176 Stockholm, Sweden
| | | |
Collapse
|
17
|
Dawes ML, Soeller C, Scholpp S. Studying molecular interactions in the intact organism: fluorescence correlation spectroscopy in the living zebrafish embryo. Histochem Cell Biol 2020; 154:507-519. [PMID: 33067656 PMCID: PMC7609432 DOI: 10.1007/s00418-020-01930-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2020] [Indexed: 02/07/2023]
Abstract
Cell behaviour and function is determined through the interactions of a multitude of molecules working in concert. To observe these molecular dynamics, biophysical studies have been developed that track single interactions. Fluorescence correlation spectroscopy (FCS) is an optical biophysical technique that non-invasively resolves single molecules through recording the signal intensity at the femtolitre scale. However, recording the behaviour of these biomolecules using in vitro-based assays often fails to recapitulate the full range of variables in vivo that directly confer dynamics. Therefore, there has been an increasing interest in observing the state of these biomolecules within living organisms such as the zebrafish Danio rerio. In this review, we explore the advancements of FCS within the zebrafish and compare and contrast these findings to those found in vitro.
Collapse
Affiliation(s)
- Michael L Dawes
- Living Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Christian Soeller
- Living Systems Institute, College of Engineering, Mathematics, and Physical Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Steffen Scholpp
- Living Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK.
| |
Collapse
|
18
|
Hobson CM, O'Brien ET, Falvo MR, Superfine R. Combined Selective Plane Illumination Microscopy and FRAP Maps Intranuclear Diffusion of NLS-GFP. Biophys J 2020; 119:514-524. [PMID: 32681822 DOI: 10.1016/j.bpj.2020.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/16/2020] [Accepted: 07/02/2020] [Indexed: 11/27/2022] Open
Abstract
Since its initial development in 1976, fluorescence recovery after photobleaching (FRAP) has been one of the most popular tools for studying diffusion and protein dynamics in living cells. Its popularity is derived from the widespread availability of confocal microscopes and the relative ease of the experiment and analysis. FRAP, however, is limited in its ability to resolve spatial heterogeneity. Here, we combine selective plane illumination microscopy (SPIM) and FRAP to create SPIM-FRAP, wherein we use a sheet of light to bleach a two-dimensional (2D) plane and subsequently image the recovery of the same image plane. This provides simultaneous quantification of diffusion or protein recovery for every pixel in a given 2D slice, thus moving FRAP measurements beyond these previous limitations. We demonstrate this technique by mapping both intranuclear diffusion of NLS-GFP and recovery of 53BP1-mCherry, a marker for DNA damage, in live MDA-MB-231 cells. SPIM-FRAP proves to be an order of magnitude faster than fluorescence-correlation-spectroscopy-based techniques for such measurements. We observe large length-scale (>∼500 nm) heterogeneity in the recovery times of NLS-GFP, which is validated against simulated data sets. 2D maps of NLS-GFP recovery times showed no pixel-by-pixel correlation with histone density, although slower diffusion was observed in nucleoli. Additionally, recovery of 53BP1-mCherry was observed to be slowed at sites of DNA damage. We finally developed a diffusion simulation for our SPIM-FRAP experiments to compare across techniques. Our measured diffusion coefficients are on the order of previously reported results, thus validating the quantitative accuracy of SPIM-FRAP relative to well-established methods. With the recent rise of accessibility of SPIM systems, SPIM-FRAP is set to provide a straightforward means of quantifying the spatial distribution of protein recovery or diffusion in living cells.
Collapse
Affiliation(s)
- Chad M Hobson
- Department of Physics and Astronomy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
| | - E Timothy O'Brien
- Department of Physics and Astronomy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael R Falvo
- Department of Physics and Astronomy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Richard Superfine
- Department of Applied Physical Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
| |
Collapse
|
19
|
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: 14] [Impact Index Per Article: 3.5] [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.
Collapse
|
20
|
Rehó B, Lau L, Mocsár G, Müller G, Fadel L, Brázda P, Nagy L, Tóth K, Vámosi G. Simultaneous Mapping of Molecular Proximity and Comobility Reveals Agonist-Enhanced Dimerization and DNA Binding of Nuclear Receptors. Anal Chem 2020; 92:2207-2215. [PMID: 31870146 DOI: 10.1021/acs.analchem.9b04902] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Single Plane Illumination Microscopy (SPIM) revolutionized time lapse imaging of live cells and organisms due to its high speed and reduced photodamage. Quantitative mapping of molecular (co)mobility by fluorescence (cross-)correlation spectroscopy (F(C)CS) in a SPIM has been introduced to reveal molecular diffusion and binding. A complementary aspect of interactions is proximity, which can be studied by Förster resonance energy transfer (FRET). Here, we extend SPIM-FCCS by alternating laser excitation, which reduces false positive cross-correlation and facilitates comapping of FRET. Thus, different aspects of interacting systems can be studied simultaneously, and molecular subpopulations can be discriminated by multiparameter analysis. After demonstrating the benefits of the method on the AP-1 transcription factor, the dimerization and DNA binding behavior of retinoic acid receptor (RAR) and retinoid X receptor (RXR) is revealed, and an extension of the molecular switch model of the nuclear receptor action is proposed. Our data imply that RAR agonist enhances RAR-RXR heterodimerization, and chromatin binding/dimerization are positively correlated. We also propose a ligand induced conformational change bringing the N-termini of RAR and RXR closer together. The RXR agonist increased homodimerization of RXR suggesting that RXR may act as an autonomous transcription factor.
Collapse
Affiliation(s)
- Bálint Rehó
- Department of Biophysics and Cell Biology, Doctoral School of Molecular Medicine, Faculty of Medicine , University of Debrecen , Egyetem tér 1 , H-4032 Debrecen , Hungary
| | - Lukas Lau
- Division Biophysics of Macromolecules , German Cancer Research Center , Im Neuenheimer Feld 280 , D-69120 Heidelberg , Germany
| | - Gábor Mocsár
- Department of Biophysics and Cell Biology, Doctoral School of Molecular Medicine, Faculty of Medicine , University of Debrecen , Egyetem tér 1 , H-4032 Debrecen , Hungary
| | - Gabriele Müller
- Division Biophysics of Macromolecules , German Cancer Research Center , Im Neuenheimer Feld 280 , D-69120 Heidelberg , Germany
| | - Lina Fadel
- Department of Biophysics and Cell Biology, Doctoral School of Molecular Medicine, Faculty of Medicine , University of Debrecen , Egyetem tér 1 , H-4032 Debrecen , Hungary
| | - Péter Brázda
- Department of Biochemistry and Molecular Biology, Faculty of Medicine , University of Debrecen , Egyetem tér 1 , H-4032 Debrecen , Hungary
| | - László Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine , University of Debrecen , Egyetem tér 1 , H-4032 Debrecen , Hungary.,Johns Hopkins University School of Medicine , Department of Medicine and Biological Chemistry, Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital , 600 Fifth Street South Saint Petersburg , Florida 33701-4634 , United States
| | - Katalin Tóth
- Division Biophysics of Macromolecules , German Cancer Research Center , Im Neuenheimer Feld 280 , D-69120 Heidelberg , Germany
| | - György Vámosi
- Department of Biophysics and Cell Biology, Doctoral School of Molecular Medicine, Faculty of Medicine , University of Debrecen , Egyetem tér 1 , H-4032 Debrecen , Hungary
| |
Collapse
|
21
|
Li Y, Zhao L, Yao Y, Guo X. Single-Molecule Nanotechnologies: An Evolution in Biological Dynamics Detection. ACS APPLIED BIO MATERIALS 2019; 3:68-85. [DOI: 10.1021/acsabm.9b00840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Lihua Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Yuan Yao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| |
Collapse
|
22
|
Azbazdar Y, Ozalp O, Sezgin E, Veerapathiran S, Duncan AL, Sansom MSP, Eggeling C, Wohland T, Karaca E, Ozhan G. More Favorable Palmitic Acid Over Palmitoleic Acid Modification of Wnt3 Ensures Its Localization and Activity in Plasma Membrane Domains. Front Cell Dev Biol 2019; 7:281. [PMID: 31803740 PMCID: PMC6873803 DOI: 10.3389/fcell.2019.00281] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/31/2019] [Indexed: 12/17/2022] Open
Abstract
While the lateral organization of plasma membrane components has been shown to control binding of Wnt ligands to their receptors preferentially in the ordered membrane domains, the role of posttranslational lipid modification of Wnt on this selective binding is unknown. Here, we identify that the canonical Wnt is presumably acylated by palmitic acid, a saturated 16-carbon fatty acid, at a conserved serine residue. Acylation of Wnt3 is dispensable for its secretion and binding to Fz8 while it is essential for Wnt3's proper binding and domain-like diffusion in the ordered membrane domains. We further unravel that non-palmitoylated Wnt3 is unable to activate Wnt/β-catenin signaling either in zebrafish embryos or in mammalian cells. Based on these results, we propose that the lipidation of canonical Wnt, presumably by a saturated fatty acid, determines its competence in interacting with the receptors in the appropriate domains of the plasma membrane, ultimately keeping the signaling activity under control.
Collapse
Affiliation(s)
- Yagmur Azbazdar
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, Izmir, Turkey
| | - Ozgun Ozalp
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, Izmir, Turkey
| | - Erdinc Sezgin
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Sapthaswaran Veerapathiran
- Department of Biological Sciences and Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Anna L. Duncan
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Department of Super-Resolution Microscopy, Institute for Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Jena, Germany
- Department of Biophysical Imaging, Leibniz Institute of Photonic Technology e.V., Jena, Germany
| | - 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
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, Izmir, Turkey
| | - Gunes Ozhan
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, Izmir, Turkey
| |
Collapse
|
23
|
Sankaran J, Tan NJHJ, But KP, Cohen Y, Rice SA, Wohland T. Single microcolony diffusion analysis in Pseudomonas aeruginosa biofilms. NPJ Biofilms Microbiomes 2019; 5:35. [PMID: 31728202 PMCID: PMC6841743 DOI: 10.1038/s41522-019-0107-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 10/04/2019] [Indexed: 01/25/2023] Open
Abstract
The influence of the biofilm matrix on molecular diffusion is commonly hypothesized to be responsible for emergent characteristics of biofilms such as nutrient trapping, signal accumulation and antibiotic tolerance. Hence quantifying the molecular diffusion coefficient is important to determine whether there is an influence of biofilm microenvironment on the mobility of molecules. Here, we use single plane illumination microscopy fluorescence correlation spectroscopy (SPIM-FCS) to obtain 3D diffusion coefficient maps with micrometre spatial and millisecond temporal resolution of entire Pseudomonas aeruginosa microcolonies. We probed how molecular properties such as size and charge as well as biofilm properties such as microcolony size and depth influence diffusion of fluorescently labelled dextrans inside biofilms. The 2 MDa dextran showed uneven penetration and a reduction in diffusion coefficient suggesting that the biofilm acts as a molecular sieve. Its diffusion coefficient was negatively correlated with the size of the microcolony. Positively charged dextran molecules and positively charged antibiotic tobramycin preferentially partitioned into the biofilm and remained mobile inside the microcolony, albeit with a reduced diffusion coefficient. Lastly, we measured changes of diffusion upon induction of dispersal and detected an increase in diffusion coefficient inside the biofilm before any loss of biomass. Thus, the change in diffusion is a proxy to detect early stages of dispersal. Our work shows that 3D diffusion maps are very sensitive to physiological changes in biofilms, viz. dispersal. However, this study also shows that diffusion, as mediated by the biofilm matrix, does not account for the high level of antibiotic tolerance associated with biofilms.
Collapse
Affiliation(s)
- Jagadish Sankaran
- 1Department of Biological Sciences, National University of Singapore, 117558 Singapore, Singapore.,2Centre for BioImaging Sciences, National University of Singapore, 117557 Singapore, Singapore
| | - Nicholas J H J Tan
- 3Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551 Singapore, Singapore.,4School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore
| | - Ka Pui But
- 2Centre for BioImaging Sciences, National University of Singapore, 117557 Singapore, Singapore.,5Department of Chemistry, National University of Singapore, 117543 Singapore, Singapore
| | - Yehuda Cohen
- 3Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551 Singapore, Singapore.,4School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore
| | - Scott A Rice
- 3Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551 Singapore, Singapore.,4School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore.,6ithree Institute, University of Technology Sydney, Sydney, Australia
| | - Thorsten Wohland
- 1Department of Biological Sciences, National University of Singapore, 117558 Singapore, Singapore.,2Centre for BioImaging Sciences, National University of Singapore, 117557 Singapore, Singapore.,5Department of Chemistry, National University of Singapore, 117543 Singapore, Singapore
| |
Collapse
|
24
|
Su D, Hou Y, Dong C, Ren J. Fluctuation correlation spectroscopy and its applications in homogeneous analysis. Anal Bioanal Chem 2019; 411:4523-4540. [DOI: 10.1007/s00216-019-01884-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/12/2019] [Accepted: 04/29/2019] [Indexed: 12/11/2022]
|
25
|
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.
Collapse
|
26
|
Cutrale F, Rodriguez D, Hortigüela V, Chiu CL, Otterstrom J, Mieruszynski S, Seriola A, Larrañaga E, Raya A, Lakadamyali M, Fraser SE, Martinez E, Ojosnegros S. Using enhanced number and brightness to measure protein oligomerization dynamics in live cells. Nat Protoc 2019; 14:616-638. [DOI: 10.1038/s41596-018-0111-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
27
|
Betaneli V, Mücksch J, Schwille P. Fluorescence Correlation Spectroscopy to Examine Protein-Lipid Interactions in Membranes. Methods Mol Biol 2019; 2003:415-447. [PMID: 31218628 DOI: 10.1007/978-1-4939-9512-7_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a versatile technique to study membrane dynamics and protein-lipid interactions. It can provide information about diffusion coefficients, concentrations, and molecular interactions of proteins and lipids in the membrane. These parameters allow for the determination of protein partitioning into different lipid environments, the identification of lipid domains, and the detection of lipid-protein complexes on the membrane. During the last decades, FCS studies were successfully performed on model membrane systems as also on living cells, to characterize protein-lipid interactions. Recent developments of the method described here improved quantitative measurements on membranes and decreased the number of potential artifacts. The aim of this chapter is to provide the reader with the necessary information and some practical guidelines to perform FCS studies on artificial and cellular membranes.
Collapse
Affiliation(s)
- Viktoria Betaneli
- Medical Faculty "Carl Gustav Carus", Institute of Physiological Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Jonas Mücksch
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Martinsried, Germany.
| |
Collapse
|
28
|
Chatterjee K, Pratiwi FW, Wu FCM, Chen P, Chen BC. Recent Progress in Light Sheet Microscopy for Biological Applications. APPLIED SPECTROSCOPY 2018; 72:1137-1169. [PMID: 29926744 DOI: 10.1177/0003702818778851] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The introduction of light sheet fluorescence microscopy (LSFM) has overcome the challenges in conventional optical microscopy. Among the recent breakthroughs in fluorescence microscopy, LSFM had been proven to provide a high three-dimensional spatial resolution, high signal-to-noise ratio, fast imaging acquisition rate, and minuscule levels of phototoxic and photodamage effects. The aforementioned auspicious properties are crucial in the biomedical and clinical research fields, covering a broad range of applications: from the super-resolution imaging of intracellular dynamics in a single cell to the high spatiotemporal resolution imaging of developmental dynamics in an entirely large organism. In this review, we provided a systematic outline of the historical development of LSFM, detailed discussion on the variants and improvements of LSFM, and delineation on the most recent technological advancements of LSFM and its potential applications in single molecule/particle detection, single-molecule super-resolution imaging, imaging intracellular dynamics of a single cell, multicellular imaging: cell-cell and cell-matrix interactions, plant developmental biology, and brain imaging and developmental biology.
Collapse
Affiliation(s)
- Krishnendu Chatterjee
- 1 Nanoscience and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- 3 Department of Engineering and System Science, National Tsing-Hua University, Hsinchu, Taiwan
| | - Feby Wijaya Pratiwi
- 1 Nanoscience and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- 4 Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | | | - Peilin Chen
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Bi-Chang Chen
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
29
|
|
30
|
Random Motion of Chromatin Is Influenced by Lamin A Interconnections. Biophys J 2018; 114:2465-2472. [PMID: 29759373 DOI: 10.1016/j.bpj.2018.04.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/11/2018] [Accepted: 04/19/2018] [Indexed: 01/30/2023] Open
Abstract
Using fluorescence correlation spectroscopy in single-plane illumination microscopy, we investigated the dynamics of chromatin in interphase mouse adult fibroblast cell nuclei under the influence of the intermediate filament protein lamin A. We find that 1) lamin A-eGFP and histone H2A-mRFP show significant comobility, indicating that their motions are clearly interconnected in the nucleus, and 2) that the random motion of histones H2A within the chromatin network is subdiffusive, i.e., the effective diffusion coefficient decreases for slow timescales. Knocking out lamin A changes the diffusion back to normal. Thus, lamin A influences the dynamics of the entire chromatin network. Our conclusion is that lamin A plays a central role in determining the viscoelasticity of the chromatin network and helping to maintain local ordering of interphase chromosomes.
Collapse
|
31
|
Buchholz J, Krieger J, Bruschini C, Burri S, Ardelean A, Charbon E, Langowski J. Widefield High Frame Rate Single-Photon SPAD Imagers for SPIM-FCS. Biophys J 2018; 114:2455-2464. [PMID: 29753448 DOI: 10.1016/j.bpj.2018.04.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 04/06/2018] [Accepted: 04/13/2018] [Indexed: 11/24/2022] Open
Abstract
Photon-counting sensors based on standard complementary metal-oxide-semiconductor single-photon avalanche diodes (SPADs) represent an emerging class of imagers that enable the counting and/or timing of single photons at zero readout noise (better than high-speed electron-multiplying charge-coupling devices) and over large arrays. They have seen substantial progress over the last 15 years, increasing their spatial resolution, timing accuracy, and sensitivity while reducing spurious signals such as afterpulsing and dark counts. They are increasingly being applied for time-resolved applications with the added advantage of enabling real-time options such as autocorrelation. We report in this study on the use of such a state-of-the-art 512 × 128 SPAD array, capable of a time resolution of 10-5-10-6 s for full frames while retaining acceptable photosensitivity thanks to the use of dedicated microlenses, in a selective plane illumination-fluorescence correlation spectroscopy setup. The latter allows us to perform thousands of fluorescence-correlation spectroscopy measurements simultaneously in a two-dimensional slice of the sample. This high-speed SPAD imager enables the measurement of molecular motion of small fluorescent particles such as single chemical dye molecules. Inhomogeneities in the molecular detection efficiency were compensated for by means of a global fit of the auto- and cross-correlation curves, which also made a calibration-free measurement of various samples possible. The afterpulsing effect could also be mitigated, making the measurement of the diffusion of Alexa-488 possible, and the overall result quality was further improved by spatial binning. The particle concentrations in the focus tend to be overestimated by a factor of 1.7 compared to a confocal setup; a calibration is thus required if absolute concentrations need to be measured. The first high-speed selective plane illumination-fluorescence correlation spectroscopy in vivo measurements to our knowledge were also recorded: although two-component fit models could not be employed because of noise, the diffusion of eGFP oligomers in HeLa cells could be measured. Sensitivity and noise will be further improved in the next generation of SPAD-based widefield sensors, which are currently under testing.
Collapse
Affiliation(s)
- Jan Buchholz
- German Cancer Research Center, Heidelberg, Germany
| | - Jan Krieger
- German Cancer Research Center, Heidelberg, Germany
| | | | - Samuel Burri
- École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Andrei Ardelean
- École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Edoardo Charbon
- École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | | |
Collapse
|
32
|
Stortz M, Angiolini J, Mocskos E, Wolosiuk A, Pecci A, Levi V. Mapping the dynamical organization of the cell nucleus through fluorescence correlation spectroscopy. Methods 2018; 140-141:10-22. [DOI: 10.1016/j.ymeth.2017.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/01/2017] [Accepted: 12/13/2017] [Indexed: 11/28/2022] Open
|
33
|
Circle scanning STED fluorescence correlation spectroscopy to quantify membrane dynamics and compartmentalization. Methods 2018; 140-141:188-197. [DOI: 10.1016/j.ymeth.2017.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/30/2017] [Accepted: 12/10/2017] [Indexed: 01/07/2023] Open
|
34
|
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.
Collapse
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.
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
Struntz P, Weiss M. The hitchhiker's guide to quantitative diffusion measurements. Phys Chem Chem Phys 2018; 20:28910-28919. [DOI: 10.1039/c8cp06158k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Quantitative comparison of three widely used techniques for diffusion measurements, implemented on a light sheet microscope.
Collapse
Affiliation(s)
- Philipp Struntz
- Experimental Physics I
- University of Bayreuth
- D-95447 Bayreuth
- Germany
| | - Matthias Weiss
- Experimental Physics I
- University of Bayreuth
- D-95447 Bayreuth
- Germany
| |
Collapse
|
37
|
Briddon SJ, Kilpatrick LE, Hill SJ. Studying GPCR Pharmacology in Membrane Microdomains: Fluorescence Correlation Spectroscopy Comes of Age. Trends Pharmacol Sci 2017; 39:158-174. [PMID: 29277246 DOI: 10.1016/j.tips.2017.11.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 12/17/2022]
Abstract
G protein-coupled receptors (GPCRs) are organised within the cell membrane into highly ordered macromolecular complexes along with other receptors and signalling proteins. Understanding how heterogeneity in these complexes affects the pharmacology and functional response of these receptors is crucial for developing new and more selective ligands. Fluorescence correlation spectroscopy (FCS) and related techniques such as photon counting histogram (PCH) analysis and image-based FCS can be used to interrogate the properties of GPCRs in these membrane microdomains, as well as their interaction with fluorescent ligands. FCS analyses fluorescence fluctuations within a small-defined excitation volume to yield information about their movement, concentration and molecular brightness (aggregation). These techniques can be used on live cells with single-molecule sensitivity and high spatial resolution. Once the preserve of specialist equipment, FCS techniques can now be applied using standard confocal microscopes. This review describes how FCS and related techniques have revealed novel insights into GPCR biology.
Collapse
Affiliation(s)
- Stephen J Briddon
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK; Centre for Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, The Midlands, UK
| | - Laura E Kilpatrick
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK; Centre for Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, The Midlands, UK
| | - Stephen J Hill
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK; Centre for Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, The Midlands, UK.
| |
Collapse
|
38
|
Abstract
Researchers striving to convert biology into an exact science foremost rely on structural biology and biochemical reconstitution approaches to obtain quantitative data. However, cell biological research is moving at an ever-accelerating speed into areas where these approaches lose much of their edge. Intrinsically unstructured proteins and biochemical interaction networks composed of interchangeable, multivalent, and unspecific interactions pose unique challenges to quantitative biology, as do processes that occur in discrete cellular microenvironments. Here we argue that a conceptual change in our way of conducting biochemical experiments is required to take on these new challenges. We propose that reconstitution of cellular processes in vitro should be much more focused on mimicking the cellular environment in vivo, an approach that requires detailed knowledge of the material properties of cellular compartments, essentially requiring a material science of the cell. In a similar vein, we suggest that quantitative biochemical experiments in vitro should be accompanied by corresponding experiments in vivo, as many newly relevant cellular processes are highly context-dependent. In essence, this constitutes a call for chemical biologists to convert their discipline from a proof-of-principle science to an area that could rightfully be called quantitative biochemistry in living cells. In this essay, we discuss novel techniques and experimental strategies with regard to their potential to fulfill such ambitious aims.
Collapse
Affiliation(s)
- Alf Honigmann
- Max Planck Institute of Molecular Cell Biology and Genetics , Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - André Nadler
- Max Planck Institute of Molecular Cell Biology and Genetics , Pfotenhauerstraße 108, 01307 Dresden, Germany
| |
Collapse
|
39
|
Sawant M, Schwarz N, Windoffer R, Magin TM, Krieger J, Mücke N, Obara B, Jankowski V, Jankowski J, Wally V, Lettner T, Leube RE. Threonine 150 Phosphorylation of Keratin 5 Is Linked to Epidermolysis Bullosa Simplex and Regulates Filament Assembly and Cell Viability. J Invest Dermatol 2017; 138:627-636. [PMID: 29080682 DOI: 10.1016/j.jid.2017.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/11/2017] [Accepted: 10/08/2017] [Indexed: 10/18/2022]
Abstract
A characteristic feature of the skin blistering disease epidermolysis bullosa simplex is keratin filament (KF) network collapse caused by aggregation of the basal epidermal keratin type II (KtyII) K5 and its type I partner keratin 14 (K14). Here, we examine the role of keratin phosphorylation in KF network rearrangement and cellular functions. We detect phosphorylation of the K5 head domain residue T150 in cytoplasmic epidermolysis bullosa simplex granules containing R125C K14 mutants. Expression of phosphomimetic T150D K5 mutants results in impaired KF formation in keratinocytes. The phenotype is enhanced upon combination with other phosphomimetic K5 head domain mutations. Remarkably, introduction of T150D K5 mutants into KtyII-lacking (KtyII-/-) keratinocytes prevents keratin network formation altogether. In contrast, phosphorylation-deficient T150A K5 leads to KFs with reduced branching and turnover. Assembly of T150D K5 is arrested at the heterotetramer stage coinciding with increased heat shock protein association. Finally, reduced cell viability and elevated response to stressors is noted in T150 mutant cells. Taken together, our findings identify T150 K5 phosphorylation as an important determinant of KF network formation and function with a possible role in epidermolysis bullosa simplex pathogenesis.
Collapse
Affiliation(s)
- Mugdha Sawant
- Institute of Molecular and Cellular Anatomy, RWTH Aachen University, Aachen, Germany
| | - Nicole Schwarz
- Institute of Molecular and Cellular Anatomy, RWTH Aachen University, Aachen, Germany
| | - Reinhard Windoffer
- Institute of Molecular and Cellular Anatomy, RWTH Aachen University, Aachen, Germany
| | - Thomas M Magin
- Institute of Biology and Translational Center for Regenerative Medicine, University of Leipzig, Leipzig, Germany
| | - Jan Krieger
- Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Norbert Mücke
- Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Boguslaw Obara
- School of Engineering and Computing Sciences, Durham University, Durham, UK
| | - Vera Jankowski
- Institut für Molekulare Herz-Kreislaufforschung, RWTH Aachen University, Aachen, Germany
| | - Joachim Jankowski
- Institut für Molekulare Herz-Kreislaufforschung, RWTH Aachen University, Aachen, Germany; School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Verena Wally
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Thomas Lettner
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Rudolf E Leube
- Institute of Molecular and Cellular Anatomy, RWTH Aachen University, Aachen, Germany.
| |
Collapse
|
40
|
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.
Collapse
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.
| |
Collapse
|
41
|
Mikuni S, Yamamoto J, Horio T, Kinjo M. Negative Correlation between the Diffusion Coefficient and Transcriptional Activity of the Glucocorticoid Receptor. Int J Mol Sci 2017; 18:ijms18091855. [PMID: 28841150 PMCID: PMC5618504 DOI: 10.3390/ijms18091855] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 12/17/2022] Open
Abstract
The glucocorticoid receptor (GR) is a transcription factor, which interacts with DNA and other cofactors to regulate gene transcription. Binding to other partners in the cell nucleus alters the diffusion properties of GR. Raster image correlation spectroscopy (RICS) was applied to quantitatively characterize the diffusion properties of EGFP labeled human GR (EGFP-hGR) and its mutants in the cell nucleus. RICS is an image correlation technique that evaluates the spatial distribution of the diffusion coefficient as a diffusion map. Interestingly, we observed that the averaged diffusion coefficient of EGFP-hGR strongly and negatively correlated with its transcriptional activities in comparison to that of EGFP-hGR wild type and mutants with various transcriptional activities. This result suggests that the decreasing of the diffusion coefficient of hGR was reflected in the high-affinity binding to DNA. Moreover, the hyper-phosphorylation of hGR can enhance the transcriptional activity by reduction of the interaction between the hGR and the nuclear corepressors.
Collapse
Affiliation(s)
- Shintaro Mikuni
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo 0010021, Japan.
| | - Johtaro Yamamoto
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo 0010021, Japan.
| | - Takashi Horio
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo 0010021, Japan.
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo 0010021, Japan.
| |
Collapse
|
42
|
Sezgin E, Azbazdar Y, Ng XW, Teh C, Simons K, Weidinger G, Wohland T, Eggeling C, Ozhan G. Binding of canonical Wnt ligands to their receptor complexes occurs in ordered plasma membrane environments. FEBS J 2017. [PMID: 28626941 PMCID: PMC5599997 DOI: 10.1111/febs.14139] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
While the cytosolic events of Wnt/β‐catenin signaling (canonical Wnt signaling) pathway have been widely studied, only little is known about the molecular mechanisms involved in Wnt binding to its receptors at the plasma membrane. Here, we reveal the influence of the immediate plasma membrane environment on the canonical Wnt–receptor interaction. While the receptors are distributed both in ordered and disordered environments, Wnt binding to its receptors selectively occurs in more ordered membrane environments which appear to cointernalize with the Wnt‐receptor complex. Moreover, Wnt/β‐catenin signaling is significantly reduced when the membrane order is disturbed by specific inhibitors of certain lipids that prefer to localize at the ordered environments. Similarly, a reduction in Wnt signaling activity is observed in Niemann–Pick Type C disease cells where trafficking of ordered membrane lipid components to the plasma membrane is genetically impaired. We thus conclude that ordered plasma membrane environments are essential for binding of canonical Wnts to their receptor complexes and downstream signaling activity.
Collapse
Affiliation(s)
- Erdinc Sezgin
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Yagmur Azbazdar
- Izmir International Biomedicine and Genome Institute (iBG-izmir), Dokuz Eylul University, Izmir, Turkey.,Department of Medical Biology and Genetics, Dokuz Eylul University Medical School, Izmir, Turkey
| | - Xue W Ng
- Department of Chemistry and Center for BioImaging Sciences, National University of Singapore, Singapore
| | - Cathleen Teh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Kai Simons
- Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
| | - Gilbert Weidinger
- Institute of Biochemistry and Molecular Biology, Ulm University, Germany
| | - Thorsten Wohland
- Department of Chemistry and Center for BioImaging Sciences, National University of Singapore, Singapore
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Gunes Ozhan
- Izmir International Biomedicine and Genome Institute (iBG-izmir), Dokuz Eylul University, Izmir, Turkey.,Department of Medical Biology and Genetics, Dokuz Eylul University Medical School, Izmir, Turkey
| |
Collapse
|
43
|
Quantifying transcription factor–DNA binding in single cells in vivo with photoactivatable fluorescence correlation spectroscopy. Nat Protoc 2017; 12:1458-1471. [DOI: 10.1038/nprot.2017.051] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
44
|
Hendrix J, Dekens T, Schrimpf W, Lamb DC. Arbitrary-Region Raster Image Correlation Spectroscopy. Biophys J 2017; 111:1785-1796. [PMID: 27760364 PMCID: PMC5073057 DOI: 10.1016/j.bpj.2016.09.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/04/2016] [Accepted: 09/12/2016] [Indexed: 11/23/2022] Open
Abstract
Combining imaging with correlation spectroscopy, as in raster image correlation spectroscopy (RICS), makes it possible to extract molecular translational diffusion constants and absolute concentrations, and determine intermolecular interactions from single-channel or multicolor confocal laser-scanning microscopy (CLSM) images. Region-specific RICS analysis remains very challenging because correlations are always calculated in a square region-of-interest (ROI). In this study, we describe a generalized image correlation spectroscopy algorithm that accepts arbitrarily shaped ROIs. We show that an image series can be cleaned up before arbitrary-region RICS (ARICS) analysis. We demonstrate the power of ARICS by simultaneously measuring molecular mobility in the cell membrane and the cytosol. Mobility near dynamic subcellular structures can be investigated with ARICS by generating a dynamic ROI. Finally, we derive diffusion and concentration pseudo-maps using the ARICS method. ARICS is a powerful expansion of image correlation spectroscopy with the potential of becoming the new standard for extracting biophysical parameters from confocal fluorescence images.
Collapse
Affiliation(s)
- Jelle Hendrix
- Laboratory for Photochemistry and Spectroscopy, Division of Molecular Imaging and Photonics, KU Leuven, Leuven, Belgium.
| | - Tomas Dekens
- Department of ETRO, Vrije Universiteit Brussel, Brussels, Belgium; iMinds vzw, Zwijnaarde, Belgium
| | - Waldemar Schrimpf
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Don C Lamb
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| |
Collapse
|
45
|
Ng XW, Teh C, Korzh V, Wohland T. The Secreted Signaling Protein Wnt3 Is Associated with Membrane Domains In Vivo: A SPIM-FCS Study. Biophys J 2017; 111:418-429. [PMID: 27463143 DOI: 10.1016/j.bpj.2016.06.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 06/10/2016] [Accepted: 06/16/2016] [Indexed: 10/21/2022] Open
Abstract
Wnt3 is a morphogen that activates the Wnt signaling pathway and regulates a multitude of biological processes ranging from cell proliferation and cell fate specification to differentiation over embryonic induction to neural patterning. Recent studies have shown that the palmitoylation of Wnt3 by Porcupine, a membrane-bound O-acyltransferase, plays a significant role in the intracellular membrane trafficking of Wnt3 and subsequently, its secretion in live zebrafish embryos, where chemical inhibition of Porcupine reduced the membrane-bound and secreted fractions of Wnt3 and eventually led to defective brain development. However, the membrane distribution of Wnt3 in cells remains not fully understood. Here, we determine the membrane organization of functionally active Wnt3-EGFP in cerebellar cells of live transgenic zebrafish embryos and the role of palmitoylation in its organization using single plane illumination microscopy-fluorescence correlation spectroscopy (SPIM-FCS), a multiplexed modality of FCS, which generates maps of molecular dynamics, concentration, and interaction of biomolecules. The FCS diffusion law was applied to SPIM-FCS data to study the subresolution membrane organization of Wnt3. We find that at the plasma membrane in vivo, Wnt3 is associated with cholesterol-dependent domains. This association reduces with increasing concentrations of Porcupine inhibitor (C59), confirming the importance of palmitoylation of Wnt3 for its association with cholesterol-dependent domains. Reduction of membrane cholesterol also results in a decrease of Wnt3 association with cholesterol-dependent domains in live zebrafish. This demonstrates for the first time, to our knowledge, in live vertebrate embryos that Wnt3 is associated with cholesterol-dependent domains.
Collapse
Affiliation(s)
- Xue Wen Ng
- Department of Chemistry, National University of Singapore, Singapore, Singapore; Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Cathleen Teh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Vladimir Korzh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Thorsten Wohland
- Department of Chemistry, National University of Singapore, Singapore, Singapore; Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
| |
Collapse
|
46
|
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.
Collapse
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.
| |
Collapse
|
47
|
Karampatzakis A, Sankaran J, Kandaswamy K, Rice SA, Cohen Y, Wohland T. Measurement of oxygen concentrations in bacterial biofilms using transient state monitoring by single plane illumination microscopy. Biomed Phys Eng Express 2017. [DOI: 10.1088/2057-1976/aa6db7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
48
|
Strobl F, Schmitz A, Stelzer EHK. Improving your four-dimensional image: traveling through a decade of light-sheet-based fluorescence microscopy research. Nat Protoc 2017; 12:1103-1109. [DOI: 10.1038/nprot.2017.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
49
|
csiLSFM combines light-sheet fluorescence microscopy and coherent structured illumination for a lateral resolution below 100 nm. Proc Natl Acad Sci U S A 2017; 114:4869-4874. [PMID: 28438995 DOI: 10.1073/pnas.1609278114] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Light-sheet-based fluorescence microscopy (LSFM) features optical sectioning in the excitation process. It minimizes fluorophore bleaching as well as phototoxic effects and provides a true axial resolution. The detection path resembles properties of conventional fluorescence microscopy. Structured illumination microscopy (SIM) is attractive for superresolution because of its moderate excitation intensity, high acquisition speed, and compatibility with all fluorophores. We introduce SIM to LSFM because the combination pushes the lateral resolution to the physical limit of linear SIM. The instrument requires three objective lenses and relies on methods to control two counterpropagating coherent light sheets that generate excitation patterns in the focal plane of the detection lens. SIM patterns with the finest line spacing in the far field become available along multiple orientations. Flexible control of rotation, frequency, and phase shift of the perfectly modulated light sheet are demonstrated. Images of beads prove a near-isotropic lateral resolution of sub-100 nm. Images of yeast endoplasmic reticulum show that coherent structured illumination (csi) LSFM performs with physiologically relevant specimens.
Collapse
|
50
|
Zhao ZW, White MD, Bissiere S, Levi V, Plachta N. Quantitative imaging of mammalian transcriptional dynamics: from single cells to whole embryos. BMC Biol 2016; 14:115. [PMID: 28010727 PMCID: PMC5180410 DOI: 10.1186/s12915-016-0331-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Probing dynamic processes occurring within the cell nucleus at the quantitative level has long been a challenge in mammalian biology. Advances in bio-imaging techniques over the past decade have enabled us to directly visualize nuclear processes in situ with unprecedented spatial and temporal resolution and single-molecule sensitivity. Here, using transcription as our primary focus, we survey recent imaging studies that specifically emphasize the quantitative understanding of nuclear dynamics in both time and space. These analyses not only inform on previously hidden physical parameters and mechanistic details, but also reveal a hierarchical organizational landscape for coordinating a wide range of transcriptional processes shared by mammalian systems of varying complexity, from single cells to whole embryos.
Collapse
Affiliation(s)
- Ziqing W Zhao
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Melanie D White
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Stephanie Bissiere
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Valeria Levi
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Conicet, Buenos Aires, C1428EHA, Argentina
| | - Nicolas Plachta
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore.
| |
Collapse
|