1
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Iyer SS, Srivastava A. Membrane lateral organization from potential energy disconnectivity graph. Biophys Chem 2024; 313:107284. [PMID: 39002248 DOI: 10.1016/j.bpc.2024.107284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/15/2024]
Abstract
Understanding the thermodynamic and kinetic properties of biomolecules requires elucidation of their complex energy landscape. A disconnectivity graph analysis of the energy landscape provides a framework for mapping the multi-dimensional landscape onto a two-dimensional representation while preserving the key features of the energy landscape. Several studies show that the structure or shape of the disconnectity graph is directly associated with the function of protein and nucleic acid molecules. In this review, we discuss how disconnectivity analysis of the potential energy surface can be extended to lipid molecules to glean important information about membrane organization. The shape of the disconnectivity graphs can be used to predict the lateral organization of multi-component lipid bilayer. We hope that this review encourages the use of disconnectivity graphs routinely by membrane biophysicists to predict the lateral organization of lipids.
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Affiliation(s)
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, C. V. Raman Road, Bangalore, Karnataka 560012, India.
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2
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Lin CC, Suzuki A. Calibrating Fluorescence Microscopy With 3D-Speckler (3D Fluorescence Speckle Analyzer). Bio Protoc 2024; 14:e5051. [PMID: 39210955 PMCID: PMC11349494 DOI: 10.21769/bioprotoc.5051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/04/2024] [Accepted: 07/11/2024] [Indexed: 09/04/2024] Open
Abstract
Fluorescence microscopy has been widely accessible and indispensable in cell biology research. This technique enables researchers to label targets, ranging from individual entities to multiple groups, with fluorescent markers. It offers precise determinations of localization, size, and shape, along with accurate quantifications of fluorescence signal intensities. Furthermore, an ideal fluorescence microscope can achieve approximately 250 nm in lateral and 600 nm in axial resolution. Despite its integral role in these measurements, the calibration of fluorescence microscopes is often overlooked. This protocol introduces the use of 3D-Speckler (3D fluorescence speckle analyzer), a semi-automated software tool we have recently developed, for calibrating fluorescence microscopy. Calibration of fluorescence microscopy includes determining resolution limits, validating accuracy in size measurements, evaluating illumination flatness, and determining chromatic aberrations. 3D-Speckler is user-friendly and enables precise quantification of fluorescence puncta, including nanoscale 2D/3D particle size, precise locations, and intensity information. By utilizing multispectral fluorescence beads of known sizes alongside 3D-Speckler, the software can effectively calibrate imaging systems. We emphasize the importance of routine calibration for imaging systems to maintain their integrity and reproducibility, ensuring accurate quantification. This protocol provides a detailed step-by-step guide on using 3D-Speckler to calibrate imaging systems. Key features • Semi-automated particle detection. • Accurate three-dimensional measurement of fluorescent particle sizes. • High-precision three-dimensional localization of fluorescent particles. • Precision analysis of point spread function and chromatic aberration in fluorescence microscopy.
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Affiliation(s)
- Chieh-Chang Lin
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, WI, USA
| | - Aussie Suzuki
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, WI, USA
- Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
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3
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Bullard MR, Cervantes JCM, Quaicoe NB, Jin A, Adams DA, Lin JM, Iliadis E, Seidler TM, Cervantes-Sandoval I, He HY. Accelerated protein retention expansion microscopy using microwave radiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.11.593228. [PMID: 38766072 PMCID: PMC11100821 DOI: 10.1101/2024.05.11.593228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Protein retention expansion microscopy (ExM) retains genetically encoded fluorescent proteins or antibody-conjugated fluorescent probes in fixed tissue and isotropically expands the tissue through a swellable polymer network to allow nanoscale (<70 nm) resolution on diffraction-limited confocal microscopes. Despite numerous advantages ExM brings to biological studies, the full protocol is time-consuming and can take multiple days to complete. Here, we adapted the ExM protocol to the vibratome-sectioned brain tissue of Xenopus laevis tadpoles and implemented a microwave-assisted protocol to reduce the workflow from days to hours. In addition to the significantly accelerated processing time, our microwave-assisted ExM (M/WExM) protocol maintains the superior resolution and signal-to-noise ratio of the original ExM protocol. Furthermore, the M/WExM protocol yields higher magnitude of expansion, suggesting that in addition to accelerating the process through increased diffusion rate of reagents, microwave radiation may also facilitate the expansion process. To demonstrate the applicability of this method to other specimens and protocols, we adapted the microwave-accelerated protocol to whole mount adult brain tissue of Drosophila melanogaster fruit flies, and successfully reduced the total processing time of a widely-used Drosophila IHC-ExM protocol from 6 days to 2 days. Our results demonstrate that with appropriate adjustment of the microwave parameters (wattage, pulse duration, interval, and number of cycles), this protocol can be readily adapted to different model organisms and tissue types to greatly increase the efficiency of ExM experiments.
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Affiliation(s)
| | | | | | - Amanda Jin
- Department of Biology, Georgetown University, Washington, DC 20057
| | - Danya A. Adams
- Department of Biology, Georgetown University, Washington, DC 20057
| | - Jessica M. Lin
- Department of Biology, Georgetown University, Washington, DC 20057
| | - Elena Iliadis
- Department of Biology, Georgetown University, Washington, DC 20057
| | - Tess M. Seidler
- Department of Biology, Georgetown University, Washington, DC 20057
| | | | - Hai-yan He
- Department of Biology, Georgetown University, Washington, DC 20057
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4
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Mlinac-Jerkovic K, Kalanj-Bognar S, Heffer M, Blažetić S. Methodological Pitfalls of Investigating Lipid Rafts in the Brain: What Are We Still Missing? Biomolecules 2024; 14:156. [PMID: 38397393 PMCID: PMC10886647 DOI: 10.3390/biom14020156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
The purpose of this review is to succinctly examine the methodologies used in lipid raft research in the brain and to highlight the drawbacks of some investigative approaches. Lipid rafts are biochemically and biophysically different from the bulk membrane. A specific lipid environment within membrane domains provides a harbor for distinct raftophilic proteins, all of which in concert create a specialized platform orchestrating various cellular processes. Studying lipid rafts has proved to be arduous due to their elusive nature, mobility, and constant dynamic reorganization to meet the cellular needs. Studying neuronal lipid rafts is particularly cumbersome due to the immensely complex regional molecular architecture of the central nervous system. Biochemical fractionation, performed with or without detergents, is still the most widely used method to isolate lipid rafts. However, the differences in solubilization when various detergents are used has exposed a dire need to find more reliable methods to study particular rafts. Biochemical methods need to be complemented with other approaches such as live-cell microscopy, imaging mass spectrometry, and the development of specific non-invasive fluorescent probes to obtain a more complete image of raft dynamics and to study the spatio-temporal expression of rafts in live cells.
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Affiliation(s)
| | | | - Marija Heffer
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Senka Blažetić
- Department of Biology, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
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5
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Puchkov D, Müller PM, Lehmann M, Matthaeus C. Analyzing the cellular plasma membrane by fast and efficient correlative STED and platinum replica EM. Front Cell Dev Biol 2023; 11:1305680. [PMID: 38099299 PMCID: PMC10720448 DOI: 10.3389/fcell.2023.1305680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
The plasma membrane of mammalian cells links transmembrane receptors, various structural components, and membrane-binding proteins to subcellular processes, allowing inter- and intracellular communication. Therefore, membrane-binding proteins, together with structural components such as actin filaments, modulate the cell membrane in their flexibility, stiffness, and curvature. Investigating membrane components and curvature in cells remains challenging due to the diffraction limit in light microscopy. Preparation of 5-15-nm-thin plasma membrane sheets and subsequent inspection by metal replica transmission electron microscopy (TEM) reveal detailed information about the cellular membrane topology, including the structure and curvature. However, electron microscopy cannot identify proteins associated with specific plasma membrane domains. Here, we describe a novel adaptation of correlative super-resolution light microscopy and platinum replica TEM (CLEM-PREM), allowing the analysis of plasma membrane sheets with respect to their structural details, curvature, and associated protein composition. We suggest a number of shortcuts and troubleshooting solutions to contemporary PREM protocols. Thus, implementation of super-resolution stimulated emission depletion (STED) microscopy offers significant reduction in sample preparation time and reduced technical challenges for imaging and analysis. Additionally, highly technical challenges associated with replica preparation and transfer on a TEM grid can be overcome by scanning electron microscopy (SEM) imaging. The combination of STED microscopy and platinum replica SEM or TEM provides the highest spatial resolution of plasma membrane proteins and their underlying membrane and is, therefore, a suitable method to study cellular events like endocytosis, membrane trafficking, or membrane tension adaptations.
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Affiliation(s)
- Dmytro Puchkov
- Cellular Imaging Facility, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Paul Markus Müller
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Martin Lehmann
- Cellular Imaging Facility, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Claudia Matthaeus
- Cellular Physiology of Nutrition, Institute for Nutritional Science, University of Potsdam, Potsdam, Germany
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6
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Löwe M, Hänsch S, Hachani E, Schmitt L, Weidtkamp-Peters S, Kedrov A. Probing macromolecular crowding at the lipid membrane interface with genetically-encoded sensors. Protein Sci 2023; 32:e4797. [PMID: 37779215 PMCID: PMC10578116 DOI: 10.1002/pro.4797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Biochemical processes within the living cell occur in a highly crowded environment, where macromolecules, first of all proteins and nucleic acids, occupy up to 30% of the volume. The phenomenon of macromolecular crowding is not an exclusive feature of the cytoplasm and can be observed in the densely protein-packed, nonhomogeneous cellular membranes and at the membrane interfaces. Crowding affects diffusional and conformational dynamics of proteins within the lipid bilayer, alters kinetic and thermodynamic properties of biochemical reactions, and modulates the membrane organization. Despite its importance, the non-invasive quantification of the membrane crowding is not trivial. Here, we developed a genetically-encoded fluorescence-based sensor for probing the macromolecular crowding at the membrane interfaces. Two sensor variants, both composed of fluorescent proteins and a membrane anchor, but differing by flexible linker domains were characterized in vitro, and the procedures for the membrane reconstitution were established. Steric pressure induced by membrane-tethered synthetic and protein crowders altered the sensors' conformation, causing increase in the intramolecular Förster's resonance energy transfer. Notably, the effect of protein crowders only weakly correlated with their molecular weight, suggesting that other factors, such as shape and charge contribute to the crowding via the quinary interactions. Finally, measurements performed in inner membrane vesicles of Escherichia coli validated the crowding-dependent dynamics of the sensors in the physiologically relevant environment. The sensors offer broad opportunities to study interfacial crowding in a complex environment of native membranes, and thus add to the toolbox of methods for studying membrane dynamics and proteostasis.
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Affiliation(s)
- Maryna Löwe
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sebastian Hänsch
- Center for Advanced imaging, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eymen Hachani
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Alexej Kedrov
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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7
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Zou W, Yang L, Lu H, Li M, Ji D, Slone J, Huang T. Application of super-resolution microscopy in mitochondria-dynamic diseases. Adv Drug Deliv Rev 2023; 200:115043. [PMID: 37536507 DOI: 10.1016/j.addr.2023.115043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Limited by spatial and temporal resolution, traditional optical microscopy cannot image the delicate ultra-structure organelles and sub-organelles. The emergence of super-resolution microscopy makes it possible. In this review, we focus on mitochondria. We summarize the process of mitochondrial dynamics, the primary proteins that regulate mitochondrial morphology, the diseases related to mitochondrial dynamics. The purpose is to apply super-resolution microscopy developed during recent years to the mitochondrial research. By providing the right research tools, we will help to promote the application of this technique to the in-depth elucidation of the pathogenesis of diseases related to mitochondrial dynamics, assistdiagnosis and develop the therapeutic treatment.
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Affiliation(s)
- Weiwei Zou
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Li Yang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Hedong Lu
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Min Li
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Dongmei Ji
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jesse Slone
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Taosheng Huang
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA.
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8
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Kumar V, Kymissis I. MicroLED/LED electro-optical integration techniques for non-display applications. APPLIED PHYSICS REVIEWS 2023; 10:021306. [PMID: 37265477 PMCID: PMC10155219 DOI: 10.1063/5.0125103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/20/2023] [Indexed: 06/03/2023]
Abstract
MicroLEDs offer an extraordinary combination of high luminance, high energy efficiency, low cost, and long lifetime. These characteristics are highly desirable in various applications, but their usage has, to date, been primarily focused toward next-generation display technologies. Applications of microLEDs in other technologies, such as projector systems, computational imaging, communication systems, or neural stimulation, have been limited. In non-display applications which use microLEDs as light sources, modifications in key electrical and optical characteristics such as external efficiency, output beam shape, modulation bandwidth, light output power, and emission wavelengths are often needed for optimum performance. A number of advanced fabrication and processing techniques have been used to achieve these electro-optical characteristics in microLEDs. In this article, we review the non-display application areas of the microLEDs, the distinct opto-electrical characteristics required for these applications, and techniques that integrate the optical and electrical components on the microLEDs to improve system-level efficacy and performance.
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Affiliation(s)
- V. Kumar
- Department of Electrical Engineering, Columbia University, New York, New York 10027, USA
| | - I. Kymissis
- Department of Electrical Engineering, Columbia University, New York, New York 10027, USA
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9
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Kinnun JJ, Scott HL, Bolmatov D, Collier CP, Charlton TR, Katsaras J. Biophysical studies of lipid nanodomains using different physical characterization techniques. Biophys J 2023; 122:931-949. [PMID: 36698312 PMCID: PMC10111277 DOI: 10.1016/j.bpj.2023.01.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
For the past 50 years, evidence for the existence of functional lipid domains has been steadily accumulating. Although the notion of functional lipid domains, also known as "lipid rafts," is now widely accepted, this was not always the case. This ambiguity surrounding lipid domains could be partly attributed to the fact that they are highly dynamic, nanoscopic structures. Since most commonly used techniques are sensitive to microscale structural features, it is therefore, not surprising that it took some time to reach a consensus regarding their existence. In this review article, we will discuss studies that have used techniques that are inherently sensitive to nanoscopic structural features (i.e., neutron scatting, nuclear magnetic resonance, and Förster resonance energy transfer). We will also mention techniques that may be of use in the future (i.e., cryoelectron microscopy, droplet interface bilayers, inelastic x-ray scattering, and neutron reflectometry), which can further our understanding of the different and unique physicochemical properties of nanoscopic lipid domains.
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Affiliation(s)
- Jacob J Kinnun
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Haden L Scott
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Dima Bolmatov
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee
| | - C Patrick Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Timothy R Charlton
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - John Katsaras
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee; Labs and Soft Matter Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
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10
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Isik OA, Cizmecioglu O. Rafting on the Plasma Membrane: Lipid Rafts in Signaling and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1436:87-108. [PMID: 36648750 DOI: 10.1007/5584_2022_759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The plasma membrane is not a uniform phospholipid bilayer; it has specialized membrane nano- or microdomains called lipid rafts. Lipid rafts are small cholesterol and sphingolipid-rich plasma membrane islands. Although their existence was long debated, their presence in the plasma membrane of living cells is now well accepted with the advent of super-resolution imaging techniques. It is interesting to note that lipid rafts function to compartmentalize receptors and their regulators and substantially modulate cellular signaling. In this review, we will examine the role of lipid rafts and caveolae-lipid raft-like microdomains with a distinct 3D morphology-in cellular signaling. Moreover, we will investigate how raft compartmentalized signaling regulates diverse physiological processes such as proliferation, apoptosis, immune signaling, and development. Also, the deregulation of lipid raft-mediated signaling during tumorigenesis and metastasis will be explored.
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Affiliation(s)
- Ozlem Aybuke Isik
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Onur Cizmecioglu
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.
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11
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Heberle FA, Welsch D, Scott HL, Waxham MN. Optimization of cryo-electron microscopy for quantitative analysis of lipid bilayers. BIOPHYSICAL REPORTS 2022; 3:100090. [PMID: 36593976 PMCID: PMC9804012 DOI: 10.1016/j.bpr.2022.100090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Cryogenic electron microscopy (cryo-EM) is among the most powerful tools available for interrogating nanoscale structure of biological materials. We recently showed that cryo-EM can be used to measure the bilayer thickness of lipid vesicles and biological membranes with subangstrom precision, resulting in the direct visualization of nanoscopic domains of different thickness in multicomponent lipid mixtures and giant plasma membrane vesicles. Despite the great potential of cryo-EM for revealing the lateral organization of biomembranes, a large parameter space of experimental conditions remains to be optimized. Here, we systematically investigate the influence of instrument parameters and image postprocessing steps on the ability to accurately measure bilayer thickness and discriminate regions of different thickness within unilamellar liposomes. This unique application of cryo-EM places particular demands on image acquisition optimization and analysis due to the facts that 1) each vesicle is a different size with different curvature, 2) the domains in each vesicle can be heterogenous in size, and 3) the random orientation of vesicles amplifies the variability of domain size in projected images. We also demonstrate a spatial autocorrelation analysis to extract additional information about lateral heterogeneity.
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Affiliation(s)
- Frederick A. Heberle
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee,Corresponding author
| | - Doug Welsch
- Department of Neurobiology and Anatomy, University of Texas Health Science Center, Houston, Texas
| | - Haden L. Scott
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - M. Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center, Houston, Texas,Corresponding author
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12
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Nieto-Garai JA, Olazar-Intxausti J, Anso I, Lorizate M, Terrones O, Contreras FX. Super-Resolution Microscopy to Study Interorganelle Contact Sites. Int J Mol Sci 2022; 23:15354. [PMID: 36499680 PMCID: PMC9739495 DOI: 10.3390/ijms232315354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/29/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Interorganelle membrane contact sites (MCS) are areas of close vicinity between the membranes of two organelles that are maintained by protein tethers. Recently, a significant research effort has been made to study MCS, as they are implicated in a wide range of biological functions, such as organelle biogenesis and division, apoptosis, autophagy, and ion and phospholipid homeostasis. Their composition, characteristics, and dynamics can be studied by different techniques, but in recent years super-resolution fluorescence microscopy (SRFM) has emerged as a powerful tool for studying MCS. In this review, we first explore the main characteristics and biological functions of MCS and summarize the different approaches for studying them. Then, we center on SRFM techniques that have been used to study MCS. For each of the approaches, we summarize their working principle, discuss their advantages and limitations, and explore the main discoveries they have uncovered in the field of MCS.
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Affiliation(s)
- Jon Ander Nieto-Garai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - June Olazar-Intxausti
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Itxaso Anso
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, 48903 Barakaldo, Spain
| | - Maier Lorizate
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Oihana Terrones
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Francesc-Xabier Contreras
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, 48940 Leioa, Spain
- Ikerbasque, Basque Foundation of Science, 48011 Bilbao, Spain
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13
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Andersson A, Fornasier M, Makasewicz K, Pálmadóttir T, Linse S, Sparr E, Jönsson P. Single-vesicle intensity and colocalization fluorescence microscopy to study lipid vesicle fusion, fission, and lipid exchange. Front Mol Neurosci 2022; 15:1007699. [PMID: 36533132 PMCID: PMC9751204 DOI: 10.3389/fnmol.2022.1007699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/18/2022] [Indexed: 12/19/2023] Open
Abstract
Interactions of lipid vesicles play important roles in a large variety of functions and dysfunctions in the human body. Vital for several biochemical functions is the interaction between monomeric proteins and lipid membranes, and the induced phenomena such as fusion between vesicles and cell membranes, lipid exchange between the membranes, or vesicle fission. Identification of single events and their frequency of occurrence would provide valuable information about protein-lipid interactions in both healthy and degenerative pathways. In this work, we present a single-vesicle intensity and colocalization fluorescence microscopy assay with a custom-written MATLAB analysis program. The assay can be used to study lipid exchange as well as vesicle fusion and fission between two vesicle populations labeled with different fluorescent dyes. Vesicles from the two populations are first mixed and docked to a glass surface. The sample is then simultaneously imaged using two separate wavelength channels monitoring intensity changes and colocalization of vesicles from the two populations. The monomeric pre-synaptic protein α-synuclein (α-syn) and small unilamellar vesicles consisting of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dioleoyl-sn-glycero-3-phospho-L-serine, (DOPS), and monosialotetrahexosylganglioside (GM1) were used as a model system to evaluate the method. From our analysis, neither α-syn induced fusion nor lipid exchange was observed for vesicles consisting of DOPC:DOPS (7:3). However, including 10% GM1 in the vesicles resulted in a 91% increase of the number of vesicles within 10 min, combined with a 57% decrease in the average fluorescence intensity per vesicle, indicating that approximately half of the vesicles underwent fission. The method facilitates the study of lipid vesicle fusion, fission, and lipid exchange under controlled conditions. It also allows these events to be studied for systems with more complex composition including exosomes and lipid-based drug carriers, to enable a better understanding of their physicochemical properties.
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Affiliation(s)
| | | | | | | | | | | | - Peter Jönsson
- Department of Chemistry, Lund University, Lund, Sweden
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14
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Fuentes-Domínguez R, Naznin S, La Cavera III S, Cousins R, Pérez-Cota F, Smith RJ, Clark M. Polarization-Sensitive Super-Resolution Phononic Reconstruction of Nanostructures. ACS PHOTONICS 2022; 9:1919-1925. [PMID: 35726241 PMCID: PMC9204812 DOI: 10.1021/acsphotonics.1c01607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Indexed: 05/28/2023]
Abstract
In this paper, we show for the first time the polarization-sensitive super-resolution phononic reconstruction of multiple nanostructures in a liquid environment by overcoming the diffraction limit of the optical system (1 μm). By using time-resolved pump-probe spectroscopy, we measure the acoustic signature of nanospheres and nanorods at different polarizations. This enables the size, position, and orientation characterization of multiple nanoparticles in a single point spread function with the precision of 5 nm, 3 nm, and 1.4°, respectively. Unlike electron microscopy where a high vacuum environment is needed for imaging, this technique performs measurements in liquids at ambient pressure, ideal to study the insights of living specimens. This is a potential path toward super-resolution phononic imaging where the acoustic signatures of multiple nanostructures could act as an alternative to fluorescent labels. In this context, phonons also offer the opportunity to extract information about the mechanical properties of the surrounding medium as well as access to subsurface features.
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Affiliation(s)
- Rafael Fuentes-Domínguez
- Optics
and Photonics Group, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Shakila Naznin
- Optics
and Photonics Group, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Salvatore La Cavera III
- Optics
and Photonics Group, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Richard Cousins
- Nanoscale
and Microscale Research Centre, University
of Nottingham, University Park, Nottingham NG7 2RD, United
Kingdom
| | - Fernando Pérez-Cota
- Optics
and Photonics Group, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Richard J. Smith
- Optics
and Photonics Group, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Matt Clark
- Optics
and Photonics Group, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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15
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Marchetti L, Porciani D, Mitola S, Giacomelli C. Editorial: Molecular Insights Into Ligand-Receptor Interactions on the Cell Surface. Front Mol Biosci 2022; 9:921677. [PMID: 35647034 PMCID: PMC9140802 DOI: 10.3389/fmolb.2022.921677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - David Porciani
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
- Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Stefania Mitola
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Chiara Giacomelli
- Department of Pharmacy, University of Pisa, Pisa, Italy
- *Correspondence: Chiara Giacomelli,
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16
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Abstract
Fluorescence microscopy has represented a crucial technique to explore the cellular and molecular mechanisms in the field of biomedicine. However, the conventional one-photon microscopy exhibits many limitations when living samples are imaged. The new technologies, including two-photon microscopy (2PM), have considerably improved the in vivo study of pathophysiological processes, allowing the investigators to overcome the limits displayed by previous techniques. 2PM enables the real-time intravital imaging of the biological functions in different organs at cellular and subcellular resolution thanks to its improved laser penetration and less phototoxicity. The development of more sensitive detectors and long-wavelength fluorescent dyes as well as the implementation of semi-automatic software for data analysis allowed to gain insights in essential physiological functions, expanding the frontiers of cellular and molecular imaging. The future applications of 2PM are promising to push the intravital microscopy beyond the existing limits. In this review, we provide an overview of the current state-of-the-art methods of intravital microscopy, focusing on the most recent applications of 2PM in kidney physiology.
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17
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El-Beyrouthy J, Makhoul-Mansour MM, Freeman EC. Studying the Mechanics of Membrane Permeabilization through Mechanoelectricity. ACS APPLIED MATERIALS & INTERFACES 2022; 14:6120-6130. [PMID: 35073482 DOI: 10.1021/acsami.1c19880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In this research, real-time monitoring of lipid membrane disruption is made possible by exploiting the dynamic properties of model lipid bilayers formed at oil-water interfaces. This involves tracking an electrical signal generated through rhythmic membrane perturbation translated into the adsorption and penetration of charged species within the membrane. Importantly, this allows for the detection of membrane surface interactions that occur prior to pore formation that may be otherwise undetected. The requisite dynamic membranes for this approach are made possible through the droplet interface bilayer (DIB) technique. Membranes are formed at the interface of lipid monolayer-coated aqueous droplets submerged in oil. We present how cyclically alternating the membrane area leads to the generation of mechanoelectric current. This current is negligible without a transmembrane voltage until a composition mismatch between the membrane monolayers is produced, such as a one-sided accumulation of disruptive agents. The generated mechanoelectric current is then eliminated when an applied electric field compensates for this asymmetry, enabling measurement of the transmembrane potential offset. Tracking the compensating voltage with respect to time then reveals the gradual accumulation of disruptive agents prior to membrane permeabilization. The innovation of this work is emphasized in its ability to continuously track membrane surface activity, highlighting the initial interaction steps of membrane disruption. In this paper, we begin by validating our proposed approach against measurements taken for fixed composition membranes using standard electrophysiological techniques. Next, we investigate surfactant adsorption, including hexadecyltrimethylammonium bromide (CTAB, cationic) and sodium decyl sulfate (SDS, anionic), demonstrating the ability to track adsorption prior to disruption. Finally, we investigate the penetration of lipid membranes by melittin, confirming that the peptide insertion and disruption mechanics are, in part, modulated by membrane composition.
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Affiliation(s)
- Joyce El-Beyrouthy
- Biomembranes Engineering Laboratory, School of Environment, Civil, Agriculture and Mechanical Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Michelle M Makhoul-Mansour
- Biomembranes Engineering Laboratory, School of Environment, Civil, Agriculture and Mechanical Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Eric C Freeman
- Biomembranes Engineering Laboratory, School of Environment, Civil, Agriculture and Mechanical Engineering, The University of Georgia, Athens, Georgia 30602, United States
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18
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Soñora M, Barrera EE, Pantano S. The stressed life of a lipid in the Zika virus membrane. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183804. [PMID: 34656553 DOI: 10.1016/j.bbamem.2021.183804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 09/30/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Protein-lipid interactions modulate a plethora of physiopathologic processes and have been the subject of countless studies. However, these kinds of interactions in the context of viral envelopes have remained relatively unexplored, partially because the intrinsically small dimensions of the molecular systems escape to the current resolution of experimental techniques. However, coarse-grained and multiscale simulations may fill that niche, providing nearly atomistic resolution at an affordable computational price. Here we use multiscale simulations to characterize the lipid-protein interactions in the envelope of the Zika Virus, a prominent member of the Flavivirus genus. Comparisons between the viral envelope and simpler molecular systems indicate that the viral membrane is under extreme pressures and asymmetric forces. Furthermore, the dense net of protein-protein contacts established by the envelope proteins creates poorly solvated regions that destabilize the external leaflet leading to a decoupled dynamics between both membrane layers. These findings lead to the idea that the Flaviviral membrane may store a significant amount of elastic energy, playing an active role in the membrane fusion process.
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Affiliation(s)
- Martín Soñora
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Exequiel E Barrera
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay; Instituto de Histología y Embriología (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CC56, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay.
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19
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Nieto-Garai JA, Lorizate M, Contreras FX. Shedding light on membrane rafts structure and dynamics in living cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2022; 1864:183813. [PMID: 34748743 DOI: 10.1016/j.bbamem.2021.183813] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 12/12/2022]
Abstract
Cellular membranes are fundamental building blocks regulating an extensive repertoire of biological functions. These structures contain lipids and membrane proteins that are known to laterally self-aggregate in the plane of the membrane, forming defined membrane nanoscale domains essential for protein activity. Membrane rafts are described as heterogeneous, dynamic, and short-lived cholesterol- and sphingolipid-enriched membrane nanodomains (10-200 nm) induced by lipid-protein and lipid-lipid interactions. Those membrane nanodomains have been extensively characterized using model membranes and in silico methods. However, despite the development of advanced fluorescence microscopy techniques, undoubted nanoscale visualization by imaging techniques of membrane rafts in the membrane of unperturbed living cells is still uncompleted, increasing the skepticism about their existence. Here, we broadly review recent biochemical and microscopy techniques used to investigate membrane rafts in living cells and we enumerate persistent open questions to answer before unlocking the mystery of membrane rafts in living cells.
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Affiliation(s)
- Jon Ander Nieto-Garai
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Bilbao, Spain.
| | - Maier Lorizate
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Bilbao, Spain; Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, 48940 Bilbao, Spain
| | - F-Xabier Contreras
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Bilbao, Spain; Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, 48940 Bilbao, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
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20
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A biophysical perspective of the regulatory mechanisms of ezrin/radixin/moesin proteins. Biophys Rev 2022; 14:199-208. [PMID: 35340609 PMCID: PMC8921360 DOI: 10.1007/s12551-021-00928-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/14/2021] [Indexed: 02/08/2023] Open
Abstract
Many signal transductions resulting from ligand-receptor interactions occur at the cell surface. These signaling pathways play essential roles in cell polarization, membrane morphogenesis, and the modulation of membrane tension at the cell surface. However, due to the large number of membrane-binding proteins, including actin-membrane linkers, and transmembrane proteins present at the cell surface, the molecular mechanisms underlying the regulation at the cell surface are yet unclear. Here, we describe the molecular functions of one of the key players at the cell surface, ezrin/radixin/moesin (ERM) proteins from a biophysical point of view. We focus our discussion on biophysical properties of ERM proteins revealed by using biophysical tools in live cells and in vitro reconstitution systems. We first describe the structural properties of ERM proteins and then discuss the interactions of ERM proteins with PI(4,5)P2 and the actin cytoskeleton. These properties of ERM proteins revealed by using biophysical approaches have led to a better understanding of their physiological functions in cells and tissues. Supplementary Information The online version contains supplementary material available at 10.1007/s12551-021-00928-0.
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21
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Identifying Membrane Lateral Organization by Contrast-Matched Small Angle Neutron Scattering. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2402:163-177. [PMID: 34854044 DOI: 10.1007/978-1-0716-1843-1_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Lipid domains in model membranes are routinely studied to provide insight into the physical interactions that drive raft formation in cellular membranes. Using small angle neutron scattering, contrast-matching techniques enable the detection of lipid domains ranging from tens to hundreds of nanometers which are not accessible to other techniques without the use of extrinsic probes. Here, we describe a probe-free experimental approach and model-free analysis to identify lipid domains in freely floating vesicles of ternary phase separating lipid mixtures.
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22
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Carravilla P, Dasgupta A, Zhurgenbayeva G, Danylchuk DI, Klymchenko AS, Sezgin E, Eggeling C. Long-term STED imaging of membrane packing and dynamics by exchangeable polarity-sensitive dyes. BIOPHYSICAL REPORTS 2021; 1:None. [PMID: 34939048 PMCID: PMC8651516 DOI: 10.1016/j.bpr.2021.100023] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/08/2021] [Indexed: 12/28/2022]
Abstract
Understanding the plasma membrane nanoscale organization and dynamics in living cells requires microscopy techniques with high spatial and temporal resolution that permit for long acquisition times and allow for the quantification of membrane biophysical properties, such as lipid ordering. Among the most popular super-resolution techniques, stimulated emission depletion (STED) microscopy offers one of the highest temporal resolutions, ultimately defined by the scanning speed. However, monitoring live processes using STED microscopy is significantly limited by photobleaching, which recently has been circumvented by exchangeable membrane dyes that only temporarily reside in the membrane. Here, we show that NR4A, a polarity-sensitive exchangeable plasma membrane probe based on Nile red, permits the super-resolved quantification of membrane biophysical parameters in real time with high temporal and spatial resolution as well as long acquisition times. The potential of this polarity-sensitive exchangeable dye is showcased by live-cell real-time three-dimensional STED recordings of bleb formation and lipid exchange during membrane fusion as well as by STED-fluorescence correlation spectroscopy experiments for the simultaneous quantification of membrane dynamics and lipid packing that correlate in model and live-cell membranes.
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Affiliation(s)
- Pablo Carravilla
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
| | - Anindita Dasgupta
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
| | - Gaukhar Zhurgenbayeva
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
- Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Dmytro I. Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Illkirch, France
| | - Andrey S. Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Illkirch, France
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Christian Eggeling
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
- Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Jena Center for Soft Matter, Jena, Germany
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23
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Rapid ensemble measurement of protein diffusion and probe blinking dynamics in cells. BIOPHYSICAL REPORTS 2021; 1:100015. [PMID: 36425455 PMCID: PMC9680803 DOI: 10.1016/j.bpr.2021.100015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/30/2021] [Indexed: 12/25/2022]
Abstract
We present a fluorescence fluctuation image correlation analysis method that can rapidly and simultaneously measure the diffusion coefficient, photoblinking rates, and fraction of diffusing particles of fluorescent molecules in cells. Unlike other image correlation techniques, we demonstrated that our method could be applied irrespective of a nonuniformly distributed, immobile blinking fluorophore population. This allows us to measure blinking and transport dynamics in complex cell morphologies, a benefit for a range of super-resolution fluorescence imaging approaches that rely on probe emission blinking. Furthermore, we showed that our technique could be applied without directly accounting for photobleaching. We successfully employed our technique on several simulations with realistic EMCCD noise and photobleaching models, as well as on Dronpa-C12-labeled β-actin in living NIH/3T3 and HeLa cells. We found that the diffusion coefficients measured using our method were consistent with previous literature values. We further found that photoblinking rates measured in the live HeLa cells varied as expected with changing excitation power.
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24
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Placidi G, Campa CC. Deliver on Time or Pay the Fine: Scheduling in Membrane Trafficking. Int J Mol Sci 2021; 22:11773. [PMID: 34769203 PMCID: PMC8583995 DOI: 10.3390/ijms222111773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/23/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
Membrane trafficking is all about time. Automation in such a biological process is crucial to ensure management and delivery of cellular cargoes with spatiotemporal precision. Shared molecular regulators and differential engagement of trafficking components improve robustness of molecular sorting. Sequential recruitment of low affinity protein complexes ensures directionality of the process and, concomitantly, serves as a kinetic proofreading mechanism to discriminate cargoes from the whole endocytosed material. This strategy helps cells to minimize losses and operating errors in membrane trafficking, thereby matching the appealed deadline. Here, we summarize the molecular pathways of molecular sorting, focusing on their timing and efficacy. We also highlight experimental procedures and genetic approaches to robustly probe these pathways, in order to guide mechanistic studies at the interface between biochemistry and quantitative biology.
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Affiliation(s)
- Giampaolo Placidi
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy;
- Candiolo Cancer Institute, FPO-IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy
| | - Carlo C. Campa
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy;
- Candiolo Cancer Institute, FPO-IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy
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25
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Wi JH, Heo CH, Gwak H, Jung C, Kim SY. Probing Physical Properties of the Cellular Membrane in Senescent Cells by Fluorescence Imaging. J Phys Chem B 2021; 125:10182-10194. [PMID: 34473497 DOI: 10.1021/acs.jpcb.1c05403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cellular senescence is the irreversible cell cycle arrest in response to various types of stress. Although the plasma membrane and its composition are significantly affected by cellular senescence, detailed studies on the physical properties of the plasma membrane have shown inconclusive results. In this study, we utilized both ensemble and single-molecule fluorescence imaging to investigate how membrane properties, such as fluidity, hydrophobicity, and ganglioside GM1 level are affected by cellular senescence. The diffusion coefficient of lipid probes, as well as the type of diffusion determined by an exponent α, which is the slope of the log-log plot of mean squared displacement as a function of time lag, were analyzed. We found that the number of molecules with a lower diffusion coefficient increased as cells became senescent. The changes in the population with a lower diffusion coefficient, observed after methyl-β-cyclodextrin treatment, and the increase in ceramide levels, detected using a ceramide-specific antibody, suggest that ceramide-rich lipid rafts were enhanced in senescent cells. Our results emphasize the importance of membrane properties in cellular senescence and might serve as a base for in-depth studies to determine how such domains facilitate the signaling pathway specific to cellular senescence.
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Affiliation(s)
- Ji Hun Wi
- Theragnosis Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.,Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Cheol Ho Heo
- Theragnosis Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - HyeRan Gwak
- Theragnosis Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Cheulhee Jung
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - So Yeon Kim
- Theragnosis Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul 02792, Republic of Korea
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26
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Jing Y, Zhang C, Yu B, Lin D, Qu J. Super-Resolution Microscopy: Shedding New Light on In Vivo Imaging. Front Chem 2021; 9:746900. [PMID: 34595156 PMCID: PMC8476955 DOI: 10.3389/fchem.2021.746900] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/26/2021] [Indexed: 12/28/2022] Open
Abstract
Over the past two decades, super-resolution microscopy (SRM), which offered a significant improvement in resolution over conventional light microscopy, has become a powerful tool to visualize biological activities in both fixed and living cells. However, completely understanding biological processes requires studying cells in a physiological context at high spatiotemporal resolution. Recently, SRM has showcased its ability to observe the detailed structures and dynamics in living species. Here we summarized recent technical advancements in SRM that have been successfully applied to in vivo imaging. Then, improvements in the labeling strategies are discussed together with the spectroscopic and chemical demands of the fluorophores. Finally, we broadly reviewed the current applications for super-resolution techniques in living species and highlighted some inherent challenges faced in this emerging field. We hope that this review could serve as an ideal reference for researchers as well as beginners in the relevant field of in vivo super resolution imaging.
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Affiliation(s)
| | | | | | - Danying Lin
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
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27
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Xu X, Wang Y, Choi WS, Sun X, Godbout R. Super resolution microscopy reveals DHA-dependent alterations in glioblastoma membrane remodelling and cell migration. NANOSCALE 2021; 13:9706-9722. [PMID: 34018532 DOI: 10.1039/d1nr02128a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Brain fatty acid binding protein (FABP7; B-FABP) promotes glioblastoma (GBM) cell migration and is associated with tumor infiltration, properties associated with a poor prognosis in GBM patients. FABP7-expressing neural stem-like cells are known to drive tumor migration/infiltration and resistance to treatment. We have previously shown that FABP7's effects on cell migration can be reversed when GBM cells are cultured in medium supplemented with the omega-3 fatty acid, docosahexaenoic acid (DHA). Here, we use super-resolution imaging on patient-derived GBM stem-like cells to examine the importance of FABP7 and its fatty acid ligands in mitigating GBM cell migration. As FABPs are involved in fatty acid transport from membrane to cytosol, we focus on the effect of FABP7 and its ligand DHA on GBM membrane remodeling, as well as FABP7 nanoscale domain formation on GBM membrane. Using quantitative plasma membrane lipid order imaging, we show that FABP7 expression in GBM cells correlates with increased membrane lipid order, with DHA dramatically decreasing lipid order. Using super-resolution stimulated emission depletion (STED) microscopy, we observe non-uniform distribution of FABP7 on the surface of GBM cells, with FABP7 forming punctate nanoscale domains of ∼100 nm in diameter. These nanodomains are particularly enriched at the migrating front of GBM cells. Interestingly, FABP7 nanodomains are disrupted when GBM cells are cultured in DHA-supplemented medium. We demonstrate a tight link between cell migration, a higher membrane lipid order and increased FABP7 nanoscale domains. We propose that DHA-mediated disruption of membrane lipid order and FABP7 nanodomains forms the basis of FABP7/DHA-mediated inhibition of cell migration in GBM.
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Affiliation(s)
- Xia Xu
- Cross Cancer Institute, University of Alberta, Department of Oncology, 11560 University Avenue, Edmonton, Alberta, Canada.
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28
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One Raft to Guide Them All, and in Axon Regeneration Inhibit Them. Int J Mol Sci 2021; 22:ijms22095009. [PMID: 34066896 PMCID: PMC8125918 DOI: 10.3390/ijms22095009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 12/15/2022] Open
Abstract
Central nervous system damage caused by traumatic injuries, iatrogenicity due to surgical interventions, stroke and neurodegenerative diseases is one of the most prevalent reasons for physical disability worldwide. During development, axons must elongate from the neuronal cell body to contact their precise target cell and establish functional connections. However, the capacity of the adult nervous system to restore its functionality after injury is limited. Given the inefficacy of the nervous system to heal and regenerate after damage, new therapies are under investigation to enhance axonal regeneration. Axon guidance cues and receptors, as well as the molecular machinery activated after nervous system damage, are organized into lipid raft microdomains, a term typically used to describe nanoscale membrane domains enriched in cholesterol and glycosphingolipids that act as signaling platforms for certain transmembrane proteins. Here, we systematically review the most recent findings that link the stability of lipid rafts and their composition with the capacity of axons to regenerate and rebuild functional neural circuits after damage.
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29
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Munnik T, Mongrand S, Zársky V, Blatt M. Dynamic membranes-the indispensable platform for plant growth, signaling, and development. PLANT PHYSIOLOGY 2021; 185:547-549. [PMID: 33822219 PMCID: PMC8133590 DOI: 10.1093/plphys/kiaa107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- Teun Munnik
- Research Cluster Green Life Sciences, Section Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, PO Box 94215, Amsterdam, 1090GE, The Netherlands
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire, UMR5200, Université de Bordeaux, CNRS, 33140 Villenave d’Ornon, France
| | - Viktor Zársky
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 165 02 Prague 6, Czech Republic
| | - Mike Blatt
- Laboratory of Plant Physiology and Biophysics, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK
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Liu Z, Gao J, Cui Y, Klumpe S, Xiang Y, Erdmann PS, Jiang L. Membrane imaging in the plant endomembrane system. PLANT PHYSIOLOGY 2021; 185:562-576. [PMID: 33793889 PMCID: PMC8133680 DOI: 10.1093/plphys/kiaa040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/11/2020] [Indexed: 05/10/2023]
Abstract
Recent studies on membrane imaging in the plant endomembrane system by 2-D/3-D CLSM and TEM provide future perspectives of whole-cell ET and cryo-FIB-aided cryo-ET analysis.
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Affiliation(s)
- Zhiqi Liu
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jiayang Gao
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yong Cui
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sven Klumpe
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Yun Xiang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Philipp S Erdmann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Liwen Jiang
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
- CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
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31
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Kluczyk-Korch K, Palazzo D, Waag A, Diéguez A, Prades JD, Di Carlo A, der Maur MA. Optical design of InGaN/GaN nanoLED arrays on a chip: toward: highly resolved illumination. NANOTECHNOLOGY 2021; 32:105203. [PMID: 33232943 DOI: 10.1088/1361-6528/abcd60] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The physical laws of diffraction limit the spatial resolution of optical systems. In contrary to most superresolution microscopy approaches used today, in our novel idea we are aiming to overcome this limit by developing a spatially resolved illumination source based on semiconductor nanoscale light emitting diode (nanoLED) arrays with individual pixel control. We present and discuss the results of optical simulations performed for such nanoLED emitter arrays and analyze the theoretical limits of this approach. As possible designs we study arrays of GaN nanofins and nanorods (obtained by etching nanofin arrays), with InGaN/GaN multi quantum wells embedded as active regions. We find that a suitable choice of the array dimensions leads to a reasonably directed light output and concentration of the optical power in the near field around an activated pixel. As a consequence, the spatial resolution for this type of microscopy should only be limited by the pixel pitch, and no longer by the optical diffraction. Realization of optimized nanoLED arrays has a potential to open new field of chip based superresolution microscopy, making super-high spatial resolution ubiquitously available.
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Affiliation(s)
- K Kluczyk-Korch
- Department of Electronic Engineering, University of Rome 'Tor Vergata', Via del Politechnico 1, 00133 Rome, Italy
| | - D Palazzo
- Department of Electronic Engineering, University of Rome 'Tor Vergata', Via del Politechnico 1, 00133 Rome, Italy
| | - A Waag
- Institute for Semiconductor Technology, University of Technology Braunschweig, Braunschweig, Germany
- Laboratory for Emerging Nanometrology LENA, Braunschweig, Germany
| | - A Diéguez
- Department of Electronic and Biomedical Engineering, University of Barcelona, Barcelona, Spain
| | - J D Prades
- Department of Electronic and Biomedical Engineering, University of Barcelona, Barcelona, Spain
| | - A Di Carlo
- Department of Electronic Engineering, University of Rome 'Tor Vergata', Via del Politechnico 1, 00133 Rome, Italy
- ISM-CNR, Via Fosso del Cavaliere 100, 00133 Rome, Italy
| | - M Auf der Maur
- Department of Electronic Engineering, University of Rome 'Tor Vergata', Via del Politechnico 1, 00133 Rome, Italy
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Schniete JK, Tinning PW, Scrimgeour RC, Robb G, Kölln LS, Wesencraft K, Paul NR, Bushell TJ, McConnell G. An evaluation of multi-excitation-wavelength standing-wave fluorescence microscopy (TartanSW) to improve sampling density in studies of the cell membrane and cytoskeleton. Sci Rep 2021; 11:2903. [PMID: 33536463 PMCID: PMC7858599 DOI: 10.1038/s41598-020-78282-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022] Open
Abstract
Conventional standing-wave (SW) fluorescence microscopy uses a single wavelength to excite fluorescence from the specimen, which is normally placed in contact with a first surface reflector. The resulting excitation SW creates a pattern of illumination with anti-nodal maxima at multiple evenly-spaced planes perpendicular to the optical axis of the microscope. These maxima are approximately 90 nm thick and spaced 180 nm apart. Where the planes intersect fluorescent structures, emission occurs, but between the planes are non-illuminated regions which are not sampled for fluorescence. We evaluate a multi-excitation-wavelength SW fluorescence microscopy (which we call TartanSW) as a method for increasing the density of sampling by using SWs with different axial periodicities, to resolve more of the overall cell structure. The TartanSW method increased the sampling density from 50 to 98% over seven anti-nodal planes, with no notable change in axial or lateral resolution compared to single-excitation-wavelength SW microscopy. We demonstrate the method with images of the membrane and cytoskeleton of living and fixed cells.
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Affiliation(s)
- Jana K Schniete
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK.
| | - Peter W Tinning
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
| | - Ross C Scrimgeour
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
| | - Gillian Robb
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
| | - Lisa S Kölln
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
| | - Katrina Wesencraft
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
| | - Nikki R Paul
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
| | - Trevor J Bushell
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Gail McConnell
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
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Ventura AE, Santos TCB, Marquês JT, de Almeida RFM, Silva LC. Biophysical Analysis of Lipid Domains by Fluorescence Microscopy. Methods Mol Biol 2021; 2187:223-245. [PMID: 32770510 DOI: 10.1007/978-1-0716-0814-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
The study of the structure and dynamics of membrane domains in vivo is a challenging task. However, major advances could be achieved through the application of microscopic and spectroscopic techniques coupled with the use of model membranes, where the relations between lipid composition and the type, amount and properties of the domains present can be quantitatively studied.This chapter provides protocols to study membrane organization and visualize membrane domains by fluorescence microscopy both in artificial membrane and living cell models of Gaucher Disease (GD ). We describe a bottom-up multiprobe methodology, which enables understanding how the specific lipid interactions established by glucosylceramide, the lipid that accumulates in GD , affect the biophysical properties of model and cell membranes, focusing on its ability to influence the formation, properties and organization of lipid raft domains. In this context, we address the preparation of (1) raft-mimicking giant unilamellar vesicles labeled with a combination of fluorophores that allow for the visualization and comprehensive characterization of those membrane domains and (2) human fibroblasts exhibiting GD phenotype to assess the biophysical properties of biological membrane in living cells using fluorescence microscopy.
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Affiliation(s)
- Ana E Ventura
- Research Institute for medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- CQFM-IN and IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Tânia C B Santos
- Research Institute for medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- CQFM-IN and IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Joaquim T Marquês
- Centro de Química e Bioquímica, Centro de Química Estrutural, DQB, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Rodrigo F M de Almeida
- Centro de Química e Bioquímica, Centro de Química Estrutural, DQB, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Liana C Silva
- Research Institute for medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
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Modulation and dynamics of cell membrane heterogeneities. Chem Phys Lipids 2020; 233:105006. [PMID: 33144069 DOI: 10.1016/j.chemphyslip.2020.105006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 01/02/2023]
Abstract
Numerous studies provide evidence that the lipid bilayer of the plasma membrane contains lateral nanodomains, and that these are functionally important regulators of transmembrane cell signaling. Depending on their chemical composition and the biophysical mechanism bringing the lipids together, multiple types of nanodomains exist in the inner and the outer leaflet of the plasma membrane bilayer. In intact cells, these domains are smaller than the optical resolution limit of light microscopy and also highly dynamic. Recently, advanced fluorescence methods have provided data to characterize many biophysical and thermodynamic aspects of these nanodomains. In this review, we summarize the physicochemical determinants of nanodomain formation, stability and extent. Then, we detail how these nanodomains play a structural role by anchoring nucleation sites for the membrane cytoskeleton on the lipid bilayer. Further, we review the existing literature on mechanisms that modulate the nanodomain size and stability, both acute and chronic events. We conclude that regulation of the nanodomains distribution in the lipid bilayer of the plasma membrane is important for modulation of transmembrane signaling. However, only very few modulators of nanodomain stability and size have been quantified in cells, suggesting interesting directions for future studies.
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Drolle E, Ngo W, Leonenko Z, Subbaraman L, Jones L. Nanoscale Characteristics of Ocular Lipid Thin Films Using Kelvin Probe Force Microscopy. Transl Vis Sci Technol 2020; 9:41. [PMID: 32832246 PMCID: PMC7414624 DOI: 10.1167/tvst.9.7.41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/05/2020] [Indexed: 02/02/2023] Open
Abstract
Purpose To describe the use of Kelvin probe force microscopy (KPFM) to investigate the electrical surface potential of human meibum and to demonstrate successful use of this instrument on both human meibum and a meibum model system (six-lipid stock [6LS]) to elucidate nanoscale surface chemistry and self-assembly characteristics. Materials and Methods 6LS and meibum were analyzed in this study. Mica-supported thin films were created using the Langmuir-Blodgett trough. Topography and electrical surface potential were quantified using simultaneous atomic force microscopy/KPFM imaging. Results Both lipid mixtures formed thin film patches on the surface of the mica substrate, with large aggregates resting atop. The 6LS had aggregate heights ranging from 41 to 153 nm. The range in surface potential was 33.0 to 125.9 mV. The meibum thin films at P = 5 mN/m had aggregates of 170 to 459 nm in height and surface potential ranging from 15.9 to 76.1 mV, while thin films at P = 10 mN/m showed an aggregate size range of 147 to 407 nm and a surface potential range of 11.5 to 255.1 mV. Conclusions This study showed imaging of the differences in electrical surface potential of meibum via KPFM and showed similarities in nanoscale topography. 6LS was also successfully analyzed, showing the capabilities of this method for use in both in vitro and ex vivo ocular research. Translational Relevance This study describes the use of KPFM for the study of ocular surface lipids for the first time and outlines possibilities for future studies to be carried out using this concept.
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Affiliation(s)
- Elizabeth Drolle
- Centre for Ocular Research & Education (CORE), School of Optometry & Vision Science, University of Waterloo, Waterloo, Ontario, Canada
| | - William Ngo
- Centre for Ocular Research & Education (CORE), School of Optometry & Vision Science, University of Waterloo, Waterloo, Ontario, Canada
| | - Zoya Leonenko
- Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada.,Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Lakshman Subbaraman
- Centre for Ocular Research & Education (CORE), School of Optometry & Vision Science, University of Waterloo, Waterloo, Ontario, Canada
| | - Lyndon Jones
- Centre for Ocular Research & Education (CORE), School of Optometry & Vision Science, University of Waterloo, Waterloo, Ontario, Canada.,Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada.,Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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36
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Direct imaging of liquid domains in membranes by cryo-electron tomography. Proc Natl Acad Sci U S A 2020; 117:19713-19719. [PMID: 32759217 DOI: 10.1073/pnas.2002245117] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Images of micrometer-scale domains in lipid bilayers have provided the gold standard of model-free evidence to understand the domains' shapes, sizes, and distributions. Corresponding techniques to directly and quantitatively assess smaller (nanoscale and submicron) liquid domains have been limited. Researchers commonly seek to correlate activities of membrane proteins with attributes of the domains in which they reside; doing so hinges on identification and characterization of membrane domains. Although some features of membrane domains can be probed by indirect methods, these methods are often constrained by the limitation that data must be analyzed in the context of models that require multiple assumptions or parameters. Here, we address this challenge by developing and testing two methods of identifying submicron domains in biomimetic membranes. Both methods leverage cryo-electron tomograms of ternary membranes under vitrified, hydrated conditions. The first method is optimized for probe-free applications: Domains are directly distinguished from the surrounding membrane by their thickness. This technique quantitatively and accurately measures area fractions of domains, in excellent agreement with known phase diagrams. The second method is optimized for applications in which a single label is deployed for imaging membranes by both high-resolution cryo-electron tomography and diffraction-limited optical microscopy. For this method, we test a panel of probes, find that a trimeric mCherry label performs best, and specify criteria for developing future high-performance, dual-use probes. These developments have led to direct and quantitative imaging of submicron membrane domains in vitrified, hydrated vesicles.
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37
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Membrane interactions in drug delivery: Model cell membranes and orthogonal techniques. Adv Colloid Interface Sci 2020; 281:102177. [PMID: 32417568 DOI: 10.1016/j.cis.2020.102177] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/05/2020] [Accepted: 05/07/2020] [Indexed: 01/22/2023]
Abstract
To generate the desired effect in the human body, the active pharmaceutical ingredient usually needs to interact with a receptor located on the cell membrane or inside the cell. Thus, understanding membrane interactions is of great importance when it comes to the development and testing of new drug molecules or new drug delivery systems. Nowadays, there is a tremendous selection of both model cell membranes and of techniques that can be used to characterize interactions between selected model cell membranes and a drug molecule, an excipient, or a drug delivery system. Having such a wide selection of model cell membranes and techniques available makes it sometimes challenging to select the optimal combination for a specific study. Furthermore, it is difficult to compare results obtained using different model cell membranes and techniques, and not all in vitro studies translate as well to an estimation of the in vivo biological activity or understanding of mode of action. This review provides an overview of the available lipid bilayer-based model cell membranes and of the most widely employed techniques for studying membrane interactions. Finally, the need for employing complimentary characterization techniques in order to acquire more reliable and in-depth information is highlighted.
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García-Calvo J, Maillard J, Fureraj I, Strakova K, Colom A, Mercier V, Roux A, Vauthey E, Sakai N, Fürstenberg A, Matile S. Fluorescent Membrane Tension Probes for Super-Resolution Microscopy: Combining Mechanosensitive Cascade Switching with Dynamic-Covalent Ketone Chemistry. J Am Chem Soc 2020; 142:12034-12038. [PMID: 32609500 DOI: 10.1021/jacs.0c04942] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We report the design, synthesis, and evaluation of fluorescent flipper probes for single-molecule super-resolution imaging of membrane tension in living cells. Reversible switching from bright-state ketones to dark-state hydrates, hemiacetals, and hemithioacetals is demonstrated for twisted and planarized mechanophores in solution and membranes. Broadband femtosecond fluorescence up-conversion spectroscopy evinces ultrafast chalcogen-bonding cascade switching in the excited state in solution. According to fluorescence lifetime imaging microscopy, the new flippers image membrane tension in live cells with record red shifts and photostability. Single-molecule localization microscopy with the new tension probes resolves membranes well below the diffraction limit.
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Affiliation(s)
- José García-Calvo
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Jimmy Maillard
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Ina Fureraj
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Karolina Strakova
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Adai Colom
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Vincent Mercier
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Aurelien Roux
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Eric Vauthey
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Naomi Sakai
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Alexandre Fürstenberg
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
| | - Stefan Matile
- School of Chemistry and Biochemistry, University of Geneva, Geneva 1211, Switzerland
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Khater IM, Nabi IR, Hamarneh G. A Review of Super-Resolution Single-Molecule Localization Microscopy Cluster Analysis and Quantification Methods. PATTERNS (NEW YORK, N.Y.) 2020; 1:100038. [PMID: 33205106 PMCID: PMC7660399 DOI: 10.1016/j.patter.2020.100038] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single-molecule localization microscopy (SMLM) is a relatively new imaging modality, winning the 2014 Nobel Prize in Chemistry, and considered as one of the key super-resolution techniques. SMLM resolution goes beyond the diffraction limit of light microscopy and achieves resolution on the order of 10-20 nm. SMLM thus enables imaging single molecules and study of the low-level molecular interactions at the subcellular level. In contrast to standard microscopy imaging that produces 2D pixel or 3D voxel grid data, SMLM generates big data of 2D or 3D point clouds with millions of localizations and associated uncertainties. This unprecedented breakthrough in imaging helps researchers employ SMLM in many fields within biology and medicine, such as studying cancerous cells and cell-mediated immunity and accelerating drug discovery. However, SMLM data quantification and interpretation methods have yet to keep pace with the rapid advancement of SMLM imaging. Researchers have been actively exploring new computational methods for SMLM data analysis to extract biosignatures of various biological structures and functions. In this survey, we describe the state-of-the-art clustering methods adopted to analyze and quantify SMLM data and examine the capabilities and shortcomings of the surveyed methods. We classify the methods according to (1) the biological application (i.e., the imaged molecules/structures), (2) the data acquisition (such as imaging modality, dimension, resolution, and number of localizations), and (3) the analysis details (2D versus 3D, field of view versus region of interest, use of machine-learning and multi-scale analysis, biosignature extraction, etc.). We observe that the majority of methods that are based on second-order statistics are sensitive to noise and imaging artifacts, have not been applied to 3D data, do not leverage machine-learning formulations, and are not scalable for big-data analysis. Finally, we summarize state-of-the-art methodology, discuss some key open challenges, and identify future opportunities for better modeling and design of an integrated computational pipeline to address the key challenges.
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Affiliation(s)
- Ismail M. Khater
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Ivan Robert Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Ghassan Hamarneh
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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Jakšić Z, Jakšić O. Biomimetic Nanomembranes: An Overview. Biomimetics (Basel) 2020; 5:E24. [PMID: 32485897 PMCID: PMC7345464 DOI: 10.3390/biomimetics5020024] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 11/30/2022] Open
Abstract
Nanomembranes are the principal building block of basically all living organisms, and without them life as we know it would not be possible. Yet in spite of their ubiquity, for a long time their artificial counterparts have mostly been overlooked in mainstream microsystem and nanosystem technologies, being a niche topic at best, instead of holding their rightful position as one of the basic structures in such systems. Synthetic biomimetic nanomembranes are essential in a vast number of seemingly disparate fields, including separation science and technology, sensing technology, environmental protection, renewable energy, process industry, life sciences and biomedicine. In this study, we review the possibilities for the synthesis of inorganic, organic and hybrid nanomembranes mimicking and in some way surpassing living structures, consider their main properties of interest, give a short overview of possible pathways for their enhancement through multifunctionalization, and summarize some of their numerous applications reported to date, with a focus on recent findings. It is our aim to stress the role of functionalized synthetic biomimetic nanomembranes within the context of modern nanoscience and nanotechnologies. We hope to highlight the importance of the topic, as well as to stress its great applicability potentials in many facets of human life.
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Affiliation(s)
- Zoran Jakšić
- Center of Microelectronic Technologies, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, 11000 Belgrade, Serbia;
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Karal MAS, Ahamed MK, Ahmed M, Ahamed S, Mahbub ZB. Location of Peptide-Induced Submicron Discontinuities in the Membranes of Vesicles Using ImageJ. J Fluoresc 2020; 30:735-740. [PMID: 32472291 DOI: 10.1007/s10895-020-02560-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/11/2020] [Indexed: 11/26/2022]
Abstract
Cell penetrating peptide transportan 10 and antimicrobial peptide melittin formed submicron pores in the lipid membranes of vesicles which are explained by the leakage of water-soluble fluorescent probes from the inside of vesicles to the outside. It is hypothesized that these submicron pores induce submicron discontinuities in the membranes. Considering this hypothesis, a technique has developed to locate the submicron discontinuities in the membranes of giant unilamellar vesicles (GUVs) using ImageJ. In this technique, at first the edges of membrane of a 'single GUV' are detected and then these edges are used to locate the submicron discontinuities. Two continuous rings are observed after applying the ImageJ in GUVs which indicated the edges of membrane. In contrast, the submicron discontinuations are detected at the edges of transportan 10 and melittin induced pore formed membranes. This investigation might be helpful for the elucidation of mechanism of the peptide-induced pore formation in the membranes of vesicles.
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Affiliation(s)
- Mohammad Abu Sayem Karal
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh.
| | - Md Kabir Ahamed
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
| | - Marzuk Ahmed
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
| | - Shareef Ahamed
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
| | - Zaid Bin Mahbub
- Department of Mathematics and Physics, North South University, Dhaka, 1229, Bangladesh
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Barbotin A, Urbančič I, Galiani S, Eggeling C, Booth M, Sezgin E. z-STED Imaging and Spectroscopy to Investigate Nanoscale Membrane Structure and Dynamics. Biophys J 2020; 118:2448-2457. [PMID: 32359408 PMCID: PMC7231928 DOI: 10.1016/j.bpj.2020.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/12/2020] [Accepted: 04/06/2020] [Indexed: 12/23/2022] Open
Abstract
Super-resolution stimulated emission depletion (STED) microcopy provides optical resolution beyond the diffraction limit. The resolution can be increased laterally (xy) or axially (z). Two-dimensional STED has been extensively used to elucidate the nanoscale membrane structure and dynamics via imaging or combined with spectroscopy techniques such as fluorescence correlation spectroscopy (FCS) and spectral imaging. On the contrary, z-STED has not been used in this context. Here, we show that a combination of z-STED with FCS or spectral imaging enables us to see previously unobservable aspects of cellular membranes. We show that thanks to an axial resolution of ∼100 nm, z-STED can be used to distinguish axially close-by membranes, early endocytic vesicles, or tubular membrane structures. Combination of z-STED with FCS and spectral imaging showed diffusion dynamics and lipid organization in these structures, respectively.
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Affiliation(s)
- Aurélien Barbotin
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Iztok Urbančič
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Jožef Stefan Institute, Ljubljana, Slovenia
| | - Silvia Galiani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Christian Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany; Leibniz Institute of Photonic Technology e.V., Jena, Germany
| | - Martin Booth
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden.
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Huang X, Jiang C, Yu L, Yang A. Current and Emerging Approaches for Studying Inter-Organelle Membrane Contact Sites. Front Cell Dev Biol 2020; 8:195. [PMID: 32292782 PMCID: PMC7118198 DOI: 10.3389/fcell.2020.00195] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/09/2020] [Indexed: 12/24/2022] Open
Abstract
Inter-organelle membrane contact sites (MCSs) are classically defined as areas of close proximity between heterologous membranes and established by specific proteins (termed tethers). The interest on MCSs has rapidly increased in the last years, since MCSs play a crucial role in the transfer of cellular components between different organelles and have been involved in important cellular functions such as apoptosis, organelle division and biogenesis, and cell growth. Recently, an unprecedented depth and breadth in insights into the details of MCSs have been uncovered. On one hand, extensive MCSs (organelles interactome) are revealed by comprehensive analysis of organelle network with high temporal-spatial resolution at the system level. On the other hand, more and more tethers involving in MCSs are identified and further works are focusing on addressing the role of these tethers in regulating the function of MCSs at the molecular level. These enormous progresses largely depend on the powerful approaches, including several different types of microscopies and various biochemical techniques. These approaches have greatly accelerated recent advances in MCSs at the system and molecular level. In this review, we summarize the current and emerging approaches for studying MCSs, such as various microscopies, proximity-driven fluorescent signal generation and proximity-dependent biotinylation. In addition, we highlight the advantages and disadvantages of the techniques to provide a general guidance for the study of MCSs.
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Affiliation(s)
- Xue Huang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Chen Jiang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lihua Yu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing, China
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44
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Picca A, Calvani R, Coelho-Junior HJ, Landi F, Bernabei R, Marzetti E. Inter-Organelle Membrane Contact Sites and Mitochondrial Quality Control during Aging: A Geroscience View. Cells 2020; 9:cells9030598. [PMID: 32138154 PMCID: PMC7140483 DOI: 10.3390/cells9030598] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial dysfunction and failing mitochondrial quality control (MQC) are major determinants of aging. Far from being standalone organelles, mitochondria are intricately related with cellular other compartments, including lysosomes. The intimate relationship between mitochondria and lysosomes is reflected by the fact that lysosomal degradation of dysfunctional mitochondria is the final step of mitophagy. Inter-organelle membrane contact sites also allow bidirectional communication between mitochondria and lysosomes as part of nondegradative pathways. This interaction establishes a functional unit that regulates metabolic signaling, mitochondrial dynamics, and, hence, MQC. Contacts of mitochondria with the endoplasmic reticulum (ER) have also been described. ER-mitochondrial interactions are relevant to Ca2+ homeostasis, transfer of phospholipid precursors to mitochondria, and integration of apoptotic signaling. Many proteins involved in mitochondrial contact sites with other organelles also participate to degradative MQC pathways. Hence, a comprehensive assessment of mitochondrial dysfunction during aging requires a thorough evaluation of degradative and nondegradative inter-organelle pathways. Here, we present a geroscience overview on (1) degradative MQC pathways, (2) nondegradative processes involving inter-organelle tethering, (3) age-related changes in inter-organelle degradative and nondegradative pathways, and (4) relevance of MQC failure to inflammaging and age-related conditions, with a focus on Parkinson’s disease as a prototypical geroscience condition.
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Affiliation(s)
- Anna Picca
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (F.L.); (E.M.)
| | - Riccardo Calvani
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (F.L.); (E.M.)
- Correspondence: (R.C.); (R.B.); Tel.: +39-(06)-3015-5559 (R.C. & R.B.); Fax: +39-(06)-3051-911 (R.C. & R.B.)
| | - Hélio José Coelho-Junior
- Institute of Internal Medicine and Geriatrics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
| | - Francesco Landi
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (F.L.); (E.M.)
- Institute of Internal Medicine and Geriatrics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
| | - Roberto Bernabei
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (F.L.); (E.M.)
- Institute of Internal Medicine and Geriatrics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
- Correspondence: (R.C.); (R.B.); Tel.: +39-(06)-3015-5559 (R.C. & R.B.); Fax: +39-(06)-3051-911 (R.C. & R.B.)
| | - Emanuele Marzetti
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (F.L.); (E.M.)
- Institute of Internal Medicine and Geriatrics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
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45
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Morrice JR, Gregory-Evans CY, Shaw CA. Investigating microglia during motor neuron degeneration using a zebrafish model. Micron 2020; 133:102852. [PMID: 32203887 DOI: 10.1016/j.micron.2020.102852] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 12/11/2022]
Abstract
Many different types of pathologies can arise in the central nervous system (CNS), such as neurodegeneration. The incidence of neurodegenerative diseases continues to increase, yet the pathogenesis underlying most neurodegenerative diseases, notably in amyotrophic lateral sclerosis (ALS), remains elusive. Neuronal support cells, or glia, are known to play a crucial role in ALS. Microglia are the resident immune cells of the CNS and also have neurotrophic support functions. These cells have a disease-modifying function in ALS, yet this role is not well understood. A likely reason for this is that the intact CNS is particularly challenging to access for investigation in patients and in most animal models, which has impeded research in this field. The zebrafish is emerging as a robust model system to investigate cells in vivo, and offer distinct advantages over other vertebrate models for investigating neurodegenerative diseases. Live imaging in vivo is a powerful technique to characterize the role of dynamic cells such as microglia during neurodegeneration, and zebrafish provide a convenient means for live imaging. Here, we discuss the zebrafish as a model for live imaging, provide a brief overview of available high resolution imaging platforms that accommodate zebrafish, and describe our own in vivo studies on the role of microglia during motor neuron degeneration. Live in vivo imaging is anticipated to provide invaluable advancements to defining the pathogenesis underlying neurodegenerative diseases, which may in turn allow for more specifically targeted therapeutics.
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Affiliation(s)
- Jessica R Morrice
- Experimental Medicine Program, University of British Columbia, 2329 West Mall, Vancouver, British Columbia, V6T 1Z4, Canada.
| | - Cheryl Y Gregory-Evans
- Experimental Medicine Program, University of British Columbia, 2329 West Mall, Vancouver, British Columbia, V6T 1Z4, Canada; Department of Ophthalmology and Visual Sciences, University of British Columbia, 2329 West Mall, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Christopher A Shaw
- Experimental Medicine Program, University of British Columbia, 2329 West Mall, Vancouver, British Columbia, V6T 1Z4, Canada; Department of Ophthalmology and Visual Sciences, University of British Columbia, 2329 West Mall, Vancouver, British Columbia, V6T 1Z4, Canada
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46
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Blatzer M, Beauvais A, Henrissat B, Latgé JP. Revisiting Old Questions and New Approaches to Investigate the Fungal Cell Wall Construction. Curr Top Microbiol Immunol 2020; 425:331-369. [PMID: 32418033 DOI: 10.1007/82_2020_209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The beginning of our understanding of the cell wall construction came from the work of talented biochemists in the 70-80's. Then came the era of sequencing. Paradoxically, the accumulation of fungal genomes complicated rather than solved the mystery of cell wall construction, by revealing the involvement of a much higher number of proteins than originally thought. The situation has become even more complicated since it is now recognized that the cell wall is an organelle whose composition continuously evolves with the changes in the environment or with the age of the fungal cell. The use of new and sophisticated technologies to observe cell wall construction at an almost atomic scale should improve our knowledge of the cell wall construction. This essay will present some of the major and still unresolved questions to understand the fungal cell wall biosynthesis and some of these exciting futurist approaches.
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Affiliation(s)
- Michael Blatzer
- Experimental Neuropathology Unit, Institut Pasteur, 25 rue du Docteur Roux, 75015, Paris, France
| | - Anne Beauvais
- Mycology Department, Institut Pasteur, 25 rue du Docteur Roux, 75015, Paris, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257-CNRS & Aix-Marseille Université, 13288, Marseille cedex 9, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jean-Paul Latgé
- Institute of Molecular Biology and Biotechnology of the Foundation for Research and Technology Hellas (IMBB-FORTH), Heraklion, Greece.
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Wilson KA, Wang L, MacDermott-Opeskin H, O'Mara ML. The Fats of Life: Using Computational Chemistry to Characterise the Eukaryotic Cell Membrane. Aust J Chem 2020. [DOI: 10.1071/ch19353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Our current knowledge of the structural dynamics and complexity of lipid bilayers is still developing. Computational techniques, especially molecular dynamics simulations, have increased our understanding significantly as they allow us to model functions that cannot currently be experimentally resolved. Here we review available computational tools and techniques, the role of the major lipid species, insights gained into lipid bilayer structure and function from molecular dynamics simulations, and recent progress towards the computational modelling of the physiological complexity of eukaryotic lipid bilayers.
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48
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Hughes HJ, Demers SME, Zhang A, Hafner JH. The orientation of a membrane probe from structural analysis by enhanced Raman scattering. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183109. [PMID: 31785235 DOI: 10.1016/j.bbamem.2019.183109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 10/10/2019] [Accepted: 10/14/2019] [Indexed: 02/04/2023]
Abstract
Small fluorescent molecules are widely used as probes of biomembranes. Different probes optically indicate membrane properties such as the lipid phase, thickness, viscosity, and electrical potential. The detailed molecular mechanisms behind probe signals are not well understood, in part due to the lack of tools to determine probe position and orientation in the membrane. Optical measurements on aligned biomembranes and lipid bilayers provide some degree of orientational information based on anisotropy in absorption, fluorescence, or nonlinear optical properties. These methods typically find the polar tilt angle between the membrane normal and the long axis of the molecule. Here we show that solution-phase surface enhanced Raman scattering (SERS) spectra of lipid membranes on gold nanorods can be used to determine molecular orientation of molecules within the membrane. The voltage sensitive dye 4-(2-(6-(dibutylamino)-2-naphthalenyl)ethenyl)-1-(3-sulfopropyl)-hydroxide, known as di-4-ANEPPS, is studied. Through the analysis of several peaks in the SERS spectrum, the polar angle from the membrane normal is found to be 66°, and the roll angle around the long axis of the molecule to be 305° from the original orientation. This structural analysis method could help elucidate the meaning of fluorescent membrane probe signals, and how they are affected by different lipid compositions.
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Affiliation(s)
- Hannah J Hughes
- Department of Physics & Astronomy, Rice University, Houston, TX, United States of America
| | - Steven M E Demers
- Department of Physics & Astronomy, Rice University, Houston, TX, United States of America
| | - Aobo Zhang
- Department of Physics & Astronomy, Rice University, Houston, TX, United States of America
| | - Jason H Hafner
- Department of Physics & Astronomy, Rice University, Houston, TX, United States of America; Department of Chemistry, Rice University, Houston, TX, United States of America.
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49
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Moltedo O, Remondelli P, Amodio G. The Mitochondria-Endoplasmic Reticulum Contacts and Their Critical Role in Aging and Age-Associated Diseases. Front Cell Dev Biol 2019; 7:172. [PMID: 31497601 PMCID: PMC6712070 DOI: 10.3389/fcell.2019.00172] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/07/2019] [Indexed: 02/03/2023] Open
Abstract
The recent discovery of interconnections between the endoplasmic reticulum (ER) membrane and those of almost all the cell compartments is providing novel perspectives for the understanding of the molecular events underlying cellular mechanisms in both physiological and pathological conditions. In particular, growing evidence strongly supports the idea that the molecular interactions occurring between ER and mitochondrial membranes, referred as the mitochondria (MT)-ER contacts (MERCs), may play a crucial role in aging and in the development of age-associated diseases. As emerged in the last decade, MERCs behave as signaling hubs composed by structural components that act as critical players in different age-associated disorders, such as neurodegenerative diseases and motor disorders, cancer, metabolic syndrome, as well as cardiovascular diseases. Age-associated disorders often derive from mitochondrial or ER dysfunction as consequences of oxidative stress, mitochondrial DNA mutations, accumulation of misfolded proteins, and defective organelle turnover. In this review, we discuss the recent advances associating MERCs to aging in the context of ER-MT crosstalk regulating redox signaling, ER-to MT lipid transfer, mitochondrial dynamics, and autophagy.
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Affiliation(s)
- Ornella Moltedo
- Department of Pharmacy, University of Salerno, Fisciano, Italy
| | - Paolo Remondelli
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," University of Salerno, Baronissi, Italy
| | - Giuseppina Amodio
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," University of Salerno, Baronissi, Italy
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50
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Proteomic Analysis of Lipid Rafts from RBL-2H3 Mast Cells. Int J Mol Sci 2019; 20:ijms20163904. [PMID: 31405203 PMCID: PMC6720779 DOI: 10.3390/ijms20163904] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/01/2019] [Accepted: 08/08/2019] [Indexed: 12/15/2022] Open
Abstract
Lipid rafts are highly ordered membrane microdomains enriched in cholesterol, glycosphingolipids, and certain proteins. They are involved in the regulation of cellular processes in diverse cell types, including mast cells (MCs). The MC lipid raft protein composition was assessed using qualitative mass spectrometric characterization of the proteome from detergent-resistant membrane fractions from RBL-2H3 MCs. Using two different post-isolation treatment methods, a total of 949 lipid raft associated proteins were identified. The majority of these MC lipid raft proteins had already been described in the RaftProtV2 database and are among highest cited/experimentally validated lipid raft proteins. Additionally, more than half of the identified proteins had lipid modifications and/or transmembrane domains. Classification of identified proteins into functional categories showed that the proteins were associated with cellular membrane compartments, and with some biological and molecular functions, such as regulation, localization, binding, catalytic activity, and response to stimulus. Furthermore, functional enrichment analysis demonstrated an intimate involvement of identified proteins with various aspects of MC biological processes, especially those related to regulated secretion, organization/stabilization of macromolecules complexes, and signal transduction. This study represents the first comprehensive proteomic profile of MC lipid rafts and provides additional information to elucidate immunoregulatory functions coordinated by raft proteins in MCs.
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