1
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Germer G, Schwartze L, García-Miller J, Balansin-Rigon R, Groth LJ, Rühl I, Patoka P, Zoschke C, Rühl E. Label-free mapping of cetuximab in multi-layered tumor oral mucosa models by atomic force-microscopy-based infrared spectroscopy. Analyst 2024; 149:2122-2130. [PMID: 38436119 DOI: 10.1039/d3an01877f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
Sensitive mapping of drugs and drug delivery systems is pivotal for the understanding and improvement of treatment options. Since labeling alters the physicochemical and potentially the pharmacological properties of the molecule of interest, its label-free detection by photothermal expansion is investigated. We report on a proof-of-concept study to map the cetuximab distribution by atomic-force microscopy-based infrared spectroscopy (AFM-IR). The monoclonal antibody cetuximab was applied to a human tumor oral mucosa model, consisting of a tumor epithelium on a lamina propria equivalent. Hyperspectral imaging in the wavenumber regime between 903 cm-1 and 1312 cm-1 and a probing distance between the data points down to 10 × 10 nm are used for determining the local drug distribution. The local distinction of cetuximab from the tissue background is gained by linear combination modeling making use of reference spectra of the drug and untreated models. The results from this approach are compared to principal component analyses, yielding comparable results. Even single molecule detection appears feasible. The results indicate that cetuximab penetrates the cytosol of tumor cells but does not bind to structures in the cell membrane. In conclusion, AFM-IR mapping of cetuximab proved to sensitively determine drug concentrations at an unprecedented spatial resolution without the need for drug labeling.
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Affiliation(s)
- Gregor Germer
- Physical Chemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany. ruehl@
| | - Leonie Schwartze
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise Str. 2+4, 14195 Berlin, Germany.
| | - Jill García-Miller
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise Str. 2+4, 14195 Berlin, Germany.
| | - Roberta Balansin-Rigon
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise Str. 2+4, 14195 Berlin, Germany.
- School of Pharmaceutical Sciences, University of Campinas, R. Candido Portinari, 200 - Cidade Universitária, Campinas, SP, 13083-871, Brazil
| | - Lucie J Groth
- Physical Chemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany. ruehl@
| | - Isabel Rühl
- Physical Chemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany. ruehl@
| | - Piotr Patoka
- Physical Chemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany. ruehl@
| | - Christian Zoschke
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise Str. 2+4, 14195 Berlin, Germany.
- Department of Veterinary Medicines, Federal Office of Consumer Protection and Food Safety, Gerichtstr. 49, 13347 Berlin, Germany
| | - Eckart Rühl
- Physical Chemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany. ruehl@
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2
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Chen T, Karedla N, Enderlein J. Measuring sub-nanometer undulations at microsecond temporal resolution with metal- and graphene-induced energy transfer spectroscopy. Nat Commun 2024; 15:1789. [PMID: 38413608 PMCID: PMC10899616 DOI: 10.1038/s41467-024-45822-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 02/01/2024] [Indexed: 02/29/2024] Open
Abstract
Out-of-plane fluctuations, also known as stochastic displacements, of biological membranes play a crucial role in regulating many essential life processes within cells and organelles. Despite the availability of various methods for quantifying membrane dynamics, accurately quantifying complex membrane systems with rapid and tiny fluctuations, such as mitochondria, remains a challenge. In this work, we present a methodology that combines metal/graphene-induced energy transfer (MIET/GIET) with fluorescence correlation spectroscopy (FCS) to quantify out-of-plane fluctuations of membranes with simultaneous spatiotemporal resolution of approximately one nanometer and one microsecond. To validate the technique and spatiotemporal resolution, we measure bending undulations of model membranes. Furthermore, we demonstrate the versatility and applicability of MIET/GIET-FCS for studying diverse membrane systems, including the widely studied fluctuating membrane system of human red blood cells, as well as two unexplored membrane systems with tiny fluctuations, a pore-spanning membrane, and mitochondrial inner/outer membranes.
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Affiliation(s)
- Tao Chen
- Third Institute of Physics - Biophysics, Georg August University, Friedrich-Hund-Platz 1, Göttingen, 37077, Germany
| | - Narain Karedla
- The Rosalind Franklin Institute, Harwell Campus, Didcot, OX11 OFA, UK
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7LF, UK
| | - Jörg Enderlein
- Third Institute of Physics - Biophysics, Georg August University, Friedrich-Hund-Platz 1, Göttingen, 37077, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Universitätsmedizin Göttingen, Robert-Koch-Str. 40, Göttingen, 37075, Germany.
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3
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Wang DX, Liu B, Han GM, Li Q, Kong DM, Enderlein J, Chen T. Metal-Induced Energy Transfer (MIET) Imaging of Cell Surface Engineering with Multivalent DNA Nanobrushes. ACS NANO 2024. [PMID: 38231016 PMCID: PMC10883130 DOI: 10.1021/acsnano.3c10162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The spacing between cells has a significant impact on cell-cell interactions, which are critical to the fate and function of both individual cells and multicellular organisms. However, accurately measuring the distance between cell membranes and the variations between different membranes has proven to be a challenging task. In this study, we employ metal-induced energy transfer (MIET) imaging/spectroscopy to determine and track the intermembrane distance and variations with nanometer precision. We have developed a DNA-based molecular adhesive called the DNA nanobrush, which serves as a cellular adhesive for connecting the plasma membranes of different cells. By manipulating the number of base pairs within the DNA nanobrush, we can modify various aspects of membrane-membrane interactions such as adhesive directionality, distance, and forces. We demonstrate that such nanometer-level changes can be detected with MIET imaging/spectroscopy. Moreover, we successfully employed MIET to measure distance variations between a cellular plasma membrane and a model membrane. This experiment not only showcases the effectiveness of MIET as a powerful tool for accurately quantifying membrane-membrane interactions but also validates the potential of DNA nanobrushes as cellular adhesives. This innovative method holds significant implications for advancing the study of multicellular interactions.
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Affiliation(s)
- Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for Cell Responses, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- III. Institute of Physics - Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Bo Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for Cell Responses, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Gui-Mei Han
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for Cell Responses, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Qingnan Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for Cell Responses, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for Cell Responses, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University, 37077 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Universitätsmedizin Göttingen, Robert-Koch-Strasse 40, Göttingen 37075, Germany
| | - Tao Chen
- III. Institute of Physics - Biophysics, Georg August University, 37077 Göttingen, Germany
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4
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Zhang L, Liu N, Wang X. Probe the nanoparticle-nucleus interaction via coarse-grained molecular model. Phys Chem Chem Phys 2023; 25:30319-30329. [PMID: 37908190 DOI: 10.1039/d3cp02981f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The present study reports on a computational model that systematically evaluates the effect of physical factors, including size, surface modification, and rigidity, on the nuclear uptake of nanoparticles (NPs). The NP-nucleus interaction is a crucial factor in biomedical applications such as drug delivery and cellular imaging. While experimental studies have provided evidence for the influence of size, shape, and surface modification on nuclear uptake, theoretical investigations on how these physical factors affect the entrance of NPs through the nuclear pore are lacking. Our results demonstrate that larger NPs require a higher amount of energy to enter the nucleus compared to smaller NPs. This highlights the importance of size as a critical factor in NP design for nuclear uptake. Additionally, surface modification of NPs can impact the nuclear uptake pathway, indicating the potential for tailored NP design for specific applications. Notably, our findings also reveal that the rigidity of NPs has a significant effect on the transport process. The interplay between physicochemical properties and nuclear pore is found to determine nuclear uptake efficiency. Taken together, our study provides new insights into the design of NPs for precise and controllable NP-nucleus interaction, with potential implications for the development of efficient and targeted drug delivery systems and imaging agents.
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Affiliation(s)
- Liuyang Zhang
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, People's Republic of China
| | - Ning Liu
- School of Aerospace Engineering and Applied Mechanics, Tongji University, Shanghai 200092, P. R. China.
| | - Xianqiao Wang
- College of Engineering, University of Georgia, Athens, GA 30602, USA
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5
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Grandy C, Port F, Radzinski M, Singh K, Erz D, Pfeil J, Reichmann D, Gottschalk KE. Remodeling of the focal adhesion complex by hydrogen-peroxide-induced senescence. Sci Rep 2023; 13:9735. [PMID: 37322076 PMCID: PMC10272183 DOI: 10.1038/s41598-023-36347-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Cellular senescence is a phenotype characterized by cessation of cell division, which can be caused by exhaustive replication or environmental stress. It is involved in age-related pathophysiological conditions and affects both the cellular cytoskeleton and the prime cellular mechanosensors, focal adhesion complexes. While the size of focal adhesions increases during senescence, it is unknown if and how this is accompanied by a remodeling of the internal focal adhesion structure. Our study uses metal-induced energy transfer to study the axial dimension of focal adhesion proteins from oxidative-stress-induced senescent cells with nanometer precision, and compares these to unstressed cells. We influenced cytoskeletal tension and the functioning of mechanosensitive ion channels using drugs and studied the combined effect of senescence and drug intervention on the focal adhesion structure. We found that H2O2-induced restructuring of the focal adhesion complex indicates a loss of tension and altered talin complexation. Mass spectroscopy-based proteomics confirmed the differential regulation of several cytoskeletal proteins induced by H2O2 treatment.
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Affiliation(s)
- Carolin Grandy
- Institute of Experimental Physics, Ulm University, 89081, Ulm, Baden-Württemberg, Germany
| | - Fabian Port
- Institute of Experimental Physics, Ulm University, 89081, Ulm, Baden-Württemberg, Germany
| | - Meytal Radzinski
- Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, 9190401, Jerusalem, Israel
| | - Karmveer Singh
- Department of Dermatology and Allergic Diseases, Ulm University, 89081, Ulm,, Baden-Württemberg, Germany
| | - Dorothee Erz
- Institute of Experimental Physics, Ulm University, 89081, Ulm, Baden-Württemberg, Germany
| | - Jonas Pfeil
- Institute of Experimental Physics, Ulm University, 89081, Ulm, Baden-Württemberg, Germany
| | - Dana Reichmann
- Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, 9190401, Jerusalem, Israel
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6
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Hauke L, Isbaner S, Ghosh A, Guido I, Turco L, Chizhik AI, Gregor I, Karedla N, Rehfeldt F, Enderlein J. Metal-Induced Energy Transfer (MIET) for Live-Cell Imaging with Fluorescent Proteins. ACS NANO 2023; 17:8242-8251. [PMID: 36995274 PMCID: PMC10173696 DOI: 10.1021/acsnano.2c12372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Metal-induced energy transfer (MIET) imaging is an easy-to-implement super-resolution modality that achieves nanometer resolution along the optical axis of a microscope. Although its capability in numerous biological and biophysical studies has been demonstrated, its implementation for live-cell imaging with fluorescent proteins is still lacking. Here, we present its applicability and capabilities for live-cell imaging with fluorescent proteins in diverse cell types (adult human stem cells, human osteo-sarcoma cells, and Dictyostelium discoideum cells), and with various fluorescent proteins (GFP, mScarlet, RFP, YPet). We show that MIET imaging achieves nanometer axial mapping of living cellular and subcellular components across multiple time scales, from a few milliseconds to hours, with negligible phototoxic effects.
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Affiliation(s)
- Lara Hauke
- Third Institute of Physics - Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Sebastian Isbaner
- Third Institute of Physics - Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Arindam Ghosh
- Third Institute of Physics - Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Isabella Guido
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Laura Turco
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Alexey I Chizhik
- Third Institute of Physics - Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Ingo Gregor
- Third Institute of Physics - Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Narain Karedla
- Third Institute of Physics - Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Florian Rehfeldt
- Third Institute of Physics - Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Jörg Enderlein
- Third Institute of Physics - Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Universitätsmedizin Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
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7
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Grandy C, Port F, Pfeil J, Oliva MAG, Vassalli M, Gottschalk KE. Cell shape and tension alter focal adhesion structure. BIOMATERIALS ADVANCES 2023; 145:213277. [PMID: 36621197 DOI: 10.1016/j.bioadv.2022.213277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/25/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023]
Abstract
Cells are not only anchored to the extracellular matrix via the focal adhesion complex, the focal adhesion complex also serves as a sensor for force transduction. How tension influences the structure of focal adhesions is not well understood. Here, we analyse the effect of tension on the location of key focal adhesion proteins, namely vinculin, paxillin and actin. We use micropatterning on gold surfaces to manipulate the cell shape, to create focal adhesions at specific cell areas, and to perform metal-induced energy transfer (MIET) measurements on the patterned cells. MIET resolves the different protein locations with respect to the gold surface with nanometer accuracy. Further, we use drugs influencing the cellular motor protein myosin or mechanosensitive ion channels to get deeper insight into focal adhesions at different tension states. We show here that in particular actin is affected by the rationally tuned force balance. Blocking mechanosensitive ion channels has a particularly high influence on the actin and focal adhesion architecture, resulting in larger focal adhesions with elevated paxillin and vinculin and strongly lowered actin stress fibres. Our results can be explained by a balance of adhesion tension with cellular tension together with ion channel-controlled focal adhesion homeostasis, where high cellular tension leads to an elevation of vinculin and actin, while high adhesion tension lowers these proteins.
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Affiliation(s)
- Carolin Grandy
- University Ulm, Institute of Experimental Physics, Ulm, Baden-Württemberg, 89081, Germany
| | - Fabian Port
- University Ulm, Institute of Experimental Physics, Ulm, Baden-Württemberg, 89081, Germany
| | - Jonas Pfeil
- University Ulm, Institute of Experimental Physics, Ulm, Baden-Württemberg, 89081, Germany
| | | | - Massimo Vassalli
- University of Glasgow, James Watt School of Engineering, Glasgow G12 8QQ, United Kingdom
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8
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Thiele JC, Jungblut M, Helmerich DA, Tsukanov R, Chizhik A, Chizhik AI, Schnermann MJ, Sauer M, Nevskyi O, Enderlein J. Isotropic three-dimensional dual-color super-resolution microscopy with metal-induced energy transfer. SCIENCE ADVANCES 2022; 8:eabo2506. [PMID: 35675401 PMCID: PMC9176750 DOI: 10.1126/sciadv.abo2506] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/25/2022] [Indexed: 05/25/2023]
Abstract
Over the past two decades, super-resolution microscopy has seen a tremendous development in speed and resolution, but for most of its methods, there exists a remarkable gap between lateral and axial resolution, which is by a factor of 2 to 3 worse. One recently developed method to close this gap is metal-induced energy transfer (MIET) imaging, which achieves an axial resolution down to nanometers. It exploits the distance-dependent quenching of fluorescence when a fluorescent molecule is brought close to a metal surface. In the present manuscript, we combine the extreme axial resolution of MIET imaging with the extraordinary lateral resolution of single-molecule localization microscopy, in particular with direct stochastic optical reconstruction microscopy (dSTORM). This combination allows us to achieve isotropic three-dimensional super-resolution imaging of subcellular structures. Moreover, we used spectral demixing for implementing dual-color MIET-dSTORM that allows us to image and colocalize, in three dimensions, two different cellular structures simultaneously.
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Affiliation(s)
- Jan Christoph Thiele
- Third Institute of Physics–Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Marvin Jungblut
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Dominic A. Helmerich
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Roman Tsukanov
- Third Institute of Physics–Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Anna Chizhik
- Third Institute of Physics–Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Alexey I. Chizhik
- Third Institute of Physics–Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Martin J. Schnermann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Oleksii Nevskyi
- Third Institute of Physics–Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Jörg Enderlein
- Third Institute of Physics–Biophysics, Georg August University, 37077 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells” (MBExC), Georg August University, Göttingen, Germany
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9
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Grandy C, Port F, Pfeil J, Gottschalk KE. Influence of ROCK Pathway Manipulation on the Actin Cytoskeleton Height. Cells 2022; 11:cells11030430. [PMID: 35159239 PMCID: PMC8834639 DOI: 10.3390/cells11030430] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
The actin cytoskeleton with its dynamic properties serves as the driving force for the movement and division of cells and gives the cell shape and structure. Disorders in the actin cytoskeleton occur in many diseases. Deeper understanding of its regulation is essential in order to better understand these biochemical processes. In our study, we use metal-induced energy transfer (MIET) as a tool to quantitatively examine the rarely considered third dimension of the actin cytoskeleton with nanometer accuracy. In particular, we investigate the influence of different drugs acting on the ROCK pathway on the three-dimensional actin organization. We find that cells treated with inhibitors have a lower actin height to the substrate while treatment with a stimulator for the ROCK pathway increases the actin height to the substrate, while the height of the membrane remains unchanged. This reveals the precise tuning of adhesion and cytoskeleton tension, which leads to a rich three-dimensional structural behaviour of the actin cytoskeleton. This finetuning is differentially affected by either inhibition or stimulation. The high axial resolution shows the importance of the precise finetuning of the actin cytoskeleton and the disturbed regulation of the ROCK pathway has a significant impact on the actin behavior in the z dimension.
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Affiliation(s)
- Carolin Grandy
- Institute of Experimental Physics, University Ulm, 89081 Ulm, Baden-Württemberg, Germany
| | - Fabian Port
- Institute of Experimental Physics, University Ulm, 89081 Ulm, Baden-Württemberg, Germany
| | - Jonas Pfeil
- Institute of Experimental Physics, University Ulm, 89081 Ulm, Baden-Württemberg, Germany
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10
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Xing Z, Zhao S, Guo W, Guo X, Wang S, Ma J, He H. Coal Wall and Roof Segmentation in the Coal Mine Working Face Based on Dynamic Graph Convolution Neural Networks. ACS OMEGA 2021; 6:31699-31715. [PMID: 34869994 PMCID: PMC8638012 DOI: 10.1021/acsomega.1c04393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
The intersection line information of the point cloud between the coal wall and the roof can not only accurately reflect the direction information of the scraper conveyor but also provide a preliminary basis for realizing the intelligent coal mine. However, the indirect method of using deep learning to segment the point cloud of coal mine working face cannot make full use of the rich information provided by the point cloud data. The direct method of using deep learning to segment the point cloud ignores the local feature relationship between points. Therefore, we propose to use dynamic graph convolution neural networks (DGCNNs) to segment the point cloud of the coal wall and roof so as to obtain the intersection line between them. First, in view of the characteristics of heavy dust and strong electromagnetic interference in the environment of the coal mine working face, we have installed an underground inspection robot so that we use light detection and ranging to obtain the point cloud of the coal mine working face. At the same time, we put forward a fast labeling method of the point cloud of the coal mine working face and an efficient training method of the depth neural network. Second, on the basis of edge convolution, being the greatest innovation of DGCNNs, we analyze the influence of the number of layers, K value, and output feature dimension of edge convolution on the effect of DGCNNs segmenting the point cloud of the coal mine working face and obtaining the intersection line of the coal wall and roof. Finally, we compare DGCNNs with PointNet and PointNet++. The results show that the DGCNN exhibits the best performance. What is more, the results provide a research foundation for the application of DGCNNs in the field of energy. Last but not least, the research results provide a direct and key basis for the adjustment of the scraper conveyor, which is of great significance for an intelligent coal mine working face and accurate construction of a geological information model.
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Affiliation(s)
- Zhizhong Xing
- College
of Mechanical Engineering, Xi’an
University of Science and Technology, Xi’an 710054, China
| | - Shuanfeng Zhao
- College
of Mechanical Engineering, Xi’an
University of Science and Technology, Xi’an 710054, China
| | - Wei Guo
- College
of Mechanical Engineering, Xi’an
University of Science and Technology, Xi’an 710054, China
| | - Xiaojun Guo
- School
of Mechanical & Automotive Engineering, South China University of Technology, Guangzhou 510641, China
| | - Shenquan Wang
- College
of Mechanical Engineering, Xi’an
University of Science and Technology, Xi’an 710054, China
| | - Junjie Ma
- College
of Mechanical Engineering, Xi’an
University of Science and Technology, Xi’an 710054, China
| | - Haitao He
- College
of Mechanical Engineering, Xi’an
University of Science and Technology, Xi’an 710054, China
- Shendong
Coal Group Co., Ltd. of National Energy Group, Yulin 719315, China
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11
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Brown D, Deng HY. Hydrodynamic effects on the energy transfer from dipoles to metal slab. J Chem Phys 2021; 155:114109. [PMID: 34551526 DOI: 10.1063/5.0062708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A systematic study of nonlocal and size effects on the energy transfer of a dipole (e.g., a molecule or a quantum dot) induced by the proximity of a metal slab is presented. Nonlocal effects are accounted for using the hydrodynamic model (HDM). We derive a general relation that connects the energy transfer rate to the linear charge density-density response function of the slab. This function is explicitly evaluated for the HDM and the local Drude model. We show that a thin metal slab can support a series of higher-frequency surface plasma wave (SPW) modes in addition to the normal SPW modes, thanks to the nonlocal effects. These modes markedly alter the response and the energy transfer process, as revealed in the structure of the energy transfer rate in the parameter space. Our findings are important for applications such as the recently developed metal-induced energy transfer imaging, which relies on accurate modeling of the energy transfer rate.
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Affiliation(s)
- Daniel Brown
- School of Physics and Astronomy, Cardiff University, 5 The Parade, Cardiff CF24 3AA, Wales, United Kingdom
| | - Hai-Yao Deng
- School of Physics and Astronomy, Cardiff University, 5 The Parade, Cardiff CF24 3AA, Wales, United Kingdom
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12
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Ghosh A, Chizhik AI, Karedla N, Enderlein J. Graphene- and metal-induced energy transfer for single-molecule imaging and live-cell nanoscopy with (sub)-nanometer axial resolution. Nat Protoc 2021; 16:3695-3715. [PMID: 34099942 DOI: 10.1038/s41596-021-00558-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/19/2021] [Indexed: 02/05/2023]
Abstract
Super-resolution fluorescence imaging that surpasses the classical optical resolution limit is widely utilized for resolving the spatial organization of biological structures at molecular length scales. In one example, single-molecule localization microscopy, the lateral positions of single molecules can be determined more precisely than the diffraction limit if the camera collects individual photons separately. Using several schemes that introduce engineered optical aberrations in the imaging optics, super-resolution along the optical axis (perpendicular to the sample plane) has been achieved, and single-molecule localization microscopy has been successfully applied for the study of 3D biological structures. Nonetheless, the achievable axial localization accuracy is typically three to five times worse than the lateral localization accuracy. Only a few exceptional methods based on interferometry exist that reach nanometer 3D super-resolution, but they involve enormous technical complexity and restricted sample preparations that inhibit their widespread application. We developed metal-induced energy transfer imaging for localizing fluorophores along the axial direction with nanometer accuracy, using only a conventional fluorescence lifetime imaging microscope. In metal-induced energy transfer, experimentally measured fluorescence lifetime values increase linearly with axial distance in the range of 0-100 nm, making it possible to calculate their axial position using a theoretical model. If graphene is used instead of the metal (graphene-induced energy transfer), the same range of lifetime values occurs over a shorter axial distance (~25 nm), meaning that it is possible to get very accurate axial information at the scale of a membrane bilayer or a molecular complex in a membrane. Here, we provide a step-by-step protocol for metal- and graphene-induced energy transfer imaging in single molecules, supported lipid bilayer and live-cell membranes. Depending on the sample preparation time, the complete duration of the protocol is 1-3 d.
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Affiliation(s)
- Arindam Ghosh
- Third Institute of Physics-Biophysics, Georg August University, Göttingen, Germany
| | - Alexey I Chizhik
- Third Institute of Physics-Biophysics, Georg August University, Göttingen, Germany
| | - Narain Karedla
- Rosalind Franklin Institute, Didcot, UK.,Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Jörg Enderlein
- Third Institute of Physics-Biophysics, Georg August University, Göttingen, Germany. .,Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), Georg August University, Göttingen, Germany.
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13
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Hwang W, Seo J, Kim D, Lee CJ, Choi IH, Yoo KH, Kim DY. Large field-of-view nanometer-sectioning microscopy by using metal-induced energy transfer and biexponential lifetime analysis. Commun Biol 2021; 4:91. [PMID: 33469155 PMCID: PMC7815909 DOI: 10.1038/s42003-020-01628-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/24/2020] [Indexed: 12/04/2022] Open
Abstract
Total internal reflection fluorescence (TIRF) microscopy, which has about 100-nm axial excitation depth, is the method of choice for nanometer-sectioning imaging for decades. Lately, several new imaging techniques, such as variable angle TIRF microscopy, supercritical-angle fluorescence microscopy, and metal-induced energy transfer imaging, have been proposed to enhance the axial resolution of TIRF. However, all of these methods use high numerical aperture (NA) objectives, and measured images inevitably have small field-of-views (FOVs). Small-FOV can be a serious limitation when multiple cells need to be observed. We propose large-FOV nanometer-sectioning microscopy, which breaks the complementary relations between the depth of focus and axial sectioning by using MIET. Large-FOV imaging is achieved with a low-magnification objective, while nanometer-sectioning is realized utilizing metal-induced energy transfer and biexponential fluorescence lifetime analysis. The feasibility of our proposed method was demonstrated by imaging nanometer-scale distances between the basal membrane of human aortic endothelial cells and a substrate. Hwang et al. demonstrate that a high axial resolution can be achieved even with low numerical aperture (NA) objectives. They show the nano-profile of a basal cell membrane using metal-induced energy transfer and biexponential fluorescence lifetime analysis. The low-NA objective provides a larger field-of-view (FOV), thereby overcoming the limitations of a small FOV of the usually used high-NA objectives.
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Affiliation(s)
- Wonsang Hwang
- Department of Physics, Yonsei University, Seoul, Republic of Korea
| | - Jinwon Seo
- Department of Microbiology, Institute for Immunology and Immunological Diseases, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - DongEun Kim
- Department of Physics, Yonsei University, Seoul, Republic of Korea
| | - Chang Jun Lee
- Department of Physics, Yonsei University, Seoul, Republic of Korea
| | - In-Hong Choi
- Department of Microbiology, Institute for Immunology and Immunological Diseases, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Kyung-Hwa Yoo
- Department of Physics, Yonsei University, Seoul, Republic of Korea
| | - Dug Young Kim
- Department of Physics, Yonsei University, Seoul, Republic of Korea.
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14
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Schneider F, Colin-York H, Fritzsche M. Quantitative Bio-Imaging Tools to Dissect the Interplay of Membrane and Cytoskeletal Actin Dynamics in Immune Cells. Front Immunol 2021; 11:612542. [PMID: 33505401 PMCID: PMC7829180 DOI: 10.3389/fimmu.2020.612542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Cellular function is reliant on the dynamic interplay between the plasma membrane and the actin cytoskeleton. This critical relationship is of particular importance in immune cells, where both the cytoskeleton and the plasma membrane work in concert to organize and potentiate immune signaling events. Despite their importance, there remains a critical gap in understanding how these respective dynamics are coupled, and how this coupling in turn may influence immune cell function from the bottom up. In this review, we highlight recent optical technologies that could provide strategies to investigate the simultaneous dynamics of both the cytoskeleton and membrane as well as their interplay, focusing on current and future applications in immune cells. We provide a guide of the spatio-temporal scale of each technique as well as highlighting novel probes and labels that have the potential to provide insights into membrane and cytoskeletal dynamics. The quantitative biophysical tools presented here provide a new and exciting route to uncover the relationship between plasma membrane and cytoskeletal dynamics that underlies immune cell function.
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Affiliation(s)
- Falk Schneider
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Huw Colin-York
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Marco Fritzsche
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
- Rosalind Franklin Institute, Harwell Campus, Didcot, United Kingdom
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15
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Grandy C, Kolb P, Port F, Gottschalk KE. Micropatterning of Cells on Gold Surfaces for Biophysical Applications. STAR Protoc 2020; 1:100106. [PMID: 33377002 PMCID: PMC7756938 DOI: 10.1016/j.xpro.2020.100106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We developed a reproducible micropatterning method to manipulate and normalize cell shape and cell-cell separation on gold. We used methoxy polyethylene glycol thiol (PEG-SH) to create a self-assembled monolayer that can be oxidized at desired shapes through a photomask with deep UV light. The oxidized PEG can be coated with extracellular matrix proteins and seeded with cells adopting the pre-defined shape. The developed and analyzed surfaces can be used in a wide range of biophysical applications.
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Affiliation(s)
- Carolin Grandy
- University Ulm, Institute of Experimental Physics, Ulm, Baden-Württemberg 89081, Germany
| | - Peter Kolb
- University Ulm, Institute of Experimental Physics, Ulm, Baden-Württemberg 89081, Germany
| | - Fabian Port
- University Ulm, Institute of Experimental Physics, Ulm, Baden-Württemberg 89081, Germany
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16
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Zelená A, Isbaner S, Ruhlandt D, Chizhik A, Cassini C, Klymchenko AS, Enderlein J, Chizhik A, Köster S. Time-resolved MIET measurements of blood platelet spreading and adhesion. NANOSCALE 2020; 12:21306-21315. [PMID: 33073832 DOI: 10.1039/d0nr05611a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Human blood platelets are non-nucleated fragments of megakaryocytes and of high importance for early hemostasis. To form a blood clot, platelets adhere to the blood vessel wall, spread and attract other platelets. Despite the importance for biomedicine, the exact mechanism of platelet spreading and adhesion to surfaces remains elusive. Here, we employ metal-induced energy transfer (MIET) imaging with a leaflet-specific fluorescent membrane probe to quantitatively determine, with nanometer resolution and in a time-resolved manner, the height profile of the basal and the apical platelet membrane above a rigid substrate during platelet spreading. We observe areas, where the platelet membrane approaches the substrate particularly closely and these areas are stable on a time scale of minutes. Time-resolved MIET measurements reveal distinct behaviors of the outermost rim and the central part of the platelets, respectively. Our findings quantify platelet adhesion and spreading and improve our understanding of early steps in blood clotting. Furthermore, the results of this study demonstrate the potential of MIET for simultaneous imaging of two close-by membranes and thus three-dimensional reconstruction of the cell shape.
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Affiliation(s)
- Anna Zelená
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
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17
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Lee YU, Zhao J, Mo GCH, Li S, Li G, Ma Q, Yang Q, Lal R, Zhang J, Liu Z. Metamaterial-Assisted Photobleaching Microscopy with Nanometer Scale Axial Resolution. NANO LETTERS 2020; 20:6038-6044. [PMID: 32597659 DOI: 10.1021/acs.nanolett.0c02056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The past two decades have witnessed a dramatic progress in the development of novel super-resolution fluorescence microscopy technologies. Here, we report a new fluorescence imaging method, called metamaterial-assisted photobleaching microscopy (MAPM), which possesses a nanometer-scale axial resolution and is suitable for broadband operation across the entire visible spectrum. The photobleaching kinetics of fluorophores can be greatly modified via a separation-dependent energy transfer process to a nearby metamaterial. The corresponding photobleaching rate is thus linked to the distance between the fluorophores and the metamaterial layer, leading to a reconstructed image with exceptionally high axial resolution. We apply the MAPM technology to image the HeLa cell membranes tagged with fluorescent proteins and demonstrate an axial resolution of ∼2.4 nm with multiple colors. MAPM utilizes a metamaterial-coated substrate to achieve super-resolution without altering anything else in a conventional microscope, representing a simple solution for fluorescence imaging at nanometer axial resolution.
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Affiliation(s)
- Yeon Ui Lee
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Junxiang Zhao
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Gary C H Mo
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department of Pharmacology, University of Illinois at Chicago, 835 S. Wolcott Avenue, Chicago, Illinois 60612, United States
| | - Shilong Li
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Guangru Li
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Qian Ma
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Qingqing Yang
- Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Ratnesh Lal
- Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Zhaowei Liu
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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18
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Dual-Color Metal-Induced Energy Transfer (MIET) Imaging for Three-Dimensional Reconstruction of Nuclear Envelope Architecture. Methods Mol Biol 2020. [PMID: 32681482 DOI: 10.1007/978-1-0716-0763-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The nuclear envelope, comprising the inner and the outer nuclear membrane, separates the nucleus from the cytoplasm and plays a key role in cellular functions. Nuclear pore complexes (NPCs) are embedded in the nuclear envelope and control transport of macromolecules between the two compartments. Recently, it has been shown that the axial distance between the inner nuclear membrane and the cytoplasmic side of the NPC can be measured using dual-color metal-induced energy transfer (MIET). This chapter focuses on experimental aspects of this method and discusses the details of data analysis.
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19
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Oleksiievets N, Thiele JC, Weber A, Gregor I, Nevskyi O, Isbaner S, Tsukanov R, Enderlein J. Wide-Field Fluorescence Lifetime Imaging of Single Molecules. J Phys Chem A 2020; 124:3494-3500. [PMID: 32255633 DOI: 10.1021/acs.jpca.0c01513] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Fluorescence lifetime imaging (FLIM) has become an important microscopy technique in bioimaging. The two most important of its applications are lifetime-multiplexing for imaging many different structures in parallel, and lifetime-based measurements of Förster resonance energy transfer. There are two principal FLIM techniques, one based on confocal-laser scanning microscopy (CLSM) and time-correlated single-photon counting (TCSPC) and the other based on wide-field microscopy and phase fluorometry. Although the first approach (CLSM-TCSPC) assures high sensitivity and allows one to detect single molecules, it is slow and has a small photon yield. The second allows, in principal, high frame rates (by 2-3 orders of magnitude faster than CLSM), but it suffers from low sensitivity, which precludes its application for single-molecule imaging. Here, we demonstrate that a novel wide-field TCSPC camera (LINCam25, Photonscore GmbH) can be successfully used for single-molecule FLIM, although its quantum yield of detection in the red spectral region is only ∼5%. This is due to the virtually absent background and readout noise of the camera, assuring high signal-to-noise ratio even at low detection efficiency. We performed single-molecule FLIM of different red fluorophores, and we use the lifetime information for successfully distinguishing between different molecular species. Finally, we demonstrate single-molecule metal-induced energy transfer (MIET) imaging which is a first step for three-dimensional single-molecule localization microscopy (SMLM) with nanometer resolution.
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Affiliation(s)
- Nazar Oleksiievets
- III. Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Jan Christoph Thiele
- III. Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany
| | - André Weber
- Special Laboratory for Electron and Laser Scanning Microscopy, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany
| | - Ingo Gregor
- III. Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Oleksii Nevskyi
- III. Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Sebastian Isbaner
- III. Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Roman Tsukanov
- III. Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Jörg Enderlein
- III. Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Georg August University, 37077 Göttingen, Germany
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20
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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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21
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Zelger P, Bodner L, Velas L, Schütz GJ, Jesacher A. Defocused imaging exploits supercritical-angle fluorescence emission for precise axial single molecule localization microscopy. BIOMEDICAL OPTICS EXPRESS 2020; 11:775-790. [PMID: 32206395 PMCID: PMC7041438 DOI: 10.1364/boe.375678] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 05/07/2023]
Abstract
Single molecule localization microscopy (SMLM) is one of the key techniques that break the classical resolution limit in optical imaging. It is based on taking multiple recordings of a sample, each showing only a sparse arrangement of spatially well separated fluorescent molecules which can be localized at nanometer precision. While localizing along the lateral directions is usually straightforward, estimating axial positions at a comparable precision is known to be much harder, which is due to the relatively large depth of focus provided by the microscope optics. Whenever a molecule is sufficiently close to the coverslip, it becomes feasible to draw additional information from near field coupling effects: super-critical angle fluorescence (SAF) appears and can be exploited to boost the axial localization precision. Here we propose defocused imaging as a SMLM strategy that is capable of leveraging the information contained in SAF. We show that, regarding axial localization precision, our approach is superior to established SAF-based approaches. At the same time it is simple and can be conducted on any research-grade microscope where controlled defocusing on the order of a few hundred nanometers is possible.
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Affiliation(s)
- Philipp Zelger
- Division for Biomedical Physics, Medical University of Innsbruck, Müllerstraße 44, 6020 Innsbruck, Austria
| | - Lisa Bodner
- Division for Biomedical Physics, Medical University of Innsbruck, Müllerstraße 44, 6020 Innsbruck, Austria
| | - Lukas Velas
- Institute of Applied Physics, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Gerhard J. Schütz
- Institute of Applied Physics, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Alexander Jesacher
- Division for Biomedical Physics, Medical University of Innsbruck, Müllerstraße 44, 6020 Innsbruck, Austria
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22
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Casting a Wider Net: Differentiating between Inner Nuclear Envelope and Outer Nuclear Envelope Transmembrane Proteins. Int J Mol Sci 2019; 20:ijms20215248. [PMID: 31652739 PMCID: PMC6862087 DOI: 10.3390/ijms20215248] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 12/11/2022] Open
Abstract
The nuclear envelope (NE) surrounds the nucleus with a double membrane in eukaryotic cells. The double membranes are embedded with proteins that are synthesized on the endoplasmic reticulum and often destined specifically for either the outer nuclear membrane (ONM) or the inner nuclear membrane (INM). These nuclear envelope transmembrane proteins (NETs) play important roles in cellular function and participate in transcription, epigenetics, splicing, DNA replication, genome architecture, nuclear structure, nuclear stability, nuclear organization, and nuclear positioning. These vital functions are dependent upon both the correct localization and relative concentrations of NETs on the appropriate membrane of the NE. It is, therefore, important to understand the distribution and abundance of NETs on the NE. This review will evaluate the current tools and methodologies available to address this important topic.
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23
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Figueiras E, Silvestre OF, Ihalainen TO, Nieder JB. Phasor-assisted nanoscopy reveals differences in the spatial organization of major nuclear lamina proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118530. [PMID: 31415840 DOI: 10.1016/j.bbamcr.2019.118530] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/18/2019] [Accepted: 08/05/2019] [Indexed: 11/15/2022]
Abstract
Phasor-assisted Metal Induced Energy Transfer-Fluorescence Lifetime Imaging Microscopy (MIET-FLIM) nanoscopy is introduced as a powerful tool for functional cell biology research. Thin metal substrates can be used to obtain axial super-resolution via nanoscale distance-dependent MIET from fluorescent dyes towards a nearby metal layer, thereby creating fluorescence lifetime contrast between dyes located at different nanoscale distance from the metal. Such data can be used to achieve axially super-resolved microscopy images, a process known as MIET-FLIM nanoscopy. Suitability of the phasor approach in MIET-FLIM nanoscopy is first demonstrated using nanopatterned substrates, and furthermore applied to characterize the distance distribution of the epithelial basal membrane of a biological cell from the gold substrate. The phasor plot of an entire cell can be used to characterize the full Förster resonance energy transfer (FRET) trajectory as a large distance heterogeneity within the sensing range of about 100 nm from the metal surface is present due to the extended shape of cell with curvatures. In contrast, the different proteins of nuclear lamina show strong confinement close to the nuclear envelope in nanoscale. We find the lamin B layer resides in average at shorter distances from the gold surface compared to the lamin A/C layer located in more extended ranges. This and the observed heterogeneity of the protein layer thicknesses suggests that A- and B-type lamins form distinct networks in the nuclear lamina. Our results provide detailed insights for the study of the different roles of lamin proteins in chromatin tethering and nuclear mechanics.
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Affiliation(s)
- Edite Figueiras
- Department of Nanophotonics, Ultrafast Bio- and Nanophotonics Group, INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal
| | - Oscar F Silvestre
- Department of Nanophotonics, Ultrafast Bio- and Nanophotonics Group, INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal
| | - Teemu O Ihalainen
- Faculty of Medicine and Health Technology, BioMediTech, Tampere University, 33014 Tampere, Finland
| | - Jana B Nieder
- Department of Nanophotonics, Ultrafast Bio- and Nanophotonics Group, INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal.
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24
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Vallotton P, Rajoo S, Wojtynek M, Onischenko E, Kralt A, Derrer CP, Weis K. Mapping the native organization of the yeast nuclear pore complex using nuclear radial intensity measurements. Proc Natl Acad Sci U S A 2019; 116:14606-14613. [PMID: 31262825 PMCID: PMC6642398 DOI: 10.1073/pnas.1903764116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Selective transport across the nuclear envelope (NE) is mediated by the nuclear pore complex (NPC), a massive ∼100-MDa assembly composed of multiple copies of ∼30 nuclear pore proteins (Nups). Recent advances have shed light on the composition and structure of NPCs, but approaches that could map their organization in live cells are still lacking. Here, we introduce an in vivo method to perform nuclear radial intensity measurements (NuRIM) using fluorescence microscopy to determine the average position of NE-localized proteins along the nucleocytoplasmic transport axis. We apply NuRIM to study the organization of the NPC and the mobile transport machinery in budding yeast. This reveals a unique snapshot of the intact yeast NPC and identifies distinct steady-state localizations for various NE-associated proteins and nuclear transport factors. We find that the NPC architecture is robust against compositional changes and could also confirm that in contrast to Chlamydomonas reinhardtii, the scaffold Y complex is arranged symmetrically in the yeast NPC. Furthermore, NuRIM was applied to probe the orientation of intrinsically disordered FG-repeat segments, providing insight into their roles in selective NPC permeability and structure.
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Affiliation(s)
- Pascal Vallotton
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zürich (ETH Zürich), 8093 Zürich, Switzerland;
| | - Sasikumar Rajoo
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zürich (ETH Zürich), 8093 Zürich, Switzerland
| | - Matthias Wojtynek
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zürich (ETH Zürich), 8093 Zürich, Switzerland
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Evgeny Onischenko
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zürich (ETH Zürich), 8093 Zürich, Switzerland
| | - Annemarie Kralt
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zürich (ETH Zürich), 8093 Zürich, Switzerland
| | - Carina Patrizia Derrer
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zürich (ETH Zürich), 8093 Zürich, Switzerland
| | - Karsten Weis
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zürich (ETH Zürich), 8093 Zürich, Switzerland;
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Mateos N, Molenaar R, Claessens MMAE, Blum C. Photonic emitter manipulation to sample nanoscale topography. OPTICS EXPRESS 2019; 27:11698-11708. [PMID: 31053012 DOI: 10.1364/oe.27.011698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/22/2019] [Indexed: 06/09/2023]
Abstract
We demonstrate that photonic emitter manipulation can be used to image the nanoscale topography of a fluorescently labeled layer in confocal imaging. We exploit the fact that a metallic probe manipulates a fluorophore's photonic environment, and thereby its fluorescent lifetime, in a strongly distance-dependent manner. To image surface topography, a metallic probe that is not in contact with the surface is rasterscanned over a fluorescently labeled sample. The axial position of the probe is kept constant. At each lateral probe position, the fluorescence decay is recorded and analyzed to obtain probe - sample distances and hence, the topography of the sample. We present images resolving a microfabricated step of 14 nm in topography, with the probe positioned at different axial positions.
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Ghosh A, Karedla N, Thiele JC, Gregor I, Enderlein J. Fluorescence lifetime correlation spectroscopy: Basics and applications. Methods 2018; 140-141:32-39. [DOI: 10.1016/j.ymeth.2018.02.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/09/2018] [Accepted: 02/10/2018] [Indexed: 10/18/2022] Open
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Isbaner S, Karedla N, Kaminska I, Ruhlandt D, Raab M, Bohlen J, Chizhik A, Gregor I, Tinnefeld P, Enderlein J, Tsukanov R. Axial Colocalization of Single Molecules with Nanometer Accuracy Using Metal-Induced Energy Transfer. NANO LETTERS 2018; 18:2616-2622. [PMID: 29562123 DOI: 10.1021/acs.nanolett.8b00425] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-molecule localization based super-resolution microscopy has revolutionized optical microscopy and routinely allows for resolving structural details down to a few nanometers. However, there exists a rather large discrepancy between lateral and axial localization accuracy, the latter typically three to five times worse than the former. Here, we use single-molecule metal-induced energy transfer (smMIET) to localize single molecules along the optical axis, and to measure their axial distance with an accuracy of 5 nm. smMIET relies only on fluorescence lifetime measurements and does not require additional complex optical setups.
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Affiliation(s)
- Sebastian Isbaner
- Third Institute of Physics - Biophysics , Georg August University , 37077 Göttingen , Germany
| | - Narain Karedla
- Third Institute of Physics - Biophysics , Georg August University , 37077 Göttingen , Germany
- DFG Research Center "Nanoscale Microscopy and Molecular Physiology of the Brain" (CNMPB) , 37077 Göttingen , Germany
| | - Izabela Kaminska
- Institute for Physical and Theoretical Chemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA) , Braunschweig University of Technology , 38106 Braunschweig , Germany
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics , Nicolaus Copernicus University , 87-100 Torun , Poland
| | - Daja Ruhlandt
- Third Institute of Physics - Biophysics , Georg August University , 37077 Göttingen , Germany
| | - Mario Raab
- Institute for Physical and Theoretical Chemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA) , Braunschweig University of Technology , 38106 Braunschweig , Germany
- Department of Chemistry and Center for NanoScience , Ludwig-Maximilians-Universität München , 80539 München , Germany
| | - Johann Bohlen
- Institute for Physical and Theoretical Chemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA) , Braunschweig University of Technology , 38106 Braunschweig , Germany
- Department of Chemistry and Center for NanoScience , Ludwig-Maximilians-Universität München , 80539 München , Germany
| | - Alexey Chizhik
- Third Institute of Physics - Biophysics , Georg August University , 37077 Göttingen , Germany
| | - Ingo Gregor
- Third Institute of Physics - Biophysics , Georg August University , 37077 Göttingen , Germany
| | - Philip Tinnefeld
- Institute for Physical and Theoretical Chemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA) , Braunschweig University of Technology , 38106 Braunschweig , Germany
- Department of Chemistry and Center for NanoScience , Ludwig-Maximilians-Universität München , 80539 München , Germany
| | - Jörg Enderlein
- Third Institute of Physics - Biophysics , Georg August University , 37077 Göttingen , Germany
- DFG Research Center "Nanoscale Microscopy and Molecular Physiology of the Brain" (CNMPB) , 37077 Göttingen , Germany
| | - Roman Tsukanov
- Third Institute of Physics - Biophysics , Georg August University , 37077 Göttingen , Germany
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Simoncelli S, Makarova M, Wardley W, Owen DM. Toward an Axial Nanoscale Ruler for Fluorescence Microscopy. ACS NANO 2017; 11:11762-11767. [PMID: 29161014 DOI: 10.1021/acsnano.7b07133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In the discussion of resolution in optical microscopy, axial precision has often come second to its lateral counterpart. However, biological systems make no special arrangements for our preferred direction of imaging. The ability to measure axial distances, that is, the heights of fluorophores relative to a plane of reference, is thus of paramount importance and has been the subject of several recent advances. A novel method is to modify the fluorescence emission based on the height of the individual fluorophore, such that its z-position is encoded somehow in the detected signal. One such approach is metal-enhanced energy transfer, recently extended to multicolor distance measurements and applied to study the topography of the nuclear membrane. Here, the fluorescence lifetime is shortened due to the proximity of the fluorophores to a thin metallic surface. Fluorescence lifetime imaging can therefore be used as an axial ruler with nanometer precision.
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Affiliation(s)
- Sabrina Simoncelli
- Blackett Laboratory, Department of Physics, Imperial College London , London SW7 2AZ, United Kingdom
| | - Maria Makarova
- Francis Crick Institute and Randall Division of Cell and Molecular Biophysics, King's College London , London NW1 1AT, United Kingdom
| | - William Wardley
- Department of Physics, King's College London , London WC2R 2LS, United Kingdom
| | - Dylan M Owen
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London , London SE1 1UL, United Kingdom
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