1
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Chen F, Liu K, Shang L, Wang Y, Tang X, Liang P, Li B. Precision isolation and cultivation of single cells by vortex and flat-top laser ejection. Front Microbiol 2024; 15:1369506. [PMID: 38659989 PMCID: PMC11039905 DOI: 10.3389/fmicb.2024.1369506] [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: 01/12/2024] [Accepted: 03/19/2024] [Indexed: 04/26/2024] Open
Abstract
Single-cell isolation stands as a critical step in single-cell studies, and single-cell ejection technology based on laser induced forward transfer technology (LIFT) is considered one of the most promising methods in this regard for its ability of visible isolating single cell from complex samples. In this study, we improve the LIFT technology and introduce optical vortex laser-induced forward transfer (OV-LIFT) and flat-top laser-induced forward transfer (FT-LIFT) by utilizing spatial light modulator (SLM), aiming to enhance the precision of single-cell sorting and the cell's viability after ejection. Experimental results demonstrate that applying vortex and flat-top beams during the sorting and collection process enables precise retrieval of single cells within diameter ranges of 50 μm and 100 μm, respectively. The recovery rates of Saccharomyces cerevisiae and Escherichia coli DH5α single cell ejected by vortex beam are 89 and 78%, by flat-top beam are 85 and 57%. When employing Gaussian beam sorting, the receiving range extends to 400 μm, with cultivation success rates of S. cerevisiae and E. coli DH5α single cell are 48 and 19%, respectively. This marks the first application of different mode beams in the ejection and cultivation of single cells, providing a novel and effective approach for the precise isolation and improving the viability of single cells.
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Affiliation(s)
- Fuyuan Chen
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kunxiang Liu
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lindong Shang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuntong Wang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xusheng Tang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Liang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bei Li
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
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2
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Sankaran J, Wohland T. Current capabilities and future perspectives of FCS: super-resolution microscopy, machine learning, and in vivo applications. Commun Biol 2023; 6:699. [PMID: 37419967 PMCID: PMC10328937 DOI: 10.1038/s42003-023-05069-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
Fluorescence correlation spectroscopy (FCS) is a single molecule sensitive tool for the quantitative measurement of biomolecular dynamics and interactions. Improvements in biology, computation, and detection technology enable real-time FCS experiments with multiplexed detection even in vivo. These new imaging modalities of FCS generate data at the rate of hundreds of MB/s requiring efficient data processing tools to extract information. Here, we briefly review FCS's capabilities and limitations before discussing recent directions that address these limitations with a focus on imaging modalities of FCS, their combinations with super-resolution microscopy, new evaluation strategies, especially machine learning, and applications in vivo.
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Affiliation(s)
- Jagadish Sankaran
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138632, Singapore.
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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3
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Galiani S, Reglinski K, Carravilla P, Barbotin A, Urbančič I, Ott J, Sehr J, Sezgin E, Schneider F, Waithe D, Hublitz P, Schliebs W, Erdmann R, Eggeling C. Diffusion and interaction dynamics of the cytosolic peroxisomal import receptor PEX5. BIOPHYSICAL REPORTS 2022; 2:None. [PMID: 36299769 PMCID: PMC9586885 DOI: 10.1016/j.bpr.2022.100055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/24/2022] [Indexed: 11/18/2022]
Abstract
Cellular functions rely on proper actions of organelles such as peroxisomes. These organelles rely on the import of proteins from the cytosol. The peroxisomal import receptor PEX5 takes up target proteins in the cytosol and transports them to the peroxisomal matrix. However, its cytosolic molecular interactions have so far not directly been disclosed. Here, we combined advanced optical microscopy and spectroscopy techniques such as fluorescence correlation spectroscopy and stimulated emission depletion microscopy with biochemical tools to present a detailed characterization of the cytosolic diffusion and interaction dynamics of PEX5. Among other features, we highlight a slow diffusion of PEX5, independent of aggregation or target binding, but associated with cytosolic interaction partners via its N-terminal domain. This sheds new light on the functionality of the receptor in the cytosol as well as highlighting the potential of using complementary microscopy tools to decipher molecular interactions in the cytosol by studying their diffusion dynamics.
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Affiliation(s)
- S. Galiani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - K. Reglinski
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Leibniz-Institute of Photonic Technologies e.V., Jena, Germany
- Institute of Applied Optic and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- University Hospital Jena, Jena, Germany
| | - P. Carravilla
- Leibniz-Institute of Photonic Technologies e.V., Jena, Germany
- Institute of Applied Optic and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain
| | - A. Barbotin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - I. Urbančič
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Laboratory of Biophysics, Condensed Matter Physics Department, Jožef Stefan Institute, Ljubljana, Slovenia
| | - J. Ott
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - J. Sehr
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - E. Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - F. Schneider
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - D. Waithe
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- WIMM Centre for Computational Biology , MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - P. Hublitz
- WIMM Genome Engineering Services, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - W. Schliebs
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - R. Erdmann
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - C. Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Leibniz-Institute of Photonic Technologies e.V., Jena, Germany
- Institute of Applied Optic and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- Jena Center for Soft Matter (JCSM), Jena, Germany
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4
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Liang P, Shang L, Wang Y, Booth MJ, Li B. Laser induced forward transfer isolating complex-shaped cell by beam shaping. BIOMEDICAL OPTICS EXPRESS 2021; 12:7024-7032. [PMID: 34858696 PMCID: PMC8606160 DOI: 10.1364/boe.439054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 05/31/2023]
Abstract
Beam shaping techniques have been widely used in holographic optical tweezers to accurately manipulate tiny particles and hologram optimization algorithms have also been widely reported to improve the optical trapping performance. In this paper, we presented a beam shaping laser induced forward transfer (BS-LIFT) technique to isolate complex-shaped cells. To do this, we built up a BS-LIFT instrument which combined beam shaping methods and laser induced forward transfer using liquid-crystal-on-silicon spatial light modulator. The laser beam was modulated into multiple desired points at the focal plane employing the Gerchberg-Saxton (GS) algorithm. Feasibility was verified through transferring various samples. To our knowledge, this is the first demonstration of BS-LIFT applied to the transfer complex-shaped cells. We successfully transferred cells whose size ranged from 1 µm to 100 µm. Our design will provide a novel approach for the application of this beam shaping technique and the isolation of single cells with variable shapes.
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Affiliation(s)
- Peng Liang
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Changchun, 130033, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lindong Shang
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Changchun, 130033, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuntong Wang
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Changchun, 130033, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Martin J. Booth
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom
| | - Bei Li
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Changchun, 130033, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Bancelin S, Mercier L, Murana E, Nägerl UV. Aberration correction in stimulated emission depletion microscopy to increase imaging depth in living brain tissue. NEUROPHOTONICS 2021; 8:035001. [PMID: 34136589 PMCID: PMC8200361 DOI: 10.1117/1.nph.8.3.035001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/18/2021] [Indexed: 05/30/2023]
Abstract
Significance: Stimulated emission depletion (STED) microscopy enables nanoscale imaging of live samples, but it requires a specific spatial beam shaping that is highly sensitive to optical aberrations, limiting its depth penetration. Therefore, there is a need for methods to reduce optical aberrations and improve the spatial resolution of STED microscopy inside thick biological tissue. Aim: The aim of our work was to develop and validate a method based on adaptive optics to achieve an a priori correction of spherical aberrations as a function of imaging depth. Approach: We first measured the aberrations in a phantom sample of gold and fluorescent nanoparticles suspended in an agarose gel with a refractive index closely matching living brain tissue. We then used a spatial light modulator to apply corrective phase shifts and validate this calibration approach by imaging neurons in living brain slices. Results: After quantifying the spatial resolution in depth in phantom samples, we demonstrated that the corrections can substantially increase image quality in living brain slices. Specifically, we could measure structures as small as 80 nm at a depth of 90 μ m inside the biological tissue and obtain a 60% signal increase after correction. Conclusion: We propose a simple and robust approach to calibrate and compensate the distortions of the STED beam profile introduced by spherical aberrations with increasing imaging depth and demonstrated that this method offers significant improvements in microscopy performance for nanoscale cellular imaging in live tissue.
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Affiliation(s)
- Stéphane Bancelin
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux, France
| | - Luc Mercier
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux, France
| | - Emanuele Murana
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux, France
| | - U. Valentin Nägerl
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux, France
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6
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Chemically-powered swimming and diffusion in the microscopic world. Nat Rev Chem 2021; 5:500-510. [PMID: 37118434 DOI: 10.1038/s41570-021-00281-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 12/20/2022]
Abstract
The past decade has seen intriguing reports and heated debates concerning the chemically-driven enhanced motion of objects ranging from small molecules to millimetre-size synthetic robots. These objects, in solutions in which chemical reactions were occurring, were observed to diffuse (spread non-directionally) or swim (move directionally) at rates exceeding those expected from Brownian motion alone. The debates have focused on whether observed enhancement is an experimental artefact or a real phenomenon. If the latter were true, then we would also need to explain how the chemical energy is converted into mechanical work. In this Perspective, we summarize and discuss recent observations and theories of active diffusion and swimming. Notably, the chemomechanical coupling and magnitude of diffusion enhancement are strongly size-dependent and should vanish as the size of the swimmers approaches the molecular scale. We evaluate the reliability of common techniques to measure diffusion coefficients and finish by considering the potential applications and chemical to mechanical energy conversion efficiencies of typical nanoswimmers and microswimmers.
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7
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Velasco MGM, Zhang M, Antonello J, Yuan P, Allgeyer ES, May D, M’Saad O, Kidd P, Barentine AES, Greco V, Grutzendler J, Booth MJ, Bewersdorf J. 3D super-resolution deep-tissue imaging in living mice. OPTICA 2021; 8:442-450. [PMID: 34239948 PMCID: PMC8243577 DOI: 10.1364/optica.416841] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 05/08/2023]
Abstract
Stimulated emission depletion (STED) microscopy enables the three-dimensional (3D) visualization of dynamic nanoscale structures in living cells, offering unique insights into their organization. However, 3D-STED imaging deep inside biological tissue is obstructed by optical aberrations and light scattering. We present a STED system that overcomes these challenges. Through the combination of two-photon excitation, adaptive optics, red-emitting organic dyes, and a long-working-distance water-immersion objective lens, our system achieves aberration-corrected 3D super-resolution imaging, which we demonstrate 164 µm deep in fixed mouse brain tissue and 76 µm deep in the brain of a living mouse.
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Affiliation(s)
- Mary Grace M. Velasco
- Department of Biomedical Engineering, Yale School of Engineering & Applied Science, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Mengyang Zhang
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Jacopo Antonello
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Peng Yuan
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Current Address: Department of Biology, Stanford University, Stanford, California 94304, USA
| | - Edward S. Allgeyer
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Current Address: The Gurdon Institute, University of Cambridge, Cambridge CB21QN, UK
| | - Dennis May
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Ons M’Saad
- Department of Biomedical Engineering, Yale School of Engineering & Applied Science, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Phylicia Kidd
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Andrew E. S. Barentine
- Department of Biomedical Engineering, Yale School of Engineering & Applied Science, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Valentina Greco
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Dermatology, Yale Stem Cell Center, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Jaime Grutzendler
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Martin J. Booth
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Joerg Bewersdorf
- Department of Biomedical Engineering, Yale School of Engineering & Applied Science, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Corresponding author:
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8
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Abstract
Over the last 30 years, confocal microscopy has emerged as a primary tool for biological investigation across many disciplines. The simplicity of use and widespread accessibility of confocal microscopy ensure that it will have a prominent place in biological imaging for many years to come, even with the recent advances in light sheet and field synthesis microscopy. Since these more advanced technologies still require significant expertise to effectively implement and carry through to analysis, confocal microscopy-based approaches still remain the easiest way for biologists with minimal imaging experience to address fundamental questions about how their systems are arranged through space and time. In this review, we discuss a number of advanced applications of confocal microscopy for probing the spatiotemporal dynamics of biological systems.
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Affiliation(s)
- W Matt Reilly
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.,Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, USA
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9
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Xin W, Zhang Q, Gu M. Inverse design of optical needles with central zero-intensity points by artificial neural networks. OPTICS EXPRESS 2020; 28:38718-38732. [PMID: 33379435 DOI: 10.1364/oe.410073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
Optical needles with central zero-intensity points have attracted much attention in the field of 3D super-resolution microscopy, optical lithography, optical storage and Raman spectroscopy. Nevertheless, most of the studies create few types of optical needles with central zero-intensity points based on the theory and intuition with time-consuming parameter sweeping and complex pre-select of parameters. Here, we report on the inverse design of optical needles with central zero-intensity points by dipole-based artificial neural networks (DANNs), permitting the creation of needles which are close to specific length and amplitude. The resolution of these optical needles with central zero-intensity points is close to axial diffraction limit (∼1λ). Additionally, the DANNs can realize the inverse design of several types on-axis distributions, such as optical needles and multifocal distributions.
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10
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Saha D, Schmidt U, Zhang Q, Barbotin A, Hu Q, Ji N, Booth MJ, Weigert M, Myers EW. Practical sensorless aberration estimation for 3D microscopy with deep learning. OPTICS EXPRESS 2020; 28:29044-29053. [PMID: 33114810 PMCID: PMC7679184 DOI: 10.1364/oe.401933] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Estimation of optical aberrations from volumetric intensity images is a key step in sensorless adaptive optics for 3D microscopy. Recent approaches based on deep learning promise accurate results at fast processing speeds. However, collecting ground truth microscopy data for training the network is typically very difficult or even impossible thereby limiting this approach in practice. Here, we demonstrate that neural networks trained only on simulated data yield accurate predictions for real experimental images. We validate our approach on simulated and experimental datasets acquired with two different microscopy modalities and also compare the results to non-learned methods. Additionally, we study the predictability of individual aberrations with respect to their data requirements and find that the symmetry of the wavefront plays a crucial role. Finally, we make our implementation freely available as open source software in Python.
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Affiliation(s)
- Debayan Saha
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
- Center for Systems Biology Dresden, Dresden, Saxony 01307, Germany
| | - Uwe Schmidt
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
- Center for Systems Biology Dresden, Dresden, Saxony 01307, Germany
| | - Qinrong Zhang
- University of California, Berkeley, California 94720, USA
| | - Aurelien Barbotin
- University of Oxford, Department of Engineering Science, Oxford OX13PJ, UK
| | - Qi Hu
- University of Oxford, Department of Engineering Science, Oxford OX13PJ, UK
| | - Na Ji
- University of California, Berkeley, California 94720, USA
| | - Martin J. Booth
- University of Oxford, Department of Engineering Science, Oxford OX13PJ, UK
| | - Martin Weigert
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
- Center for Systems Biology Dresden, Dresden, Saxony 01307, Germany
- Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne CH1015, Switzerland
| | - Eugene W. Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
- Center for Systems Biology Dresden, Dresden, Saxony 01307, Germany
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11
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Lamparter L, Galic M. Cellular Membranes, a Versatile Adaptive Composite Material. Front Cell Dev Biol 2020; 8:684. [PMID: 32850810 PMCID: PMC7419611 DOI: 10.3389/fcell.2020.00684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 07/06/2020] [Indexed: 12/17/2022] Open
Abstract
Cellular membranes belong to the most vital yet least understood biomaterials of live matter. For instance, its biomechanical requirements substantially vary across species and subcellular sites, raising the question how membranes manage to adjust to such dramatic changes. Central to its adaptability at the cell surface is the interplay between the plasma membrane and the adjacent cell cortex, forming an adaptive composite material that dynamically adjusts its mechanical properties. Using a hypothetical composite material, we identify core challenges, and discuss how cellular membranes solved these tasks. We further muse how pathological changes in material properties affect membrane mechanics and cell function, before closing with open questions and future challenges arising when studying cellular membranes.
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Affiliation(s)
- Lucas Lamparter
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Münster, Münster, Germany.,Cells in Motion Interfaculty Centre, University of Müenster, Münster, Germany
| | - Milos Galic
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Münster, Münster, Germany.,Cells in Motion Interfaculty Centre, University of Müenster, Münster, Germany
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12
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Barbotin A, Urbančič I, Galiani S, Eggeling C, Booth M. Background Reduction in STED-FCS Using a Bivortex Phase Mask. ACS PHOTONICS 2020; 7:1742-1753. [PMID: 32685609 PMCID: PMC7366504 DOI: 10.1021/acsphotonics.0c00388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Indexed: 05/04/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) is a valuable tool to study the molecular dynamics in living cells. When used together with a super-resolution stimulated emission depletion (STED) microscope, STED-FCS can measure diffusion processes on the nanoscale in living cells. In two-dimensional (2D) systems like the cellular plasma membrane, a ring-shaped depletion focus is most commonly used to increase the lateral resolution, leading to more than 25-fold decrease in the observation volume, reaching the relevant scale of supramolecular arrangements. However, STED-FCS faces severe limitations when measuring diffusion in three dimensions (3D), largely due to the spurious background contributions from undepleted areas of the excitation focus that reduce the signal quality and ultimately limit the resolution. In this paper, we investigate how different STED confinement modes can mitigate this issue. By simulations as well as experiments with fluorescent probes in solution and in cells, we demonstrate that the coherent-hybrid (CH) depletion pattern created by a bivortex phase mask reduces background most efficiently and thus provides superior signal quality under comparable reduction of the observation volume. Featuring also the highest robustness to common optical aberrations, CH-STED can be considered the method of choice for reliable STED-FCS-based investigations of 3D diffusion on the subdiffraction scale.
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Affiliation(s)
- Aurélien Barbotin
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United
Kingdom
| | - Iztok Urbančič
- MRC
Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
- “Jožef
Stefan” Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Silvia Galiani
- MRC
Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
- Wolfson
Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Christian Eggeling
- MRC
Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
- Wolfson
Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
- Institute
of Applied Optics and Biophysics, Friedrich-Schiller-University
Jena, Max-Wien Platz
4, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology e.V., Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - Martin Booth
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United
Kingdom
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13
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Tröger J, Hoischen C, Perner B, Monajembashi S, Barbotin A, Löschberger A, Eggeling C, Kessels MM, Qualmann B, Hemmerich P. Comparison of Multiscale Imaging Methods for Brain Research. Cells 2020; 9:E1377. [PMID: 32492970 PMCID: PMC7349602 DOI: 10.3390/cells9061377] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/11/2022] Open
Abstract
A major challenge in neuroscience is how to study structural alterations in the brain. Even small changes in synaptic composition could have severe outcomes for body functions. Many neuropathological diseases are attributable to disorganization of particular synaptic proteins. Yet, to detect and comprehensively describe and evaluate such often rather subtle deviations from the normal physiological status in a detailed and quantitative manner is very challenging. Here, we have compared side-by-side several commercially available light microscopes for their suitability in visualizing synaptic components in larger parts of the brain at low resolution, at extended resolution as well as at super-resolution. Microscopic technologies included stereo, widefield, deconvolution, confocal, and super-resolution set-ups. We also analyzed the impact of adaptive optics, a motorized objective correction collar and CUDA graphics card technology on imaging quality and acquisition speed. Our observations evaluate a basic set of techniques, which allow for multi-color brain imaging from centimeter to nanometer scales. The comparative multi-modal strategy we established can be used as a guide for researchers to select the most appropriate light microscopy method in addressing specific questions in brain research, and we also give insights into recent developments such as optical aberration corrections.
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Affiliation(s)
- Jessica Tröger
- Institute of Biochemistry I, Jena University Hospital—Friedrich Schiller University Jena, Nonnenplan 2-4, 07743 Jena, Germany;
| | - Christian Hoischen
- Core Facility Imaging, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (C.H.); (B.P.); (S.M.)
| | - Birgit Perner
- Core Facility Imaging, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (C.H.); (B.P.); (S.M.)
- Molecular Genetics Lab, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Shamci Monajembashi
- Core Facility Imaging, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (C.H.); (B.P.); (S.M.)
| | - Aurélien Barbotin
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX13PJ, UK;
| | - Anna Löschberger
- Advanced Development Light Microscopy, Carl Zeiss Microscopy GmbH, Carl-Zeiss-Promenade 10, 07745 Jena, Germany;
| | - Christian Eggeling
- MRC Human Immunology Unit & Wolfson Imaging Center Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX39DS, UK;
- Dep. Biophysical Imaging, Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, and Institute for Applied Optics and Biophysics, Faculty of Physics and Astronomy, Friedrich Schiller University Jena, Max-Wien-Platz 1, 07743 Jena, Germany
| | - Michael M. Kessels
- Institute of Biochemistry I, Jena University Hospital—Friedrich Schiller University Jena, Nonnenplan 2-4, 07743 Jena, Germany;
| | - Britta Qualmann
- Institute of Biochemistry I, Jena University Hospital—Friedrich Schiller University Jena, Nonnenplan 2-4, 07743 Jena, Germany;
| | - Peter Hemmerich
- Core Facility Imaging, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (C.H.); (B.P.); (S.M.)
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14
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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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15
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Schneider F, Hernandez-Varas P, Christoffer Lagerholm B, Shrestha D, Sezgin E, Julia Roberti M, Ossato G, Hecht F, Eggeling C, Urbančič I. High photon count rates improve the quality of super-resolution fluorescence fluctuation spectroscopy. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2020; 53:164003. [PMID: 33191951 PMCID: PMC7655148 DOI: 10.1088/1361-6463/ab6cca] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/19/2019] [Accepted: 01/16/2020] [Indexed: 05/15/2023]
Abstract
Probing the diffusion of molecules has become a routine measurement across the life sciences, chemistry and physics. It provides valuable insights into reaction dynamics, oligomerisation, molecular (re-)organisation or cellular heterogeneities. Fluorescence correlation spectroscopy (FCS) is one of the widely applied techniques to determine diffusion dynamics in two and three dimensions. This technique relies on the temporal autocorrelation of intensity fluctuations but recording these fluctuations has thus far been limited by the detection electronics, which could not efficiently and accurately time-tag photons at high count rates. This has until now restricted the range of measurable dye concentrations, as well as the data quality of the FCS recordings, especially in combination with super-resolution stimulated emission depletion (STED) nanoscopy. Here, we investigate the applicability and reliability of (STED-)FCS at high photon count rates (average intensities of more than 1 MHz) using novel detection equipment, namely hybrid detectors and real-time gigahertz sampling of the photon streams implemented on a commercial microscope. By measuring the diffusion of fluorophores in solution and cytoplasm of live cells, as well as in model and cellular membranes, we show that accurate diffusion and concentration measurements are possible in these previously inaccessible high photon count regimes. Specifically, it offers much greater flexibility of experiments with biological samples with highly variable intensity, e.g. due to a wide range of expression levels of fluorescent proteins. In this context, we highlight the independence of diffusion properties of cytosolic GFP in a concentration range of approx. 0.01-1 µm. We further show that higher photon count rates also allow for much shorter acquisition times, and improved data quality. Finally, this approach also pronouncedly increases the robustness of challenging live cell STED-FCS measurements of nanoscale diffusion dynamics, which we testify by confirming a free diffusion pattern for a fluorescent lipid analogue on the apical membrane of adherent cells.
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Affiliation(s)
- Falk Schneider
- MRC Human Immunology Unit and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Pablo Hernandez-Varas
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
- Core Facility for Integrated Microscopy, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - B Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Dilip Shrestha
- MRC Human Immunology Unit and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Erdinc Sezgin
- MRC Human Immunology Unit and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - M Julia Roberti
- Leica Microsystems CMS GmbH, Am Friedensplatz 3, 68163 Mannheim, Germany
| | - Giulia Ossato
- Leica Microsystems CMS GmbH, Am Friedensplatz 3, 68163 Mannheim, Germany
| | - Frank Hecht
- Leica Microsystems CMS GmbH, Am Friedensplatz 3, 68163 Mannheim, Germany
| | - Christian Eggeling
- MRC Human Immunology Unit and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Iztok Urbančič
- MRC Human Immunology Unit and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
- Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
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16
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Carravilla P, Nieva JL, Eggeling C. Fluorescence Microscopy of the HIV-1 Envelope. Viruses 2020; 12:E348. [PMID: 32245254 PMCID: PMC7150788 DOI: 10.3390/v12030348] [Citation(s) in RCA: 4] [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: 02/22/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 12/18/2022] Open
Abstract
Human immunodeficiency virus (HIV) infection constitutes a major health and social issue worldwide. HIV infects cells by fusing its envelope with the target cell plasma membrane. This process is mediated by the viral Env glycoprotein and depends on the envelope lipid composition. Fluorescent microscopy has been employed to investigate the envelope properties, and the processes of viral assembly and fusion, but the application of this technique to the study of HIV is still limited by a number of factors, such as the small size of HIV virions or the difficulty to label the envelope components. Here, we review fluorescence imaging studies of the envelope lipids and proteins, focusing on labelling strategies and model systems.
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Affiliation(s)
- Pablo Carravilla
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 1, 07743 Jena, Germany;
- Leibniz Institute of Photonic Technology, Albert Einstein Strasse 9, 07743 Jena, Germany
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain;
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, E-48940 Leioa, Spain
| | - José L. Nieva
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain;
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, E-48940 Leioa, Spain
| | - Christian Eggeling
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 1, 07743 Jena, Germany;
- Leibniz Institute of Photonic Technology, Albert Einstein Strasse 9, 07743 Jena, Germany
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
- Jena Center for Soft Matter (JCSM), Friedrich-Schiller-University Jena, Philosophenweg 7, 07743 Jena, Germany
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