1
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Haak A, Lesslich HM, Dietzel ID. Visualization of the membrane surface and cytoskeleton of oligodendrocyte progenitor cell growth cones using a combination of scanning ion conductance and four times expansion microscopy. Biol Chem 2024; 405:31-41. [PMID: 37950644 DOI: 10.1515/hsz-2023-0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/17/2023] [Indexed: 11/13/2023]
Abstract
Growth cones of oligodendrocyte progenitor cells (OPCs) are challenging to investigate with conventional light microscopy due to their small size. Especially substructures such as filopodia, lamellipodia and their underlying cytoskeleton are difficult to resolve with diffraction limited microscopy. Light microscopy techniques, which surpass the diffraction limit such as stimulated emission depletion microscopy, often require expensive setups and specially trained personnel rendering them inaccessible to smaller research groups. Lately, the invention of expansion microscopy (ExM) has enabled super-resolution imaging with any light microscope without the need for additional equipment. Apart from the necessary resolution, investigating OPC growth cones comes with another challenge: Imaging the topography of membranes, especially label- and contact-free, is only possible with very few microscopy techniques one of them being scanning ion conductance microscopy (SICM). We here present a new imaging workflow combining SICM and ExM, which enables the visualization of OPC growth cone nanostructures. We correlated SICM recordings and ExM images of OPC growth cones captured with a conventional widefield microscope. This enabled the visualization of the growth cones' membrane topography as well as their underlying actin and tubulin cytoskeleton.
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Affiliation(s)
- Annika Haak
- Nanoscopy, RUBION, Ruhr-Universität Bochum, Universitätsstraße 150, D-44801 Bochum, Germany
| | - Heiko M Lesslich
- Nanoscopy, RUBION, Ruhr-Universität Bochum, Universitätsstraße 150, D-44801 Bochum, Germany
| | - Irmgard D Dietzel
- Department of Biochemistry II, Electrobiochemistry of Neural Cells, Ruhr-Universität Bochum, D-44801 Bochum, Germany
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2
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Xu X, Qiu K, Tian Z, Aryal C, Rowan F, Chen R, Sun Y, Diao J. Probing the dynamic crosstalk of lysosomes and mitochondria with structured illumination microscopy. Trends Analyt Chem 2023; 169:117370. [PMID: 37928815 PMCID: PMC10621629 DOI: 10.1016/j.trac.2023.117370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Structured illumination microscopy (SIM) is a super-resolution technology for imaging living cells and has been used for studying the dynamics of lysosomes and mitochondria. Recently, new probes and analyzing methods have been developed for SIM imaging, enabling the quantitative analysis of these subcellular structures and their interactions. This review provides an overview of the working principle and advances of SIM, as well as the organelle-targeting principles and types of fluorescence probes, including small molecules, metal complexes, nanoparticles, and fluorescent proteins. Additionally, quantitative methods based on organelle morphology and distribution are outlined. Finally, the review provides an outlook on the current challenges and future directions for improving the combination of SIM imaging and image analysis to further advance the study of organelles. We hope that this review will be useful for researchers working in the field of organelle research and help to facilitate the development of SIM imaging and analysis techniques.
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Affiliation(s)
- Xiuqiong Xu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Kangqiang Qiu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Zhiqi Tian
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Chinta Aryal
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Fiona Rowan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Rui Chen
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Yujie Sun
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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3
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Kraft N, Muenz TS, Reinhard S, Werner C, Sauer M, Groh C, Rössler W. Expansion microscopy in honeybee brains for high-resolution neuroanatomical analyses in social insects. Cell Tissue Res 2023; 393:489-506. [PMID: 37421435 PMCID: PMC10484815 DOI: 10.1007/s00441-023-03803-4] [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: 01/27/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023]
Abstract
The diffraction limit of light microscopy poses a problem that is frequently faced in structural analyses of social insect brains. With the introduction of expansion microscopy (ExM), a tool became available to overcome this limitation by isotropic physical expansion of preserved specimens. Our analyses focus on synaptic microcircuits (microglomeruli, MG) in the mushroom body (MB) of social insects, high-order brain centers for sensory integration, learning, and memory. MG undergo significant structural reorganizations with age, sensory experience, and during long-term memory formation. However, the changes in subcellular architecture involved in this plasticity have only partially been accessed yet. Using the western honeybee Apis mellifera as an experimental model, we established ExM for the first time in a social insect species and applied it to investigate plasticity in synaptic microcircuits within MG of the MB calyces. Using combinations of antibody staining and neuronal tracing, we demonstrate that this technique enables quantitative and qualitative analyses of structural neuronal plasticity at high resolution in a social insect brain.
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Affiliation(s)
- Nadine Kraft
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany.
| | - Thomas S Muenz
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Sebastian Reinhard
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Christian Werner
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Claudia Groh
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Wolfgang Rössler
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
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4
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Ueda S, Yagi M, Tomoda E, Matsumoto S, Ueyanagi Y, Do Y, Setoyama D, Matsushima Y, Nagao A, Suzuki T, Ide T, Mori Y, Oyama N, Kang D, Uchiumi T. Mitochondrial haplotype mutation alleviates respiratory defect of MELAS by restoring taurine modification in tRNA with 3243A > G mutation. Nucleic Acids Res 2023; 51:7480-7495. [PMID: 37439353 PMCID: PMC10415116 DOI: 10.1093/nar/gkad591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
The 3243A > G in mtDNA is a representative mutation in mitochondrial diseases. Mitochondrial protein synthesis is impaired due to decoding disorder caused by severe reduction of 5-taurinomethyluridine (τm5U) modification of the mutant mt-tRNALeu(UUR) bearing 3243A > G mutation. The 3243A > G heteroplasmy in peripheral blood reportedly decreases exponentially with age. Here, we found three cases with mild respiratory symptoms despite bearing high rate of 3243A > G mutation (>90%) in blood mtDNA. These patients had the 3290T > C haplotypic mutation in addition to 3243A > G pathogenic mutation in mt-tRNALeu(UUR) gene. We generated cybrid cells of these cases to examine the effects of the 3290T > C mutation on mitochondrial function and found that 3290T > C mutation improved mitochondrial translation, formation of respiratory chain complex, and oxygen consumption rate of pathogenic cells associated with 3243A > G mutation. We measured τm5U frequency of mt-tRNALeu(UUR) with 3243A > G mutation in the cybrids by a primer extension method assisted with chemical derivatization of τm5U, showing that hypomodification of τm5U was significantly restored by the 3290T > C haplotypic mutation. We concluded that the 3290T > C is a haplotypic mutation that suppresses respiratory deficiency of mitochondrial disease by restoring hypomodified τm5U in mt-tRNALeu(UUR) with 3243A > G mutation, implying a potential therapeutic measure for mitochondrial disease associated with pathogenic mutations in mt-tRNAs.
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Affiliation(s)
- Saori Ueda
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mikako Yagi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ena Tomoda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shinya Matsumoto
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yasushi Ueyanagi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yura Do
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Daiki Setoyama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuichi Matsushima
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Japan
| | - Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tomomi Ide
- Department of Cardiovascular Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yusuke Mori
- Department of Internal Medicine Kitakyushu City Yahata Hospital, 2-6-2 Ogura, Yahatahigashi-ku, Kitakyushu 805-8534, Japan
| | - Noriko Oyama
- Department of Endocrinology and Metabolism, Fukuoka Children's Hospital, 5-1-1 Kashiiteriha, Higashi-ku, Fukuoka 813-0017, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takeshi Uchiumi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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5
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Ng EL, Reed AL, O'Connell CB, Alder NN. Using Live Cell STED Imaging to Visualize Mitochondrial Inner Membrane Ultrastructure in Neuronal Cell Models. J Vis Exp 2023:10.3791/65561. [PMID: 37458423 PMCID: PMC11067429 DOI: 10.3791/65561] [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] [Indexed: 07/20/2023] Open
Abstract
Mitochondria play many essential roles in the cell, including energy production, regulation of Ca2+ homeostasis, lipid biosynthesis, and production of reactive oxygen species (ROS). These mitochondria-mediated processes take on specialized roles in neurons, coordinating aerobic metabolism to meet the high energy demands of these cells, modulating Ca2+ signaling, providing lipids for axon growth and regeneration, and tuning ROS production for neuronal development and function. Mitochondrial dysfunction is therefore a central driver in neurodegenerative diseases. Mitochondrial structure and function are inextricably linked. The morphologically complex inner membrane with structural infolds called cristae harbors many molecular systems that perform the signature processes of the mitochondrion. The architectural features of the inner membrane are ultrastructural and therefore, too small to be visualized by traditional diffraction-limited resolved microscopy. Thus, most insights on mitochondrial ultrastructure have come from electron microscopy on fixed samples. However, emerging technologies in super-resolution fluorescence microscopy now provide resolution down to tens of nanometers, allowing visualization of ultrastructural features in live cells. Super-resolution imaging therefore offers an unprecedented ability to directly image fine details of mitochondrial structure, nanoscale protein distributions, and cristae dynamics, providing fundamental new insights that link mitochondria to human health and disease. This protocol presents the use of stimulated emission depletion (STED) super-resolution microscopy to visualize the mitochondrial ultrastructure of live human neuroblastoma cells and primary rat neurons. This procedure is organized into five sections: (1) growth and differentiation of the SH-SY5Y cell line, (2) isolation, plating, and growth of primary rat hippocampal neurons, (3) procedures for staining cells for live STED imaging, (4) procedures for live cell STED experiments using a STED microscope for reference, and (5) guidance for segmentation and image processing using examples to measure and quantify morphological features of the inner membrane.
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Affiliation(s)
- Emery L Ng
- Center for Open Research Resources and Equipment, University of Connecticut
| | - Ashley L Reed
- Department of Molecular and Cell Biology, University of Connecticut
| | | | - Nathan N Alder
- Department of Molecular and Cell Biology, University of Connecticut;
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6
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Holsapple JS, Schnitzler L, Rusch L, Baldeweg TH, Neubert E, Kruss S, Erpenbeck L. Expansion microscopy of neutrophil nuclear structure and extracellular traps. BIOPHYSICAL REPORTS 2022; 3:100091. [PMID: 36619899 PMCID: PMC9813678 DOI: 10.1016/j.bpr.2022.100091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Neutrophils are key players of the immune system and possess an arsenal of effector functions, including the ability to form and expel neutrophil extracellular traps (NETs) in a process termed NETosis. During NETosis, the nuclear DNA/chromatin expands until it fills the whole cell and is released into the extracellular space. NETs are composed of DNA decorated with histones, proteins, or peptides, and NETosis is implicated in many diseases. Resolving the structure of the nucleus in great detail is essential to understand the underlying processes, but so far, superresolution methods have not been applied. Here, we developed an expansion-microscopy-based method and determined the spatial distribution of chromatin/DNA, histone H1, and nucleophosmin with an over fourfold improved resolution (<40-50 nm) and increased information content. It allowed us to identify the punctate localization of nucleophosmin in the nucleus and histone-rich domains in NETotic cells with a size of 54-66 nm. The technique could also be applied to components of the nuclear envelope (lamins B1 and B2) and myeloperoxidase, providing a complete picture of nuclear composition and structure. In conclusion, expansion microscopy enables superresolved imaging of the highly dynamic structure of nuclei in immune cells.
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Affiliation(s)
| | - Lena Schnitzler
- Department of Chemistry, Ruhr-University Bochum, Bochum, Germany
| | - Louisa Rusch
- Department of Dermatology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Elsa Neubert
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Sebastian Kruss
- Department of Chemistry, Ruhr-University Bochum, Bochum, Germany,Fraunhofer Institute for Microelectronic Circuits and Systems, Duisburg, Germany,Center for Nanointegration Duisburg-Essen (CENIDE), Duisburg, Germany,Corresponding author
| | - Luise Erpenbeck
- Department of Dermatology, University Hospital Münster, Münster, Germany,Corresponding author
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7
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Gayan S, Joshi G, Dey T. Biomarkers of mitochondrial origin: a futuristic cancer diagnostic. Integr Biol (Camb) 2022; 14:77-88. [PMID: 35780307 DOI: 10.1093/intbio/zyac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/17/2022] [Accepted: 05/27/2022] [Indexed: 11/12/2022]
Abstract
Cancer is a highly fatal disease without effective early-stage diagnosis and proper treatment. Along with the oncoproteins and oncometabolites, several organelles from cancerous cells are also emerging as potential biomarkers. Mitochondria isolated from cancer cells are one such biomarker candidates. Cancerous mitochondria exhibit different profiles compared with normal ones in morphology, genomic, transcriptomic, proteomic and metabolic landscape. Here, the possibilities of exploring such characteristics as potential biomarkers through single-cell omics and Artificial Intelligence (AI) are discussed. Furthermore, the prospects of exploiting the biomarker-based diagnosis and its futuristic utilization through circulatory tumor cell technology are analyzed. A successful alliance of circulatory tumor cell isolation protocols and a single-cell omics platform can emerge as a next-generation diagnosis and personalized treatment procedure.
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Affiliation(s)
- Sukanya Gayan
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, India
| | - Gargee Joshi
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, India
| | - Tuli Dey
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, India
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8
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Amodio A, Cassani M, Mummolo L, Cortez-Jugo C, Bhangu SK, Symons J, Ahlenstiel CL, Forte G, Ricci F, Kelleher AD, Lewin SR, Cavalieri F, Caruso F. Nanoscale probing and imaging of HIV-1 RNA in cells with a chimeric LNA-DNA sensor. NANOSCALE 2022; 14:3049-3061. [PMID: 35142755 DOI: 10.1039/d1nr08418f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Real-time detection and nanoscale imaging of human immunodeficiency virus type 1 ribonucleic acid (HIV-1 RNA) in latently infected cells that persist in people living with HIV-1 on antiretroviral therapy in blood and tissue may reveal new insights needed to cure HIV-1 infection. Herein, we develop a strategy combining DNA nanotechnology and super-resolution expansion microscopy (ExM) to detect and image a 22 base sequence transcribed from the HIV-1 promoter in model live and fixed cells. We engineer a chimeric locked nucleic acid (LNA)-DNA sensor via hybridization chain reaction to probe HIV-1 RNA in the U3 region of the HIV-1 long terminal repeat (LTR) by signal amplification in live cells. We find that the viral RNA transcript of the U3 region of the HIV-1 LTR, namely PromA, is a valid and specific biomarker to detect infected live cells. The efficiency and selectivity of the LNA-DNA sensor are evaluated in combination with ExM. Unlike standard ExM methods, which rely on additional custom linkers to anchor and immobilize RNA molecules in the intracellular polymeric network, in the current strategy, we probe and image the HIV-1 RNA target at nanoscale resolution, without resorting to chemical linkers or additional preparation steps. This is achieved by physical entrapment of the HIV-1 viral transcripts in the cells post-expansion by finely tuning the mesh size of the intracellular polymeric network.
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Affiliation(s)
- Alessia Amodio
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.
- Dipartimento di Scienze e Tecnologie Chimiche, Università degli Studi di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Marco Cassani
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.
- International Clinical Research Center (ICRC), St Anne's University Hospital, CZ-65691 Brno, Czech Republic
| | - Liviana Mummolo
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Christina Cortez-Jugo
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | | | - Jori Symons
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | | | - Giancarlo Forte
- International Clinical Research Center (ICRC), St Anne's University Hospital, CZ-65691 Brno, Czech Republic
| | - Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, Università degli Studi di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Anthony D Kelleher
- Kirby Institute, University of New South Wales, New South Wales 2052, Australia
| | - Sharon R Lewin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Victoria 3004, Australia
| | - Francesca Cavalieri
- Dipartimento di Scienze e Tecnologie Chimiche, Università degli Studi di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- School of Science, RMIT University, Victoria 3000, Australia.
| | - Frank Caruso
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Teranikar T, Lim J, Ijaseun T, Lee J. Development of Planar Illumination Strategies for Solving Mysteries in the Sub-Cellular Realm. Int J Mol Sci 2022; 23:ijms23031643. [PMID: 35163562 PMCID: PMC8835835 DOI: 10.3390/ijms23031643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 02/04/2023] Open
Abstract
Optical microscopy has vastly expanded the frontiers of structural and functional biology, due to the non-invasive probing of dynamic volumes in vivo. However, traditional widefield microscopy illuminating the entire field of view (FOV) is adversely affected by out-of-focus light scatter. Consequently, standard upright or inverted microscopes are inept in sampling diffraction-limited volumes smaller than the optical system's point spread function (PSF). Over the last few decades, several planar and structured (sinusoidal) illumination modalities have offered unprecedented access to sub-cellular organelles and 4D (3D + time) image acquisition. Furthermore, these optical sectioning systems remain unaffected by the size of biological samples, providing high signal-to-noise (SNR) ratios for objective lenses (OLs) with long working distances (WDs). This review aims to guide biologists regarding planar illumination strategies, capable of harnessing sub-micron spatial resolution with a millimeter depth of penetration.
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Affiliation(s)
| | | | | | - Juhyun Lee
- Correspondence: ; Tel.: +1-817-272-6534; Fax: +1-817-272-2251
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10
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Trinks N, Reinhard S, Drobny M, Heilig L, Löffler J, Sauer M, Terpitz U. Subdiffraction-resolution fluorescence imaging of immunological synapse formation between NK cells and A. fumigatus by expansion microscopy. Commun Biol 2021; 4:1151. [PMID: 34608260 PMCID: PMC8490467 DOI: 10.1038/s42003-021-02669-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Expansion microscopy (ExM) enables super-resolution fluorescence imaging on standard microscopes by physical expansion of the sample. However, the investigation of interactions between different organisms such as mammalian and fungal cells by ExM remains challenging because different cell types require different expansion protocols to ensure identical, ideally isotropic expansion of both partners. Here, we introduce an ExM method that enables super-resolved visualization of the interaction between NK cells and Aspergillus fumigatus hyphae. 4-fold expansion in combination with confocal fluorescence imaging allows us to resolve details of cytoskeleton rearrangement as well as NK cells' lytic granules triggered by contact with an RFP-expressing A. fumigatus strain. In particular, subdiffraction-resolution images show polarized degranulation upon contact formation and the presence of LAMP1 surrounding perforin at the NK cell-surface post degranulation. Our data demonstrate that optimized ExM protocols enable the investigation of immunological synapse formation between two different species with so far unmatched spatial resolution.
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Affiliation(s)
- Nora Trinks
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, Germany
| | - Sebastian Reinhard
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, Germany
| | - Matthias Drobny
- Department of Internal Medicine II, WÜ4i, University Hospital Würzburg, Würzburg, Germany
| | - Linda Heilig
- Department of Internal Medicine II, WÜ4i, University Hospital Würzburg, Würzburg, Germany
| | - Jürgen Löffler
- Department of Internal Medicine II, WÜ4i, University Hospital Würzburg, Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, Germany
| | - Ulrich Terpitz
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, Germany.
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11
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Campbell LA, Pannoni KE, Savory NA, Lal D, Farris S. Protein-retention expansion microscopy for visualizing subcellular organelles in fixed brain tissue. J Neurosci Methods 2021; 361:109285. [PMID: 34242703 PMCID: PMC8370715 DOI: 10.1016/j.jneumeth.2021.109285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 11/21/2022]
Abstract
BACKGROUND Protein expansion microscopy (proExM) is a powerful technique that crosslinks proteins to a swellable hydrogel to physically expand and optically clear biological samples. The resulting increased resolution (~70 nm) and physical separation of labeled proteins make it an attractive tool for studying the localization of subcellular organelles in densely packed tissues, such as the brain. However, the digestion and expansion process greatly reduce fluorescence signals making it necessary to optimize ExM conditions per sample for specific end goals. NEW METHOD Here we compare the staining and digestion conditions of existing proExM workflows to identify the optimal protocol for visualizing subcellular organelles (mitochondria and the Golgi apparatus) within reporter-labeled neurons in fixed mouse brain tissue. RESULTS We found that immunostaining before proExM and using a proteinase K based digestion for 8 h consistently resulted in robust fluorescence retention for immunolabeled subcellular organelles and genetically-encoded reporters. COMPARISON WITH EXISTING METHODS With these methods, we more accurately quantified mitochondria size and number and better visualized Golgi ultrastructure in individual CA2 neurons in the mouse hippocampus. CONCLUSIONS This organelle optimized proExM protocol will be broadly useful for investigators interested in visualizing the spatial distribution of immunolabeled subcellular organelles in various reporter mouse lines, reducing effort, time and resources on the optimization process.
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Affiliation(s)
- Logan A Campbell
- Fralin Biomedical Research Institute, Center for Neurobiology Research, Virginia Tech Carilion, Roanoke, VA, USA
| | - Katy E Pannoni
- Fralin Biomedical Research Institute, Center for Neurobiology Research, Virginia Tech Carilion, Roanoke, VA, USA
| | - Niesha A Savory
- Fralin Biomedical Research Institute, Center for Neurobiology Research, Virginia Tech Carilion, Roanoke, VA, USA; School of Neuroscience, Virginia Tech, Blacksburg, VA, USA
| | - Dinesh Lal
- Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | - Shannon Farris
- Fralin Biomedical Research Institute, Center for Neurobiology Research, Virginia Tech Carilion, Roanoke, VA, USA; Virginia Tech Carilion School of Medicine, Roanoke, VA, USA; Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA.
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12
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Yao L, Zhang L, Fei Y, Chen L, Mi L, Ma J. Application of SNAP-Tag in Expansion Super-Resolution Microscopy Using DNA Oligostrands. Front Chem 2021; 9:640519. [PMID: 33996746 PMCID: PMC8119759 DOI: 10.3389/fchem.2021.640519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Expansion super-resolution technology is a new technology developed in recent years. It anchors the dye on the hydrogel and the dye expands with the expansion of the hydrogel so that a super-resolution map can be obtained under an ordinary microscope. However, by labeling the target protein with a first antibody and secondary antibody, the distance between the fluorescent group and the actual target protein is greatly increased. Although fluorescent proteins can also be used for expansion super-resolution to reduce this effect, the fluorescent protein is often destroyed during sample preparation. To solve this problem, we developed a novel label system for expansion microscopy, based on a DNA oligostrand linked with a fluorescent dye, acrylamide group (linker), and benzoylguanine (BG, a small substrate molecule for SNAP-tag). This protocol greatly reduced the error between the position of fluorescent group and the actual target protein, and also reduced loss of the fluorescent group during sample preparation.
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Affiliation(s)
- Longfang Yao
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Li Zhang
- Shanghai Engineering Research Center of Industrial Microorganisms, The Multiscale Research Institute of Complex Systems, School of Life Sciences, Fudan University, Shanghai, China
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Liwen Chen
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Lan Mi
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Jiong Ma
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Industrial Microorganisms, The Multiscale Research Institute of Complex Systems, School of Life Sciences, Fudan University, Shanghai, China.,Insititute of Biomedical Engineering and Technology, Academy for Engineering and Technology, Fudan University, Shanghai, China
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13
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Kunz TC, Rühling M, Moldovan A, Paprotka K, Kozjak-Pavlovic V, Rudel T, Fraunholz M. The Expandables: Cracking the Staphylococcal Cell Wall for Expansion Microscopy. Front Cell Infect Microbiol 2021; 11:644750. [PMID: 33796486 PMCID: PMC8008081 DOI: 10.3389/fcimb.2021.644750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/08/2021] [Indexed: 12/03/2022] Open
Abstract
Expansion Microscopy (ExM) is a novel tool improving the resolution of fluorescence microscopy by linking the sample into a hydrogel that gets physically expanded in water. Previously, we have used ExM to visualize the intracellular Gram-negative pathogens Chlamydia trachomatis, Simkania negevensis, and Neisseria gonorrhoeae. Gram-positive bacteria have a rigid and thick cell wall that impedes classic expansion strategies. Here we developed an approach, which included a series of enzymatic treatments resulting in isotropic 4× expansion of the Gram-positive pathogen Staphylococcus aureus. We further demonstrate the suitability of the technique for imaging of planktonic bacteria as well as endocytosed, intracellular bacteria at a spatial resolution of approximately 60 nm with conventional confocal laser scanning microscopy.
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Affiliation(s)
- Tobias C Kunz
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Marcel Rühling
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Adriana Moldovan
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Kerstin Paprotka
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Vera Kozjak-Pavlovic
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Thomas Rudel
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Martin Fraunholz
- Department of Microbiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
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