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Cremer C, Schock F, Failla AV, Birk U. Modulated illumination microscopy: Application perspectives in nuclear nanostructure analysis. J Microsc 2024. [PMID: 38618985 DOI: 10.1111/jmi.13297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 02/26/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
Abstract
The structure of the cell nucleus of higher organisms has become a major topic of advanced light microscopy. So far, a variety of methods have been applied, including confocal laser scanning fluorescence microscopy, 4Pi, STED and localisation microscopy approaches, as well as different types of patterned illumination microscopy, modulated either laterally (in the object plane) or axially (along the optical axis). Based on our experience, we discuss here some application perspectives of Modulated Illumination Microscopy (MIM) and its combination with single-molecule localisation microscopy (SMLM). For example, spatially modulated illumination microscopy/SMI (illumination modulation along the optical axis) has been used to determine the axial extension (size) of small, optically isolated fluorescent objects between ≤ 200 nm and ≥ 40 nm diameter with a precision down to the few nm range; it also allows the axial positioning of such structures down to the 1 nm scale; combined with laterally structured illumination/SIM, a 3D localisation precision of ≤1 nm is expected using fluorescence yields typical for SMLM applications. Together with the nanosizing capability of SMI, this can be used to analyse macromolecular nuclear complexes with a resolution approaching that of cryoelectron microscopy.
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Affiliation(s)
- Christoph Cremer
- Kirchhoff Institute for Physics (KIP), Heidelberg, Germany
- Interdisciplinary Centre for Scientific Computing (IWR), University of Heidelberg, Heidelberg, Germany
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Florian Schock
- Kirchhoff Institute for Physics (KIP), Heidelberg, Germany
| | - Antonio Virgilio Failla
- UKE Microscopy Imaging Facility, University Medical Centre Hamburg Eppendorf, Hamburg, Germany
| | - Udo Birk
- Institute for Photonics and Robotics (IPR), Department of Applied Future Technologies, University of Applied Sciences of the Grisons (FH Graubünden), Chur, Switzerland
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2
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Pluthero FG, Kahr WHA. Evaluation of human platelet granules by structured illumination laser fluorescence microscopy. Platelets 2023; 34:2157808. [PMID: 36572649 DOI: 10.1080/09537104.2022.2157808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Many roles of human platelets in health and disease are linked to their ability to transport and secrete a variety of small molecules and proteins carried in dense (δ-) and α-granules. Determination of granule number and content is important for diagnosis of platelet disorders and for studies of platelet structure, function, and development. We have optimized methods for detection and localization of platelet proteins via antibody and lectin staining, imaging via structured illumination laser fluorescence microscopy (SIM), and three-dimension (3D) image analysis. The methods were validated via comparison with published studies based on electron microscopy and high-resolution fluorescence microscopy. The α-granule cargo proteins thrombospondin-1 (TSP1), osteonectin (SPARC), fibrinogen (FGN), and Von Willebrand factor (VWF) were localized within the granule lumen, as was the proteoglycan serglycin (SRGN). Colocalization analysis indicates that staining with fluorescently labeled wheat germ agglutinin (WGA) allows detection of α-granules as effectively as immunostaining for cargo proteins, with the advantage of not requiring antibodies. RAB27B was observed to be concentrated at dense granules, allowing them to be counted via visual scoring and object analysis. We present a workflow for counting dense and α-granules via object analysis of 3D SIM images of platelets stained for RAB27B and with WGA.Abbreviation: SIM: structured illumination microscopy; WGA: wheat germ agglutinin; FGN: fibrinogen; TSP1: thrombospondin 1; ER: endoplasmic reticulum.
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Affiliation(s)
- Fred G Pluthero
- Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Walter H A Kahr
- Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,Division of Haematology/Oncology, Department of Paediatrics, University of Toronto and The Hospital for Sick Children, Toronto, ON, Canada
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3
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Eilts J, Reinhard S, Michetschläger N, Werner C, Sauer M. Enhanced synaptic protein visualization by multicolor super-resolution expansion microscopy. Neurophotonics 2023; 10:044412. [PMID: 37886043 PMCID: PMC10599331 DOI: 10.1117/1.nph.10.4.044412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 10/28/2023]
Abstract
Significance Understanding the organization of biomolecules into complexes and their dynamics is crucial for comprehending cellular functions and dysfunctions, particularly in neuronal networks connected by synapses. In the last two decades, various powerful super-resolution (SR) microscopy techniques have been developed that produced stunning images of synapses and their molecular organization. However, current SR microscopy methods do not permit multicolor fluorescence imaging with 20 to 30 nm spatial resolution. Aim We developed a method that enables 4-color fluorescence imaging of synaptic proteins in neurons with 20 to 30 nm lateral resolution. Approach We used post-expansion immunolabeling of eightfold expanded hippocampal neurons in combination with Airyscan and structured illumination microscopy (SIM). Results We demonstrate that post-expansion immunolabeling of approximately eightfold expanded hippocampal neurons enables efficient labeling of synaptic proteins in crowded compartments with minimal linkage error and enables in combination with Airyscan and SIM four-color three-dimensional fluorescence imaging with 20 to 30 nm lateral resolution. Using immunolabeling of Synaptobrevin 2 as an efficient marker of the vesicle pool allowed us to identify individual synaptic vesicles colocalized with Rab3-interacting molecule 1 and 2 (RIM1/2), a marker of pre-synaptic fusion sites. Conclusions Our optimized expansion microscopy approach improves the visualization and location of pre- and post-synaptic proteins and can thus provide invaluable insights into the spatial organization of proteins at synapses.
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Affiliation(s)
- Janna Eilts
- University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Würzburg, Germany
| | - Sebastian Reinhard
- University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Würzburg, Germany
| | - Nikolas Michetschläger
- University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Würzburg, Germany
| | - Christian Werner
- University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Würzburg, Germany
| | - Markus Sauer
- University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Würzburg, Germany
- University of Würzburg, Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, Würzburg, Germany
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Yang B, Liu W, Chen X, Chen G, Zhu X. A novel multi-frame wavelet generative adversarial network for scattering reconstruction of structured illumination microscopy. Phys Med Biol 2023; 68:185016. [PMID: 37619594 DOI: 10.1088/1361-6560/acf3cb] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/24/2023] [Indexed: 08/26/2023]
Abstract
Objective. Structured illumination microscopy (SIM) is widely used in various fields of life science research. In clinical practice, it has low phototoxicity, fast imaging speed and no special fluorescent markers. However, SIM is still affected by the scattering medium of biological tissues, resulting in insufficient resolution of the obtained images, which limits the development of life sciences. A novel multi-frame wavelet generation adversarial network (MWGAN) is proposed to improve the scattering reconstruction capability of SIM.Approach. MWGAN is based on two components derived from the original image. A generative adversarial network constructed by wavelet transform is trained to reconstruct some complex details in the cell structure. Multi-frame adversarial network is used to obtain the inter-frame information of the image and use the complementary information of the before and after frames to improve the quality of the model reconstruction.Results. To demonstrate the robustness of MWGAN, multiple low-quality SIM image datasets are tested. Compared with the state-of-the-art methods, the proposed method achieves superior performance in both of the subjective and objective evaluation.Conclusion. MWGAN is effective for improving the clarity of SIM images. Meanwhile, the SIM images reconstructed by multiple frames improve the reconstruction quality of complex regions and allow clearer and dynamic observation of cellular functions.
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Affiliation(s)
- Bin Yang
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou 350007, People's Republic of China
- Fujian Provincial Engineering Technology Research Center of Photoelectric Sensing Application, Fujian Normal University, Fuzhou 350007, People's Republic of China
| | - Weiping Liu
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou 350007, People's Republic of China
- Fujian Provincial Engineering Technology Research Center of Photoelectric Sensing Application, Fujian Normal University, Fuzhou 350007, People's Republic of China
| | - Xinghong Chen
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou 350007, People's Republic of China
- Fujian Provincial Engineering Technology Research Center of Photoelectric Sensing Application, Fujian Normal University, Fuzhou 350007, People's Republic of China
| | - Guannan Chen
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou 350007, People's Republic of China
- Fujian Provincial Engineering Technology Research Center of Photoelectric Sensing Application, Fujian Normal University, Fuzhou 350007, People's Republic of China
| | - Xiaoqin Zhu
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou 350007, People's Republic of China
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5
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Phillips TA, Caprettini V, Aggarwal N, Marcotti S, Tetley R, Mao Y, Shaw T, Chiappini C, Parsons M, Cox S. A method for reproducible high-resolution imaging of 3D cancer cell spheroids. J Microsc 2023; 291:30-42. [PMID: 36639864 PMCID: PMC10953429 DOI: 10.1111/jmi.13169] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
Multicellular tumour cell spheroids embedded within three-dimensional (3D) hydrogels or extracellular matrices (ECM) are widely used as models to study cancer growth and invasion. Standard methods to embed spheroids in 3D matrices result in random placement in space which limits the use of inverted fluorescence microscopy techniques, and thus the resolution that can be achieved to image molecular detail within the intact spheroid. Here, we leverage UV photolithography to microfabricate PDMS (polydimethylsiloxane) stamps that allow for generation of high-content, reproducible well-like structures in multiple different imaging chambers. Addition of multicellular tumour spheroids into stamped collagen structures allows for precise positioning of spheroids in 3D space for reproducible high-/super-resolution imaging. Embedded spheroids can be imaged live or fixed and are amenable to immunostaining, allowing for greater flexibility of experimental approaches. We describe the use of these spheroid imaging chambers to analyse cell invasion, cell-ECM interaction, ECM alignment, force-dependent intracellular protein dynamics and extension of fine actin-based protrusions with a variety of commonly used inverted microscope platforms. This method enables reproducible, high-/super-resolution live imaging of multiple tumour spheroids, that can be potentially extended to visualise organoids and other more complex 3D in vitro systems.
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Affiliation(s)
- Thomas A. Phillips
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
| | - Valeria Caprettini
- Centre for Craniofacial & Regenerative BiologyKing's College LondonLondonUK
| | - Nandini Aggarwal
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
- Department of Inflammation BiologySchool of Immunology & Microbial SciencesKing's College LondonLondonUK
| | - Stefania Marcotti
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
| | - Rob Tetley
- Laboratory for Molecular Cell Biology and Institute for the Physics of Living SystemsUniversity College LondonLondonUK
| | - Yanlan Mao
- Laboratory for Molecular Cell Biology and Institute for the Physics of Living SystemsUniversity College LondonLondonUK
| | - Tanya Shaw
- Department of Inflammation BiologySchool of Immunology & Microbial SciencesKing's College LondonLondonUK
| | - Ciro Chiappini
- Centre for Craniofacial & Regenerative BiologyKing's College LondonLondonUK
| | - Maddy Parsons
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
| | - Susan Cox
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
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6
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Sen Gupta A, Seidel C, Tsuchiya D, McKinney S, Yu Z, Smith S, Unruh J, Gerton JL. Defining a core configuration for human centromeres during mitosis. bioRxiv 2023:2023.05.10.539634. [PMID: 37214893 PMCID: PMC10197669 DOI: 10.1101/2023.05.10.539634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The biorientation of sister chromatids on the mitotic spindle, essential for accurate sister chromatid segregation, relies on critical centromere components including cohesin, the centromere-specific H3 variant CENP-A, and centromeric DNA. Centromeric DNA is highly variable between chromosomes yet must accomplish a similar function. Moreover, how the 50 nm cohesin ring, proposed to encircle sister chromatids, accommodates inter-sister centromeric distances of hundreds of nanometers on the metaphase spindle is a conundrum. Insight into the 3D organization of centromere components would help resolve how centromeres function on the mitotic spindle. We used ChIP-seq and super-resolution microscopy to examine the geometry of essential centromeric components on human chromosomes. ChIP-seq demonstrates that cohesin subunits are depleted in α-satellite arrays where CENP-A nucleosomes and kinetochores assemble. Cohesin is instead enriched at pericentromeric DNA. Structured illumination microscopy of sister centromeres is consistent, revealing a non-overlapping pattern of CENP-A and cohesin. We used single particle averaging of hundreds of mitotic sister chromatids to develop an average centromere model. CENP-A clusters on sister chromatids, connected by α-satellite, are separated by ~562 nm with a perpendicular intervening ~190 nM wide axis of cohesin. Two differently sized α-satellite arrays on chromosome 7 display similar inter-sister CENP-A cluster distance, demonstrating different sized arrays can achieve a common spacing. Our data suggest a working model for a common core configuration of essential centromeric components that includes CENP-A nucleosomes at the outer edge of extensible α-satellite DNA and pericentromeric cohesion. This configuration helps reconcile how centromeres function and serves as a foundation for future studies of additional components required for centromere function.
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Affiliation(s)
| | - Chris Seidel
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Dai Tsuchiya
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Zulin Yu
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Sarah Smith
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Jennifer L. Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA
- University of Kansas Department of Biochemistry and Molecular Biology, Kansas City, KS, USA
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7
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Bali K, Guffick C, McCoy R, Lu Z, Kaminski CF, Mela I, Owens RM, van Veen HW. Biosensor for Multimodal Characterization of an Essential ABC Transporter for Next-Generation Antibiotic Research. ACS Appl Mater Interfaces 2023; 15:12766-12776. [PMID: 36866935 PMCID: PMC10020959 DOI: 10.1021/acsami.2c21556] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/15/2023] [Indexed: 05/21/2023]
Abstract
As the threat of antibiotic resistance increases, there is a particular focus on developing antimicrobials against pathogenic bacteria whose multidrug resistance is especially entrenched and concerning. One such target for novel antimicrobials is the ATP-binding cassette (ABC) transporter MsbA that is present in the plasma membrane of Gram-negative pathogenic bacteria where it is fundamental to the survival of these bacteria. Supported lipid bilayers (SLBs) are useful in monitoring membrane protein structure and function since they can be integrated with a variety of optical, biochemical, and electrochemical techniques. Here, we form SLBs containing Escherichia coli MsbA and use atomic force microscopy (AFM) and structured illumination microscopy (SIM) as high-resolution microscopy techniques to study the integrity of the SLBs and incorporated MsbA proteins. We then integrate these SLBs on microelectrode arrays (MEA) based on the conducting polymer poly(3,4-ethylenedioxy-thiophene) poly(styrene sulfonate) (PEDOT:PSS) using electrochemical impedance spectroscopy (EIS) to monitor ion flow through MsbA proteins in response to ATP hydrolysis. These EIS measurements can be correlated with the biochemical detection of MsbA-ATPase activity. To show the potential of this SLB approach, we observe not only the activity of wild-type MsbA but also the activity of two previously characterized mutants along with quinoline-based MsbA inhibitor G907 to show that EIS systems can detect changes in ABC transporter activity. Our work combines a multitude of techniques to thoroughly investigate MsbA in lipid bilayers as well as the effects of potential inhibitors of this protein. We envisage that this platform will facilitate the development of next-generation antimicrobials that inhibit MsbA or other essential membrane transporters in microorganisms.
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Affiliation(s)
- Karan Bali
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Charlotte Guffick
- Department
of Pharmacology, University of Cambridge, CB2 1PD Cambridge, U. K.
| | - Reece McCoy
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Zixuan Lu
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Clemens F. Kaminski
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Ioanna Mela
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Róisín M. Owens
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Hendrik W. van Veen
- Department
of Pharmacology, University of Cambridge, CB2 1PD Cambridge, U. K.
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8
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Du Y, Zhu YJ, Zeng B, Mu XL, Liu JY. Super-Resolution Quantification of T2DM-Induced Mitochondrial Morphology Changes and Their Implications in Pharmacodynamics of Metformin and Sorafenib. Front Pharmacol 2022; 13:932116. [PMID: 35873543 PMCID: PMC9298863 DOI: 10.3389/fphar.2022.932116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/07/2022] [Indexed: 02/05/2023] Open
Abstract
Mitochondria, as the powerhouse of cells, are involved in various processes of cellular homeostasis, especially energy metabolism. The morphology of mitochondria is a critical indicator for their functions, referring to mitochondrial fusion and fission. Here, we performed structured illumination microscopy (SIM) to measure the mitochondrial morphology in living cells. Benefitting from its nano-scale resolution, this SIM-based strategy can quantify the fusion and fission of mitochondria with high sensitivity. Furthermore, as type 2 diabetes mellitus (T2DM) is caused by a disorder of energy substrate utilization, this strategy has the potential to study T2DM by analyzing the mitochondrial morphology of insulin-resistant (IR) cells. With SIM, we found that mitochondrial fission was increased in IR MRC-5, LO2, FHs 74 Int, and HepG2 cells but not in IR Huh7 cells with high-invasiveness ability. Furthermore, we found that metformin could inhibit mitochondrial fission in IR cells, and sorafenib could promote mitochondrial fusion in HepG2 cancer cells, especially in those IR cells. To conclude, mitochondrial fission is involved in T2DM, and cancer cells with high-invasiveness ability may be equipped with stronger resistance to energy metabolism disorder. In addition, the pharmacodynamics of metformin and sorafenib in cancer may be related to the inhibition of mitochondrial fission, especially for patients with T2DM.
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Affiliation(s)
- Yang Du
- Cancer Center, State Key Laboratory of Biotherapy, Department of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Ya-Juan Zhu
- Cancer Center, State Key Laboratory of Biotherapy, Department of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Bo Zeng
- Dean's Office, West China Hospital, Sichuan University, Chengdu, China
| | - Xiao-Li Mu
- Cancer Center, State Key Laboratory of Biotherapy, Department of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Ji-Yan Liu
- Cancer Center, State Key Laboratory of Biotherapy, Department of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
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9
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Plačková K, Zedek F, Schubert V, Houben A, Bureš P. Kinetochore size scales with chromosome size in bimodal karyotypes of Agavoideae. Ann Bot 2022; 130:77-84. [PMID: 35576011 PMCID: PMC9295917 DOI: 10.1093/aob/mcac063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/15/2022] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS In eukaryotes, the total kinetochore size (defined as a chromosomal region containing CENH3-positive nucleosomes) per nucleus strongly correlates with genome size, a relationship that has been hypothesized to stem from general intracellular scaling principles. However, if larger chromosomes within a karyotype required larger kinetochores to move properly, it could also be derived from the mechanics of cell division. METHODS We selected seven species of the plant subfamily Agavoideae whose karyotypes are characterized by the presence of small and very large chromosomes. We visualized the kinetochore regions and chromosomes by immunolabelling with an anti-CENH3 antibody and DAPI (6'-diamidino-2-phenylindole) staining. We then employed 2D widefield and 3D super-resolution microscopy to measure chromosome and kinetochore areas and volumes, respectively. To assess the scaling relationship of kinetochore size to chromosome size inside a karyotype, we log-transformed the data and analysed them with linear mixed models which allowed us to control for the inherent hierarchical structure of the dataset (metaphases within slides and species). KEY RESULTS We found a positive intra-karyotype relationship between kinetochore and chromosome size. The slope of the regression line of the observed relationship (0.277 for areas, 0.247 for volumes) was very close to the theoretical slope of 0.25 for chromosome width based on the expected physics of chromosome passage through the cytoplasm during cell division. We obtained similar results by reanalysing available data from human and maize. CONCLUSIONS Our findings suggest that the total kinetochore size to genome size scaling observed across eukaryotes may also originate from the mechanics of cell division. Moreover, the potential causal link between kinetochore and chromosome size indicates that evolutionary mechanisms capable of leading kinetochore size changes to fixation, such as centromere drive, could promote the size evolution of entire chromosomes and genomes.
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Affiliation(s)
- Klára Plačková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | | | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, D-06466 Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, D-06466 Seeland, Germany
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Lauriola A, Davalli P, Marverti G, Caporali A, Mai S, D’Arca D. Telomere Dysfunction Is Associated with Altered DNA Organization in Trichoplein/Tchp/Mitostatin (TpMs) Depleted Cells. Biomedicines 2022; 10:biomedicines10071602. [PMID: 35884905 PMCID: PMC9312488 DOI: 10.3390/biomedicines10071602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 12/02/2022] Open
Abstract
Recently, we highlighted a novel role for the protein Trichoplein/TCHP/Mitostatin (TpMs), both as mitotic checkpoint regulator and guardian of chromosomal stability. TpMs-depleted cells show numerical and structural chromosome alterations that lead to genomic instability. This condition is a major driving force in malignant transformation as it allows for the cells acquiring new functional capabilities to proliferate and disseminate. Here, the effect of TpMs depletion was investigated in different TpMs-depleted cell lines by means of 3D imaging and 3D Structured illumination Microscopy. We show that TpMs depletion causes alterations in the 3D architecture of telomeres in colon cancer HCT116 cells. These findings are consistent with chromosome alterations that lead to genomic instability. Furthermore, TpMs depletion changes the spatial arrangement of chromosomes and other nuclear components. Modified nuclear architecture and organization potentially induce variations that precede the onset of genomic instability and are considered as markers of malignant transformation. Our present observations connect the tumor suppression ability of TpMs with its novel functions in maintaining the proper chromosomal segregation as well as the proper telomere and nuclear architecture. Further investigations will investigate the connection between alterations in telomeres and nuclear architecture with the progression of human tumors with the aim of developing personalized therapeutic interventions.
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Affiliation(s)
- Angela Lauriola
- Department of Biotechnology, University of Verona, 37134 Verona, Italy;
| | - Pierpaola Davalli
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy; (P.D.); (G.M.)
| | - Gaetano Marverti
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy; (P.D.); (G.M.)
| | - Andrea Caporali
- The Queen’s Medical Research Institute, BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH10 4AH, UK;
| | - Sabine Mai
- CancerCare Manitoba Research Institute, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
- Correspondence: (S.M.); (D.D.); Tel.: +1-204-272-3174 (S.M.); +39-059-205-5610 (D.D.)
| | - Domenico D’Arca
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy; (P.D.); (G.M.)
- Correspondence: (S.M.); (D.D.); Tel.: +1-204-272-3174 (S.M.); +39-059-205-5610 (D.D.)
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11
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Wang Y, Guan M, Zhang Y, Zhanghao K, Xi P. Glucose increases the length and spacing of the lattice structure of the axon initial segment. Microsc Res Tech 2022; 85:2679-2691. [PMID: 35411984 DOI: 10.1002/jemt.24122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/01/2022] [Accepted: 03/31/2022] [Indexed: 11/12/2022]
Abstract
The axon initial segment (AIS) plays an important role in maintaining neuronal polarity and initiating action potentials (APs). The AIS adapts to its environment by changing its length and distance from the cell body, resulting in modulation of neuronal excitability, which is referred to as AIS plasticity. Previous studies found an ~200 nm single periodic distribution of the key AIS components ankyrinG (AnkG), Nav 1.2, and βIV-spectrin, while it remains unclear how the lattice structure is altered by AIS plasticity. In this study, we found that the length of the AIS significantly increased, resulting in increased neuronal excitability, with high-concentration glucose treatment. Structured illumination microscopy (SIM) images of the lattice structure showed a dual-spacing periodic distribution (~200 nm and ~260 nm) of AnkG, Nav 1.2, and βIV-spectrin. Moreover, 480-kDa AnkG was crucial for AIS plasticity and increased lattice structure spacing. The discovery of new regulators for modulating AIS plasticity will help us to understand and manipulate the structure and function of the AIS.
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Affiliation(s)
- Yiming Wang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | - Meiling Guan
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Yan Zhang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China.,PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Karl Zhanghao
- UTS-SUStech Joint Research Centre for Biomedical Materials & Devices, Department of Biomedical Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Peng Xi
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China.,UTS-SUStech Joint Research Centre for Biomedical Materials & Devices, Department of Biomedical Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China.,National Biomedical Imaging Center, Peking University, Beijing, China
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12
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Prakash K, Diederich B, Heintzmann R, Schermelleh L. Super-resolution microscopy: a brief history and new avenues. Philos Trans A Math Phys Eng Sci 2022; 380:20210110. [PMID: 35152764 PMCID: PMC8841785 DOI: 10.1098/rsta.2021.0110] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 05/03/2023]
Abstract
Super-resolution microscopy (SRM) is a fast-developing field that encompasses fluorescence imaging techniques with the capability to resolve objects below the classical diffraction limit of optical resolution. Acknowledged with the Nobel prize in 2014, numerous SRM methods have meanwhile evolved and are being widely applied in biomedical research, all with specific strengths and shortcomings. While some techniques are capable of nanometre-scale molecular resolution, others are geared towards volumetric three-dimensional multi-colour or fast live-cell imaging. In this editorial review, we pick on the latest trends in the field. We start with a brief historical overview of both conceptual and commercial developments. Next, we highlight important parameters for imaging successfully with a particular super-resolution modality. Finally, we discuss the importance of reproducibility and quality control and the significance of open-source tools in microscopy. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 2)'.
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Affiliation(s)
- Kirti Prakash
- Integrated Pathology Unit, Centre for Molecular Pathology, The Royal Marsden Trust and Institute of Cancer Research, Sutton SM2 5NG, UK
| | - Benedict Diederich
- Leibniz Institute for Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - Rainer Heintzmann
- Leibniz Institute for Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, 07743 Jena, Germany
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13
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Kolesnikova TD, Pokholkova GV, Dovgan VV, Zhimulev IF, Schubert V. Super-resolution microscopy reveals stochastic initiation of replication in Drosophila polytene chromosomes. Chromosome Res 2022; 30:361-83. [PMID: 35226231 DOI: 10.1007/s10577-021-09679-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 01/25/2023]
Abstract
Studying the probability distribution of replication initiation along a chromosome is a huge challenge. Drosophila polytene chromosomes in combination with super-resolution microscopy provide a unique opportunity for analyzing the probabilistic nature of replication initiation at the ultrastructural level. Here, we developed a method for synchronizing S-phase induction among salivary gland cells. An analysis of the replication label distribution in the first minutes of S phase and in the following hours after the induction revealed the dynamics of replication initiation. Spatial super-resolution structured illumination microscopy allowed identifying multiple discrete replication signals and to investigate the behavior of replication signals in the first minutes of the S phase at the ultrastructural level. We identified replication initiation zones where initiation occurs stochastically. These zones differ significantly in the probability of replication initiation per time unit. There are zones in which initiation occurs on most strands of the polytene chromosome in a few minutes. In other zones, the initiation on all strands takes several hours. Compact bands are free of replication initiation events, and the replication runs from outer edges to the middle, where band shapes may alter.
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14
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Kim GT, Bahn S, Kim N, Choi JH, Kim JS, Rah JC. Efficient and Accurate Synapse Detection With Selective Structured Illumination Microscopy on the Putative Regions of Interest of Ultrathin Serial Sections. Front Neuroanat 2021; 15:759816. [PMID: 34867216 PMCID: PMC8634652 DOI: 10.3389/fnana.2021.759816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Critical determinants of synaptic functions include subcellular locations, input sources, and specific molecular characteristics. However, there is not yet a reliable and efficient method that can detect synapses. Electron microscopy is a gold-standard method to detect synapses due to its exceedingly high spatial resolution. However, it requires laborious and time-consuming sample preparation and lengthy imaging time with limited labeling methods. Recent advances in various fluorescence microscopy methods have highlighted fluorescence microscopy as a substitute for electron microscopy in reliable synapse detection in a large volume of neural circuits. In particular, array tomography has been verified as a useful tool for neural circuit reconstruction. To further improve array tomography, we developed a novel imaging method, called “structured illumination microscopy on the putative region of interest on ultrathin sections”, which enables efficient and accurate detection of synapses-of-interest. Briefly, based on low-magnification conventional fluorescence microscopy images, synapse candidacy was determined. Subsequently, the coordinates of the regions with candidate synapses were imaged using super-resolution structured illumination microscopy. Using this system, synapses from the high-order thalamic nucleus, the posterior medial nucleus in the barrel cortex were rapidly and accurately imaged.
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Affiliation(s)
- Gyeong Tae Kim
- Korea Brain Research Institute, Daegu, South Korea.,Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Sangkyu Bahn
- Korea Brain Research Institute, Daegu, South Korea
| | - Nari Kim
- Korea Brain Research Institute, Daegu, South Korea
| | - Joon Ho Choi
- Korea Brain Research Institute, Daegu, South Korea
| | - Jinseop S Kim
- Korea Brain Research Institute, Daegu, South Korea.,Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Jong-Cheol Rah
- Korea Brain Research Institute, Daegu, South Korea.,Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology, Daegu, South Korea
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15
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Lee YU, Posner C, Nie Z, Zhao J, Li S, Bopp SE, Wisna GBM, Ha J, Song C, Zhang J, Yang S, Zhang X, Liu Z. Organic Hyperbolic Material Assisted Illumination Nanoscopy. Adv Sci (Weinh) 2021; 8:e2102230. [PMID: 34436815 PMCID: PMC8596137 DOI: 10.1002/advs.202102230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/09/2021] [Indexed: 06/07/2023]
Abstract
Resolution capability of the linear structured illumination microscopy (SIM) plays a key role in its applications in physics, medicine, biology, and life science. Many advanced methodologies have been developed to extend the resolution of structured illumination by using subdiffraction-limited optical excitation patterns. However, obtaining SIM images with a resolution beyond 40 nm at visible frequency remains as an insurmountable obstacle due to the intrinsic limitation of spatial frequency bandwidth of the involved materials and the complexity of the illumination system. Here, a low-loss natural organic hyperbolic material (OHM) that can support record high spatial-frequency modes beyond 50k0 , i.e., effective refractive index larger than 50, at visible frequencies is reported. OHM-based speckle structured illumination microscopy demonstrates imaging resolution at 30 nm scales with enhanced fluorophore photostability, biocompatibility, easy to use and low cost. This study will open up a new route in super-resolution microscopy by utilizing OHM films for various applications including bioimaging and sensing.
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Affiliation(s)
- Yeon Ui Lee
- Department of Electrical and Computer EngineeringUniversity of CaliforniaSan Diego, 9500 Gilman DriveLa JollaCA92093USA
- Department of PhysicsChungbuk National UniversityCheongjuChungbuk28644South Korea
| | - Clara Posner
- Department of PharmacologyUniversity of CaliforniaSan Diego, 9500 Gilman DriveLa JollaCA92093USA
| | - Zhaoyu Nie
- Department of Mechanical EngineeringUniversity of CaliforniaBerkeleyCA94720USA
| | - Junxiang Zhao
- Department of Electrical and Computer EngineeringUniversity of CaliforniaSan Diego, 9500 Gilman DriveLa JollaCA92093USA
| | - Shilong Li
- Department of Electrical and Computer EngineeringUniversity of CaliforniaSan Diego, 9500 Gilman DriveLa JollaCA92093USA
| | - Steven Edward Bopp
- Materials Science and EngineeringUniversity of CaliforniaSan Diego, 9500 Gilman DriveLa JollaCA92093USA
| | | | - Jeongho Ha
- Department of Electrical and Computer EngineeringUniversity of CaliforniaSan Diego, 9500 Gilman DriveLa JollaCA92093USA
| | - Chengyu Song
- National Center for Electron MicroscopyThe Molecular FoundryOne Cyclotron RoadBerkeleyCA94720USA
| | - Jin Zhang
- Department of PharmacologyUniversity of CaliforniaSan Diego, 9500 Gilman DriveLa JollaCA92093USA
| | - Sui Yang
- Materials Science and Engineering, School for Engineering of Matter Transport and EnergyArizona State UniversityTempeAZ85287USA
| | - Xiang Zhang
- Department of Mechanical EngineeringUniversity of CaliforniaBerkeleyCA94720USA
| | - Zhaowei Liu
- Department of Electrical and Computer EngineeringUniversity of CaliforniaSan Diego, 9500 Gilman DriveLa JollaCA92093USA
- Materials Science and EngineeringUniversity of CaliforniaSan Diego, 9500 Gilman DriveLa JollaCA92093USA
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16
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Tank RG, Lund VA, Kumar S, Turner RD, Lafage L, Pasquina Lemonche L, Bullough PA, Cadby A, Foster SJ, Hobbs JK. Correlative Super-Resolution Optical and Atomic Force Microscopy Reveals Relationships Between Bacterial Cell Wall Architecture and Synthesis in Bacillus subtilis. ACS Nano 2021; 15:16011-16018. [PMID: 34533301 PMCID: PMC8552488 DOI: 10.1021/acsnano.1c04375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Indexed: 06/13/2023]
Abstract
Understanding how bacteria grow and divide requires insight into both the molecular-level dynamics of ultrastructure and the chemistry of the constituent components. Atomic force microscopy (AFM) can provide near molecular resolution images of biological systems but typically provides limited chemical information. Conversely, while super-resolution optical microscopy allows localization of particular molecules and chemistries, information on the molecular context is difficult to obtain. Here, we combine these approaches into STORMForce (stochastic optical reconstruction with atomic force microscopy) and the complementary SIMForce (structured illumination with atomic force microscopy), to map the synthesis of the bacterial cell wall structural macromolecule, peptidoglycan, during growth and division in the rod-shaped bacterium Bacillus subtilis. Using "clickable" d-amino acid incorporation, we fluorescently label and spatially localize a short and controlled period of peptidoglycan synthesis and correlate this information with high-resolution AFM of the resulting architecture. During division, septal synthesis occurs across its developing surface, suggesting a two-stage process with incorporation at the leading edge and with considerable in-filling behind. During growth, the elongation of the rod occurs through bands of synthesis, spaced by ∼300 nm, and corresponds to denser regions of the internal cell wall as revealed by AFM. Combining super-resolution optics and AFM can provide insights into the synthesis processes that produce the complex architectures of bacterial structural biopolymers.
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Affiliation(s)
- Raveen
K. G. Tank
- Department
of Physics and Astronomy, University of
Sheffield, Sheffield S3 7RH, United Kingdom
| | - Victoria A. Lund
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Sandip Kumar
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Robert D. Turner
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
- Department
of Computer Science, University of Sheffield, Sheffield, S1 4DP, United Kingdom
| | - Lucia Lafage
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Laia Pasquina Lemonche
- Department
of Physics and Astronomy, University of
Sheffield, Sheffield S3 7RH, United Kingdom
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Per A. Bullough
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Ashley Cadby
- Department
of Physics and Astronomy, University of
Sheffield, Sheffield S3 7RH, United Kingdom
| | - Simon J. Foster
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Jamie K. Hobbs
- Department
of Physics and Astronomy, University of
Sheffield, Sheffield S3 7RH, United Kingdom
- The
Florey Institute for Host−Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, United Kingdom
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17
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Liu Z, Luo Z, Chen H, Yin A, Sun H, Zhuang Z, Chen T. Optical section structured illumination-based Förster resonance energy transfer imaging. Cytometry A 2021; 101:264-272. [PMID: 34490985 DOI: 10.1002/cyto.a.24500] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/11/2021] [Accepted: 08/31/2021] [Indexed: 01/04/2023]
Abstract
Förster resonance energy transfer (FRET) microscopy is an important tool suitable for studying molecular interactions in living cells. Optical section structured illumination microscopy (OS-SIM), like confocal microscopy, has about 200 nm spatial resolution. In this report, we performed quantitative 3-cube FRET imaging in OS-SIM mode and widefield microscopy (WF) mode, respectively, for living cells expressing FRET constructs consisting of Cerulean (C, donor) and Venus (V, acceptor). OS-SIM images exhibited higher resolution than WF images. Four spectral crosstalk coefficients measured under OS-SIM mode are consistent with those measured under WF mode. Similarly, the system calibration factors G and k measured under OS-SIM mode were consistent with those measured under WF mode. The measured FRET efficiency (E) values of C32V and C17V as well as C5V constructs, standard FRET plasmids, in living Hela cells were E C 32 V OSF = 0.32 ± 0.02 , E C 17 V OSF = 0.38 ± 0.02 , and E C 5 V OSF = 0.45 ± 0.03 , and the measured acceptor-to-donor concentration ratios ( R c ) were R C 32 V OSF = 1.07 ± 0.03 , R C 17 V OSF = 1.09 ± 0.03 , and R C 5 V OSF = 1.02 ± 0.04 , consistent with the reported values. Collectively, our data demonstrates that OS-SIM can be integrated into FRET microscopy to build an OS-SIM-FRET with confocal microscopy-like resolution.
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Affiliation(s)
- Zhi Liu
- Key Laboratory of Laser Life Science, Ministry of Education, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
| | - Zewei Luo
- Key Laboratory of Laser Life Science, Ministry of Education, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
| | - Hongce Chen
- Key Laboratory of Laser Life Science, Ministry of Education, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
| | - Ao Yin
- Key Laboratory of Laser Life Science, Ministry of Education, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
| | - Han Sun
- Key Laboratory of Laser Life Science, Ministry of Education, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
| | - Zhengfei Zhuang
- Key Laboratory of Laser Life Science, Ministry of Education, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China.,SCNU Qingyuan Institute of Science and Technology Innovation Co., Ltd., South China Normal University, Qingyuan, China
| | - Tongsheng Chen
- Key Laboratory of Laser Life Science, Ministry of Education, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China.,SCNU Qingyuan Institute of Science and Technology Innovation Co., Ltd., South China Normal University, Qingyuan, China
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18
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Abstract
Super-resolution (diffraction unlimited) microscopy was developed 15 years ago; the developers were awarded the Nobel Prize in Chemistry in recognition of their work in 2014. Super-resolution microscopy is increasingly being applied to diverse scientific fields, from single molecules to cell organelles, viruses, bacteria, plants, and animals, especially the mammalian model organism Mus musculus. In this review, we explain how super-resolution microscopy, along with fluorescence microscopy from which it grew, has aided the renaissance of the light microscope. We cover experiment planning and specimen preparation and explain structured illumination microscopy, super-resolution radial fluctuations, stimulated emission depletion microscopy, single-molecule localization microscopy, and super-resolution imaging by pixel reassignment. The final section of this review discusses the strengths and weaknesses of each super-resolution technique and how to choose the best approach for your research. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Jessica Valli
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
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19
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Hou X, Nozumi M, Nakamura H, Igarashi M, Sugiyama S. Coactosin Promotes F-Actin Protrusion in Growth Cones Under Cofilin-Related Signaling Pathway. Front Cell Dev Biol 2021; 9:660349. [PMID: 34235144 PMCID: PMC8256272 DOI: 10.3389/fcell.2021.660349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/31/2021] [Indexed: 12/03/2022] Open
Abstract
During brain development, axon outgrowth and its subsequent pathfinding are reliant on a highly motile growth cone located at the tip of the axon. Actin polymerization that is regulated by actin-depolymerizing factors homology (ADF-H) domain-containing family drives the formation of lamellipodia and filopodia at the leading edge of growth cones for axon guidance. However, the precise localization and function of ADF-H domain-containing proteins involved in axon extension and retraction remain unclear. We have previously shown that transcripts and proteins of coactosin-like protein 1 (COTL1), an ADF-H domain-containing protein, are observed in neurites and axons in chick embryos. Coactosin overexpression analysis revealed that this protein was localized to axonal growth cones and involved in axon extension in the midbrain. We further examined the specific distribution of coactosin and cofilin within the growth cone using superresolution microscopy, structured illumination microscopy, which overcomes the optical diffraction limitation and is suitable to the analysis of cellular dynamic movements. We found that coactosin was tightly associated with F-actin bundles at the growth cones and that coactosin overexpression promoted the expansion of lamellipodia and extension of growth cones. Coactosin knockdown in oculomotor neurons resulted in an increase in the levels of the inactive, phosphorylated form of cofilin and dysregulation of actin polymerization and axonal elongation, which suggests that coactosin promoted axonal growth in a cofilin-dependent manner. Indeed, the application of a dominant-negative form of LIMK1, a downstream effector of GTPases, reversed the effect of coactosin knockdown on axonal growth by enhancing cofilin activity. Combined, our results indicate that coactosin functions promote the assembly of protrusive actin filament arrays at the leading edge for growth cone motility.
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Affiliation(s)
- Xubin Hou
- Laboratory of Neuronal Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.,Department of Molecular Neurobiology, Graduate School of Life Sciences, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Motohiro Nozumi
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Harukazu Nakamura
- Department of Molecular Neurobiology, Graduate School of Life Sciences, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Michihiro Igarashi
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Sayaka Sugiyama
- Laboratory of Neuronal Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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20
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Prakash K, Diederich B, Reichelt S, Heintzmann R, Schermelleh L. Super-resolution structured illumination microscopy: past, present and future. Philos Trans A Math Phys Eng Sci 2021; 379:20200143. [PMID: 33896205 PMCID: PMC8366908 DOI: 10.1098/rsta.2020.0143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Structured illumination microscopy (SIM) has emerged as an essential technique for three-dimensional (3D) and live-cell super-resolution imaging. However, to date, there has not been a dedicated workshop or journal issue covering the various aspects of SIM, from bespoke hardware and software development and the use of commercial instruments to biological applications. This special issue aims to recap recent developments as well as outline future trends. In addition to SIM, we cover related topics such as complementary super-resolution microscopy techniques, computational imaging, visualization and image processing methods. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.
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Affiliation(s)
- Kirti Prakash
- National Physical Laboratory, TW11 0LW Teddington, UK
- Department of Paediatrics, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Benedict Diederich
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, Jena, Germany
| | - Stefanie Reichelt
- CRUK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE, UK
| | - Rainer Heintzmann
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, Jena, Germany
- Faculty of Physics and Astronomy, Friedrich-Schiller-University, Jena, Germany
| | - Lothar Schermelleh
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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21
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Mo Y, Feng F, Mao H, Fan J, Chen L. Structured illumination microscopy artefacts caused by illumination scattering. Philos Trans A Math Phys Eng Sci 2021; 379:20200153. [PMID: 33896197 DOI: 10.1098/rsta.2020.0153] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/03/2020] [Indexed: 05/19/2023]
Abstract
Despite its wide application in live-cell super-resolution (SR) imaging, structured illumination microscopy (SIM) suffers from aberrations caused by various sources. Although artefacts generated from inaccurate reconstruction parameter estimation and noise amplification can be minimized, aberrations due to the scattering of excitation light on samples have rarely been investigated. In this paper, by simulating multiple subcellular structure with the distinct refractive index from water, we study how different thicknesses of this subcellular structure scatter incident light on its optical path of SIM excitation. Because aberrant interference light aggravates with the increase in sample thickness, the reconstruction of the 2D-SIM SR image degraded with the change of focus along the axial axis. Therefore, this work may guide the future development of algorithms to suppress SIM artefacts caused by scattering in thick samples. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.
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Affiliation(s)
- Yanquan Mo
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, School of Future Technology, Peking University, Beijing 100871, People's Republic of China
| | - Fan Feng
- Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Heng Mao
- School of Mathematical Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Junchao Fan
- Chongqing Key Laboratory of Image Cognition, College of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing 400065, People's Republic of China
| | - Liangyi Chen
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, School of Future Technology, Peking University, Beijing 100871, People's Republic of China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, People's Republic of China
- Beijing Academy of Artificial Intelligence, Beijing 100871, People's Republic of China
- Shenzhen Bay Laboratory, Shenzhen 518055, People's Republic of China
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22
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Gong H, Guo W, Neil MAA. GPU-accelerated real-time reconstruction in Python of three-dimensional datasets from structured illumination microscopy with hexagonal patterns. Philos Trans A Math Phys Eng Sci 2021; 379:20200162. [PMID: 33896199 PMCID: PMC8072201 DOI: 10.1098/rsta.2020.0162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We present a structured illumination microscopy system that projects a hexagonal pattern by the interference among three coherent beams, suitable for implementation in a light-sheet geometry. Seven images acquired as the illumination pattern is shifted laterally can be processed to produce a super-resolved image that surpasses the diffraction-limited resolution by a factor of over 2 in an exemplar light-sheet arrangement. Three methods of processing data are discussed depending on whether the raw images are available in groups of seven, individually in a stream or as a larger batch representing a three-dimensional stack. We show that imaging axially moving samples can introduce artefacts, visible as fine structures in the processed images. However, these artefacts are easily removed by a filtering operation carried out as part of the batch processing algorithm for three-dimensional stacks. The reconstruction algorithms implemented in Python include specific optimizations for calculation on a graphics processing unit and we demonstrate its operation on experimental data of static objects and on simulated data of moving objects. We show that the software can process over 239 input raw frames per second at 512 × 512 pixels, generating over 34 super-resolved frames per second at 1024 × 1024 pixels. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.
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Affiliation(s)
- Hai Gong
- Department of Physics, Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2AZ, UK
| | - Wenjun Guo
- Department of Physics, Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2AZ, UK
| | - Mark A. A. Neil
- Department of Physics, Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2AZ, UK
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Sheppard CJR. Structured illumination microscopy and image scanning microscopy: a review and comparison of imaging properties. Philos Trans A Math Phys Eng Sci 2021; 379:20200154. [PMID: 33896206 DOI: 10.1098/rsta.2020.0154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/10/2020] [Indexed: 05/19/2023]
Abstract
Structured illumination microscopy and image scanning microscopy are two microscopical tech- niques, rapidly increasing in practical application, that can result in improvement in transverse spatial resolution, and/or improvement in axial imaging performance. The history and principles of these techniques are reviewed, and the imaging properties of the two methods compared. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.
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MESH Headings
- Animals
- Humans
- Image Processing, Computer-Assisted/methods
- Image Processing, Computer-Assisted/statistics & numerical data
- Imaging, Three-Dimensional/methods
- Imaging, Three-Dimensional/statistics & numerical data
- Light
- Microscopy, Confocal/methods
- Microscopy, Confocal/statistics & numerical data
- Microscopy, Fluorescence/methods
- Microscopy, Fluorescence/statistics & numerical data
- Microscopy, Fluorescence, Multiphoton/methods
- Microscopy, Fluorescence, Multiphoton/statistics & numerical data
- Optical Phenomena
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Affiliation(s)
- Colin J R Sheppard
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83 Edificio B, 16152 Genova, Italy
- Molecular Horizons, School of Chemistry and Molecular Biology, University of Wollongong, Wollongong 2522, New South Wales, Australia
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Abstract
This article presents answers to the questions on superresolution and structured illumination microscopy (SIM) as raised in the editorial of this collection of articles (https://doi.org/10.1098/rsta.2020.0143). These answers are based on my personal views on superresolution in light microscopy, supported by reasoning. Discussed are the definition of superresolution, Abbe's resolution limit and the classification of superresolution methods into nonlinear-, prior knowledge- and near-field-based superresolution. A further focus is put on the capabilities and technical aspects of present and future SIM methods. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.
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Affiliation(s)
- Rainer Heintzmann
- Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, Jena, Germany
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Korobchevskaya K, Colin-York H, Barbieri L, Fritzsche M. Extended mechanical force measurements using structured illumination microscopy. Philos Trans A Math Phys Eng Sci 2021; 379:20200151. [PMID: 33896200 PMCID: PMC7612033 DOI: 10.1098/rsta.2020.0151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Quantifying cell generated mechanical forces is key to furthering our understanding of mechanobiology. Traction force microscopy (TFM) is one of the most broadly applied force probing technologies, but its sensitivity is strictly dependent on the spatio-temporal resolution of the underlying imaging system. In previous works, it was demonstrated that increased sampling densities of cell derived forces permitted by super-resolution fluorescence imaging enhanced the sensitivity of the TFM method. However, these recent advances to TFM based on super-resolution techniques were limited to slow acquisition speeds and high illumination powers. Here, we present three novel TFM approaches that, in combination with total internal reflection, structured illumination microscopy and astigmatism, improve the spatial and temporal performance in either two-dimensional or three-dimensional mechanical force quantification, while maintaining low illumination powers. These three techniques can be straightforwardly implemented on a single optical set-up offering a powerful platform to provide new insights into the physiological force generation in a wide range of biological studies. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.
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Affiliation(s)
- Kseniya Korobchevskaya
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom
| | - Huw Colin-York
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom
| | - Liliana Barbieri
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford. OX3 9DS, United Kingdom
| | - Marco Fritzsche
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford. OX3 9DS, United Kingdom
- Rosalind Franklin Institute, Harwell Campus, Didcot, OX11 0FA, United Kingdom
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Russell CT, Shaw M. mmSIM: an open toolbox for accessible structured illumination microscopy. Philos Trans A Math Phys Eng Sci 2021; 379:20200353. [PMID: 33896202 DOI: 10.1098/rsta.2020.0353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/12/2021] [Indexed: 05/19/2023]
Abstract
Since the first practical super-resolution structured illumination fluorescence microscopes (SIM) were demonstrated more than two decades ago, the method has become increasingly popular for a wide range of bioimaging applications. The high cost and relative inflexibility of commercial systems, coupled with the conceptual simplicity of the approach and the desire to exploit and customize existing hardware, have led to the development of a large number of home-built systems. Several detailed hardware designs are available in the scientific literature, complemented by open-source software tools for SIM image validation and reconstruction. However, there remains a lack of simple open-source software to control these systems and manage the synchronization between hardware components, which is critical for effective SIM imaging. This article describes a new suite of software tools based on the popular Micro-Manager package, which enable the keen microscopist to develop and run a SIM system. We use the software to control two custom-built, high-speed, spatial light modulator-based SIM systems, evaluating their performance by imaging a range of fluorescent samples. By simplifying the process of SIM hardware development, we aim to support wider adoption of the technique. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.
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Affiliation(s)
- Craig T Russell
- EBI, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Michael Shaw
- Biometrology Group, National Physical Laboratory, Teddington TW11 OLW, UK
- Department of Computer Science, Faculty of Engineering Sciences, University College London, London WC1E 6BT, UK
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Pilger C, Pospíšil J, Müller M, Ruoff M, Schütte M, Spiecker H, Huser T. Super-resolution fluorescence microscopy by line-scanning with an unmodified two-photon microscope. Philos Trans A Math Phys Eng Sci 2021; 379:20200300. [PMID: 33896201 PMCID: PMC8072199 DOI: 10.1098/rsta.2020.0300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/20/2020] [Indexed: 05/19/2023]
Abstract
Fluorescence-based microscopy as one of the standard tools in biomedical research benefits more and more from super-resolution methods, which offer enhanced spatial resolution allowing insights into new biological processes. A typical drawback of using these methods is the need for new, complex optical set-ups. This becomes even more significant when using two-photon fluorescence excitation, which offers deep tissue imaging and excellent z-sectioning. We show that the generation of striped-illumination patterns in two-photon laser scanning microscopy can readily be exploited for achieving optical super-resolution and contrast enhancement using open-source image reconstruction software. The special appeal of this approach is that even in the case of a commercial two-photon laser scanning microscope no optomechanical modifications are required to achieve this modality. Modifying the scanning software with a custom-written macro to address the scanning mirrors in combination with rapid intensity switching by an electro-optic modulator is sufficient to accomplish the acquisition of two-photon striped-illumination patterns on an sCMOS camera. We demonstrate and analyse the resulting resolution improvement by applying different recently published image resolution evaluation procedures to the reconstructed filtered widefield and super-resolved images. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.
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Affiliation(s)
- Christian Pilger
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Jakub Pospíšil
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
- Department of Radioelectronics, Faculty of Electrical Engineering, Czech Technical University in Prague, Technická 2, 166 27 Prague 6, Czech Republic
| | - Marcel Müller
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Martin Ruoff
- LaVision BioTec GmbH, Astastraße 14, 33617 Bielefeld, Germany
| | - Martin Schütte
- LaVision BioTec GmbH, Astastraße 14, 33617 Bielefeld, Germany
| | | | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
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Lachetta M, Sandmeyer H, Sandmeyer A, Esch JSA, Huser T, Müller M. Simulating digital micromirror devices for patterning coherent excitation light in structured illumination microscopy. Philos Trans A Math Phys Eng Sci 2021; 379:20200147. [PMID: 33896207 PMCID: PMC8072202 DOI: 10.1098/rsta.2020.0147] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Digital micromirror devices (DMDs) are spatial light modulators that employ the electro-mechanical movement of miniaturized mirrors to steer and thus modulate the light reflected off a mirror array. Their wide availability, low cost and high speed make them a popular choice both in consumer electronics such as video projectors, and scientific applications such as microscopy. High-end fluorescence microscopy systems typically employ laser light sources, which by their nature provide coherent excitation light. In super-resolution microscopy applications that use light modulation, most notably structured illumination microscopy (SIM), the coherent nature of the excitation light becomes a requirement to achieve optimal interference pattern contrast. The universal combination of DMDs and coherent light sources, especially when working with multiple different wavelengths, is unfortunately not straight forward. The substructure of the tilted micromirror array gives rise to a blazed grating, which has to be understood and which must be taken into account when designing a DMD-based illumination system. Here, we present a set of simulation frameworks that explore the use of DMDs in conjunction with coherent light sources, motivated by their application in SIM, but which are generalizable to other light patterning applications. This framework provides all the tools to explore and compute DMD-based diffraction effects and to simulate possible system alignment configurations computationally, which simplifies the system design process and provides guidance for setting up DMD-based microscopes. This article is part of the Theo Murphy meeting 'Super-resolution structured illumination microscopy (part 1)'.
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Affiliation(s)
- Mario Lachetta
- Biomolecular Photonics, Faculty of Physics, Bielefeld University, Universitätsstraße 25, 33501 Bielefeld, Germany
- Department of General and Visceral Surgery, Evangelisches Klinikum Bethel GmbH, University Hospital OWL of Bielefeld University, Campus Bielefeld-Bethel, Bielefeld, Germany
| | - Hauke Sandmeyer
- Numerical Simulations and Field Theory, Faculty of Physics, Bielefeld University, Universitätsstraße 25, 33501 Bielefeld, Germany
| | - Alice Sandmeyer
- Biomolecular Photonics, Faculty of Physics, Bielefeld University, Universitätsstraße 25, 33501 Bielefeld, Germany
| | - Jan Schulte am Esch
- Department of General and Visceral Surgery, Evangelisches Klinikum Bethel GmbH, University Hospital OWL of Bielefeld University, Campus Bielefeld-Bethel, Bielefeld, Germany
| | - Thomas Huser
- Biomolecular Photonics, Faculty of Physics, Bielefeld University, Universitätsstraße 25, 33501 Bielefeld, Germany
| | - Marcel Müller
- Biomolecular Photonics, Faculty of Physics, Bielefeld University, Universitätsstraße 25, 33501 Bielefeld, Germany
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Yoon S, Parnell E, Penzes P. TGF-β-Induced Phosphorylation of Usp9X Stabilizes Ankyrin-G and Regulates Dendritic Spine Development and Maintenance. Cell Rep 2021; 31:107685. [PMID: 32460012 PMCID: PMC7324065 DOI: 10.1016/j.celrep.2020.107685] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/02/2020] [Accepted: 05/04/2020] [Indexed: 12/30/2022] Open
Abstract
Signaling by the cytokine transforming growth factor β (TGF-β) has been implicated in a multitude of biological functions; however, TGF-β signaling, particularly in the CNS, remains largely unexplored. ANK3 variants (encoding ankyrin-G) are associated with bipolar disorder, intellectual disability, and autism spectrum disorder, while mutations in USP9X, which encodes a deubiquitinase, are associated with X-linked intellectual disability and autism in humans. Here, we show that TGF-β signaling promotes Usp9X phosphorylation, which enhances its interaction with ankyrin-G and stabilizes ankyrin-G in spines, leading to spine enlargement. Using in situ proximity ligation combined with structured illumination superresolution microscopy, we characterize the postsynaptic spatial organization of phosphorylation-dependent regulation of Usp9X/ankyrin-G interactions in dendrites and its quantitative relationship with spine morphology and number. These data reveal a cytokine-mediated mechanism regulating protein stability in spines and suggest a role for deubiquitination and TGF-β signaling in neurodevelopmental disorder pathogenesis and treatment. Yoon et al. show that phosphorylation of a deubiquitinating enzyme by a cytokine enhances the stabilization of synaptic scaffolding protein during dendritic spine development, and its alterations result in deficient synaptic structural maintenance, with relevance for neurodevelopmental disorders.
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Affiliation(s)
- Sehyoun Yoon
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Euan Parnell
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Peter Penzes
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Northwestern University, Center for Autism and Neurodevelopment, Chicago, IL 60611, USA.
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Matsumoto A, Matsui I, Katsuma Y, Yasuda S, Shimada K, Namba-Hamano T, Sakaguchi Y, Kaimori JY, Takabatake Y, Inoue K, Isaka Y. Quantitative Analyses of Foot Processes, Mitochondria, and Basement Membranes by Structured Illumination Microscopy Using Elastica-Masson- and Periodic-Acid-Schiff-Stained Kidney Sections. Kidney Int Rep 2021; 6:1923-1938. [PMID: 34307987 PMCID: PMC8258503 DOI: 10.1016/j.ekir.2021.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 04/16/2021] [Indexed: 11/28/2022] Open
Abstract
Introduction Foot process effacement and mitochondrial fission associate with kidney disease pathogenesis. Electron microscopy is the gold-standard method for their visualization, but the observable area of electron microscopy is smaller than light microscopy. It is important to develop alternative ways to quantitatively evaluate these microstructural changes because the lesion site of renal diseases can be focal. Methods We analyzed elastica-Masson trichrome (EMT) and periodic acid-Schiff (PAS) stained kidney sections using structured illumination microscopy (SIM). Results EMT staining revealed three-dimensional (3D) structures of foot process, whereas ponceau xylidine acid fuchsin azophloxine solution induced fluorescence. Conversion of foot process images into their constituent frequencies by Fourier transform showed that the concentric square of (1/4)2-(1/16)2 in the power spectra (PS) included information for normal periodic structures of foot processes. Foot process integrity, assessed by PS, negatively correlated with proteinuria. EMT-stained sections revealed fragmented mitochondria in mice with mitochondrial injuries and patients with tubulointerstitial nephritis; Fourier transform quantified associated mitochondrial injury. Quantified mitochondrial damage in patients with immunoglobulin A (IgA) nephropathy predicted a decline in estimated glomerular filtration rate (eGFR) after kidney biopsy but did not correlate with eGFR at biopsy. PAS-stained sections, excited by a 640 nm laser, combined with the coefficient of variation values, quantified subtle changes in the basement membranes of patients with membranous nephropathy stage I. Conclusions Kidney microstructures are quantified from sections prepared in clinical practice using SIM.
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Affiliation(s)
- Ayumi Matsumoto
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Isao Matsui
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yusuke Katsuma
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Seiichi Yasuda
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Karin Shimada
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Tomoko Namba-Hamano
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yusuke Sakaguchi
- Department of Inter-Organ Communication Research in Kidney Disease, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Jun-Ya Kaimori
- Department of Inter-Organ Communication Research in Kidney Disease, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshitsugu Takabatake
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kazunori Inoue
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshitaka Isaka
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
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Park HM, Joo KN. Motionless Polarizing Structured Illumination Microscopy. Sensors (Basel) 2021; 21:2837. [PMID: 33920615 DOI: 10.3390/s21082837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 11/17/2022]
Abstract
In this investigation, we propose a motionless polarizing structured illumination microscopy as an axially sectioning and reflective-type device to measure the 3D surface profiles of specimens. Based on the spatial phase-shifting technique to obtain the visibility of the illumination pattern. Instead of using a grid, a Wollaston prism is used to generate the light pattern by the stable interference of two beams. As the polarization states of two beams are orthogonal with each other, a polarization pixelated CMOS camera can simultaneously obtain four phase-shifted patterns with the beams after passing through a quarter wave plate based on the spatial phase-shifting technique with polarization. In addition, a focus tunable lens is used to eliminate a mechanical moving part for the axial scanning of the specimen. In the experimental result, a step height sample and a concave mirror were measured with 0.05 µm and 0.2 mm repeatabilities of step height and the radius of curvature, respectively.
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Yang G, Li L, Liu Y, Liang K, Wei L, Chen L. Hyperglycemia-Induced Dysregulated Fusion Intermediates in Insulin-Secreting Cells Visualized by Super-Resolution Microscopy. Front Cell Dev Biol 2021; 9:650167. [PMID: 33937248 PMCID: PMC8083903 DOI: 10.3389/fcell.2021.650167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/15/2021] [Indexed: 11/23/2022] Open
Abstract
Impaired insulin release is a hallmark of type 2 diabetes and is closely related to chronically elevated glucose concentrations, known as “glucotoxicity.” However, the molecular mechanisms by which glucotoxicity impairs insulin secretion remain poorly understood. In addition to known kiss-and-run and kiss-and-stay fusion events in INS-1 cells, ultrafast Hessian structured illumination microscopy (Hessian SIM) enables full fusion to be categorized according to the newly identified structures, such as ring fusion (those with enlarged pores) or dot fusion (those without apparent pores). In addition, we identified four fusion intermediates during insulin exocytosis: initial pore opening, vesicle collapse, enlarged pore formation, and final pore dilation. Long-term incubation in supraphysiological doses of glucose reduced exocytosis in general and increased the occurrence of kiss-and-run events at the expense of reduced full fusion. In addition, hyperglycemia delayed pore opening, vesicle collapse, and enlarged pore formation in full fusion events. It also reduced the size of apparently enlarged pores, all of which contributed to the compromised insulin secretion. These phenotypes were mostly due to the hyperglycemia-induced reduction in syntaxin-1A (Stx-1A) and SNAP-25 protein, since they could be recapitulated by the knockdown of endogenous Stx-1A and SNAP-25. These findings suggest essential roles for the vesicle fusion type and intermediates in regulating insulin secretion from pancreatic beta cells in normal and disease conditions.
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Affiliation(s)
- Guoyi Yang
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, School of Future Technology, Peking University, Beijing, China
| | - Liuju Li
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, School of Future Technology, Peking University, Beijing, China
| | - Yanmei Liu
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, School of Future Technology, Peking University, Beijing, China.,Institute for Brain Research and Rehabilitation, Key Laboratory of Brain, Cognition and Education Science, South China Normal University, Guangzhou, China
| | - Kuo Liang
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Lisi Wei
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, School of Future Technology, Peking University, Beijing, China
| | - Liangyi Chen
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, School of Future Technology, Peking University, Beijing, China.,PKU-IDG/McGovern Institute for Brain Research, Beijing, China.,Beijing Academy of Artificial Intelligence, Beijing, China.,Shenzhen Bay Laboratory, Shenzhen, China
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Wanuske M, Brantschen D, Schinner C, Stüdle C, Walter E, Hiermaier M, Vielmuth F, Waschke J, Spindler V. Clustering of desmosomal cadherins by desmoplakin is essential for cell-cell adhesion. Acta Physiol (Oxf) 2021; 231:e13609. [PMID: 33354837 DOI: 10.1111/apha.13609] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/19/2020] [Accepted: 12/20/2020] [Indexed: 12/14/2022]
Abstract
AIM Desmoplakin (Dp) is a crucial component of the desmosome, a supramolecular cell junction complex anchoring intermediate filaments. The mechanisms how Dp modulates cell-cell adhesion are only partially understood. Here, we studied the impact of Dp on the function of desmosomal adhesion molecules, desmosome turnover and intercellular adhesion. METHODS CRISPR/Cas9 was used for gene editing of human keratinocytes which were characterized by Western blot and immunostaining. Desmosomal ultrastructure and function were assessed by electron microscopy and cell adhesion assays. Single molecule binding properties and localization of desmosomal cadherins were studied by atomic force microscopy and super-resolution imaging. RESULTS Knockout (ko) of Dp impaired cell cohesion to drastically higher extents as ko of another desmosomal protein, plakoglobin (Pg). In contrast to Pg ko, desmosomes were completely absent in Dp ko. Binding properties of the desmosomal adhesion molecules desmocollin (Dsc) 3 and desmoglein (Dsg) 3 remained unaltered under loss of Dp. Dp was required for assembling desmosomal cadherins into large clusters, as Dsg2 and Dsc3, adhesion molecules primarily localized within desmosomes, were redistributed into small puncta in the cell membrane of Dp ko cells. Additional silencing of desmosomal cadherins in Dp ko did not further increase loss of intercellular adhesion. CONCLUSION Our data demonstrate that Dp is essential for desmosome formation but does not influence intercellular adhesion on the level of individual cadherin binding properties. Rather, macro-clustering of desmosomal adhesion molecules through Dp is crucial. These results may help to better understand severe diseases which are caused by Dp dysfunction.
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Affiliation(s)
- Marie‐Therès Wanuske
- Department of Biomedicine University of Basel Basel Switzerland
- Faculty of Medicine Ludwig‐Maximilians‐Universität Munich Munich Germany
| | | | - Camilla Schinner
- Department of Biomedicine University of Basel Basel Switzerland
- Faculty of Medicine Ludwig‐Maximilians‐Universität Munich Munich Germany
| | - Chiara Stüdle
- Department of Biomedicine University of Basel Basel Switzerland
| | - Elias Walter
- Faculty of Medicine Ludwig‐Maximilians‐Universität Munich Munich Germany
| | - Matthias Hiermaier
- Department of Biomedicine University of Basel Basel Switzerland
- Faculty of Medicine Ludwig‐Maximilians‐Universität Munich Munich Germany
| | - Franziska Vielmuth
- Faculty of Medicine Ludwig‐Maximilians‐Universität Munich Munich Germany
| | - Jens Waschke
- Faculty of Medicine Ludwig‐Maximilians‐Universität Munich Munich Germany
| | - Volker Spindler
- Department of Biomedicine University of Basel Basel Switzerland
- Faculty of Medicine Ludwig‐Maximilians‐Universität Munich Munich Germany
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Liu W, Luque M, Li H, Schrott-Fischer A, Glueckert R, Tylstedt S, Rajan G, Ladak H, Agrawal S, Rask-Andersen H. Spike Generators and Cell Signaling in the Human Auditory Nerve: An Ultrastructural, Super-Resolution, and Gene Hybridization Study. Front Cell Neurosci 2021; 15:642211. [PMID: 33796009 PMCID: PMC8008129 DOI: 10.3389/fncel.2021.642211] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/22/2021] [Indexed: 11/23/2022] Open
Abstract
Background: The human auditory nerve contains 30,000 nerve fibers (NFs) that relay complex speech information to the brain with spectacular acuity. How speech is coded and influenced by various conditions is not known. It is also uncertain whether human nerve signaling involves exclusive proteins and gene manifestations compared with that of other species. Such information is difficult to determine due to the vulnerable, "esoteric," and encapsulated human ear surrounded by the hardest bone in the body. We collected human inner ear material for nanoscale visualization combining transmission electron microscopy (TEM), super-resolution structured illumination microscopy (SR-SIM), and RNA-scope analysis for the first time. Our aim was to gain information about the molecular instruments in human auditory nerve processing and deviations, and ways to perform electric modeling of prosthetic devices. Material and Methods: Human tissue was collected during trans-cochlear procedures to remove petro-clival meningioma after ethical permission. Cochlear neurons were processed for electron microscopy, confocal microscopy (CM), SR-SIM, and high-sensitive in situ hybridization for labeling single mRNA transcripts to detect ion channel and transporter proteins associated with nerve signal initiation and conductance. Results: Transport proteins and RNA transcripts were localized at the subcellular level. Hemi-nodal proteins were identified beneath the inner hair cells (IHCs). Voltage-gated ion channels (VGICs) were expressed in the spiral ganglion (SG) and axonal initial segments (AISs). Nodes of Ranvier (NR) expressed Nav1.6 proteins, and encoding genes critical for inter-cellular coupling were disclosed. Discussion: Our results suggest that initial spike generators are located beneath the IHCs in humans. The first NRs appear at different places. Additional spike generators and transcellular communication may boost, sharpen, and synchronize afferent signals by cell clusters at different frequency bands. These instruments may be essential for the filtering of complex sounds and may be challenged by various pathological conditions.
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Affiliation(s)
- Wei Liu
- Section of Otolaryngology, Department of Surgical Sciences, Head and Neck Surgery, Uppsala University Hospital, Uppsala, Sweden
| | - Maria Luque
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | - Hao Li
- Section of Otolaryngology, Department of Surgical Sciences, Head and Neck Surgery, Uppsala University Hospital, Uppsala, Sweden
| | | | - Rudolf Glueckert
- Department of Otorhinolaryngology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sven Tylstedt
- Department of Olaryngology, Västerviks Hospital, Västervik, Sweden
| | - Gunesh Rajan
- Department of Otolaryngology, Head & Neck Surgery, Luzerner Kantonsspital, Luzern, Switzerland
- Department of Otolaryngology, Head & Neck Surgery, Division of Surgery, Medical School, University of Western Australia, Perth, WA, Australia
| | - Hanif Ladak
- Department of Otolaryngology-Head and Neck Surgery, Department of Medical Biophysics and Department of Electrical and Computer Engineering, Western University, London, ON, Canada
| | - Sumit Agrawal
- Department of Otolaryngology-Head and Neck Surgery, Western University, London, ON, Canada
| | - Helge Rask-Andersen
- Section of Otolaryngology, Department of Surgical Sciences, Head and Neck Surgery, Uppsala University Hospital, Uppsala, Sweden
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Okabe S. Recent advances in computational methods for measurement of dendritic spines imaged by light microscopy. Microscopy (Oxf) 2021; 69:196-213. [PMID: 32244257 DOI: 10.1093/jmicro/dfaa016] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 02/04/2020] [Accepted: 03/23/2020] [Indexed: 12/13/2022] Open
Abstract
Dendritic spines are small protrusions that receive most of the excitatory inputs to the pyramidal neurons in the neocortex and the hippocampus. Excitatory neural circuits in the neocortex and hippocampus are important for experience-dependent changes in brain functions, including postnatal sensory refinement and memory formation. Several lines of evidence indicate that synaptic efficacy is correlated with spine size and structure. Hence, precise and accurate measurement of spine morphology is important for evaluation of neural circuit function and plasticity. Recent advances in light microscopy and image analysis techniques have opened the way toward a full description of spine nanostructure. In addition, large datasets of spine nanostructure can be effectively analyzed using machine learning techniques and other mathematical approaches, and recent advances in super-resolution imaging allow researchers to analyze spine structure at an unprecedented level of precision. This review summarizes computational methods that can effectively identify, segment and quantitate dendritic spines in either 2D or 3D imaging. Nanoscale analysis of spine structure and dynamics, combined with new mathematical approaches, will facilitate our understanding of spine functions in physiological and pathological conditions.
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Affiliation(s)
- Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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Cainero I, Cerutti E, Faretta M, Dellino GI, Pelicci PG, Diaspro A, Lanzanò L. Measuring Nanoscale Distances by Structured Illumination Microscopy and Image Cross-Correlation Spectroscopy (SIM-ICCS). Sensors (Basel) 2021; 21:2010. [PMID: 33809144 PMCID: PMC8001887 DOI: 10.3390/s21062010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/27/2022]
Abstract
Since the introduction of super-resolution microscopy, there has been growing interest in quantifying the nanoscale spatial distributions of fluorescent probes to better understand cellular processes and their interactions. One way to check if distributions are correlated or not is to perform colocalization analysis of multi-color acquisitions. Among all the possible methods available to study and quantify the colocalization between multicolor images, there is image cross-correlation spectroscopy (ICCS). The main advantage of ICCS, in comparison with other co-localization techniques, is that it does not require pre-segmentation of the sample into single objects. Here we show that the combination of structured illumination microscopy (SIM) with ICCS (SIM-ICCS) is a simple approach to quantify colocalization and measure nanoscale distances from multi-color SIM images. We validate the SIM-ICCS analysis on SIM images of optical nanorulers, DNA-origami-based model samples containing fluorophores of different colors at a distance of 80 nm. The SIM-ICCS analysis is compared with an object-based analysis performed on the same samples. Finally, we show that SIM-ICCS can be used to quantify the nanoscale spatial distribution of functional nuclear sites in fixed cells.
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Affiliation(s)
- Isotta Cainero
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152 Genoa, Italy; (I.C.); (E.C.)
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16143 Genoa, Italy
| | - Elena Cerutti
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152 Genoa, Italy; (I.C.); (E.C.)
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, Via S. Sofia 64, 95123 Catania, Italy
| | - Mario Faretta
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20100 Milan, Italy; (M.F.); (G.I.D.); (P.G.P.)
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20100 Milan, Italy; (M.F.); (G.I.D.); (P.G.P.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20100 Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20100 Milan, Italy; (M.F.); (G.I.D.); (P.G.P.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20100 Milan, Italy
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152 Genoa, Italy; (I.C.); (E.C.)
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16143 Genoa, Italy
| | - Luca Lanzanò
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152 Genoa, Italy; (I.C.); (E.C.)
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, Via S. Sofia 64, 95123 Catania, Italy
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Kubalová I, Němečková A, Weisshart K, Hřibová E, Schubert V. Comparing Super-Resolution Microscopy Techniques to Analyze Chromosomes. Int J Mol Sci 2021; 22:ijms22041903. [PMID: 33672992 PMCID: PMC7917581 DOI: 10.3390/ijms22041903] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/21/2022] Open
Abstract
The importance of fluorescence light microscopy for understanding cellular and sub-cellular structures and functions is undeniable. However, the resolution is limited by light diffraction (~200–250 nm laterally, ~500–700 nm axially). Meanwhile, super-resolution microscopy, such as structured illumination microscopy (SIM), is being applied more and more to overcome this restriction. Instead, super-resolution by stimulated emission depletion (STED) microscopy achieving a resolution of ~50 nm laterally and ~130 nm axially has not yet frequently been applied in plant cell research due to the required specific sample preparation and stable dye staining. Single-molecule localization microscopy (SMLM) including photoactivated localization microscopy (PALM) has not yet been widely used, although this nanoscopic technique allows even the detection of single molecules. In this study, we compared protein imaging within metaphase chromosomes of barley via conventional wide-field and confocal microscopy, and the sub-diffraction methods SIM, STED, and SMLM. The chromosomes were labeled by DAPI (4′,6-diamidino-2-phenylindol), a DNA-specific dye, and with antibodies against topoisomerase IIα (Topo II), a protein important for correct chromatin condensation. Compared to the diffraction-limited methods, the combination of the three different super-resolution imaging techniques delivered tremendous additional insights into the plant chromosome architecture through the achieved increased resolution.
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Affiliation(s)
- Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466 Seeland, Germany;
| | - Alžběta Němečková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic; (A.N.); (E.H.)
| | | | - Eva Hřibová
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic; (A.N.); (E.H.)
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466 Seeland, Germany;
- Correspondence: ; Tel.: +49-394-825-212
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Zheng Y, Chen J, Wu C, Gong W, Si K. Adaptive optics for structured illumination microscopy based on deep learning. Cytometry A 2021; 99:622-631. [PMID: 33543823 DOI: 10.1002/cyto.a.24319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/10/2021] [Accepted: 02/01/2021] [Indexed: 11/10/2022]
Abstract
Structured illumination microscopy (SIM) is widely used in biological imaging for its high resolution, fast imaging speed, and simple optical setup. However, when imaging thick samples, the structured illumination patterns in SIM will suffer from optical aberrations, leading to a serious deterioration in resolution. Therefore, it is necessary to reconstruct structured illumination patterns with high quality and efficiency in deep tissue imaging. Here we demonstrate an adaptive optics (AO) correction method based on deep learning in wide-field SIM imaging system. The mapping between the coefficients of the first 15 Zernike modes and their corresponding distorted patterns is established to train the convolution neural network (CNN). The results show that the optimized CNN can predict the aberration phase within ~10.1 ms with a personal computer. The correlation index between the aberration phases and their corresponding predicted aberration phase is up to 0.9986. This method is highly robust and effective for patterns with various spatial densities and illumination conditions and able to effectively correct the imaging distortion caused by optical aberration in SIM system.
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Affiliation(s)
- Yao Zheng
- Department of Neurology of the First Affiliated Hospital, State Key Laboratory of Modern Optical Instrumentation, Zhejiang University School of Medicine, Hangzhou, China.,College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Jiajia Chen
- College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Chenxue Wu
- College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Wei Gong
- Research Units for Emotion and Emotion Disorders, Chinese Academy of Medical Sciences, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, China
| | - Ke Si
- Department of Neurology of the First Affiliated Hospital, State Key Laboratory of Modern Optical Instrumentation, Zhejiang University School of Medicine, Hangzhou, China.,College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.,Research Units for Emotion and Emotion Disorders, Chinese Academy of Medical Sciences, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, China
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Bandini G, Agop-Nersesian C, van der Wel H, Mandalasi M, Kim HW, West CM, Samuelson J. The nucleocytosolic O-fucosyltransferase SPINDLY affects protein expression and virulence in Toxoplasma gondii. J Biol Chem 2021; 296:100039. [PMID: 33158988 PMCID: PMC7949088 DOI: 10.1074/jbc.ra120.015883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/23/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
Once considered unusual, nucleocytoplasmic glycosylation is now recognized as a conserved feature of eukaryotes. While in animals, O-GlcNAc transferase (OGT) modifies thousands of intracellular proteins, the human pathogen Toxoplasma gondii transfers a different sugar, fucose, to proteins involved in transcription, mRNA processing, and signaling. Knockout experiments showed that TgSPY, an ortholog of plant SPINDLY and paralog of host OGT, is required for nuclear O-fucosylation. Here we verify that TgSPY is the nucleocytoplasmic O-fucosyltransferase (OFT) by 1) complementation with TgSPY-MYC3, 2) its functional dependence on amino acids critical for OGT activity, and 3) its ability to O-fucosylate itself and a model substrate and to specifically hydrolyze GDP-Fuc. While many of the endogenous proteins modified by O-Fuc are important for tachyzoite fitness, O-fucosylation by TgSPY is not essential. Growth of Δspy tachyzoites in fibroblasts is modestly affected, despite marked reductions in the levels of ectopically expressed proteins normally modified with O-fucose. Intact TgSPY-MYC3 localizes to the nucleus and cytoplasm, whereas catalytic mutants often displayed reduced abundance. Δspy tachyzoites of a luciferase-expressing type II strain exhibited infection kinetics in mice similar to wild-type but increased persistence in the chronic brain phase, potentially due to an imbalance of regulatory protein levels. The modest changes in parasite fitness in vitro and in mice, despite profound effects on reporter protein accumulation, and the characteristic punctate localization of O-fucosylated proteins suggest that TgSPY controls the levels of proteins to be held in reserve for response to novel stresses.
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Affiliation(s)
- Giulia Bandini
- Department of Molecular and Cell Biology, Boston University Henry Goldman School of Dental Medicine, Boston, Massachusetts, USA.
| | - Carolina Agop-Nersesian
- Department of Molecular and Cell Biology, Boston University Henry Goldman School of Dental Medicine, Boston, Massachusetts, USA
| | - Hanke van der Wel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Msano Mandalasi
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Hyun W Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Christopher M West
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - John Samuelson
- Department of Molecular and Cell Biology, Boston University Henry Goldman School of Dental Medicine, Boston, Massachusetts, USA
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40
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Di Pietro S, Iacopini D, Storti B, Nifosì R, Di Bussolo V, Pineschi M, Moscardini A, Signore G, Bizzarri R. New 1,3-Disubstituted Benzo[ h]Isoquinoline Cyclen-Based Ligand Platform: Synthesis, Eu 3+ Multiphoton Sensitization and Imaging Applications. Molecules 2020; 26:E58. [PMID: 33374449 DOI: 10.3390/molecules26010058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 11/17/2022] Open
Abstract
The development of lanthanide-based luminescent probes with a long emission lifetime has the potential to revolutionize imaging-based diagnostic techniques. By a rational design strategy taking advantage of computational predictions, a novel, water-soluble Eu3+ complex from a cyclen-based ligand bearing 1,3-disubstituted benzo[h]isoquinoline arms was realized. The ligand has been obtained overcoming the lack of reactivity of position 3 of the isoquinoline moiety. Notably, steric hindrance of the heteroaromatic chromophore allowed selective and stoichiometry-controlled insertion of two or three antennas on the cyclen platform without any protection strategy. The complex bears a fourth heptanoic arm for easy conjugation to biomolecules. This new chromophore allowed the sensitization of the metal center either with one or two photons excitation. The suitability as a luminescent bioprobe was validated by imaging BMI1 oncomarker in lung carcinoma cells following an established immunofluorescence approach. The use of a conventional epifluorescence microscope equipped with a linear structured illumination module disclosed a simple and inexpensive way to image confocally Ln-bioprobes by single photon excitation in the 350–400 nm window, where ordinary confocal systems have no excitation sources.
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Lally PJ, Matthews PM, Bangerter NK. Unbalanced SSFP for super-resolution in MRI. Magn Reson Med 2020; 85:2477-2489. [PMID: 33201538 PMCID: PMC8972796 DOI: 10.1002/mrm.28593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/18/2020] [Accepted: 10/20/2020] [Indexed: 11/13/2022]
Abstract
Purpose: To achieve rapid, low specific absorption rate (SAR) super-resolution imaging by exploiting the characteristic magnetization off-resonance profile in SSFP. Theory and Methods: In the presented technique, low flip angle unbalanced SSFP imaging is used to acquire a series of images at a low nominal resolution that are then combined in a super-resolution strategy analogous to non-linear structured illumination microscopy. This is demonstrated in principle via Bloch simulations and synthetic phantoms, and the performance is quantified in terms of point-spread function (PSF) and SNR for gray and white matter from field strengths of 0.35T to 9.4T. A k-space reconstruction approach is proposed to account for B0 effects. This was applied to reconstruct super-resolution images from a test object at 9.4T. Results: Artifact-free super-resolution images were produced after incorporating sufficient preparation time for the magnetization to approach the steady state. High-resolution images of a test object were obtained at 9.4T, in the presence of considerable B0 inhomogeneity. For gray matter, the highest achievable resolution ranges from 3% of the acquired voxel dimension at 0.35T, to 9% at 9.4T. For white matter, this corresponds to 3% and 10%, respectively. Compared to an equivalent segmented gradient echo acquisition at the optimal flip angle, with a fixed TR of 8 ms, gray matter has up to 34% of the SNR at 9.4T while using a ×10 smaller flip angle. For white matter, this corresponds to 29% with a ×11 smaller flip angle. Conclusion: This approach achieves high degrees of super-resolution enhancement with minimal RF power requirements.
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Affiliation(s)
- Peter J Lally
- Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Paul M Matthews
- Department of Brain Sciences, Imperial College London, London, United Kingdom.,UK Dementia Research Institute Centre at Imperial College London, London, United Kingdom
| | - Neal K Bangerter
- Department of Bioengineering, Imperial College London, London, United Kingdom
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Mateu-Regué À, Christiansen J, Bagger FO, Winther O, Hellriegel C, Nielsen FC. Single mRNP Analysis Reveals that Small Cytoplasmic mRNP Granules Represent mRNA Singletons. Cell Rep 2020; 29:736-748.e4. [PMID: 31618640 DOI: 10.1016/j.celrep.2019.09.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/19/2018] [Accepted: 09/06/2019] [Indexed: 12/24/2022] Open
Abstract
Small cytoplasmic mRNP granules are implicated in mRNA transport, translational control, and decay. Using super-resolution microscopy and fluorescence correlation spectroscopy, we analyzed the molecular composition and dynamics of single cytoplasmic YBX1_IMP1 mRNP granules in live cells. Granules appeared elongated and branched, with patches of IMP1 and YBX1 distributed along mRNA, reflecting the attachment of the two RNA-binding proteins in cis. Particles form at the nuclear pore and do not associate with translating ribosomes, so the mRNP is a repository for mRNAs awaiting translation. In agreement with the average number of mRNA-binding sites derived from crosslinked immunoprecipitation (CLIP) analyses, individual mRNPs contain 5-15 molecules of YBX1 and IMP1 and a single poly(A) tail identified by PABPC1. Taken together, we conclude that small cytoplasmic mRNP granules are mRNA singletons, thus depicting the cellular transcriptome. Consequently, expression of functionally related mRNAs in RNA regulons is unlikely to result from coordinated assembly.
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Affiliation(s)
- Àngels Mateu-Regué
- Center for Genomic Medicine, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Jan Christiansen
- Department of Biology, Copenhagen Biocenter, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Frederik Otzen Bagger
- Center for Genomic Medicine, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Ole Winther
- Center for Genomic Medicine, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Christian Hellriegel
- Carl Zeiss RMS, Harvard Center for Biological Imaging, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark.
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Kounatidis I, Stanifer ML, Phillips MA, Paul-Gilloteaux P, Heiligenstein X, Wang H, Okolo CA, Fish TM, Spink MC, Stuart DI, Davis I, Boulant S, Grimes JM, Dobbie IM, Harkiolaki M. 3D Correlative Cryo-Structured Illumination Fluorescence and Soft X-ray Microscopy Elucidates Reovirus Intracellular Release Pathway. Cell 2020; 182:515-530.e17. [PMID: 32610083 PMCID: PMC7391008 DOI: 10.1016/j.cell.2020.05.051] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/14/2020] [Accepted: 05/28/2020] [Indexed: 01/15/2023]
Abstract
Imaging of biological matter across resolution scales entails the challenge of preserving the direct and unambiguous correlation of subject features from the macroscopic to the microscopic level. Here, we present a correlative imaging platform developed specifically for imaging cells in 3D under cryogenic conditions by using X-rays and visible light. Rapid cryo-preservation of biological specimens is the current gold standard in sample preparation for ultrastructural analysis in X-ray imaging. However, cryogenic fluorescence localization methods are, in their majority, diffraction-limited and fail to deliver matching resolution. We addressed this technological gap by developing an integrated, user-friendly platform for 3D correlative imaging of cells in vitreous ice by using super-resolution structured illumination microscopy in conjunction with soft X-ray tomography. The power of this approach is demonstrated by studying the process of reovirus release from intracellular vesicles during the early stages of infection and identifying intracellular virus-induced structures.
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Affiliation(s)
- Ilias Kounatidis
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Megan L Stanifer
- Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Michael A Phillips
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Perrine Paul-Gilloteaux
- Université de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France; Nantes Université, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS3556, Nantes, France
| | | | - Hongchang Wang
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Chidinma A Okolo
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Thomas M Fish
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Matthew C Spink
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - David I Stuart
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Ilan Davis
- Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Steeve Boulant
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; Research Group "Cellular polarity and viral infection," German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jonathan M Grimes
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Ian M Dobbie
- Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Maria Harkiolaki
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
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Sciurano RB, Rahn IM, González Arias B, Rey Valzacchi G, Benavente R, Solari AJ. Selective advantage of euploid spermatocytes I in an azoospermic 47,XYY man with gonadal mosaicism. Hum Reprod 2020; 34:568-573. [PMID: 30597018 DOI: 10.1093/humrep/dey387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/23/2018] [Accepted: 12/11/2018] [Indexed: 11/13/2022] Open
Abstract
Although most XYY men have normal sperm counts and are fertile (supposedly due to the loss of the extra Y before meiosis), there is a minority who are infertile. In these cases, the XYY spermatocytes are able to enter meiosis and form different synaptic configurations. With regard to mosaics, there is scarce well-defined information on the presence of the second Y and its meiotic behaviour. In this study, the chromosome constitution and the synaptic behaviour of pachytene spermatocytes from an azoospermic man with testicular hypotrophy and non-mosaic 47,XYY karyotype were analysed. Furthermore, we determined the chromosome constitution of the somatic Sertoli cells. Five karyotypically normal men with obstructive azoospermia, but having complete spermatogenesis, were included as controls. Immuno-FISH using specific protein markers of synapsis and recombination (SYCP3, SYCP1, BRCA1, MLH1, CREST) and a specific Yq12 DNA probe were used. In addition, we used the newly developed Super-Resolution Structured Illumination Microscopy (SR-SIM) to clearly define the synaptic configurations. FISH analysis was also performed on Sertoli cells. The histopathological analysis showed variable degrees of spermatogenesis development in the testicular tissue of the propositus. Immuno-FISH analysis showed that most of the primary spermatocytes were euploid 46, XY. The use of SR-SIM confirmed the existence of this euploidy. Only a few pachytene spermatocytes showed an aneuploid X + YY constitution. Sertoli cells showed two different populations with one or two Y chromosomes, in similar proportions. Thus an abnormal niche of sex-trisomic Sertoli cells should be also considered when searching for the origin of spermatogenesis failure in XYY men.
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Affiliation(s)
- R B Sciurano
- 2nd. A.U. Cell Biology, Histology, Embryology and Genetics, School of Medicine, University of Buenos Aires.,CONICET, Procrearte/Servicio de Urología, Hospital Italiano.,Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Germany
| | - I M Rahn
- 2nd. A.U. Cell Biology, Histology, Embryology and Genetics, School of Medicine, University of Buenos Aires.,CONICET, Procrearte/Servicio de Urología, Hospital Italiano
| | - B González Arias
- 2nd. A.U. Cell Biology, Histology, Embryology and Genetics, School of Medicine, University of Buenos Aires
| | | | - R Benavente
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Germany
| | - A J Solari
- 2nd. A.U. Cell Biology, Histology, Embryology and Genetics, School of Medicine, University of Buenos Aires.,CONICET, Procrearte/Servicio de Urología, Hospital Italiano
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45
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Zaccard CR, Shapiro L, Martin-de-Saavedra MD, Pratt C, Myczek K, Song A, Forrest MP, Penzes P. Rapid 3D Enhanced Resolution Microscopy Reveals Diversity in Dendritic Spinule Dynamics, Regulation, and Function. Neuron 2020; 107:522-537.e6. [PMID: 32464088 DOI: 10.1016/j.neuron.2020.04.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 12/19/2019] [Accepted: 04/27/2020] [Indexed: 12/31/2022]
Abstract
Dendritic spinules are thin protrusions, formed by neuronal spines, not adequately resolved by diffraction-limited light microscopy, which has limited our understanding of their behavior. Here we performed rapid structured illumination microscopy and enhanced resolution confocal microscopy to study spatiotemporal spinule dynamics in cortical pyramidal neurons. Spinules recurred at the same locations on mushroom spine heads. Most were short-lived, dynamic, exploratory, and originated near simple PSDs, whereas a subset was long-lived, elongated, and associated with complex PSDs. These subtypes were differentially regulated by Ca2+ transients. Furthermore, the postsynaptic Rac1-GEF kalirin-7 regulated spinule formation, elongation, and recurrence. Long-lived spinules often contained PSD fragments, contacted distal presynaptic terminals, and formed secondary synapses. NMDAR activation increased spinule number, length, and contact with distal presynaptic elements. Spinule subsets, dynamics, and recurrence were validated in cortical neurons of acute brain slices. Thus, we identified unique properties, regulatory mechanisms, and functions of spinule subtypes, supporting roles in neuronal connectivity.
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Affiliation(s)
- Colleen R Zaccard
- Department of Physiology, Northwestern University, Chicago, IL 60611, USA
| | - Lauren Shapiro
- Department of Physiology, Northwestern University, Chicago, IL 60611, USA
| | | | - Christopher Pratt
- Department of Physiology, Northwestern University, Chicago, IL 60611, USA
| | - Kristoffer Myczek
- Department of Physiology, Northwestern University, Chicago, IL 60611, USA
| | - Amy Song
- Department of Physiology, Northwestern University, Chicago, IL 60611, USA
| | - Marc P Forrest
- Department of Physiology, Northwestern University, Chicago, IL 60611, USA
| | - Peter Penzes
- Department of Physiology, Northwestern University, Chicago, IL 60611, USA; Department of Psychiatry and Behavioral Sciences, Northwestern University, Chicago, IL 60611, USA.
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Qiu K, Du Y, Liu J, Guan JL, Chao H, Diao J. Super-resolution observation of lysosomal dynamics with fluorescent gold nanoparticles. Theranostics 2020; 10:6072-6081. [PMID: 32483439 PMCID: PMC7254985 DOI: 10.7150/thno.42134] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/30/2020] [Indexed: 02/05/2023] Open
Abstract
Because lysosomes play critical roles in multiple cellular functions and are associated with many diseases, studying them at the subcellular level could elucidate their functionality and support the discovery of therapeutic drugs for treating those diseases. The commonly used dyes for super-resolution imaging of lysosomes are the commercial molecular LysoTrackers. But the tolerance to changes in the lysosomal microenvironment and to lysosomal membrane permeabilization (LMP) and the photostability of the LysoTrackers are worrisome. The purpose of our study was to evaluate the feasibility of performing a fluorescent gold nanoprobe for super-resolution observation of lysosomal dynamics in living cells and compare it to the commercial LysoTrackers. Methods: The nanoprobe Cy5@Au NP contained three parts: a bio-inert gold core, a biocompatible polyethylene glycol spacer, and a fluorophore cyanine 5. Structured illumination microscopy (SIM) was employed to capture the fluorescence of Cy5@Au NPs in cells. The tolerance assays to changes in the lysosomal microenvironment and to LMP, the photobleaching assay, and the long-term lysosomes labelling assay of Cy5@Au NPs were compared with commercial LysoTrackers. The super-resolution observation of lysosomal dynamics with Cy5@Au NPs was performed. Results: Cy5@Au NPs can light up lysosomes specifically under SIM. Compared with commercial lysosomal molecular probes, Cy5@Au NPs exhibited stronger tolerance in lysosomes during various treatments, and changes in the lysosomal microenvironment and LMP did not cause Cy5@Au NPs to lose track of their targets. Cy5@Au NPs demonstrated an excellent anti-photobleaching ability, and a long-term labelling assay revealed that they could label lysosomes more than 3 d. Biological events of lysosomes such as the kiss-and-run process, fusion, fission, and mitophagy were recorded with the fluorescent Cy5@Au NPs under SIM. Conclusions: The nanoprobe Cy5@Au NP was successfully used as a lysosomal probe for the super-resolution observation in living cells and found to overcome the limitations of commercial LysoTrackers. Our results thus confirm that nanoparticles can be useful tools for subcellular super-resolution imaging and highlight new avenues for using nanoparticles in biology.
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Schubert V, Neumann P, Marques A, Heckmann S, Macas J, Pedrosa-Harand A, Schubert I, Jang TS, Houben A. Super-Resolution Microscopy Reveals Diversity of Plant Centromere Architecture. Int J Mol Sci 2020; 21:E3488. [PMID: 32429054 PMCID: PMC7278974 DOI: 10.3390/ijms21103488] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/11/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022] Open
Abstract
Centromeres are essential for proper chromosome segregation to the daughter cells during mitosis and meiosis. Chromosomes of most eukaryotes studied so far have regional centromeres that form primary constrictions on metaphase chromosomes. These monocentric chromosomes vary from point centromeres to so-called "meta-polycentromeres", with multiple centromere domains in an extended primary constriction, as identified in Pisum and Lathyrus species. However, in various animal and plant lineages centromeres are distributed along almost the entire chromosome length. Therefore, they are called holocentromeres. In holocentric plants, centromere-specific proteins, at which spindle fibers usually attach, are arranged contiguously (line-like), in clusters along the chromosomes or in bands. Here, we summarize findings of ultrastructural investigations using immunolabeling with centromere-specific antibodies and super-resolution microscopy to demonstrate the structural diversity of plant centromeres. A classification of the different centromere types has been suggested based on the distribution of spindle attachment sites. Based on these findings we discuss the possible evolution and advantages of holocentricity, and potential strategies to segregate holocentric chromosomes correctly.
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Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
| | - Pavel Neumann
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; (P.N.); (J.M.); (T.-S.J.)
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
| | - Jiri Macas
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; (P.N.); (J.M.); (T.-S.J.)
| | - Andrea Pedrosa-Harand
- Department of Botany, Federal University of Pernambuco (UFPE), Recife 50670-901, Pernambuco, Brazil;
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
| | - Tae-Soo Jang
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; (P.N.); (J.M.); (T.-S.J.)
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
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48
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Crosby KC, Gookin SE, Garcia JD, Hahm KM, Dell'Acqua ML, Smith KR. Nanoscale Subsynaptic Domains Underlie the Organization of the Inhibitory Synapse. Cell Rep 2020; 26:3284-3297.e3. [PMID: 30893601 DOI: 10.1016/j.celrep.2019.02.070] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/03/2019] [Accepted: 02/19/2019] [Indexed: 12/15/2022] Open
Abstract
Inhibitory synapses mediate the majority of synaptic inhibition in the brain, thereby controlling neuronal excitability, firing, and plasticity. Although essential for neuronal function, the central question of how these synapses are organized at the subsynaptic level remains unanswered. Here, we use three-dimensional (3D) super-resolution microscopy to image key components of the inhibitory postsynaptic domain and presynaptic terminal, revealing that inhibitory synapses are organized into nanoscale subsynaptic domains (SSDs) of the gephyrin scaffold, GABAARs and the active-zone protein Rab3-interacting molecule (RIM). Gephyrin SSDs cluster GABAAR SSDs, demonstrating nanoscale architectural interdependence between scaffold and receptor. GABAAR SSDs strongly associate with active-zone RIM SSDs, indicating an important role for GABAAR nanoscale organization near sites of GABA release. Finally, we find that in response to elevated activity, synapse growth is mediated by an increase in the number of postsynaptic SSDs, suggesting a modular mechanism for increasing inhibitory synaptic strength.
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Affiliation(s)
- Kevin C Crosby
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Sara E Gookin
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Joshua D Garcia
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Katlin M Hahm
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Mark L Dell'Acqua
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Katharine R Smith
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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49
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Johnson KA, Hagen GM. Artifact-free whole-slide imaging with structured illumination microscopy and Bayesian image reconstruction. Gigascience 2020; 9:giaa035. [PMID: 32285910 PMCID: PMC7155289 DOI: 10.1093/gigascience/giaa035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/06/2019] [Accepted: 03/24/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Structured illumination microscopy (SIM) is a method that can be used to image biological samples and can achieve both optical sectioning and super-resolution effects. Optimization of the imaging set-up and data-processing methods results in high-quality images without artifacts due to mosaicking or due to the use of SIM methods. Reconstruction methods based on Bayesian estimation can be used to produce images with a resolution beyond that dictated by the optical system. FINDINGS Five complete datasets are presented including large panoramic SIM images of human tissues in pathophysiological conditions. Cancers of the prostate, skin, ovary, and breast, as well as tuberculosis of the lung, were imaged using SIM. The samples are available commercially and are standard histological preparations stained with hematoxylin-eosin. CONCLUSION The use of fluorescence microscopy is increasing in histopathology. There is a need for methods that reduce artifacts caused by the use of image-stitching methods or optical sectioning methods such as SIM. Stitched SIM images produce results that may be useful for intraoperative histology. Releasing high-quality, full-slide images and related data will aid researchers in furthering the field of fluorescent histopathology.
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Affiliation(s)
- Karl A Johnson
- UCCS BioFrontiers Center, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA
| | - Guy M Hagen
- UCCS BioFrontiers Center, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA
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50
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Lisjak M, Potokar M, Zorec R, Jorgačevski J. Indirect Role of AQP4b and AQP4d Isoforms in Dynamics of Astrocyte Volume and Orthogonal Arrays of Particles. Cells 2020; 9:cells9030735. [PMID: 32192013 PMCID: PMC7140617 DOI: 10.3390/cells9030735] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/10/2020] [Accepted: 03/13/2020] [Indexed: 01/10/2023] Open
Abstract
Water channel aquaporin 4 (AQP4) plays a key role in the regulation of water homeostasis in the central nervous system (CNS). It is predominantly expressed in astrocytes lining blood–brain and blood–liquor boundaries. AQP4a (M1), AQP4c (M23), and AQP4e, present in the plasma membrane, participate in the cell volume regulation of astrocytes. The function of their splicing variants, AQP4b and AQP4d, predicted to be present in the cytoplasm, is unknown. We examined the cellular distribution of AQP4b and AQP4d in primary rat astrocytes and their role in cell volume regulation. The AQP4b and AQP4d isoforms exhibited extensive cytoplasmic localization in early and late endosomes/lysosomes and in the Golgi apparatus. Neither isoform localized to orthogonal arrays of particles (OAPs) in the plasma membrane. The overexpression of AQP4b and AQP4d isoforms in isoosmotic conditions reduced the density of OAPs; in hypoosmotic conditions, they remained absent from OAPs. In hypoosmotic conditions, the AQP4d isoform was significantly redistributed to early endosomes, which correlated with the increased trafficking of AQP4-laden vesicles. The overexpression of AQP4d facilitated the kinetics of cell swelling, without affecting the regulatory volume decrease. Therefore, although they reside in the cytoplasm, AQP4b and AQP4d isoforms may play an indirect role in astrocyte volume changes.
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Affiliation(s)
- Marjeta Lisjak
- Laboratory of Neuroendocrinology–Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia; (M.L.); (M.P.); (R.Z.)
| | - Maja Potokar
- Laboratory of Neuroendocrinology–Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia; (M.L.); (M.P.); (R.Z.)
- Celica Biomedical, Tehnološki park 24, 1000 Ljubljana, Slovenia
| | - Robert Zorec
- Laboratory of Neuroendocrinology–Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia; (M.L.); (M.P.); (R.Z.)
- Celica Biomedical, Tehnološki park 24, 1000 Ljubljana, Slovenia
| | - Jernej Jorgačevski
- Laboratory of Neuroendocrinology–Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia; (M.L.); (M.P.); (R.Z.)
- Celica Biomedical, Tehnološki park 24, 1000 Ljubljana, Slovenia
- Correspondence: ; Tel.: +38615437081
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