101
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Abstract
Newly developed tissue clearing techniques can be used to render intact tissues transparent. When combined with fluorescent labeling technologies and optical sectioning microscopy, this allows visualization of fine structure in three dimensions. Gene-transfection techniques have proved very useful in visualizing cellular structures in animal models, but they are not applicable to human brain tissue. Here, we discuss the characteristics of an ideal chemical fluorescent probe for use in brain and other cleared tissues, and offer a comprehensive overview of currently available chemical probes. We describe their working principles and compare their performance with the goal of simplifying probe selection for neuropathologists and stimulating probe development by chemists. We propose several approaches for the development of innovative chemical labeling methods which, when combined with tissue clearing, have the potential to revolutionize how we study the structure and function of the human brain.
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Affiliation(s)
- Hei Ming Lai
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Neuropathology Unit, Division of Brain Sciences, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Wai-Lung Ng
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Steve M Gentleman
- Neuropathology Unit, Division of Brain Sciences, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Wutian Wu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; State Key Laboratory of Brain and Cognitive Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Research Center of Reproduction, Development and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Joint Laboratory of Jinan University and The University of Hong Kong, GHM Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China.
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102
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Nehrhoff I, Ripoll J, Samaniego R, Desco M, Gómez-Gaviro MV. Looking inside the heart: a see-through view of the vascular tree. BIOMEDICAL OPTICS EXPRESS 2017; 8:3110-3118. [PMID: 28663930 PMCID: PMC5480453 DOI: 10.1364/boe.8.003110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 05/20/2017] [Accepted: 05/21/2017] [Indexed: 06/07/2023]
Abstract
The ability to acquire 3D images of the heart and its vasculature at cellular resolution facilitates a more detailed study of many heart diseases. Here, we describe a novel technique to image in 3D the heart vasculature by combining the CUBIC clearing protocol combined with in vivo administration of fluorescent-labeled lectin. The use of these techniques in combination with Selective Plane Illumination Microscopy (SPIM) made it possible to obtain high resolution 3D images of the cardiac vascular tree. This methodological approach may enhance the visualization of 3D images of the cardiac vasculature remodeling associated with coronary disease.
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Affiliation(s)
- Imke Nehrhoff
- Instituto de Investigación Sanitaria Gregorio Marañón, (IiSGM), Madrid, Spain
| | - Jorge Ripoll
- Instituto de Investigación Sanitaria Gregorio Marañón, (IiSGM), Madrid, Spain
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Spain
| | - Rafael Samaniego
- Unidad de Microscopía Confocal, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Manuel Desco
- Instituto de Investigación Sanitaria Gregorio Marañón, (IiSGM), Madrid, Spain
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Spain
| | - Maria Victoria Gómez-Gaviro
- Instituto de Investigación Sanitaria Gregorio Marañón, (IiSGM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain
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103
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Männ L, Klingberg A, Gunzer M, Hasenberg M. Quantitative Visualization of Leukocyte Infiltrate in a Murine Model of Fulminant Myocarditis by Light Sheet Microscopy. J Vis Exp 2017. [PMID: 28605364 DOI: 10.3791/55450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Light-sheet fluorescence microscopy (LSFM), in combination with chemical clearing protocols, has become the gold standard for analyzing fluorescently labelled structures in large biological specimens, and is down to cellular resolution. Meanwhile, the constant refinement of underlying protocols and the enhanced availability of specialized commercial systems enable us to investigate the microstructure of whole mouse organs and even allow for the characterization of cellular behavior in various live-cell imaging approaches. Here, we describe a protocol for the spatial whole-mount visualization and quantification of the CD45+ leukocyte population in inflamed mouse hearts. The method employs a transgenic mouse strain (CD11c.DTR)that has recently been shown to serve as a robust, inducible model for the study of the development of fulminant fatal myocarditis, characterized by lethal cardiac arrhythmias. This protocol includes myocarditis induction, intravital antibody-mediated cell staining, organ preparation, and LSFM with subsequent computer-assisted image post-processing. Although presented as a highly-adapted method for our particular scientific question, the protocol represents the blueprint of an easily adjustable system that can also target completely different fluorescent structures in other organs and even in other species.
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Affiliation(s)
- Linda Männ
- Department of Translational Skin Cancer Research, University of Duisburg/Essen
| | - Anika Klingberg
- Institute for Experimental Immunology and Imaging, University of Duisburg/Essen
| | - Matthias Gunzer
- Institute for Experimental Immunology and Imaging, University of Duisburg/Essen
| | - Mike Hasenberg
- Imaging Center Essen, Electron Microscopy Unit, University Hospital of Essen;
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104
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Lu CY, Hour MJ, Wang CY, Huang SH, Mu WX, Chang YC, Lin CW. Single-Round Infectious Particle Antiviral Screening Assays for the Japanese Encephalitis Virus. Viruses 2017; 9:v9040076. [PMID: 28394283 PMCID: PMC5408682 DOI: 10.3390/v9040076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/13/2022] Open
Abstract
Japanese Encephalitis virus (JEV) is a mosquito-borne flavivirus with a positive-sense single-stranded RNA genome that contains a big open reading frame (ORF) flanked by 5′- and 3′- untranslated regions (UTRs). Nearly 30,000 JE cases with 10,000 deaths are still annually reported in East Asia. Although the JEV genotype III vaccine has been licensed, it elicits a lower protection against other genotypes. Moreover, no effective treatment for a JE case is developed. This study constructed a pBR322-based and cytomegaloviruses (CMV) promoter-driven JEV replicon for the production of JEV single-round infectious particles (SRIPs) in a packaging cell line expressing viral structural proteins. Genetic instability of JEV genome cDNA in the pBR322 plasmid was associated with the prokaryotic promoter at 5′ end of the JEV genome that triggers the expression of the structural proteins in E. coli. JEV structural proteins were toxic E. coli, thus the encoding region for structural proteins was replaced by a reporter gene (enhanced green fluorescent protein, EGFP) that was in-frame fused with the first eight amino acids of the C protein at N-terminus and the foot-and-mouth disease virus (FMDV) 2A peptide at C-terminus in a pBR322-based JEV-EGFP replicon. JEV-EGFP SRIPs generated from JEV-EGFP replicon-transfected packaging cells displayed the infectivity with cytopathic effect induction, self-replication of viral genomes, and the expression of EGFP and viral proteins. Moreover, the combination of JEV-EGFP SRIP plus flow cytometry was used to determine the half maximal inhibitory concentration (IC50) values of antiviral agents according to fluorescent intensity and positivity of SRIP-infected packaging cells post treatment. MJ-47, a quinazolinone derivative, significantly inhibited JEV-induced cytopathic effect, reducing the replication and expression of JEV-EGFP replicon in vitro. The IC50 value of 6.28 µM for MJ-47 against JEV was determined by the assay of JEV-EGFP SRIP infection in packaging cells plus flow cytometry that was more sensitive, effective, and efficient compared to the traditional plaque assay. Therefore, the system of JEV-EGFP SRIPs plus flow cytometry was a rapid and reliable platform for screening antiviral agents and evaluating antiviral potency.
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Affiliation(s)
- Chien-Yi Lu
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan.
| | - Mann-Jen Hour
- School of Pharmacy, China Medical University, Taichung 40402, Taiwan.
| | - Ching-Ying Wang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan.
| | - Su-Hua Huang
- Department of Biotechnology, Asia University, Taichung 41354, Taiwan.
| | - Wen-Xiang Mu
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan.
| | - Yu-Chun Chang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan.
| | - Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan.
- Department of Biotechnology, Asia University, Taichung 41354, Taiwan.
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105
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High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis. Sci Rep 2017; 7:43012. [PMID: 28211501 PMCID: PMC5314416 DOI: 10.1038/srep43012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/17/2017] [Indexed: 12/17/2022] Open
Abstract
Zebrafish testis has become a powerful model for reproductive biology of teleostean fishes and other vertebrates and encompasses multiple applications in applied and basic research. Many studies have focused on 2D images, which is time consuming and implies extrapolation of results. Three-dimensional imaging of whole organs recently became an important challenge to better understand their architecture and allow cell enumeration. Several protocols have thus been developed to enhance sample transparency, a limiting step for imaging large biological samples. However, none of these methods has been applied to the zebrafish testis. We tested five clearing protocols to determine if some of them could be applied with only small modifications to the testis. We compared clearing efficiency at both macroscopic and microscopic levels. CUBIC and PACT were suitable for an efficient transparency, an optimal optical penetration, the GFP fluorescence preservation and avoiding meaningful tissue deformation. Finally, we succeeded in whole testis 3D capture at a cellular resolution with both CUBIC and PACT, which will be valuable in a standard workflow to investigate the 3D architecture of the testis and its cellular content. This paves the way for further development of high content phenotyping studies in several fields including development, genetic or toxicology.
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106
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Bohmbach K, Schwarz MK, Schoch S, Henneberger C. The structural and functional evidence for vesicular release from astrocytes in situ. Brain Res Bull 2017; 136:65-75. [PMID: 28122264 DOI: 10.1016/j.brainresbull.2017.01.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/17/2017] [Accepted: 01/19/2017] [Indexed: 12/31/2022]
Abstract
The concept of the tripartite synapse states that bi-directional signalling between perisynaptic astrocyte processes, presynaptic axonal boutons and postsynaptic neuronal structures defines the properties of synaptic information processing. Ca2+-dependent vesicular release from astrocytes, as one of the mechanisms of astrocyte-neuron communication, has attracted particular attention but has also been the subject of intense debate. In neurons, regulated vesicular release is a strongly coordinated process. It requires a complex release machinery comprised of many individual components ranging from vesicular neurotransmitter transporters and soluble NSF attachment protein receptors (SNARE) proteins to Ca2+-sensors and the proteins that spatially and temporally control exocytosis of synaptic vesicles. If astrocytes employ similar mechanisms to release neurotransmitters is less well understood. The aim of this review is therefore to discuss recent experimental evidence that sheds light on the central structural components responsible for vesicular release from astrocytes in situ.
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Affiliation(s)
- Kirsten Bohmbach
- Institute of Cellular Neurosciences, University of Bonn Medical School, Bonn, Germany.
| | - Martin K Schwarz
- Department of Epileptology, University of Bonn Medical School, Bonn, Germany
| | - Susanne Schoch
- Institute of Neuropathology, University of Bonn Medical School, Bonn, Germany
| | - Christian Henneberger
- Institute of Cellular Neurosciences, University of Bonn Medical School, Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; Institute of Neurology, University College London, London, United Kingdom.
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107
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Doerr J, Schwarz MK, Wiedermann D, Leinhaas A, Jakobs A, Schloen F, Schwarz I, Diedenhofen M, Braun NC, Koch P, Peterson DA, Kubitscheck U, Hoehn M, Brüstle O. Whole-brain 3D mapping of human neural transplant innervation. Nat Commun 2017; 8:14162. [PMID: 28102196 PMCID: PMC5253698 DOI: 10.1038/ncomms14162] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 12/05/2016] [Indexed: 11/22/2022] Open
Abstract
While transplantation represents a key tool for assessing in vivo functionality of neural stem cells and their suitability for neural repair, little is known about the integration of grafted neurons into the host brain circuitry. Rabies virus-based retrograde tracing has developed into a powerful approach for visualizing synaptically connected neurons. Here, we combine this technique with light sheet fluorescence microscopy (LSFM) to visualize transplanted cells and connected host neurons in whole-mouse brain preparations. Combined with co-registration of high-precision three-dimensional magnetic resonance imaging (3D MRI) reference data sets, this approach enables precise anatomical allocation of the host input neurons. Our data show that the same neural donor cell population grafted into different brain regions receives highly orthotopic input. These findings indicate that transplant connectivity is largely dictated by the circuitry of the target region and depict rabies-based transsynaptic tracing and LSFM as efficient tools for comprehensive assessment of host–donor cell innervation. Transplantation of cells into the central nervous system has developed into a major avenue for replacing neurons lost to neurodegenerative disease. Here the authors develop an approach combining viral-based transynaptic tracing labeling and whole brain imaging to trace synaptic innervation of human neurons transplanted into a mouse background.
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Affiliation(s)
- Jonas Doerr
- Institute of Reconstructive Neurobiology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany.,Life&Brain GmbH, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Martin Karl Schwarz
- Life&Brain GmbH, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany.,Department of Epileptology, Functional Neuroconnectomics Group, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Dirk Wiedermann
- Max Planck Institute for Metabolism Research, In-vivo-NMR Laboratory, Gleuelerstrasse 50, 50931 Cologne, Germany
| | - Anke Leinhaas
- Institute of Reconstructive Neurobiology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Alina Jakobs
- Institute of Reconstructive Neurobiology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Florian Schloen
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegeler Strasse 12, 53115 Bonn, Germany
| | - Inna Schwarz
- Department of Epileptology, Functional Neuroconnectomics Group, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Michael Diedenhofen
- Max Planck Institute for Metabolism Research, In-vivo-NMR Laboratory, Gleuelerstrasse 50, 50931 Cologne, Germany
| | - Nils Christian Braun
- Institute of Reconstructive Neurobiology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Philipp Koch
- Institute of Reconstructive Neurobiology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Daniel A Peterson
- Center for Stem Cell and Regenerative Medicine, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, 60064 North Chicago, Illinois, USA
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegeler Strasse 12, 53115 Bonn, Germany
| | - Mathias Hoehn
- Max Planck Institute for Metabolism Research, In-vivo-NMR Laboratory, Gleuelerstrasse 50, 50931 Cologne, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany.,Life&Brain GmbH, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
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108
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Ariel P. A beginner's guide to tissue clearing. Int J Biochem Cell Biol 2017; 84:35-39. [PMID: 28082099 DOI: 10.1016/j.biocel.2016.12.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/22/2016] [Accepted: 12/16/2016] [Indexed: 01/18/2023]
Abstract
The last decade has seen a proliferation of tissue clearing methods that render large biological samples transparent and allow unprecedented three-dimensional views of enormous volumes of tissue. For a scientist wondering whether these methods will be useful to address their research problems, it can be bewildering to sort through the ever-increasing number of papers introducing new clearing methods. Here, I provide a concise summary for the novice describing what tissue clearing is, which research problems it can be applied to, how to decide on a clearing method, and where the field is headed in the future.
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Affiliation(s)
- Pablo Ariel
- Microscopy Services Laboratory, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, United States.
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109
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Jährling N, Becker K, Saghafi S, Dodt HU. Light-Sheet Fluorescence Microscopy: Chemical Clearing and Labeling Protocols for Ultramicroscopy. Methods Mol Biol 2017; 1563:33-49. [PMID: 28324600 DOI: 10.1007/978-1-4939-6810-7_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Light-sheet microscopy is an effective technique in neuroscience, developmental biology, and cancer research for visualizing and analyzing cellular networks and whole organs in three dimensions. Because this technique requires specimens to be translucent they commonly have to be cleared before microscopy inspection. Here, we provide 3DISCO based protocols for preparing cleared samples of immuno-stained neural networks, lectin-labeled vascular networks, and Methoxy-X04 labeled beta-amyloid plaques in mice. 3DISCO utilizes the lipophilic solvents tetrahydrofuran (THF) and dibenzylether (DBE) for dehydration and successive clearing. Crucial steps for obtaining transparent tissues and preserving the fragile endogenous GFP are the transcardial perfusion, as well as the proper implementation of the 3DISCO clearing process using peroxide free chemicals. We further provide a protocol for resin embedding of 3DISCO cleared specimens that allows long term archiving of samples for years with virtually no loss in signal quality.
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Affiliation(s)
- Nina Jährling
- Department of Bioelectronics, FKE, Vienna University of Technology, Floragasse 7, 1040, Vienna, Austria.
- Center of Brain Research, Medical University of Vienna, Vienna, Austria.
| | - Klaus Becker
- Department of Bioelectronics, FKE, Vienna University of Technology, Floragasse 7, 1040, Vienna, Austria
- Center of Brain Research, Medical University of Vienna, Vienna, Austria
| | - Saiedeh Saghafi
- Department of Bioelectronics, FKE, Vienna University of Technology, Floragasse 7, 1040, Vienna, Austria
- Center of Brain Research, Medical University of Vienna, Vienna, Austria
| | - Hans-Ulrich Dodt
- Department of Bioelectronics, FKE, Vienna University of Technology, Floragasse 7, 1040, Vienna, Austria
- Center of Brain Research, Medical University of Vienna, Vienna, Austria
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110
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Lai HM, Ng HM, Wu W. Three-dimensional histology: new visual approaches to morphological changes during neural regeneration. Neural Regen Res 2017; 12:53-55. [PMID: 28250740 PMCID: PMC5319234 DOI: 10.4103/1673-5374.198974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Three-dimensional (3D) histology utilizes tissue clearing techniques to turn intact tissues transparent, allowing rapid interrogation of tissue architecture in three dimensions. In this article, we summarized the available tissue clearing methods and classified them according to their physicochemical principles of operation, which provided a framework for one to choose the best techniques for various research settings. Recent attempts in addressing various questions regarding the degenerating and regenerating nervous system have been promising with the use of 3D histological techniques.
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Affiliation(s)
- Hei Ming Lai
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Ho Man Ng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Wutian Wu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; State Key Laboratory of Brain and Cognitive Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Research Center of Reproduction, Development and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong Province, China
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111
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Justus D, Dalügge D, Bothe S, Fuhrmann F, Hannes C, Kaneko H, Friedrichs D, Sosulina L, Schwarz I, Elliott DA, Schoch S, Bradke F, Schwarz MK, Remy S. Glutamatergic synaptic integration of locomotion speed via septoentorhinal projections. Nat Neurosci 2016; 20:16-19. [PMID: 27893726 DOI: 10.1038/nn.4447] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/01/2016] [Indexed: 12/21/2022]
Abstract
The medial septum and diagonal band of Broca (MSDB) send glutamatergic axons to medial entorhinal cortex (MEC). We found that this pathway provides speed-correlated input to several MEC cell-types in layer 2/3. The speed signal is integrated most effectively by pyramidal cells but also excites stellate cells and interneurons. Thus, the MSDB conveys speed information that can be used by MEC neurons for spatial representation of self-location.
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Affiliation(s)
- Daniel Justus
- Neuronal Networks Group, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Dennis Dalügge
- Neuronal Networks Group, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Stefanie Bothe
- Neuronal Networks Group, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Falko Fuhrmann
- Neuronal Networks Group, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Christian Hannes
- Neuronal Networks Group, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Hiroshi Kaneko
- Neuronal Networks Group, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Detlef Friedrichs
- Neuronal Networks Group, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Liudmila Sosulina
- Neuronal Networks Group, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Inna Schwarz
- Functional Neuroconnectomics Group, Department of Epileptology, University of Bonn Medical Center, Bonn, Germany
| | - David Anthony Elliott
- Axon Growth and Regeneration Group, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Susanne Schoch
- Department of Epileptology, University of Bonn Medical Center, Bonn, Germany.,Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Frank Bradke
- Axon Growth and Regeneration Group, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Martin Karl Schwarz
- Functional Neuroconnectomics Group, Department of Epileptology, University of Bonn Medical Center, Bonn, Germany
| | - Stefan Remy
- Neuronal Networks Group, German Center for Neurodegenerative Diseases, Bonn, Germany.,Department of Epileptology, University of Bonn Medical Center, Bonn, Germany
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112
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Kirschbaum K, Sonner JK, Zeller MW, Deumelandt K, Bode J, Sharma R, Krüwel T, Fischer M, Hoffmann A, Costa da Silva M, Muckenthaler MU, Wick W, Tews B, Chen JW, Heiland S, Bendszus M, Platten M, Breckwoldt MO. In vivo nanoparticle imaging of innate immune cells can serve as a marker of disease severity in a model of multiple sclerosis. Proc Natl Acad Sci U S A 2016; 113:13227-13232. [PMID: 27799546 PMCID: PMC5135308 DOI: 10.1073/pnas.1609397113] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Innate immune cells play a key role in the pathogenesis of multiple sclerosis and experimental autoimmune encephalomyelitis (EAE). Current clinical imaging is restricted to visualizing secondary effects of inflammation, such as gliosis and blood-brain barrier disruption. Advanced molecular imaging, such as iron oxide nanoparticle imaging, can allow direct imaging of cellular and molecular activity, but the exact cell types that phagocytose nanoparticles in vivo and how phagocytic activity relates to disease severity is not well understood. In this study we used MRI to map inflammatory infiltrates using high-field MRI and fluorescently labeled cross-linked iron oxide nanoparticles for cell tracking. We confirmed nanoparticle uptake and MR detectability ex vivo. Using in vivo MRI, we identified extensive nanoparticle signal in the cerebellar white matter and circumscribed cortical gray matter lesions that developed during the disease course (4.6-fold increase of nanoparticle accumulation in EAE compared with healthy controls, P < 0.001). Nanoparticles showed good cellular specificity for innate immune cells in vivo, labeling activated microglia, infiltrating macrophages, and neutrophils, whereas there was only sparse uptake by adaptive immune cells. Importantly, nanoparticle signal correlated better with clinical disease than conventional gadolinium (Gd) imaging (r, 0.83 for nanoparticles vs. 0.71 for Gd-imaging, P < 0.001). We validated our approach using the Food and Drug Administration-approved iron oxide nanoparticle ferumoxytol. Our results show that noninvasive molecular imaging of innate immune responses can serve as an imaging biomarker of disease activity in autoimmune-mediated neuroinflammation with potential clinical applications in a wide range of inflammatory diseases.
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Affiliation(s)
- Klara Kirschbaum
- German Cancer Consortium, Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Neuroradiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Jana K Sonner
- German Cancer Consortium, Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Matthias W Zeller
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115
- Division of Neuroradiology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115
| | - Katrin Deumelandt
- German Cancer Consortium, Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Julia Bode
- Schaller Research Group, University of Heidelberg and DKFZ, 69120 Heidelberg, Germany
- Molecular Mechanisms of Tumor Invasion, DKFZ, 69120 Heidelberg, Germany
| | - Rakesh Sharma
- Schaller Research Group, University of Heidelberg and DKFZ, 69120 Heidelberg, Germany
- Molecular Mechanisms of Tumor Invasion, DKFZ, 69120 Heidelberg, Germany
| | - Thomas Krüwel
- Schaller Research Group, University of Heidelberg and DKFZ, 69120 Heidelberg, Germany
- Molecular Mechanisms of Tumor Invasion, DKFZ, 69120 Heidelberg, Germany
| | - Manuel Fischer
- Department of Neuroradiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Angelika Hoffmann
- Department of Neuroradiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Milene Costa da Silva
- Department of Pediatric Hematology, Oncology and Immunology, University of Heidelberg, 69120 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Graduate Program in Areas of Basic and Applied Biology, Abel Salazar Biomedical Sciences Institute, University of Porto, 4050-313 Porto, Portugal
| | - Martina U Muckenthaler
- Department of Pediatric Hematology, Oncology and Immunology, University of Heidelberg, 69120 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Wolfgang Wick
- Department of Neurology and National Center for Tumor Diseases (NCT), University Hospital Heidelberg, 69120 Heidelberg, Germany
- German Cancer Consortium, Clinical Cooperation Unit Neurooncology, DKFZ, 69120 Heidelberg, Germany
| | - Björn Tews
- Schaller Research Group, University of Heidelberg and DKFZ, 69120 Heidelberg, Germany
- Molecular Mechanisms of Tumor Invasion, DKFZ, 69120 Heidelberg, Germany
| | - John W Chen
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115
- Division of Neuroradiology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115
| | - Sabine Heiland
- Department of Neuroradiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Martin Bendszus
- Department of Neuroradiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Michael Platten
- German Cancer Consortium, Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Neurology and National Center for Tumor Diseases (NCT), University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Michael O Breckwoldt
- German Cancer Consortium, Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
- Department of Neuroradiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
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113
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Cazemier JL, Clascá F, Tiesinga PHE. Connectomic Analysis of Brain Networks: Novel Techniques and Future Directions. Front Neuroanat 2016; 10:110. [PMID: 27881953 PMCID: PMC5101213 DOI: 10.3389/fnana.2016.00110] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/25/2016] [Indexed: 12/31/2022] Open
Abstract
Brain networks, localized or brain-wide, exist only at the cellular level, i.e., between specific pre- and post-synaptic neurons, which are connected through functionally diverse synapses located at specific points of their cell membranes. "Connectomics" is the emerging subfield of neuroanatomy explicitly aimed at elucidating the wiring of brain networks with cellular resolution and a quantified accuracy. Such data are indispensable for realistic modeling of brain circuitry and function. A connectomic analysis, therefore, needs to identify and measure the soma, dendrites, axonal path, and branching patterns together with the synapses and gap junctions of the neurons involved in any given brain circuit or network. However, because of the submicron caliber, 3D complexity, and high packing density of most such structures, as well as the fact that axons frequently extend over long distances to make synapses in remote brain regions, creating connectomic maps is technically challenging and requires multi-scale approaches, Such approaches involve the combination of the most sensitive cell labeling and analysis methods available, as well as the development of new ones able to resolve individual cells and synapses with increasing high-throughput. In this review, we provide an overview of recently introduced high-resolution methods, which researchers wanting to enter the field of connectomics may consider. It includes several molecular labeling tools, some of which specifically label synapses, and covers a number of novel imaging tools such as brain clearing protocols and microscopy approaches. Apart from describing the tools, we also provide an assessment of their qualities. The criteria we use assess the qualities that tools need in order to contribute to deciphering the key levels of circuit organization. We conclude with a brief future outlook for neuroanatomic research, computational methods, and network modeling, where we also point out several outstanding issues like structure-function relations and the complexity of neural models.
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Affiliation(s)
- J Leonie Cazemier
- Department of Neuroinformatics, Donders Institute, Radboud UniversityNijmegen, Netherlands; Department of Cortical Structure and Function, Netherlands Institute for NeuroscienceAmsterdam, Netherlands
| | - Francisco Clascá
- Department of Anatomy, Histology and Neuroscience, School of Medicine, Autónoma University Madrid, Spain
| | - Paul H E Tiesinga
- Department of Neuroinformatics, Donders Institute, Radboud University Nijmegen, Netherlands
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114
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Tainaka K, Kuno A, Kubota SI, Murakami T, Ueda HR. Chemical Principles in Tissue Clearing and Staining Protocols for Whole-Body Cell Profiling. Annu Rev Cell Dev Biol 2016; 32:713-741. [DOI: 10.1146/annurev-cellbio-111315-125001] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kazuki Tainaka
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan
| | - Akihiro Kuno
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan
- PhD Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Shimpei I. Kubota
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan
| | - Tatzya Murakami
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroki R. Ueda
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka 565-0871, Japan;
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115
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Feuchtinger A, Walch A, Dobosz M. Deep tissue imaging: a review from a preclinical cancer research perspective. Histochem Cell Biol 2016; 146:781-806. [DOI: 10.1007/s00418-016-1495-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2016] [Indexed: 10/20/2022]
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116
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Shrinkage-mediated imaging of entire organs and organisms using uDISCO. Nat Methods 2016; 13:859-67. [PMID: 27548807 DOI: 10.1038/nmeth.3964] [Citation(s) in RCA: 387] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/26/2016] [Indexed: 02/06/2023]
Abstract
Recent tissue-clearing approaches have become important alternatives to standard histology approaches. However, light scattering in thick tissues and the size restrictions on samples that can be imaged with standard light-sheet microscopy pose limitations for analyzing large samples such as an entire rodent body. We developed 'ultimate DISCO' (uDISCO) clearing to overcome these limitations in volumetric imaging. uDISCO preserves fluorescent proteins over months and renders intact organs and rodent bodies transparent while reducing their size up to 65%. We used uDISCO to image neuronal connections and vasculature from head to toe over 7 cm and to perform unbiased screening of transplanted stem cells within the entire body of adult mice. uDISCO is compatible with diverse labeling methods and archival human tissue, and it can readily be used in various biomedical applications to study organization of large organ systems throughout entire organisms.
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117
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Klingberg A, Hasenberg A, Ludwig-Portugall I, Medyukhina A, Männ L, Brenzel A, Engel DR, Figge MT, Kurts C, Gunzer M. Fully Automated Evaluation of Total Glomerular Number and Capillary Tuft Size in Nephritic Kidneys Using Lightsheet Microscopy. J Am Soc Nephrol 2016; 28:452-459. [PMID: 27487796 DOI: 10.1681/asn.2016020232] [Citation(s) in RCA: 227] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 07/08/2016] [Indexed: 12/19/2022] Open
Abstract
The total number of glomeruli is a fundamental parameter of kidney function but very difficult to determine using standard methodology. Here, we counted all individual glomeruli in murine kidneys and sized the capillary tufts by combining in vivo fluorescence labeling of endothelial cells, a novel tissue-clearing technique, lightsheet microscopy, and automated registration by image analysis. Total hands-on time per organ was <1 hour, and automated counting/sizing was finished in <3 hours. We also investigated the novel use of ethyl-3-phenylprop-2-enoate (ethyl cinnamate) as a nontoxic solvent-based clearing reagent that can be handled without specific safety measures. Ethyl cinnamate rapidly cleared all tested organs, including calcified bone, but the fluorescence of proteins and immunohistochemical labels was maintained over weeks. Using ethyl cinnamate-cleared kidneys, we also quantified the average creatinine clearance rate per glomerulus. This parameter decreased in the first week of experimental nephrotoxic nephritis, whereas reduction in glomerular numbers occurred much later. Our approach delivers fundamental parameters of renal function, and because of its ease of use and speed, it is suitable for high-throughput analysis and could greatly facilitate studies of the effect of kidney diseases on whole-organ physiology.
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Affiliation(s)
- Anika Klingberg
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Anja Hasenberg
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Isis Ludwig-Portugall
- Institute for Experimental Immunology, Rheinische-Friedrichs-Wilhelms University of Bonn, Bonn, Germany
| | - Anna Medyukhina
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Leibniz-Association, Jena, Germany; and
| | - Linda Männ
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Alexandra Brenzel
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Daniel R Engel
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Marc Thilo Figge
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Leibniz-Association, Jena, Germany; and.,Friedrich Schiller University Jena, Jena, Germany
| | - Christian Kurts
- Institute for Experimental Immunology, Rheinische-Friedrichs-Wilhelms University of Bonn, Bonn, Germany
| | - Matthias Gunzer
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, Germany;
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118
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Silvestri L, Costantini I, Sacconi L, Pavone FS. Clearing of fixed tissue: a review from a microscopist's perspective. JOURNAL OF BIOMEDICAL OPTICS 2016; 21:081205. [PMID: 27020691 DOI: 10.1117/1.jbo.21.8.081205] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 02/26/2016] [Indexed: 05/18/2023]
Abstract
Chemical clearing of fixed tissues is becoming a key instrument for the three-dimensional reconstruction of macroscopic tissue portions, including entire organs. Indeed, the growing interest in this field has both triggered and been stimulated by recent advances in high-throughput microscopy and data analysis methods, which allowed imaging and management of large samples. The strong entanglement between clearing methods and imaging technology is often overlooked, as typical classification of the former is based only on the chemicals used. Here, we review the recent literature in the field, proposing a taxonomy of clearing techniques based on their mating with the major high-throughput microscopies. We hope that this application-oriented classification can help researchers to find the protocol best suited to their experiment among the many present in the literature.
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Affiliation(s)
- Ludovico Silvestri
- National Institute of Optics, National Research Council, Via Nello Carrara 1, 50019 Sesto Fiorentino, Florence, ItalybEuropean Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Florence, Italy
| | - Irene Costantini
- European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Florence, Italy
| | - Leonardo Sacconi
- National Institute of Optics, National Research Council, Via Nello Carrara 1, 50019 Sesto Fiorentino, Florence, ItalybEuropean Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Florence, Italy
| | - Francesco Saverio Pavone
- National Institute of Optics, National Research Council, Via Nello Carrara 1, 50019 Sesto Fiorentino, Florence, ItalybEuropean Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Florence, ItalycUniversity of Florence, Dep
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119
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Niedworok CJ, Brown APY, Jorge Cardoso M, Osten P, Ourselin S, Modat M, Margrie TW. aMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data. Nat Commun 2016; 7:11879. [PMID: 27384127 PMCID: PMC4941048 DOI: 10.1038/ncomms11879] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/09/2016] [Indexed: 01/16/2023] Open
Abstract
The validation of automated image registration and segmentation is crucial for accurate and reliable mapping of brain connectivity and function in three-dimensional (3D) data sets. While validation standards are necessarily high and routinely met in the clinical arena, they have to date been lacking for high-resolution microscopy data sets obtained from the rodent brain. Here we present a tool for optimized automated mouse atlas propagation (aMAP) based on clinical registration software (NiftyReg) for anatomical segmentation of high-resolution 3D fluorescence images of the adult mouse brain. We empirically evaluate aMAP as a method for registration and subsequent segmentation by validating it against the performance of expert human raters. This study therefore establishes a benchmark standard for mapping the molecular function and cellular connectivity of the rodent brain.
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Affiliation(s)
- Christian J. Niedworok
- The Division of Neurophysiology, MRC National Institute for Medical Research, London NW7 1AA, UK
- The Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London W1T 4JG, UK
| | - Alexander P. Y. Brown
- The Division of Neurophysiology, MRC National Institute for Medical Research, London NW7 1AA, UK
- The Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London W1T 4JG, UK
| | - M. Jorge Cardoso
- Translational Imaging Group, Centre for Medical Image Computing, University College London, London WC1E 6BT, UK
| | - Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Sebastien Ourselin
- Translational Imaging Group, Centre for Medical Image Computing, University College London, London WC1E 6BT, UK
| | - Marc Modat
- Translational Imaging Group, Centre for Medical Image Computing, University College London, London WC1E 6BT, UK
| | - Troy W. Margrie
- The Division of Neurophysiology, MRC National Institute for Medical Research, London NW7 1AA, UK
- The Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London W1T 4JG, UK
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120
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Alves S, Bode J, Bemelmans AP, von Kalle C, Cartier N, Tews B. Ultramicroscopy as a novel tool to unravel the tropism of AAV gene therapy vectors in the brain. Sci Rep 2016; 6:28272. [PMID: 27320056 PMCID: PMC4913310 DOI: 10.1038/srep28272] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/01/2016] [Indexed: 01/07/2023] Open
Abstract
Recombinant adeno-associated viral (AAV) vectors have advanced to the vanguard of gene therapy. Numerous naturally occurring serotypes have been used to target cells in various tissues. There is a strong need for fast and dynamic methods which efficiently unravel viral tropism in whole organs. Ultramicroscopy (UM) is a novel fluorescence microscopy technique that images optically cleared undissected specimens, achieving good resolutions at high penetration depths while being non-destructive. UM was applied to obtain high-resolution 3D analysis of AAV transduction in adult mouse brains, especially in the hippocampus, a region of interest for Alzheimer’s disease therapy. We separately or simultaneously compared transduction efficacies for commonly used serotypes (AAV9 and AAVrh10) using fluorescent reporter expression. We provide a detailed comparative and quantitative analysis of the transduction profiles. UM allowed a rapid analysis of marker fluorescence expression in neurons with intact projections deep inside the brain, in defined anatomical structures. Major hippocampal neuronal transduction was observed with both vectors, with slightly better efficacy for AAV9 in UM. Glial response and synaptic marker expression did not change post transduction.We propose UM as a novel valuable complementary tool to efficiently and simultaneously unravel tropism of different viruses in a single non-dissected adult rodent brain.
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Affiliation(s)
- Sandro Alves
- INSERM U1169/MIRCen CEA, Fontenay aux Roses 92265, France, Université Paris-Sud, Université Paris-Saclay, Orsay 91400, France
| | - Julia Bode
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany.,Molecular Mechanisms of Tumor Invasion (V077), DKFZ, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
| | - Alexis-Pierre Bemelmans
- Commissariat à l´Energie Atomique et aux Energies Alternatives (CEA), Départment de la Recherche Fondamentale (DRF), Institut d´Imagerie Biomédicale (I2BM), Molecular Imaging Research Center (MIRCen), Fontenay-aux-Roses, France.,Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, UMR 9199, Neurodegenerative Diseases Laboratory, Fontenay-aux Roses, France
| | - Christof von Kalle
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Nathalie Cartier
- INSERM U1169/MIRCen CEA, Fontenay aux Roses 92265, France, Université Paris-Sud, Université Paris-Saclay, Orsay 91400, France
| | - Björn Tews
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany.,Molecular Mechanisms of Tumor Invasion (V077), DKFZ, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
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121
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Stefaniuk M, Gualda EJ, Pawlowska M, Legutko D, Matryba P, Koza P, Konopka W, Owczarek D, Wawrzyniak M, Loza-Alvarez P, Kaczmarek L. Light-sheet microscopy imaging of a whole cleared rat brain with Thy1-GFP transgene. Sci Rep 2016; 6:28209. [PMID: 27312902 PMCID: PMC4911560 DOI: 10.1038/srep28209] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/31/2016] [Indexed: 12/03/2022] Open
Abstract
Whole-brain imaging with light-sheet fluorescence microscopy and optically cleared tissue is a new, rapidly developing research field. Whereas successful attempts to clear and image mouse brain have been reported, a similar result for rats has proven difficult to achieve. Herein, we report on creating novel transgenic rat harboring fluorescent reporter GFP under control of neuronal gene promoter. We then present data on clearing the rat brain, showing that FluoClearBABB was found superior over passive CLARITY and CUBIC methods. Finally, we demonstrate efficient imaging of the rat brain using light-sheet fluorescence microscopy.
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Affiliation(s)
| | - Emilio J. Gualda
- Institut de Ciencies Fotoniques (ICFO), Barcelona Institute of Science and Technology, 08860, Castelldefels (Barcelona), Spain
| | | | | | | | - Paulina Koza
- Nencki Institute, Pasteura 3, 02-093 Warsaw, Poland
| | | | | | | | - Pablo Loza-Alvarez
- Institut de Ciencies Fotoniques (ICFO), Barcelona Institute of Science and Technology, 08860, Castelldefels (Barcelona), Spain
| | - Leszek Kaczmarek
- Nencki Institute, Pasteura 3, 02-093 Warsaw, Poland
- Institut de Ciencies Fotoniques (ICFO), Barcelona Institute of Science and Technology, 08860, Castelldefels (Barcelona), Spain
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122
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Renier N, Adams EL, Kirst C, Wu Z, Azevedo R, Kohl J, Autry AE, Kadiri L, Umadevi Venkataraju K, Zhou Y, Wang VX, Tang CY, Olsen O, Dulac C, Osten P, Tessier-Lavigne M. Mapping of Brain Activity by Automated Volume Analysis of Immediate Early Genes. Cell 2016; 165:1789-1802. [PMID: 27238021 DOI: 10.1016/j.cell.2016.05.007] [Citation(s) in RCA: 507] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/31/2016] [Accepted: 05/01/2016] [Indexed: 11/26/2022]
Abstract
Understanding how neural information is processed in physiological and pathological states would benefit from precise detection, localization, and quantification of the activity of all neurons across the entire brain, which has not, to date, been achieved in the mammalian brain. We introduce a pipeline for high-speed acquisition of brain activity at cellular resolution through profiling immediate early gene expression using immunostaining and light-sheet fluorescence imaging, followed by automated mapping and analysis of activity by an open-source software program we term ClearMap. We validate the pipeline first by analysis of brain regions activated in response to haloperidol. Next, we report new cortical regions downstream of whisker-evoked sensory processing during active exploration. Last, we combine activity mapping with axon tracing to uncover new brain regions differentially activated during parenting behavior. This pipeline is widely applicable to different experimental paradigms, including animal species for which transgenic activity reporters are not readily available.
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Affiliation(s)
- Nicolas Renier
- Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Eliza L Adams
- Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Christoph Kirst
- Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Zhuhao Wu
- Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Ricardo Azevedo
- Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Johannes Kohl
- Department of Molecular and Cellular Biology, Center for Brain Science, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Anita E Autry
- Department of Molecular and Cellular Biology, Center for Brain Science, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | | | - Kannan Umadevi Venkataraju
- Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, USA; Certerra, Cold Spring Harbor, NY 11724, USA
| | - Yu Zhou
- Department of Radiology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Victoria X Wang
- Department of Radiology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Cheuk Y Tang
- Department of Radiology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Olav Olsen
- Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Center for Brain Science, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Pavel Osten
- Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, USA
| | - Marc Tessier-Lavigne
- Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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123
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Breckwoldt MO, Bode J, Kurz FT, Hoffmann A, Ochs K, Ott M, Deumelandt K, Krüwel T, Schwarz D, Fischer M, Helluy X, Milford D, Kirschbaum K, Solecki G, Chiblak S, Abdollahi A, Winkler F, Wick W, Platten M, Heiland S, Bendszus M, Tews B. Correlated magnetic resonance imaging and ultramicroscopy (MR-UM) is a tool kit to assess the dynamics of glioma angiogenesis. eLife 2016; 5:e11712. [PMID: 26830460 PMCID: PMC4755755 DOI: 10.7554/elife.11712] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/30/2015] [Indexed: 01/08/2023] Open
Abstract
Neoangiogenesis is a pivotal therapeutic target in glioblastoma. Tumor monitoring requires imaging methods to assess treatment effects and disease progression. Until now mapping of the tumor vasculature has been difficult. We have developed a combined magnetic resonance and optical toolkit to study neoangiogenesis in glioma models. We use in vivo magnetic resonance imaging (MRI) and correlative ultramicroscopy (UM) of ex vivo cleared whole brains to track neovascularization. T2* imaging allows the identification of single vessels in glioma development and the quantification of neovessels over time. Pharmacological VEGF inhibition leads to partial vascular normalization with decreased vessel caliber, density, and permeability. To further resolve the tumor microvasculature, we performed correlated UM of fluorescently labeled microvessels in cleared brains. UM resolved typical features of neoangiogenesis and tumor cell invasion with a spatial resolution of ~5 µm. MR-UM can be used as a platform for three-dimensional mapping and high-resolution quantification of tumor angiogenesis.
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Affiliation(s)
- Michael O Breckwoldt
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Julia Bode
- Schaller Research Group, University of Heidelberg and German Cancer Research Center, Heidelberg, Germany.,Molecular Mechanisms of Tumor Invasion, German Cancer Research Center, Heidelberg, Germany
| | - Felix T Kurz
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Angelika Hoffmann
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Katharina Ochs
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany.,Molecular Mechanisms of Tumor Invasion, German Cancer Research Center, Heidelberg, Germany
| | - Martina Ott
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany.,Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Katrin Deumelandt
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany.,Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Krüwel
- Department of Diagnostic and Interventional Radiology, University Medical Center Göttingen, Göttingen, Germany
| | - Daniel Schwarz
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Manuel Fischer
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Xavier Helluy
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany.,NeuroImaging Centre, Research Department of Neuroscience, Ruhr-University Bochum, Bochum, Germany
| | - David Milford
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Klara Kirschbaum
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Gergely Solecki
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Sara Chiblak
- German Cancer Consortium and Heidelberg Institute of Radiation Oncology, National Center for Radiation Research in Oncology, Heidelberg, Germany.,Heidelberg University School of Medicine, Heidelberg University, Heidelberg, Germany.,Translational Radiation Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Amir Abdollahi
- German Cancer Consortium and Heidelberg Institute of Radiation Oncology, National Center for Radiation Research in Oncology, Heidelberg, Germany.,Heidelberg University School of Medicine, Heidelberg University, Heidelberg, Germany.,Translational Radiation Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Frank Winkler
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Wolfgang Wick
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neurooncology, German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Michael Platten
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany.,Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Sabine Heiland
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Martin Bendszus
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Björn Tews
- Schaller Research Group, University of Heidelberg and German Cancer Research Center, Heidelberg, Germany.,Molecular Mechanisms of Tumor Invasion, German Cancer Research Center, Heidelberg, Germany
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Grinevich V, Knobloch-Bollmann HS, Eliava M, Busnelli M, Chini B. Assembling the Puzzle: Pathways of Oxytocin Signaling in the Brain. Biol Psychiatry 2016; 79:155-64. [PMID: 26001309 DOI: 10.1016/j.biopsych.2015.04.013] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/01/2015] [Accepted: 04/19/2015] [Indexed: 12/24/2022]
Abstract
Oxytocin (OT) is a neuropeptide, which can be seen to be one of the molecules of the decade due to its profound prosocial effects in nonvertebrate and vertebrate species, including humans. Although OT can be detected in various physiological fluids (blood, saliva, urine, cerebrospinal fluid) and brain tissue, it is unclear whether peripheral and central OT releases match and synergize. Moreover, the pathways of OT delivery to brain regions involved in specific behaviors are far from clear. Here, we discuss the evolutionarily and ontogenetically determined pathways of OT delivery and OT signaling, which orchestrate activity of the mesolimbic social decision-making network. Furthermore, we speculate that both the alteration in OT delivery and OT receptor expression may cause behavioral abnormalities in patients afflicted with psychosocial diseases.
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Affiliation(s)
- Valery Grinevich
- Schaller Research Group on Neuropeptides, German Cancer Research Center DKFZ, Heidelberg, Germany; CellNetworks Cluster of Excellence, University of Heidelberg, Heidelberg, Germany.
| | - H Sophie Knobloch-Bollmann
- Schaller Research Group on Neuropeptides, German Cancer Research Center DKFZ, Heidelberg, Germany; CellNetworks Cluster of Excellence, University of Heidelberg, Heidelberg, Germany
| | - Marina Eliava
- Schaller Research Group on Neuropeptides, German Cancer Research Center DKFZ, Heidelberg, Germany; CellNetworks Cluster of Excellence, University of Heidelberg, Heidelberg, Germany
| | - Marta Busnelli
- National Research Council, Institute of Neuroscience, Milan, Italy
| | - Bice Chini
- National Research Council, Institute of Neuroscience, Milan, Italy
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Susaki E, Ueda H. Whole-body and Whole-Organ Clearing and Imaging Techniques with Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals. Cell Chem Biol 2016; 23:137-157. [DOI: 10.1016/j.chembiol.2015.11.009] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 11/20/2015] [Accepted: 11/20/2015] [Indexed: 12/29/2022]
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126
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Architectonic Mapping of the Human Brain beyond Brodmann. Neuron 2015; 88:1086-1107. [DOI: 10.1016/j.neuron.2015.12.001] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 10/13/2015] [Accepted: 11/20/2015] [Indexed: 12/25/2022]
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127
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Abstract
Here we describe a protocol for advanced CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis). The CUBIC protocol enables simple and efficient organ clearing, rapid imaging by light-sheet microscopy and quantitative imaging analysis of multiple samples. The organ or body is cleared by immersion for 1-14 d, with the exact time required dependent on the sample type and the experimental purposes. A single imaging set can be completed in 30-60 min. Image processing and analysis can take <1 d, but it is dependent on the number of samples in the data set. The CUBIC clearing protocol can process multiple samples simultaneously. We previously used CUBIC to image whole-brain neural activities at single-cell resolution using Arc-dVenus transgenic (Tg) mice. CUBIC informatics calculated the Venus signal subtraction, comparing different brains at a whole-organ scale. These protocols provide a platform for organism-level systems biology by comprehensively detecting cells in a whole organ or body.
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