1
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Hussain S, Sedlacek M, Cui R, Zhang-Hooks W, Bergles D, Bum-Shin J, Kindt KS, Kachar B. Spontaneous calcium transients in hair cell stereocilia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.12.607658. [PMID: 39185174 PMCID: PMC11343103 DOI: 10.1101/2024.08.12.607658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
The hair bundle of auditory and vestibular hair cells converts mechanical stimuli into electrical signals through mechanoelectrical transduction (MET). The MET apparatus is built around a tip link that connects neighboring stereocilia that are aligned in the direction of mechanosensitivity of the hair bundle. Upon stimulation, the MET channel complex responds to changes in tip-link tension and allows a cation influx into the cell. Ca2+ influx in stereocilia has been used as a signature of MET activity. Using genetically encoded Ca2+ sensors (GCaMP3, GCaMP6s) and high-performance fluorescence confocal microscopy, we detect spontaneous Ca2+ transients in individual stereocilia in developing and fully formed hair bundles. We demonstrate that this activity is abolished by MET channel blockers and thus likely originates from putative MET channels. We observe Ca2+ transients in the stereocilia of mice in tissue explants as well as in vivo in zebrafish hair cells, indicating this activity is functionally conserved. Within stereocilia, the origin of Ca2+ transients is not limited to the canonical MET site at the stereocilia tip but is also present along the stereocilia length. Remarkably, we also observe these Ca2+ transients in the microvilli-like structures on the hair cell surface in the early stages of bundle development, prior to the onset of MET. Ca2+ transients are also present in the tallest rows of stereocilia in auditory hair cells, structures not traditionally thought to contain MET channels. We hypothesize that this newly described activity may reflect stochastic and spontaneous MET channel opening. Localization of these transients to other regions of the stereocilia indicates the presence of a pool of channels or channel precursors. Our work provides insights into MET channel assembly, maturation, function, and turnover.
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Affiliation(s)
- Saman Hussain
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Miloslav Sedlacek
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Runjia Cui
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wendy Zhang-Hooks
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dwight Bergles
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Otolaryngology-Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jung Bum-Shin
- Department of Neuroscience, University of Virginia, Charlottesville, VA 22908
| | - Katie S. Kindt
- Laboratory of Cellular Biology, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bechara Kachar
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
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2
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Culley S, Caballero AC, Burden JJ, Uhlmann V. Made to measure: An introduction to quantifying microscopy data in the life sciences. J Microsc 2024; 295:61-82. [PMID: 37269048 DOI: 10.1111/jmi.13208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/04/2023]
Abstract
Images are at the core of most modern biological experiments and are used as a major source of quantitative information. Numerous algorithms are available to process images and make them more amenable to be measured. Yet the nature of the quantitative output that is useful for a given biological experiment is uniquely dependent upon the question being investigated. Here, we discuss the 3 main types of information that can be extracted from microscopy data: intensity, morphology, and object counts or categorical labels. For each, we describe where they come from, how they can be measured, and what may affect the relevance of these measurements in downstream data analysis. Acknowledging that what makes a measurement 'good' is ultimately down to the biological question being investigated, this review aims at providing readers with a toolkit to challenge how they quantify their own data and be critical of conclusions drawn from quantitative bioimage analysis experiments.
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Affiliation(s)
- Siân Culley
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | | | | | - Virginie Uhlmann
- European Bioinformatics Institute (EMBL-EBI), EMBL, Cambridge, UK
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3
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Verwee E, Van de Walle D, De Bruyne M, Mienis E, Sekulic M, Chaerle P, Vyverman W, Foubert I, Dewettinck K. Visualisation of microalgal lipid bodies through electron microscopy. J Microsc 2024; 293:118-131. [PMID: 38149687 DOI: 10.1111/jmi.13259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 12/28/2023]
Abstract
In this study, transmission electron microscopy (TEM) and cryo-scanning electron microscopy (cryo-SEM) were evaluated for their ability to detect lipid bodies in microalgae. To do so, Phaeodactylum tricornutum and Nannochloropsis oculata cells were harvested in both the mid-exponential and early stationary growth phase. Two different cryo-SEM cutting methods were compared: cryo-planing and freeze-fracturing. The results showed that, despite the longer preparation time, TEM visualisation preceded by cryo-immobilisation allows a clear detection of lipid bodies and is preferable to cryo-SEM. Using freeze-fracturing, lipid bodies were rarely detected. This was only feasible if crystalline layers in the internal structure, most likely related to sterol esters or di-saturated triacylglycerols, were revealed. Furthermore, lipid bodies could not be detected using cryo-planing. Cryo-SEM is also not the preferred technique to recognise other organelles besides lipid bodies, yet it did reveal chloroplasts in both species and filament-containing organelles in cryo-planed Nannochloropsis oculata samples.
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Affiliation(s)
- Ellen Verwee
- Department of Food Technology, Food Structure & Function research group, Safety and Health, Ghent University, Ghent, Belgium
- Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Davy Van de Walle
- Department of Food Technology, Food Structure & Function research group, Safety and Health, Ghent University, Ghent, Belgium
| | - Michiel De Bruyne
- VIB BioImaging Core VIB, Ghent, Belgium
- VIB Center for Inflammation Research VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Esther Mienis
- Research Unit Food & Lipids, KU Leuven Kulak, Kortrijk, Belgium
- Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
| | - Mirna Sekulic
- Department of Biology, Laboratory of Protistology and Aquatic Ecology, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology VIB, Ghent, Belgium
| | - Peter Chaerle
- Department of Biology, Laboratory of Protistology and Aquatic Ecology, Ghent University, Ghent, Belgium
- Department of Biology, BCCM/DCG Diatoms Collection, Ghent University, Ghent, Belgium
| | - Wim Vyverman
- Department of Biology, Laboratory of Protistology and Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Imogen Foubert
- Research Unit Food & Lipids, KU Leuven Kulak, Kortrijk, Belgium
- Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
| | - Koen Dewettinck
- Department of Food Technology, Food Structure & Function research group, Safety and Health, Ghent University, Ghent, Belgium
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4
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Sachse M, Fernández-Sánchez SY, Tenorio R, de Castro IF, Risco C. Imaging Bunyavirus Infections by Transmission Electron Microscopy: Conventional Sample Preparation vs High-Pressure Freezing and Freeze-Substitution. Methods Mol Biol 2024; 2824:241-258. [PMID: 39039417 DOI: 10.1007/978-1-0716-3926-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Transmission electron microscopy significantly contributed to unveil the course of virus entry, replication, morphogenesis, and egress. For these studies, the most widely used approach is imaging ultrathin sections of virus-infected cells embedded in a plastic resin that is transparent to electrons. Before infiltration in a resin, cells must be processed to stabilize their components under the observation conditions in an electron microscope, such as high vacuum and irradiation with electrons. For conventional sample preparation, chemical fixation and dehydration are followed by infiltration in the resin and polymerization to produce a hard block that can be sectioned with an ultramicrotome. Another method that provides a superior preservation of cell components is high-pressure freezing (HPF) followed by freeze substitution (FS) before resin infiltration and polymerization. This chapter describes both procedures with cells infected with Bunyamwera virus (BUNV), a well characterized member of the Bunyavirales, and compares the morphological details of different viral structures imaged in the two types of samples. Advantages, disadvantages, and applications of conventional processing and HPF/FS are also presented and discussed.
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Affiliation(s)
- Martin Sachse
- Centro Nacional de Microbiología/ISCIII, Madrid, Spain.
| | - Sara Y Fernández-Sánchez
- Cell Structure Lab, Centro Nacional de Biotecnología, CNB - CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Raquel Tenorio
- Cell Structure Lab, Centro Nacional de Biotecnología, CNB - CSIC, Campus de Cantoblanco, Madrid, Spain
| | | | - Cristina Risco
- Cell Structure Lab, Centro Nacional de Biotecnología, CNB - CSIC, Campus de Cantoblanco, Madrid, Spain.
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5
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Xu CS, Pang S, Shtengel G, Müller A, Ritter AT, Hoffman HK, Takemura SY, Lu Z, Pasolli HA, Iyer N, Chung J, Bennett D, Weigel AV, Freeman M, van Engelenburg SB, Walther TC, Farese RV, Lippincott-Schwartz J, Mellman I, Solimena M, Hess HF. An open-access volume electron microscopy atlas of whole cells and tissues. Nature 2021; 599:147-151. [PMID: 34616045 PMCID: PMC9004664 DOI: 10.1038/s41586-021-03992-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 09/02/2021] [Indexed: 02/06/2023]
Abstract
Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structures with nanometre resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations in that they visualize only a single slice or a relatively small volume of the cell, respectively. Focused ion beam-scanning electron microscopy (FIB-SEM) has demonstrated the ability to image small volumes of cellular samples with 4-nm isotropic voxels1. Owing to advances in the precision and stability of FIB milling, together with enhanced signal detection and faster SEM scanning, we have increased the volume that can be imaged with 4-nm voxels by two orders of magnitude. Here we present a volume EM atlas at such resolution comprising ten three-dimensional datasets for whole cells and tissues, including cancer cells, immune cells, mouse pancreatic islets and Drosophila neural tissues. These open access data (via OpenOrganelle2) represent the foundation of a field of high-resolution whole-cell volume EM and subsequent analyses, and we invite researchers to explore this atlas and pose questions.
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Affiliation(s)
- C Shan Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Song Pang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Gleb Shtengel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Andreas Müller
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | | | - Huxley K Hoffman
- Molecular and Cellular Biophysics Program, Department of Biological Sciences, University of Denver, Denver, CO, USA
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Shin-Ya Takemura
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Zhiyuan Lu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - H Amalia Pasolli
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY, USA
| | - Nirmala Iyer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jeeyun Chung
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Davis Bennett
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Aubrey V Weigel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Melanie Freeman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Advanced Bio-imaging Center, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Schuyler B van Engelenburg
- Molecular and Cellular Biophysics Program, Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Tobias C Walther
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Robert V Farese
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | | | | | - Michele Solimena
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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6
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Velamoor S, Mitchell A, Bostina M, Harland D. Processing hair follicles for transmission electron microscopy. Exp Dermatol 2021; 31:110-121. [PMID: 34351648 DOI: 10.1111/exd.14439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 11/30/2022]
Abstract
Transmission electron microscopy (TEM) has greatly advanced our knowledge of hair growth and follicle morphogenesis, but complex preparations such as fixation, dehydration and embedding compromise ultrastructure. While recent developments with cryofixation have been shown to preserve the ultrastructure of biological materials close to native state, they do have limitations. This review will focus on each stage of the TEM sample preparation process and their effects on the structural integrity of follicles.
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Affiliation(s)
- Sailakshmi Velamoor
- Proteins and Metabolites, AgResearch Limited, Lincoln, New Zealand.,Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Allan Mitchell
- Otago Micro and Nano Imaging, University of Otago, Dunedin, New Zealand
| | - Mihnea Bostina
- Microbiology and Immunology, University of Otago, Dunedin, New Zealand.,Otago Micro and Nano Imaging, University of Otago, Dunedin, New Zealand
| | - Duane Harland
- Proteins and Metabolites, AgResearch Limited, Lincoln, New Zealand
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7
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VELAMOOR S, RICHENA M, MITCHELL A, LEQUEUX S, BOSTINA M, HARLAND D. High‐pressure freezing followed by freeze substitution of a complex and variable density miniorgan: the wool follicle. J Microsc 2020; 278:18-28. [DOI: 10.1111/jmi.12875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/16/2020] [Accepted: 02/06/2020] [Indexed: 01/15/2023]
Affiliation(s)
- S. VELAMOOR
- Lincoln Research Centre, Food & Bio‐Based ProductsAgresearch Limited Lincoln New Zealand
- Department of Immunology and MicrobiologyUniversity of Otago Dunedin New Zealand
| | - M. RICHENA
- Lincoln Research Centre, Food & Bio‐Based ProductsAgresearch Limited Lincoln New Zealand
| | - A. MITCHELL
- Otago Micro and Nano Imaging UnitUniversity of Otago Dunedin New Zealand
| | - S. LEQUEUX
- Otago Micro and Nano Imaging UnitUniversity of Otago Dunedin New Zealand
| | - M. BOSTINA
- Department of Immunology and MicrobiologyUniversity of Otago Dunedin New Zealand
- Otago Micro and Nano Imaging UnitUniversity of Otago Dunedin New Zealand
| | - D. HARLAND
- Lincoln Research Centre, Food & Bio‐Based ProductsAgresearch Limited Lincoln New Zealand
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8
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Roman M, Rigo C, Castillo-Michel H, Urgast DS, Feldmann J, Munivrana I, Vindigni V, Mičetić I, Benetti F, Barbante C, Cairns WRL. Spatiotemporal distribution and speciation of silver nanoparticles in the healing wound. Analyst 2020; 145:6456-6469. [DOI: 10.1039/d0an00607f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
First observation of AgNPs dynamics in the wounds of real patients through elemental imaging and speciation.
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Affiliation(s)
- Marco Roman
- Ca’ Foscari University of Venice
- Department of Environmental Sciences
- Informatics and Statistics (DAIS)
- 30172 Venice Mestre
- Italy
| | - Chiara Rigo
- Ca’ Foscari University of Venice
- Department of Environmental Sciences
- Informatics and Statistics (DAIS)
- 30172 Venice Mestre
- Italy
| | | | - Dagmar S. Urgast
- University of Aberdeen
- Trace Element Speciation Laboratory
- Aberdeen AB24 3UE
- UK
| | - Jörg Feldmann
- University of Aberdeen
- Trace Element Speciation Laboratory
- Aberdeen AB24 3UE
- UK
- University of Graz
| | - Ivan Munivrana
- University Hospital of Padua
- Burns Centre
- Division of Plastic Surgery
- 35128 Padua
- Italy
| | - Vincenzo Vindigni
- University Hospital of Padua
- Burns Centre
- Division of Plastic Surgery
- 35128 Padua
- Italy
| | - Ivan Mičetić
- University of Padua
- Department of Biomedical Sciences
- 35131 Padua
- Italy
| | - Federico Benetti
- EcamRicert Srl
- European Centre for the Sustainable Impact of Nanotechnology (ECSIN)
- Corso Stati Uniti 4
- 35127 Padua
- Italy
| | - Carlo Barbante
- Ca’ Foscari University of Venice
- Department of Environmental Sciences
- Informatics and Statistics (DAIS)
- 30172 Venice Mestre
- Italy
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9
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Beck T, Kilchling T, Reese S, Brühschwein A, Meyer-Lindenberg A. Influence of storage on the quality of conventional CT and µCT-imaging for the middle and inner cat ear. Anat Sci Int 2019; 95:190-201. [PMID: 31728859 DOI: 10.1007/s12565-019-00509-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
Abstract
The aim of this study was to analyze whether different fixation methods such as freezing or formaldehyde storage for different periods of time have an influence on the recognition of anatomical relevant structures in the middle and inner ear of the cat with conventional computed tomography (cCT) and micro-computed tomography (µCT). Besides, effects of freeze-thaw cycles on determined structures of the ear were investigated by means of histological slices. Three veterinarians with different radiologic expertise evaluated the scans of 30 dissected cat ears anonymously and scored predefined structures in a five-point scale with reference to visually sharp reproducibility and perfect image quality. The total scores of the different fixation groups as well as the ears within a group were compared with each other. Furthermore, an intra-reader examination including an evaluation of the identifiability of specified structures was performed for both imaging methods. cCT as well as µCT-scans have a very low variation coefficient of 1.6% and 2.3%, respectively. The results for the alterations between the different fixation methods show that the changes for cCT-scans are negligible, as the percentage alteration compared to fresh samples ranges in a very small interval with values from 1.0% better to 1.2% worse. µCT-scans are more influenced by the fixation method with a range from 1.3% better to 6.9% worse values. The scans mostly deteriorated after two freeze-thaw cycles (1.8% worse) and after storing the samples for 1 (2.4% worse), respectively, and 3 weeks in formaldehyde (6.9% worse).
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Affiliation(s)
- Tobias Beck
- Clinic for Small Animal Surgery and Reproduction, Ludwig-Maximilians-University Munich, Veterinärstraße 13, 80539, Munich, Germany. .,, Wolfratshausen, Germany.
| | - T Kilchling
- Clinic for Small Animal Surgery and Reproduction, Ludwig-Maximilians-University Munich, Veterinärstraße 13, 80539, Munich, Germany.,, Baden-Baden, Germany
| | - S Reese
- Veterinary Department, Institute of Veterinary Anatomy, Histology and Embryology, Ludwig-Maximilians-University Munich, Veterinärstraße 13, 80539, Munich, Germany
| | - A Brühschwein
- Clinic for Small Animal Surgery and Reproduction, Ludwig-Maximilians-University Munich, Veterinärstraße 13, 80539, Munich, Germany
| | - Andrea Meyer-Lindenberg
- Clinic for Small Animal Surgery and Reproduction, Ludwig-Maximilians-University Munich, Veterinärstraße 13, 80539, Munich, Germany
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10
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Numerical analysis of an enhanced cooling rate cryopreservation process in a biological tissue. J Therm Biol 2019; 81:146-153. [DOI: 10.1016/j.jtherbio.2019.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/25/2019] [Accepted: 03/01/2019] [Indexed: 01/19/2023]
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11
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Ongay S, Langelaar-Makkinje M, Stoop MP, Liu N, Overkleeft H, Luider TM, Groothuis GMM, Bischoff R. Cleavable Crosslinkers as Tissue Fixation Reagents for Proteomic Analysis. Chembiochem 2018; 19:736-743. [PMID: 29356267 DOI: 10.1002/cbic.201700625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Indexed: 12/17/2022]
Abstract
Formaldehyde fixation is widely used for long-term maintenance of tissue. However, due to formaldehyde-induced crosslinks, fixed tissue proteins are difficult to extract, which hampers mass spectrometry (MS) proteomic analyses. Recent years have seen the use of different combinations of high temperature and solubilizing agents (usually derived from antigen retrieval techniques) to unravel formaldehyde-fixed paraffin-embedded tissue proteomes. However, to achieve protein extraction yields similar to those of fresh-frozen tissue, high-temperature heating is necessary. Such harsh extraction conditions can affect sensitive amino acids and post-translational modifications, resulting in the loss of important information, while still not resulting in protein yields comparable to those of fresh-frozen tissue. Herein, the objective is to evaluate cleavable protein crosslinkers as fixatives that allow tissue preservation and efficient protein extraction from fixed tissue for MS proteomics under mild conditions. With this goal in mind, disuccinimidyl tartrate (DST) and dithiobis(succinimidylpropionate) (DSP) are investigated as cleavable fixating reagents. These compounds crosslink proteins by reacting with amino groups, leading to amide bond formation, and can be cleaved with sodium metaperiodate (cis-diols, DST) or reducing agents (disulfide bonds, DSP), respectively. Results show that cleavable protein crosslinking with DST and DSP allows tissue fixation with morphology preservation comparable to that of formaldehyde. In addition, cleavage of DSP improves protein recovery from fixed tissue by a factor of 18 and increases the number of identified proteins by approximately 20 % under mild extraction conditions compared with those of formaldehyde-fixed paraffin-embedded tissue. A major advantage of DSP is the introduction of well-defined protein modifications that can be taken into account during database searching. In contrast to DSP fixation, DST fixation followed by cleavage with sodium metaperiodate, although effective, results in side reactions that prevent effective protein extraction and interfere with protein identification. Protein crosslinkers that can be cleaved under mild conditions and result in defined modifications, such as DSP, are thus viable alternatives to formaldehyde as tissue fixatives to facilitate protein analysis from paraffin-embedded, fixed tissue.
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Affiliation(s)
- Sara Ongay
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands
| | - Miriam Langelaar-Makkinje
- Department Pharmacokinetics, Toxicology and Targeting, University of Groningen, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands
| | - Marcel P Stoop
- Department of Neurology, Erasmus University Medical Center, P. O. Box 1738, 3000 DR, Rotterdam, The Netherlands
| | - Nora Liu
- Department of Bio-Organic Synthesis, Leiden University, P. O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Hermen Overkleeft
- Department of Bio-Organic Synthesis, Leiden University, P. O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus University Medical Center, P. O. Box 1738, 3000 DR, Rotterdam, The Netherlands
| | - Geny M M Groothuis
- Department Pharmacokinetics, Toxicology and Targeting, University of Groningen, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands
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12
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Borges AA, Neta LBQ, Santos MV, Oliveira MF, Silva AR, Pereira AF. Combination of ethylene glycol with sucrose increases survival rate after vitrification of somatic tissue of collared peccaries (Pecari tajacu Linnaeus, 1758). PESQUISA VETERINARIA BRASILEIRA 2018. [DOI: 10.1590/1678-5150-pvb-5193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT: The cryopreservation of somatic tissue in collared peccaries promotes an alternative source of genetic material of this specie. The solid-surface vitrification (SSV) is a great option for tissue conservation; nevertheless, the optimization of SSV requirements is necessary, especially when referred to cryoprotectants that will compose the vitrification solution. Therefore, the aim was to evaluate the effect of the presence of 0.25 M sucrose in addition to different combinations (only or association) and concentrations (1.5 M or 3.0 M) of ethylene glycol (EG) and/or dimethyl sulfoxide (DMSO) in the somatic tissue vitrification of collared peccaries. Subsequently, we tested six combinations of cryoprotectants with or without sucrose in Dulbecco modified Eagle medium (DMEM) plus 10% fetal bovine serum (FBS). Thus, 3.0 M EG with sucrose was able to maintain normal tissue characteristics compared with non-vitrified (control), especially for the volumetric ratio of epidermis (61.2 vs. 58.7%) and dermis (34.5 vs. 36.6%), number of fibroblast (90.3 vs. 127.0), argyrophilic nucleolar organizer region (AgNOR) ratio (0.09 vs. 0.17%) and nucleus area (15.4 vs. 14.5 μm2) respectively. In conclusion, 3.0 M EG with 0.25 M sucrose and 10% FBS resulted in a better cryoprotectant composition in the SSV for somatic tissue of collared peccaries.
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13
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Cano-Garrido O, Garcia-Fruitós E, Villaverde A, Sánchez-Chardi A. Improving Biomaterials Imaging for Nanotechnology: Rapid Methods for Protein Localization at Ultrastructural Level. Biotechnol J 2018; 13:e1700388. [PMID: 29271611 DOI: 10.1002/biot.201700388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 12/07/2017] [Indexed: 11/06/2022]
Abstract
The preparation of biological samples for electron microscopy is material- and time-consuming because it is often based on long protocols that also may produce artifacts. Protein labeling for transmission electron microscopy (TEM) is such an example, taking several days. However, for protein-based nanotechnology, high resolution imaging techniques are unique and crucial tools for studying the spatial distribution of these molecules, either alone or as components of biomaterials. In this paper, we tested two new short methods of immunolocalization for TEM, and compared them with a standard protocol in qualitative and quantitative approaches by using four protein-based nanoparticles. We reported a significant increase of labeling per area of nanoparticle in both new methodologies (H = 19.811; p < 0.001) with all the model antigens tested: GFP (H = 22.115; p < 0.001), MMP-2 (H = 19.579; p < 0.001), MMP-9 (H = 7.567; p < 0.023), and IFN-γ (H = 62.110; p < 0.001). We also found that the most suitable protocol for labeling depends on the nanoparticle's tendency to aggregate. Moreover, the shorter methods reduce artifacts, time (by 30%), residues, and reagents hindering, losing, or altering antigens, and obtaining a significant increase of protein localization (of about 200%). Overall, this study makes a step forward in the development of optimized protocols for the nanoscale localization of peptides and proteins within new biomaterials.
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Affiliation(s)
- Olivia Cano-Garrido
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona 08320, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona 08320, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN)
| | - Elena Garcia-Fruitós
- Departament de Producció de Remugants, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui 08140, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona 08320, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona 08320, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN)
| | - Alejandro Sánchez-Chardi
- Servei de Microscòpia, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona 08320, Spain
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14
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Vélez-Ortega AC, Frolenkov GI. Visualization of Live Cochlear Stereocilia at a Nanoscale Resolution Using Hopping Probe Ion Conductance Microscopy. Methods Mol Biol 2017; 1427:203-21. [PMID: 27259929 DOI: 10.1007/978-1-4939-3615-1_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The mechanosensory apparatus that detects sound-induced vibrations in the cochlea is located on the apex of the auditory sensory hair cells and it is made up of actin-filled projections, called stereocilia. In young rodents, stereocilia bundles of auditory hair cells consist of 3-4 rows of stereocilia of decreasing height and varying thickness. Morphological studies of the auditory stereocilia bundles in live hair cells have been challenging because the diameter of each stereocilium is near or below the resolution limit of optical microscopy. In theory, scanning probe microscopy techniques, such as atomic force microscopy, could visualize the surface of a living cell at a nanoscale resolution. However, their implementations for hair cell imaging have been largely unsuccessful because the probe usually damages the bundle and disrupts the bundle cohesiveness during imaging. We overcome these limitations by using hopping probe ion conductance microscopy (HPICM), a non-contact scanning probe technique that is ideally suited for the imaging of live cells with a complex topography. Organ of Corti explants are placed in a physiological solution and then a glass nanopipette-which is connected to a 3D-positioning piezoelectric system and to a patch clamp amplifier-is used to scan the surface of the live hair cells at nanometer resolution without ever touching the cell surface.Here, we provide a detailed protocol for the imaging of mouse or rat stereocilia bundles in live auditory hair cells using HPICM. We provide information about the fabrication of the nanopipettes, the calibration of the HPICM setup, the parameters we have optimized for the imaging of live stereocilia bundles and, lastly, a few basic image post-processing manipulations.
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Affiliation(s)
- A Catalina Vélez-Ortega
- Department of Physiology, College of Medicine, Chandler Medical Center, University of Kentucky, MS508, 800 Rose Street, Lexington, KY, 40536, USA
| | - Gregory I Frolenkov
- Department of Physiology, College of Medicine, Chandler Medical Center, University of Kentucky, MS508, 800 Rose Street, Lexington, KY, 40536, USA.
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15
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Claeys M, Yushin VV, Leunissen JL, Claeys J, Bert W. Self-Pressurised Rapid Freezing (SPRF): an easy-to-use and low-cost alternative cryo-fixation method for nematodes. NEMATOLOGY 2017. [DOI: 10.1163/15685411-00003093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Self-Pressurised Rapid Freezing (SPRF), an easy-to-use and low-cost alternative cryo-fixation method, was evaluated based on a comparative analysis of the ultrastructure of spermatozoa of the nematodes Acrobeles complexus and Caenorhabditis elegans. Sealed copper tubes, packed with active nematodes in water, were plunged into nitrogen slush, a semi-solid form of nitrogen. The water inside the capillary copper tube expands upon cooling due to the formation of hexagonal ice, thereby generating high pressure intrinsically for cryo-fixation of the sample. For sperm cells cryo-fixed by SPRF, the preservation of the ultrastructure was comparable to that achieved with high pressure freezing. This was evidenced by the clear details in mitochondria, membranous organelles and cytoskeleton in the pseudopod. It was demonstrated that SPRF fixation did not destroy antigenicity, based on the results of the immunolocalisation of the major sperm protein in both species. In conclusion, SPRF is a low-cost alternative cryo-fixation method for nematodes.
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Affiliation(s)
- Myriam Claeys
- Nematology Research Unit, Department of Biology, Ghent University, Belgium
| | - Vladimir V. Yushin
- National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690041, Russia
- Far Eastern Federal University, Vladivostok 690950, Russia
| | | | - Jef Claeys
- Nematology Research Unit, Department of Biology, Ghent University, Belgium
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, Belgium
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16
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Parker A, Chessum L, Mburu P, Sanderson J, Bowl MR. Light and Electron Microscopy Methods for Examination of Cochlear Morphology in Mouse Models of Deafness. ACTA ACUST UNITED AC 2016; 6:272-306. [PMID: 27584554 DOI: 10.1002/cpmo.10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mice are an invaluable model organism for the study of auditory function. Even though there are differences in size and frequency response, the anatomy and physiology of the mouse and human ear are remarkably similar. In addition, the tools available for genetic manipulation in the mouse have enabled the generation of models carrying mutations in orthologous human deafness-causing genes, helping to validate these lesions and assess their functional consequence. Reciprocally, novel gene mutations discovered to cause auditory deficits in the mouse highlight potential new loci for human hearing loss, and expand our basic knowledge of the mechanisms and pathways important for the function of the mammalian ear. Microscopy and imaging are invaluable techniques that allow detailed characterization of cochlear pathologies associated with particular gene mutations. However, the highly organized, delicate, and intricate structures responsible for transduction of sound waves into nerve impulses are encapsulated in one of the hardest bones in the body - the temporal bone. This makes sample preparation without damage to the soft tissue, be it from dissection or processing, somewhat challenging. Fortunately, there are numerous methods for achieving high-quality images of the mouse cochlea. Reported in this article are a selection of sample preparation and imaging techniques that can be used routinely to assess cochlear morphology. Several protocols are also described for immunodetection of proteins in the cochlea. In addition, the advantages and disadvantages between different imaging platforms and their suitability for different types of microscopic examination are highlighted. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Andrew Parker
- Mammalian Genetics Unit, MRC Harwell, Oxfordshire, United Kingdom
| | - Lauren Chessum
- Mammalian Genetics Unit, MRC Harwell, Oxfordshire, United Kingdom
| | - Philomena Mburu
- Mammalian Genetics Unit, MRC Harwell, Oxfordshire, United Kingdom
| | - Jeremy Sanderson
- Mammalian Genetics Unit, MRC Harwell, Oxfordshire, United Kingdom
| | - Michael R Bowl
- Mammalian Genetics Unit, MRC Harwell, Oxfordshire, United Kingdom
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17
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Bullen A, West T, Moores C, Ashmore J, Fleck RA, MacLellan-Gibson K, Forge A. Association of intracellular and synaptic organization in cochlear inner hair cells revealed by 3D electron microscopy. J Cell Sci 2015; 128:2529-40. [PMID: 26045447 PMCID: PMC4510854 DOI: 10.1242/jcs.170761] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/29/2015] [Indexed: 01/12/2023] Open
Abstract
The ways in which cell architecture is modelled to meet cell function is a poorly understood facet of cell biology. To address this question, we have studied the cytoarchitecture of a cell with highly specialised organisation, the cochlear inner hair cell (IHC), using multiple hierarchies of three-dimensional (3D) electron microscopy analyses. We show that synaptic terminal distribution on the IHC surface correlates with cell shape, and the distribution of a highly organised network of membranes and mitochondria encompassing the infranuclear region of the cell. This network is juxtaposed to a population of small vesicles, which represents a potential new source of neurotransmitter vesicles for replenishment of the synapses. Structural linkages between organelles that underlie this organisation were identified by high-resolution imaging. Taken together, these results describe a cell-encompassing network of membranes and mitochondria present in IHCs that support efficient coding and transmission of auditory signals. Such techniques also have the potential for clarifying functionally specialised cytoarchitecture of other cell types. Summary: 3D electron microscopy reconstructs the highly organised structure of the infranuclear region of the cochlear inner hair cell, which supports synaptic functions.
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Affiliation(s)
- Anwen Bullen
- Centre for Auditory Research, UCL Ear Institute, London WC1X 8EE, UK
| | - Timothy West
- Centre for Auditory Research, UCL Ear Institute, London WC1X 8EE, UK
| | - Carolyn Moores
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Jonathan Ashmore
- Centre for Auditory Research, UCL Ear Institute, London WC1X 8EE, UK Neuroscience, Physiology & Pharmacology, UCL, London WC1E 6BT, UK
| | - Roland A Fleck
- Centre for Ultrastructural Imaging, King's College London, London WC2R 2LS, UK
| | | | - Andrew Forge
- Centre for Auditory Research, UCL Ear Institute, London WC1X 8EE, UK
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18
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Taylor RR, Jagger DJ, Saeed SR, Axon P, Donnelly N, Tysome J, Moffatt D, Irving R, Monksfield P, Coulson C, Freeman SR, Lloyd SK, Forge A. Characterizing human vestibular sensory epithelia for experimental studies: new hair bundles on old tissue and implications for therapeutic interventions in ageing. Neurobiol Aging 2015; 36:2068-84. [PMID: 25818177 PMCID: PMC4436436 DOI: 10.1016/j.neurobiolaging.2015.02.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/09/2015] [Accepted: 02/11/2015] [Indexed: 12/19/2022]
Abstract
Balance disequilibrium is a significant contributor to falls in the elderly. The most common cause of balance dysfunction is loss of sensory cells from the vestibular sensory epithelia of the inner ear. However, inaccessibility of inner ear tissue in humans severely restricts possibilities for experimental manipulation to develop therapies to ameliorate this loss. We provide a structural and functional analysis of human vestibular sensory epithelia harvested at trans-labyrinthine surgery. We demonstrate the viability of the tissue and labeling with specific markers of hair cell function and of ion homeostasis in the epithelium. Samples obtained from the oldest patients revealed a significant loss of hair cells across the tissue surface, but we found immature hair bundles present in epithelia harvested from patients >60 years of age. These results suggest that the environment of the human vestibular sensory epithelium could be responsive to stimulation of developmental pathways to enhance hair cell regeneration, as has been demonstrated successfully in the vestibular organs of adult mice.
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Affiliation(s)
| | | | - Shakeel R Saeed
- UCL Ear Institute, London, UK; Royal National Throat Nose and Ear Hospital, UCLH NHS Foundation Trust, London, UK
| | - Patrick Axon
- Addenbrooke's Hospital, Cambridge University NHS Foundation Trust, Cambridge, UK
| | - Neil Donnelly
- Addenbrooke's Hospital, Cambridge University NHS Foundation Trust, Cambridge, UK
| | - James Tysome
- Addenbrooke's Hospital, Cambridge University NHS Foundation Trust, Cambridge, UK
| | - David Moffatt
- Addenbrooke's Hospital, Cambridge University NHS Foundation Trust, Cambridge, UK
| | - Richard Irving
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Medical Centre, Birmingham, UK
| | - Peter Monksfield
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Medical Centre, Birmingham, UK
| | - Chris Coulson
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Medical Centre, Birmingham, UK
| | - Simon R Freeman
- Manchester Royal Infirmary, Central Manchester University Hospitals NHS Trust, Manchester, UK; Salford Royal Infirmary, Salford Royal NHS Foundation Trust, Salford, UK
| | - Simon K Lloyd
- Manchester Royal Infirmary, Central Manchester University Hospitals NHS Trust, Manchester, UK; Salford Royal Infirmary, Salford Royal NHS Foundation Trust, Salford, UK
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A short splice form of Xin-actin binding repeat containing 2 (XIRP2) lacking the Xin repeats is required for maintenance of stereocilia morphology and hearing function. J Neurosci 2015; 35:1999-2014. [PMID: 25653358 DOI: 10.1523/jneurosci.3449-14.2015] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Approximately one-third of known deafness genes encode proteins located in the hair bundle, the sensory hair cell's mechanoreceptive organelle. In previous studies, we used mass spectrometry to characterize the hair bundle's proteome, resulting in the discovery of novel bundle proteins. One such protein is Xin-actin binding repeat containing 2 (XIRP2), an actin-cross-linking protein previously reported to be specifically expressed in striated muscle. Because mutations in other actin-cross-linkers result in hearing loss, we investigated the role of XIRP2 in hearing function. In the inner ear, XIRP2 is specifically expressed in hair cells, colocalizing with actin-rich structures in bundles, the underlying cuticular plate, and the circumferential actin belt. Analysis using peptide mass spectrometry revealed that the bundle harbors a previously uncharacterized XIRP2 splice variant, suggesting XIRP2's role in the hair cell differs significantly from that reported in myocytes. To determine the role of XIRP2 in hearing, we applied clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-mediated genome-editing technology to induce targeted mutations into the mouse Xirp2 gene, resulting in the elimination of XIRP2 protein expression in the inner ear. Functional analysis of hearing in the resulting Xirp2-null mice revealed high-frequency hearing loss, and ultrastructural scanning electron microscopy analyses of hair cells demonstrated stereocilia degeneration in these mice. We thus conclude that XIRP2 is required for long-term maintenance of hair cell stereocilia, and that its dysfunction causes hearing loss in the mouse.
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