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Sağsöz ME, Sağlam B, Arslan K, Baştuğ T, Çavuş M, Puralı N. Structural, Functional and Molecular Dynamics Examination of a de novo cloned Otopetrin-like Proton Channel in crayfish. Cell Biochem Biophys 2024:10.1007/s12013-024-01310-z. [PMID: 38811473 DOI: 10.1007/s12013-024-01310-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2024] [Indexed: 05/31/2024]
Abstract
Proton channels play a crucial role in many biological functions, as they are responsible for the selective transport of protons across cell membranes. Recently, Otopetrins, a family of eukaryotic proton-selective ion channels, have attracted significant attention due to their diverse physiological roles. Despite the importance of Otopetrins, their structural and functional properties remain relatively unexplored. As a model organism, crayfish have been extensively studied to gain insights into the functioning of the nervous system. These studies cover a wide range of aspects, including the properties of individual neurons and behavioral science. However, studying the physiological systems of crayfish poses challenges for molecular research due to limited molecular sequence information available for these organisms. In the present work was identified an originally cloned mRNA, coding an Otopetrin like proton channel in the crayfish. The coded protein was modeled in silico and possible conduction mechanisms and pathways were revealed. A plasmid of the cloned mRNA was heterologously expressed in HEK293T cells. Functional experiments on transfected cells indicated that the expressed mRNA was coupled to proton conduction across the cell membrane.
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Affiliation(s)
- Mustafa Erdem Sağsöz
- Biophysics Department, Hacettepe University, Faculty of Medicine, Ankara, Türkiye
- Biophysics Department, Atatürk University, Faculty of Medicine, Erzurum, Türkiye
| | - Berk Sağlam
- Biophysics Department, Hacettepe University, Faculty of Medicine, Ankara, Türkiye
| | - Kaan Arslan
- Biophysics Department, Hacettepe University, Faculty of Medicine, Ankara, Türkiye
| | - Turgut Baştuğ
- Biophysics Department, Hacettepe University, Faculty of Medicine, Ankara, Türkiye
| | - Murat Çavuş
- Bozok University, Faculty of Education, Mathematics and Science Education, Yozgat, Türkiye
| | - Nuhan Puralı
- Biophysics Department, Hacettepe University, Faculty of Medicine, Ankara, Türkiye.
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2
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Jędrychowska J, Vardanyan V, Wieczor M, Marciniak A, Czub J, Amini R, Jain R, Shen H, Choi H, Kuznicki J, Korzh V. Mutant analysis of Kcng4b reveals how the different functional states of the voltage-gated potassium channel regulate ear development. Dev Biol 2024:S0012-1606(24)00081-2. [PMID: 38492873 DOI: 10.1016/j.ydbio.2024.03.002] [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: 08/01/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 03/18/2024]
Abstract
The voltage gated (Kv) slow-inactivating delayed rectifier channel regulates the development of hollow organs of the zebrafish. The functional channel consists of the tetramer of electrically active Kcnb1 (Kv2.1) subunits and Kcng4b (Kv6.4) modulatory or electrically silent subunits. The two mutations in zebrafish kcng4b gene - kcng4b-C1 and kcng4b-C2 (Gasanov et al., 2021) - have been studied during ear development using electrophysiology, developmental biology and in silico structural modelling. kcng4b-C1 mutation causes a C-terminal truncation characterized by mild Kcng4b loss-of-function (LOF) manifested by failure of kinocilia to extend and formation of ectopic otoliths. In contrast, the kcng4b-C2-/- mutation causes the C-terminal domain to elongate and the ectopic seventh transmembrane (TM) domain to form, converting the intracellular C-terminus to an extracellular one. Kcng4b-C2 acts as a Kcng4b gain-of-function (GOF) allele. Otoliths fail to develop and kinocilia are reduced in kcng4b-C2-/-. These results show that different mutations of the silent subunit Kcng4 can affect the activity of the Kv channel and cause a wide range of developmental defects.
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Affiliation(s)
- Justyna Jędrychowska
- International Institute of Molecular and Cell Biology in Warsaw, Poland; Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Vitya Vardanyan
- Institute of Molecular Biology, Armenian Academy of Sciences, Yerevan, Armenia
| | - Milosz Wieczor
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Antoni Marciniak
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Razieh Amini
- International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Ruchi Jain
- International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Hongyuan Shen
- Singapore Nuclear Research and Safety Initiative, National University of Singapore, Singapore
| | - Hyungwon Choi
- Cardiovascular Research Institute, National University Health Sciences, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jacek Kuznicki
- International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology in Warsaw, Poland.
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Jiang Q, Liang X, Ye T, Zhang Y, Lou B. Metabonomics and Transcriptomics Analyses Reveal the Development Process of the Auditory System in the Embryonic Development Period of the Small Yellow Croaker under Background Noise. Int J Mol Sci 2024; 25:1954. [PMID: 38396633 PMCID: PMC10888356 DOI: 10.3390/ijms25041954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Underwater noise pollution has become a potential threat to aquatic animals in the natural environment. The main causes of such pollution are frequent human activities creating underwater environmental noise, including commercial shipping, offshore energy platforms, scientific exploration activities, etc. However, in aquaculture environments, underwater noise pollution has also become an unavoidable problem due to background noise created by aquaculture equipment. Some research has shown that certain fish show adaptability to noise over a period of time. This could be due to fish's special auditory organ, i.e., their "inner ear"; meanwhile, otoliths and sensory hair cells are the important components of the inner ear and are also essential for the function of the auditory system. Recently, research in respect of underwater noise pollution has mainly focused on adult fish, and there is a lack of the research on the effects of underwater noise pollution on the development process of the auditory system in the embryonic development period. Thus, in this study, we collected embryo-larval samples of the small yellow croaker (Larimichthys polyactis) in four important stages of otic vesicle development through artificial breeding. Then, we used metabonomics and transcriptomics analyses to reveal the development process of the auditory system in the embryonic development period under background noise (indoor and underwater environment sound). Finally, we identified 4026 differentially expressed genes (DEGs) and 672 differential metabolites (DMs), including 37 DEGs associated with the auditory system, and many differences mainly existed in the neurula stage (20 h of post-fertilization/20 HPF). We also inferred the regulatory mode and process of some important DEGs (Dnmt1, CPS1, and endothelin-1) in the early development of the auditory system. In conclusion, we suggest that the auditory system development of L. polyactis begins at least in the neurula stage or earlier; the other three stages (tail bud stage, caudal fin fold stage, and heart pulsation stage, 28-35 HPF) mark the rapid development period. We speculate that the effect of underwater noise pollution on the embryo-larval stage probably begins even earlier.
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Affiliation(s)
| | | | | | | | - Bao Lou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310000, China; (Q.J.); (X.L.); (T.Y.); (Y.Z.)
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4
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Yuan M, Zeng C, Lu H, Yue Y, Sun T, Zhou X, Li G, Ai N, Ge W. Genetic and Epigenetic Evidence for Nonestrogenic Disruption of Otolith Development by Bisphenol A in Zebrafish. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16190-16205. [PMID: 37752410 DOI: 10.1021/acs.est.3c04336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Bisphenol A (BPA) is a well-known endocrine-disrupting chemical (EDC) that has estrogenic activities. In addition to disrupting reproductive development and function via estrogenic signaling pathways, BPA can also interfere with nonreproductive functions through nonestrogenic pathways; however, the mechanisms underlying such nonestrogenic activities are not well understood. In this study, we demonstrated that BPA could disrupt otolith formation during the early development of zebrafish with long-lasting ethological effects. Using multiple mutants of estrogen receptors, we provided strong genetic evidence that the BPA-induced otolith malformation was independent of estrogen signaling. Transcriptome analysis revealed that two genes related to otolith development, otopetrin 1 (otop1) and starmaker (stm), decreased their expression significantly after BPA exposure. Knockout of both otop1 and stm genes could phenocopy the BPA-induced otolith malformation, while microinjection of their mRNAs could rescue the BPA-induced abnormalities of otolith formation. Further experiments showed that BPA inhibited the expression of otop1 and stm by activating the MEK/ERK-EZH2-H3K27me3 signaling pathway. Taken together, our study provided comprehensive genetic and molecular evidence that BPA induced the otolith malformation through nonestrogenic pathway during zebrafish early development and its activities involved epigenetic control of key genes (e.g., otop1 and stm) participating in otolith formation.
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Affiliation(s)
- Mingzhe Yuan
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
- Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
| | - Chu Zeng
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
- Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
| | - Huijie Lu
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
- Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
| | - Yiming Yue
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
- Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
| | - Ting Sun
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
| | - Xianqing Zhou
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Gang Li
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
| | - Nana Ai
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
- Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
| | - Wei Ge
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
- Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
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Tu YH, Liu N, Xiao C, Gavrilova O, Reitman ML. Loss of Otopetrin 1 affects thermoregulation during fasting in mice. PLoS One 2023; 18:e0292610. [PMID: 37812612 PMCID: PMC10561838 DOI: 10.1371/journal.pone.0292610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 09/09/2023] [Indexed: 10/11/2023] Open
Abstract
OBJECTIVE Otopetrin 1 (OTOP1) is a proton channel that is highly expressed in brown adipose tissue. We examined the physiology of Otop1-/- mice, which lack functional OTOP1. METHODS Mice were studied by indirect calorimetry and telemetric ambulatory body temperature monitoring. Mitochondrial function was measured as oxygen consumption and extracellular acidification. RESULTS Otop1-/- mice had similar body temperatures as control mice at baseline and in response to cold and hot ambient temperatures. However, in response to fasting the Otop1-/- mice exhibited an exaggerated hypothermia and hypometabolism. Similarly, in ex vivo tests of Otop1-/- brown adipose tissue mitochondrial function, there was no change in baseline oxygen consumption, but the oxygen consumption was reduced after maximal uncoupling with FCCP and increased upon stimulation with the β3-adrenergic agonist CL316243. Mast cells also express Otop1, and Otop1-/- mice had intact, possibly greater hypothermia in response to mast cell activation by the adenosine A3 receptor agonist MRS5698. No increase in insulin resistance was observed in the Otop1-/- mice. CONCLUSIONS Loss of OTOP1 does not change basal function of brown adipose tissue but affects stimulated responses.
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Affiliation(s)
- Yu-Hsiang Tu
- Diabetes, Endocrinology and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Naili Liu
- Mouse Metabolism Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Cuiying Xiao
- Diabetes, Endocrinology and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Oksana Gavrilova
- Mouse Metabolism Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Marc L. Reitman
- Diabetes, Endocrinology and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States of America
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Liang Z, Wilson CE, Teng B, Kinnamon SC, Liman ER. The proton channel OTOP1 is a sensor for the taste of ammonium chloride. Nat Commun 2023; 14:6194. [PMID: 37798269 PMCID: PMC10556057 DOI: 10.1038/s41467-023-41637-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/12/2023] [Indexed: 10/07/2023] Open
Abstract
Ammonium (NH4+), a breakdown product of amino acids that can be toxic at high levels, is detected by taste systems of organisms ranging from C. elegans to humans and has been used for decades in vertebrate taste research. Here we report that OTOP1, a proton-selective ion channel expressed in sour (Type III) taste receptor cells (TRCs), functions as sensor for ammonium chloride (NH4Cl). Extracellular NH4Cl evoked large dose-dependent inward currents in HEK-293 cells expressing murine OTOP1 (mOTOP1), human OTOP1 and other species variants of OTOP1, that correlated with its ability to alkalinize the cell cytosol. Mutation of a conserved intracellular arginine residue (R292) in the mOTOP1 tm 6-tm 7 linker specifically decreased responses to NH4Cl relative to acid stimuli. Taste responses to NH4Cl measured from isolated Type III TRCs, or gustatory nerves were strongly attenuated or eliminated in an Otop1-/- mouse strain. Behavioral aversion of mice to NH4Cl, reduced in Skn-1a-/- mice lacking Type II TRCs, was entirely abolished in a double knockout with Otop1. These data together reveal an unexpected role for the proton channel OTOP1 in mediating a major component of the taste of NH4Cl and a previously undescribed channel activation mechanism.
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Affiliation(s)
- Ziyu Liang
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
- Program in Neuroscience, University of Southern California, Los Angeles, CA, 90089, USA
| | - Courtney E Wilson
- Department of Otolaryngology, University of Colorado Medical School, 12700 E 19(th) Avenue, MS 8606, Aurora, CO, 80045, USA
| | - Bochuan Teng
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
- Program in Neuroscience, University of Southern California, Los Angeles, CA, 90089, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sue C Kinnamon
- Department of Otolaryngology, University of Colorado Medical School, 12700 E 19(th) Avenue, MS 8606, Aurora, CO, 80045, USA
| | - Emily R Liman
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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Wu J, Zhang Y, Mao S, Li W, Li G, Li H, Sun S. Cross-species analysis and comparison of the inner ear between chickens and mice. J Comp Neurol 2023; 531:1443-1458. [PMID: 37462291 DOI: 10.1002/cne.25524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023]
Abstract
The inner ear of mammals includes the cochlea and vestibule, which house specialized hair cells that are responsible for hearing and balance, respectively. While cochlear hair cells fail to regenerate following damage, those of the utricle, which is part of the vestibular apparatus, show partial regeneration. In birds, the macula lagena, a unique ear structure in this clade, has the ability to regenerate hair cells similarly to the utricle. Many studies have sought to explain regeneration in terms of evolution and species differences. However, it remains unclear what the cellular and molecular basis is behind the differences in inner ear structures and between avians and mammals. In the present study, we first investigated the anatomical structures of the inner ear of both chickens and rodents. We then performed RNA sequencing (RNA-Seq) and made cross-species analyses of the expression of homologous genes obtained from the inner ear tissue from both chickens and mice. Finally, we focused on the lagena, the basilar papilla, and the utricle in chickens and identified differentially expressed genes between tissues and determined the expression patterns of genes involved in inner ear structure formation by single-cell RNA sequencing and bulk RNA-Seq. We concluded that the cellular and molecular composition of the lagena is more similar to that of the utricle than the cochlea. Taken together, our study provides a valuable resource for the study of inner ear evolution and development.
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Affiliation(s)
- Jingfang Wu
- Department of ENT Institute and Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology, NHC Key Laboratory of Hearing Medicine Research, Fudan University, Shanghai, P. R. China
| | - Yunzhong Zhang
- Department of ENT Institute and Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology, NHC Key Laboratory of Hearing Medicine Research, Fudan University, Shanghai, P. R. China
| | - Shihang Mao
- Department of ENT Institute and Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology, NHC Key Laboratory of Hearing Medicine Research, Fudan University, Shanghai, P. R. China
| | - Wen Li
- Department of ENT Institute and Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology, NHC Key Laboratory of Hearing Medicine Research, Fudan University, Shanghai, P. R. China
| | - Guangfei Li
- Department of ENT Institute and Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology, NHC Key Laboratory of Hearing Medicine Research, Fudan University, Shanghai, P. R. China
| | - Huawei Li
- Department of ENT Institute and Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology, NHC Key Laboratory of Hearing Medicine Research, Fudan University, Shanghai, P. R. China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
- The Institutes of Brain Science and the Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, P. R. China
| | - Shan Sun
- Department of ENT Institute and Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology, NHC Key Laboratory of Hearing Medicine Research, Fudan University, Shanghai, P. R. China
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Teng B, Kaplan J, Liang Z, Chyung KS, Goldschen-Ohm MP, Liman ER. Zinc activation of OTOP proton channels identifies structural elements of the gating apparatus. eLife 2023; 12:85317. [PMID: 37053086 PMCID: PMC10101688 DOI: 10.7554/elife.85317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
Otopetrin proteins (OTOPs) form proton-selective ion channels that are expressed in diverse cell types where they mediate detection of acids or regulation of pH. In vertebrates there are three family members: OTOP1 is required for formation of otoconia in the vestibular system and it forms the receptor for sour taste, while the functions of OTOP2 and OTOP3 are not yet known. Importantly, the gating mechanisms of any of the OTOP channels are not well understood. Here, we show that zinc (Zn2+), as well as other transition metals including copper (Cu2+), potently activates murine OTOP3 (mOTOP3). Zn2+ pre-exposure increases the magnitude of mOTOP3 currents to a subsequent acid stimulus by as much as 10-fold. In contrast, mOTOP2 currents are insensitive to activation by Zn2+. Swapping the extracellular tm 11-12 linker between mOTOP3 and mOTOP2 was sufficient to eliminate Zn2+ activation of mOTOP3 and confer Zn2+ activation on mOTOP2. Mutation to alanine of H531 and E535 within the tm 11-12 linker and H234 and E238 within the 5-6 linker reduced or eliminated activation of mOTOP3 by Zn2+, indicating that these residues likely contribute to the Zn2+ activating site. Kinetic modeling of the data is consistent with Zn2+ stabilizing the opn2+en state of the channel, competing with H+ for activation of the channels. These results establish the tm 11-12 and tm 5-6 linkers as part of the gating apparatus of OTOP channels and a target for drug discovery. Zn2+ is an essential micronutrient and its activation of OTOP channels will undoubtedly have important physiological sequelae.
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Affiliation(s)
- Bochuan Teng
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, United States
- Program in Neuroscience, University of Southern California, Los Angeles, United States
| | - Joshua Kaplan
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, United States
- Program in Neuroscience, University of Southern California, Los Angeles, United States
| | - Ziyu Liang
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, United States
- Program in Neuroscience, University of Southern California, Los Angeles, United States
| | - Kevin Saejin Chyung
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | | | - Emily Ruth Liman
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, United States
- Program in Neuroscience, University of Southern California, Los Angeles, United States
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9
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Li S, Al-Sheikh U, Chen Y, Kang L. Nematode homologs of the sour taste receptor Otopetrin1 are evolutionarily conserved acid-sensitive proton channels. Front Cell Dev Biol 2023; 11:1133890. [PMID: 36776560 PMCID: PMC9909269 DOI: 10.3389/fcell.2023.1133890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
Numerous taste receptors and related molecules have been identified in vertebrates and invertebrates. Otopetrin1 has recently been identified as mammalian sour taste receptor which is essential for acid sensation. However, whether other Otopetrin proteins are involved in PH-sensing remains unknown. In C. elegans, there are eight otopetrin homologous genes but their expression patterns and functions have not been reported so far. Through heterologous expression in HEK293T cells, we found that ceOTOP1a can be activated by acid in NMDG+ solution without conventional cations, which generated inward currents and can be blocked by zinc ions. Moreover, we found that Otopetrin channels are widely expressed in numerous tissues, especially in sensory neurons in the nematode. These results suggest that the biophysical characteristics of the Otopetrin channels in nematodes are generally conserved. However, a series of single gene mutations of otopetrins, which were constructed by CRISPR-Cas9 method, did not affect either calcium responses in ASH polymodal sensory neurons to acid stimulation or acid avoidance behaviors, suggesting that Otopetrin channels might have diverse functions among species. This study reveals that nematode Otopetrins are evolutionarily conserved acid-sensitive proton channels, and provides a framework for further revealing the function and mechanisms of Otopetrin channels in both invertebrates and vertebrates.
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Affiliation(s)
- Shitian Li
- Department of Neurobiology and Department of Neurosurgery of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, Hangzhou, China,NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Umar Al-Sheikh
- Department of Neurobiology and Department of Neurosurgery of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, Hangzhou, China,NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yili Chen
- Department of Neurobiology and Department of Neurosurgery of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,*Correspondence: Yili Chen, ; Lijun Kang,
| | - Lijun Kang
- Department of Neurobiology and Department of Neurosurgery of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, Hangzhou, China,NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China,*Correspondence: Yili Chen, ; Lijun Kang,
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10
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Tian L, Zhang H, Yang S, Luo A, Kamau PM, Hu J, Luo L, Lai R. Vertebrate OTOP1 is also an alkali-activated channel. Nat Commun 2023; 14:26. [PMID: 36596786 PMCID: PMC9810603 DOI: 10.1038/s41467-022-35754-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 12/23/2022] [Indexed: 01/04/2023] Open
Abstract
Although alkaline sensation is critical for survival, alkali-activated receptors are yet to be identified in vertebrates. Here, we showed that the OTOP1 channel can be directly activated by extracellular alkali. Notably, OTOP1 biphasically mediated proton influx and efflux with extracellular acid and base stimulation, respectively. Mutations of K221 and R554 at the S5-S6 and S11-S12 linkers significantly reduced alkali affinity without affecting acid activation, suggesting that different domains are responsible for acid- and alkali-activation of OTOP1. The selectivity for H+ was significantly higher in OTOP1 activated by alkali than that by acid, further suggesting that the two activations might be independent gating processes. Given that the alkali-activation of OTOP1 and the required key residues were conserved in the six representative vertebrates, we cautiously propose that OTOP1 participates in alkaline sensation in vertebrates. Thus, our study identified OTOP1 as an alkali-activated channel.
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Affiliation(s)
- Lifeng Tian
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province/National & Local Joint Engineering Center of Natural Bioactive Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, China.,National Resource Center for Non-Human Primates, Kunming Primate Research Center/National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, 650107, Kunming, Yunnan, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 310024, Hangzhou, China.,The cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, 310022, Hangzhou, China
| | - Hao Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province/National & Local Joint Engineering Center of Natural Bioactive Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, China.,National Resource Center for Non-Human Primates, Kunming Primate Research Center/National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, 650107, Kunming, Yunnan, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Shilong Yang
- College of Wildlife and Protected Area, Northeast Forestry University, 150040, Harbin, China
| | - Anna Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province/National & Local Joint Engineering Center of Natural Bioactive Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, China.,National Resource Center for Non-Human Primates, Kunming Primate Research Center/National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, 650107, Kunming, Yunnan, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Peter Muiruri Kamau
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province/National & Local Joint Engineering Center of Natural Bioactive Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, China.,National Resource Center for Non-Human Primates, Kunming Primate Research Center/National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, 650107, Kunming, Yunnan, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,Sino-African Joint Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, China
| | - Jingmei Hu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province/National & Local Joint Engineering Center of Natural Bioactive Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, China.,National Resource Center for Non-Human Primates, Kunming Primate Research Center/National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, 650107, Kunming, Yunnan, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Lei Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province/National & Local Joint Engineering Center of Natural Bioactive Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, China. .,National Resource Center for Non-Human Primates, Kunming Primate Research Center/National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, 650107, Kunming, Yunnan, China.
| | - Ren Lai
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province/National & Local Joint Engineering Center of Natural Bioactive Peptides, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, China. .,National Resource Center for Non-Human Primates, Kunming Primate Research Center/National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, 650107, Kunming, Yunnan, China. .,School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 310024, Hangzhou, China. .,Sino-African Joint Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, China.
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11
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Visual, spectral, and microchemical quantification of crystalline anomalies in otoliths of wild and cultured delta smelt. Sci Rep 2022; 12:20751. [PMID: 36456583 PMCID: PMC9715569 DOI: 10.1038/s41598-022-22813-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/19/2022] [Indexed: 12/03/2022] Open
Abstract
Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in otoliths of delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the San Francisco Estuary. Left-right asymmetry and anomalous crystalline polymorphs (i.e., vaterite) were quantified and compared between wild and cultured populations using digital image analysis. Visual estimates of vaterite were validated using X-ray diffraction, Raman spectroscopy, laser ablation ICPMS, and electron probe microanalysis. Results indicated that cultured delta smelt were 80 times more likely to contain a vateritic otolith and 18 times more likely to contain relatively large (≥ 15%) amounts of vaterite. Similarly, cultured fish exhibited 30% greater asymmetry than wild fish. These results indicate that cultured delta smelt exhibit a significantly higher frequency of vestibular abnormalities which are known to reduce fitness and survival. Such hatchery effects on otolith development could have important implications for captive culture practices and the supplementation of wild fish populations with cultured individuals.
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12
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The roles of two extracellular loops in proton sensing and permeation in human Otop1 proton channel. Commun Biol 2022; 5:1110. [PMID: 36266567 PMCID: PMC9585144 DOI: 10.1038/s42003-022-04085-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/07/2022] [Indexed: 11/08/2022] Open
Abstract
Otopetrin (Otop) proteins were recently found to function as proton channels, with Otop1 revealed to be the sour taste receptor in mammals. Otop proteins contain twelve transmembrane segments (S1-S12) which are divided into structurally similar N and C domains. The mechanisms by which Otop channels sense extracellular protons to initiate gating and conduct protons once the channels are activated remains largely elusive. Here we show that two extracellular loops are playing key roles in human Otop1 channel function. We find that residue H229 in the S5-S6 loop is critical for proton sensing of Otop1. Further, our data reveal that the S11-12 loop is structurally and functionally essential for the Otop1 channel and that residue D570 in this loop regulates proton permeation into the pore formed by the C domain. This study sheds light on the molecular mechanism behind the structure and function of this newly identified ion channel family. Electrophysiology experiments, mutagenesis, and structural modelling provide insights into the structure and function of the sour taste receptor Otopetrin 1.
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13
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Cai Z, Machado A, Chowdhury RA, Spilkin A, Vincent T, Aydin Ü, Pellegrino G, Lina JM, Grova C. Diffuse optical reconstructions of functional near infrared spectroscopy data using maximum entropy on the mean. Sci Rep 2022; 12:2316. [PMID: 35145148 PMCID: PMC8831678 DOI: 10.1038/s41598-022-06082-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 01/24/2022] [Indexed: 02/07/2023] Open
Abstract
Functional near-infrared spectroscopy (fNIRS) measures the hemoglobin concentration changes associated with neuronal activity. Diffuse optical tomography (DOT) consists of reconstructing the optical density changes measured from scalp channels to the oxy-/deoxy-hemoglobin concentration changes within the cortical regions. In the present study, we adapted a nonlinear source localization method developed and validated in the context of Electro- and Magneto-Encephalography (EEG/MEG): the Maximum Entropy on the Mean (MEM), to solve the inverse problem of DOT reconstruction. We first introduced depth weighting strategy within the MEM framework for DOT reconstruction to avoid biasing the reconstruction results of DOT towards superficial regions. We also proposed a new initialization of the MEM model improving the temporal accuracy of the original MEM framework. To evaluate MEM performance and compare with widely used depth weighted Minimum Norm Estimate (MNE) inverse solution, we applied a realistic simulation scheme which contained 4000 simulations generated by 250 different seeds at different locations and 4 spatial extents ranging from 3 to 40\documentclass[12pt]{minimal}
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\begin{document}$$\text {cm}^2$$\end{document}cm2 along the cortical surface. Our results showed that overall MEM provided more accurate DOT reconstructions than MNE. Moreover, we found that MEM was remained particularly robust in low signal-to-noise ratio (SNR) conditions. The proposed method was further illustrated by comparing to functional Magnetic Resonance Imaging (fMRI) activation maps, on real data involving finger tapping tasks with two different montages. The results showed that MEM provided more accurate HbO and HbR reconstructions in spatial agreement with the main fMRI cluster, when compared to MNE.
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Affiliation(s)
- Zhengchen Cai
- Department of Physics and PERFORM Centre, Concordia University, Montreal, Canada.
| | - Alexis Machado
- Multimodal Functional Imaging Lab, Biomedical Engineering Department, McGill University, Montreal, Canada
| | - Rasheda Arman Chowdhury
- Multimodal Functional Imaging Lab, Biomedical Engineering Department, McGill University, Montreal, Canada
| | - Amanda Spilkin
- Department of Physics and PERFORM Centre, Concordia University, Montreal, Canada
| | - Thomas Vincent
- Department of Physics and PERFORM Centre, Concordia University, Montreal, Canada.,Neurology and Neurosurgery Department, Montreal Neurological Institute, McGill University, Montreal, Canada.,Centre de médecine préventive et d'activité physique, Montréal Heart Institute, Montréal, Canada
| | - Ümit Aydin
- Department of Physics and PERFORM Centre, Concordia University, Montreal, Canada.,MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Giovanni Pellegrino
- Neurology and Neurosurgery Department, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Jean-Marc Lina
- École de technologie supérieure de l'Université du Québec, Montréal, Canada.,Centre de Recherches Mathématiques, Université de Montréal, Montréal, Canada
| | - Christophe Grova
- Department of Physics and PERFORM Centre, Concordia University, Montreal, Canada.,Multimodal Functional Imaging Lab, Biomedical Engineering Department, McGill University, Montreal, Canada.,Neurology and Neurosurgery Department, Montreal Neurological Institute, McGill University, Montreal, Canada.,Centre de Recherches Mathématiques, Université de Montréal, Montréal, Canada
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14
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Frank HER, Amato K, Trautwein M, Maia P, Liman ER, Nichols LM, Schwenk K, Breslin PAS, Dunn RR. The evolution of sour taste. Proc Biol Sci 2022; 289:20211918. [PMID: 35135352 PMCID: PMC8826303 DOI: 10.1098/rspb.2021.1918] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The evolutionary history of sour taste has been little studied. Through a combination of literature review and trait mapping on the vertebrate phylogenetic tree, we consider the origin of sour taste, potential cases of the loss of sour taste, and those factors that might have favoured changes in the valence of sour taste-from aversive to appealing. We reconstruct sour taste as having evolved in ancient fish. By contrast to other tastes, sour taste does not appear to have been lost in any major vertebrate taxa. For most species, sour taste is aversive. Animals, including humans, that enjoy the sour taste triggered by acidic foods are exceptional. We conclude by considering why sour taste evolved, why it might have persisted as vertebrates made the transition to land and what factors might have favoured the preference for sour-tasting, acidic foods, particularly in hominins, such as humans.
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Affiliation(s)
- Hannah E. R. Frank
- Department of Crop and Soil Sciences North Carolina State University, Raleigh, USA
| | - Katie Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Michelle Trautwein
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, USA
| | - Paula Maia
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Emily R. Liman
- Department of Biological Sciences, Section of Neurobiology, University of Southern California, Los Angeles, CA, USA
| | - Lauren M. Nichols
- Department of Applied Ecology, North Carolina State University, Raleigh, USA
| | - Kurt Schwenk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Paul A. S. Breslin
- Department of Nutritional Sciences, Rutgers The State University of New Jersey, New Brunswick, NJ, USA,Monell Chemical Senses Center, Philadelphia, PA, USA
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, USA,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
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15
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Teng B, Kaplan JP, Liang Z, Krieger Z, Tu YH, Burendei B, Ward AB, Liman ER. Structural motifs for subtype-specific pH-sensitive gating of vertebrate otopetrin proton channels. eLife 2022; 11:77946. [PMID: 35920807 PMCID: PMC9348849 DOI: 10.7554/elife.77946] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/19/2022] [Indexed: 01/05/2023] Open
Abstract
Otopetrin (OTOP) channels are proton-selective ion channels conserved among vertebrates and invertebrates, with no structural similarity to other ion channels. There are three vertebrate OTOP channels (OTOP1, OTOP2, and OTOP3), of which one (OTOP1) functions as a sour taste receptor. Whether extracellular protons gate OTOP channels, in addition to permeating them, was not known. Here, we compare the functional properties of the three murine OTOP channels using patch-clamp recording and cytosolic pH microfluorimetry. We find that OTOP1 and OTOP3 are both steeply activated by extracellular protons, with thresholds of pHo <6.0 and 5.5, respectively, and kinetics that are pH-dependent. In contrast, OTOP2 channels are broadly active over a large pH range (pH 5 pH 10) and carry outward currents in response to extracellular alkalinization (>pH 9.0). Strikingly, we could change the pH-sensitive gating of OTOP2 and OTOP3 channels by swapping extracellular linkers that connect transmembrane domains. Swaps of extracellular linkers in the N domain, comprising transmembrane domains 1-6, tended to change the relative conductance at alkaline pH of chimeric channels, while swaps within the C domain, containing transmembrane domains 7-12, tended to change the rates of OTOP3 current activation. We conclude that members of the OTOP channel family are proton-gated (acid-sensitive) proton channels and that the gating apparatus is distributed across multiple extracellular regions within both the N and C domains of the channels. In addition to the taste system, OTOP channels are expressed in the vertebrate vestibular and digestive systems. The distinct gating properties we describe may allow them to subserve varying cell-type specific functions in these and other biological systems.
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Affiliation(s)
- Bochuan Teng
- Section of Neurobiology, Department of Biological Sciences, University of Southern CaliforniaLos AngelesUnited States,Program in Neuroscience, University of Southern CaliforniaLos AngelesUnited States
| | - Joshua P Kaplan
- Section of Neurobiology, Department of Biological Sciences, University of Southern CaliforniaLos AngelesUnited States,Program in Neuroscience, University of Southern CaliforniaLos AngelesUnited States
| | - Ziyu Liang
- Section of Neurobiology, Department of Biological Sciences, University of Southern CaliforniaLos AngelesUnited States,Program in Neuroscience, University of Southern CaliforniaLos AngelesUnited States
| | - Zachary Krieger
- Section of Neurobiology, Department of Biological Sciences, University of Southern CaliforniaLos AngelesUnited States
| | - Yu-Hsiang Tu
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Batuujin Burendei
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Emily R Liman
- Section of Neurobiology, Department of Biological Sciences, University of Southern CaliforniaLos AngelesUnited States,Program in Neuroscience, University of Southern CaliforniaLos AngelesUnited States
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16
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Requirement for an Otopetrin-like protein for acid taste in Drosophila. Proc Natl Acad Sci U S A 2021; 118:2110641118. [PMID: 34911758 PMCID: PMC8713817 DOI: 10.1073/pnas.2110641118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 11/18/2022] Open
Abstract
Receptors for bitter, sugar, and other tastes have been identified in the fruit fly Drosophila melanogaster, while a broadly tuned receptor for the taste of acid has been elusive. Previous work showed that such a receptor was unlikely to be encoded by a gene within one of the two major families of taste receptors in Drosophila, the "gustatory receptors" and "ionotropic receptors." Here, to identify the acid taste receptor, we tested the contributions of genes encoding proteins distantly related to the mammalian Otopertrin1 (OTOP1) proton channel that functions as a sour receptor in mice. RNA interference (RNAi) knockdown or mutation by CRISPR/Cas9 of one of the genes, Otopetrin-Like A (OtopLA), but not of the others (OtopLB or OtopLC) severely impaired the behavioral rejection to a sweet solution laced with high levels of HCl or carboxylic acids and greatly reduced acid-induced action potentials measured from taste hairs. An isoform of OtopLA that we isolated from the proboscis was sufficient to restore behavioral sensitivity and acid-induced action potential firing in OtopLA mutant flies. At lower concentrations, HCl was attractive to the flies, and this attraction was abolished in the OtopLA mutant. Cell type-specific rescue experiments showed that OtopLA functions in distinct subsets of gustatory receptor neurons for repulsion and attraction to high and low levels of protons, respectively. This work highlights a functional conservation of a sensory receptor in flies and mammals and shows that the same receptor can function in both appetitive and repulsive behaviors.
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17
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Coll-Lladó C, Mittermayer F, Webb PB, Allison N, Clemmesen C, Stiasny M, Bridges CR, Göttler G, Garcia de la Serrana D. Pilot study to investigate the effect of long-term exposure to high pCO 2 on adult cod (Gadus morhua) otolith morphology and calcium carbonate deposition. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:1879-1891. [PMID: 34585317 PMCID: PMC8636414 DOI: 10.1007/s10695-021-01016-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
To date the study of ocean acidification on fish otolith formation has been mainly focused on larval and juvenile stages. In the present pilot study, wild-captured adult Atlantic cod (Gadus morhua) were exposed to two different levels of pCO2, 422µatm (ambient, low pCO2) or 1091µatm (high pCO2), for a period of 30 weeks (from mid-October to early April 2014-2015) in order to study the effects on otolith size, shape and CaCO3 crystallization amongst other biological parameters. We found that otoliths from cod exposed to high pCO2 were slightly smaller (- 3.4% in length; - 3.3% in perimeter), rounder (- 2.9% circularity and + 4% roundness) but heavier (+ 5%) than the low pCO2 group. Interestingly, there were different effects in males and females; for instance, male cods exposed to high pCO2 exhibited significant changes in circularity (- 3%) and roundness (+ 4%) compared to the low pCO2 males, but without significant changes on otolith dimensions, while females exposed to high pCO2 had smaller otoliths as shown for length (- 5.6%), width (- 2%), perimeter (- 3.5%) and area (- 4.8%). Furthermore, while the majority of the otoliths analysed showed normal aragonite deposition, 10% of fish exposed to 1091µatm of pCO2 had an abnormal accretion of calcite, suggesting a shift on calcium carbonate polymorph crystallization in some individuals under high pCO2 conditions. Our preliminary results indicate that high levels of pCO2 in adult Atlantic cod might affect otolith growth in a gender-specific way. Our findings reveal that otoliths from adult cod are affected by ocean acidification, and we believe that the present study will prompt further research into this currently under-explored area.
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Affiliation(s)
- Clara Coll-Lladó
- Scottish Oceans Institute, School of Biology, University of St Andrews, Scotland, UK
| | - Felix Mittermayer
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Nicola Allison
- School of Earth and Environmental Sciences, University of St Andrews, Scotland, UK
| | - Catriona Clemmesen
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Martina Stiasny
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Ocean and Earth Science, National Oceanography Center Southampton, University of Southampton, Waterfront Campus, Southampton, UK
| | - Christopher Robert Bridges
- Institut Für Stoffwechselphysiologie/AG Ecophysiology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Gwendolin Göttler
- Institut Für Stoffwechselphysiologie/AG Ecophysiology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Daniel Garcia de la Serrana
- Scottish Oceans Institute, School of Biology, University of St Andrews, Scotland, UK.
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain.
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18
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Abstract
Sour taste, the taste of acids, is one of the most enigmatic of the five basic taste qualities; its function is unclear and its receptor was until recently unknown. Sour tastes are transduced in taste buds on the tongue and palate epithelium by a subset of taste receptor cells, known as type III cells. Type III cells express a number of unique markers, including the PKD2L1 gene, which allow for their identification and manipulation. These cells respond to acid stimuli with action potentials and release neurotransmitters onto afferent nerve fibers, with cell bodies in geniculate and petrosal ganglia. Here, we review classical studies of sour taste leading up to the identification of the sour receptor as the proton channel, OTOP1. Expected final online publication date for the Annual Review of Physiology, Volume 84 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Heather N Turner
- Department of Biological Sciences, Section of Neurobiology, University of Southern California, Los Angeles, California, USA; ,
| | - Emily R Liman
- Department of Biological Sciences, Section of Neurobiology, University of Southern California, Los Angeles, California, USA; ,
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19
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Wang J, Wang L, Sun L, Liu R, Chi B, Zhang Y, Liu H. Simultaneous Determination and Comprehensive Evaluation of Mineral Elements in Yellow Croaker Ear-Stone on Sale in China. Chem Pharm Bull (Tokyo) 2021; 69:918-925. [PMID: 34234056 DOI: 10.1248/cpb.c21-00352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Yellow Croaker Ear-stone or Yunaoshi, is actually two kinds of fish otolith in China and has received increased attention in recent years as important folk medicine. For better understanding of this crude drug, a chaotic market circulation status investigation was carried out and seventeen samples with different varieties or producing areas were collected. In this study, pharmacodynamic components of nineteen varieties mineral elements of the seventeen samples were simultaneously determined by Inductively coupled plasma mass spectrometry (ICP-MS) method. The detected elements were categorized into the beneficial (Na, Mg, Ca, K, Fe, Mn, Zn, Sr, B) and unbeneficial elements (Cu, As, Cd, Hg, Al, Pb, Co, Ba, Cr and Ni) kinds and their concentrations were quantified. Then the principal component analysis (PCA) and hierarchical clustering analysis (HCA) were further applied to launch an exploratory analysis for Yunaoshi samples. The results showed that samples 1-3, 15-8, 15-3 ranked the top three from the perspective of beneficial elements and samples 1-3, 1-4, 15-2 ranked the top three based on the unbeneficial elements sides. Combined with HCA results, all samples can be used as the substitutes for Yunaoshi except for samples 1-3, 1-4 and 15-2 only judging from the perspective of mineral elements concentrations. In conclusion, simultaneous determination of mineral elements accompanied with PCA and HCA can not only provide pharmacogenetic reference for the medicinal material of Yunaoshi, but also establish a feasibility for exploring new crude resources or substitutes to this medicine.
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Affiliation(s)
| | - Liang Wang
- Inspection testing center of Linyi county
| | - Luping Sun
- Basic Medicine, Shandong University of Traditional Chinese Medicine
| | - Ruohan Liu
- Basic Medicine, Shandong University of Traditional Chinese Medicine
| | - Bingqing Chi
- Basic Medicine, Shandong University of Traditional Chinese Medicine
| | - Yinghan Zhang
- Basic Medicine, Shandong University of Traditional Chinese Medicine
| | - Hongyan Liu
- Experimental Center, Shandong University of Traditional Chinese Medicine
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20
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An otopetrin family proton channel promotes cellular acid efflux critical for biomineralization in a marine calcifier. Proc Natl Acad Sci U S A 2021; 118:2101378118. [PMID: 34301868 DOI: 10.1073/pnas.2101378118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Otopetrins comprise a family of proton-selective channels that are critically important for the mineralization of otoliths and statoconia in vertebrates but whose underlying cellular mechanisms remain largely unknown. Here, we demonstrate that otopetrins are critically involved in the calcification process by providing an exit route for protons liberated by the formation of CaCO3 Using the sea urchin larva, we examined the otopetrin ortholog otop2l, which is exclusively expressed in the calcifying primary mesenchymal cells (PMCs) that generate the calcitic larval skeleton. otop2l expression is stimulated during skeletogenesis, and knockdown of otop2l impairs spicule formation. Intracellular pH measurements demonstrated Zn2+-sensitive H+ fluxes in PMCs that regulate intracellular pH in a Na+/HCO3 --independent manner, while Otop2l knockdown reduced membrane proton permeability. Furthermore, Otop2l displays unique features, including strong activation by high extracellular pH (>8.0) and check-valve-like outwardly rectifying H+ flux properties, making it into a cellular proton extrusion machine adapted to oceanic living conditions. Our results provide evidence that otopetrin family proton channels are a central component of the cellular pH regulatory machinery in biomineralizing cells. Their ubiquitous occurrence in calcifying systems across the animal kingdom suggest a conserved physiological function by mediating pH at the site of mineralization. This important role of otopetrin family proton channels has strong implications for our view on the cellular mechanisms of biomineralization and their response to changes in oceanic pH.
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21
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Zhang J, Lee H, Macpherson LJ. Mechanisms for the Sour Taste. Handb Exp Pharmacol 2021; 275:229-245. [PMID: 34117536 DOI: 10.1007/164_2021_476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Sour, the taste of acids, provides important sensory information to prevent the ingestion of unripe, spoiled, or fermented foods. In mammals, acids elicit disgust and pain by simultaneously activating taste and somatosensory neurons innervating the oral cavity. Early researchers detected electrical activity in taste nerves upon presenting acids to the tongue, establishing this as the bona fide sour taste. Recent studies have made significant contributions to our understanding of the mechanisms underlying acid sensing in the taste receptor cells at the periphery and the neural circuitry that convey this information to the brain. In this chapter, we discuss the characterization of sour taste receptor cells, the twists and turns eventually leading to the identification of Otopetrin1 (OTOP1) as the sour taste receptor, the pathway of sour taste signaling from the tongue to the brainstem, and other roles sour taste receptor cells play in the taste bud.
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Affiliation(s)
- Jin Zhang
- Mortimer B. Zukerman Mind Brain and Behavior Institute, Columbia University, New York, NY, USA.
| | - Hojoon Lee
- Department of Neurobiology, Northwestern University, Evanston, IL, USA.
| | - Lindsey J Macpherson
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, USA.
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22
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Sampilo NF, Stepicheva NA, Song JL. microRNA-31 regulates skeletogenesis by direct suppression of Eve and Wnt1. Dev Biol 2021; 472:98-114. [PMID: 33484703 PMCID: PMC7956219 DOI: 10.1016/j.ydbio.2021.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/23/2020] [Accepted: 01/11/2021] [Indexed: 11/22/2022]
Abstract
microRNAs (miRNAs) play a critical role in a variety of biological processes, including embryogenesis and the physiological functions of cells. Evolutionarily conserved microRNA-31 (miR-31) has been found to be involved in cancer, bone formation, and lymphatic development. We previously discovered that, in the sea urchin, miR-31 knockdown (KD) embryos have shortened dorsoventral connecting rods, mispatterned skeletogenic primary mesenchyme cells (PMCs) and shifted and expanded Vegf3 expression domain. Vegf3 itself does not contain miR-31 binding sites; however, we identified its upstream regulators Eve and Wnt1 to be directly suppressed by miR-31. Removal of miR-31's suppression of Eve and Wnt1 resulted in skeletal and PMC patterning defects, similar to miR-31 KD phenotypes. Additionally, removal of miR-31's suppression of Eve and Wnt1 results in an expansion and anterior shift in expression of Veg1 ectodermal genes, including Vegf3 in the blastulae. This indicates that miR-31 indirectly regulates Vegf3 expression through directly suppressing Eve and Wnt1. Furthermore, removing miR-31 suppression of Eve is sufficient to cause skeletogenic defects, revealing a novel regulatory role of Eve in skeletogenesis and PMC patterning. Overall, this study provides a proposed molecular mechanism of miR-31's regulation of skeletogenesis and PMC patterning through its cross-regulation of a Wnt signaling ligand and a transcription factor of the endodermal and ectodermal gene regulatory network.
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Affiliation(s)
- Nina Faye Sampilo
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Nadezda A Stepicheva
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Jia L Song
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
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23
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Zimmer AM, Goss GG, Glover CN. Reductionist approaches to the study of ionoregulation in fishes. Comp Biochem Physiol B Biochem Mol Biol 2021; 255:110597. [PMID: 33781928 DOI: 10.1016/j.cbpb.2021.110597] [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: 01/05/2021] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
The mechanisms underlying ionoregulation in fishes have been studied for nearly a century, and reductionist methods have been applied at all levels of biological organization in this field of research. The complex nature of ionoregulatory systems in fishes makes them ideally suited to reductionist methods and our collective understanding has been dramatically shaped by their use. This review provides an overview of the broad suite of techniques used to elucidate ionoregulatory mechanisms in fishes, from the whole-animal level down to the gene, discussing some of the advantages and disadvantages of these methods. We provide a roadmap for understanding and appreciating the work that has formed the current models of organismal, endocrine, cellular, molecular, and genetic regulation of ion balance in fishes and highlight the contribution that reductionist techniques have made to some of the fundamental leaps forward in the field throughout its history.
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Affiliation(s)
- Alex M Zimmer
- Department of Biological Sciences, CW 405, Biological Sciences Bldg., University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Greg G Goss
- Department of Biological Sciences, CW 405, Biological Sciences Bldg., University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Chris N Glover
- Department of Biological Sciences, CW 405, Biological Sciences Bldg., University of Alberta, Edmonton, AB T6G 2E9, Canada; Faculty of Science and Technology and Athabasca River Basin Research Institute, Athabasca University, Athabasca, AB T9S 3A3, Canada
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24
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Abstract
Sour taste, which is evoked by low pH, is one of the original four fundamental taste qualities, recognized as a distinct taste sensation for centuries, and universally aversive across diverse species. It is generally assumed to have evolved for detection of acids in unripe fruit and spoiled food. But despite decades of study, only recently have the receptor, the neurotransmitter, and the circuits for sour taste been identified. In this review, we describe studies leading up to the identification of the sour receptor as OTOP1, an ion channel that is selectively permeable to protons. We also describe advances in our understanding of how information is transmitted from the taste receptor cells to gustatory neurons, leading to behavioral aversion to acids.
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Affiliation(s)
- Emily R Liman
- Department of Biological Sciences, Section of Neurobiology, University of Southern California, 3641 Watt Way, Los Angeles, CA 90089, USA
| | - Sue C Kinnamon
- Department of Otolaryngology and Rocky Mountain Taste and Smell Center, University of Colorado Anschutz Medical Campus, 12700 E 19(th) Avenue, Aurora, CO 80045, USA
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25
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Khor JM, Ettensohn CA. Transcription Factors of the Alx Family: Evolutionarily Conserved Regulators of Deuterostome Skeletogenesis. Front Genet 2020; 11:569314. [PMID: 33329706 PMCID: PMC7719703 DOI: 10.3389/fgene.2020.569314] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
Members of the alx gene family encode transcription factors that contain a highly conserved Paired-class, DNA-binding homeodomain, and a C-terminal OAR/Aristaless domain. Phylogenetic and comparative genomic studies have revealed complex patterns of alx gene duplications during deuterostome evolution. Remarkably, alx genes have been implicated in skeletogenesis in both echinoderms and vertebrates. In this review, we provide an overview of current knowledge concerning alx genes in deuterostomes. We highlight their evolutionarily conserved role in skeletogenesis and draw parallels and distinctions between the skeletogenic gene regulatory circuitries of diverse groups within the superphylum.
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Affiliation(s)
- Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
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26
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Patiyal RS, Mir MI, Pandey N, Rajesh M, Sarma D, Chandra S. Study on embryonic and larval developmental stages of Sucker head Garra gotyla (Gray 1830; Teleostei; Cyprinidae). ZYGOTE 2020; 28:1-11. [PMID: 32772943 DOI: 10.1017/s0967199419000698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Garra gotyla is an indigenous coldwater fish of the cyprinid family and has wide geographical distribution in India as well as in other countries of Asia and Africa. Induced breeding in G. gotyla was carried out successfully for the first time and an attempt has been made to document developmental stages chronologically from the first minute of fertilization, through all stages of embryonic development until the fifth day post hatching. This experiment was carried out at 22-24°C water temperature at the Directorate of Coldwater Fisheries Research, Bhimtal, India. During the breeding trial, the fertilization rate was observed as 70-75% and hatching rate was 85-90%. The mature fertilized ova were measured as 0.8-1.0 mm in diameter and the perivitelline membrane became thick soon after fertilization and formation of the germ pole. The periods taken for complete developmental stages were recorded; cleavage stage 111 min (min post fertilization (pf)), blastulation stage 580 min (pf), neurulation and segmentation 1250 min (pf) and hatching was completed after 1420 min. The sac fry was measured as 3 mm in length and took almost 3 days for complete absorption of the yolk content. The major structural and differential changes observed are in head, tail, fins, alimentary canal, rudiments of each organ and appearance of melanophore pigmentation in the whole body. The 5-day-old larvae were measured as 6 mm in length with almost every organ fully differentiated. The present study will be utilized for large-scale production of fingerlings for stock enhancement in rivers, lakes and possibilities of genetic improvement and manipulation at the embryonic stage.
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Affiliation(s)
- Rabindar Singh Patiyal
- ICAR, Directorate of Coldwater Fisheries Research, Bhimtal, Nanital, Uttarakhand 263136, India
| | - Mohammad Iqbal Mir
- ICAR, Directorate of Coldwater Fisheries Research, Bhimtal, Nanital, Uttarakhand 263136, India
| | - Nityanand Pandey
- ICAR, Directorate of Coldwater Fisheries Research, Bhimtal, Nanital, Uttarakhand 263136, India
| | - M Rajesh
- ICAR, Directorate of Coldwater Fisheries Research, Bhimtal, Nanital, Uttarakhand 263136, India
| | - Debajit Sarma
- ICAR, Directorate of Coldwater Fisheries Research, Bhimtal, Nanital, Uttarakhand 263136, India
| | - Suresh Chandra
- ICAR, Directorate of Coldwater Fisheries Research, Bhimtal, Nanital, Uttarakhand 263136, India
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27
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Han DG, Kim DJ. The evolutionary hypothesis of benign paroxysmal positional vertigo. Med Hypotheses 2020; 134:109445. [DOI: 10.1016/j.mehy.2019.109445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 10/17/2019] [Indexed: 01/04/2023]
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Abstract
The inner ear, which mediates the senses of hearing and balance, derives from a simple ectodermal vesicle in the vertebrate embryo. In the zebrafish, the otic placode and vesicle express a whole suite of genes required for ciliogenesis and ciliary motility. Every cell of the otic epithelium is ciliated at early stages; at least three different ciliary subtypes can be distinguished on the basis of length, motility, genetic requirements and function. In the early otic vesicle, most cilia are short and immotile. Long, immotile kinocilia on the first sensory hair cells tether the otoliths, biomineralized aggregates of calcium carbonate and protein. Small numbers of motile cilia at the poles of the otic vesicle contribute to the accuracy of otolith tethering, but neither the presence of cilia nor ciliary motility is absolutely required for this process. Instead, otolith tethering is dependent on the presence of hair cells and the function of the glycoprotein Otogelin. Otic cilia or ciliary proteins also mediate sensitivity to ototoxins and coordinate responses to extracellular signals. Other studies are beginning to unravel the role of ciliary proteins in cellular compartments other than the kinocilium, where they are important for the integrity and survival of the sensory hair cell. This article is part of the Theo Murphy meeting issue 'Unity and diversity of cilia in locomotion and transport'.
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Affiliation(s)
- Tanya T Whitfield
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
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29
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Zhang J, Jin H, Zhang W, Ding C, O'Keeffe S, Ye M, Zuker CS. Sour Sensing from the Tongue to the Brain. Cell 2019; 179:392-402.e15. [PMID: 31543264 DOI: 10.1016/j.cell.2019.08.031] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/04/2019] [Accepted: 08/15/2019] [Indexed: 12/19/2022]
Abstract
The ability to sense sour provides an important sensory signal to prevent the ingestion of unripe, spoiled, or fermented foods. Taste and somatosensory receptors in the oral cavity trigger aversive behaviors in response to acid stimuli. Here, we show that the ion channel Otopetrin-1, a proton-selective channel normally involved in the sensation of gravity in the vestibular system, is essential for sour sensing in the taste system. We demonstrate that knockout of Otop1 eliminates acid responses from sour-sensing taste receptor cells (TRCs). In addition, we show that mice engineered to express otopetrin-1 in sweet TRCs have sweet cells that also respond to sour stimuli. Next, we genetically identified the taste ganglion neurons mediating each of the five basic taste qualities and demonstrate that sour taste uses its own dedicated labeled line from TRCs in the tongue to finely tuned taste neurons in the brain to trigger aversive behaviors.
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Affiliation(s)
- Jin Zhang
- Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University, New York, NY 10032, USA; Mortimer B. Zukerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Hao Jin
- Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University, New York, NY 10032, USA; Mortimer B. Zukerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Wenyi Zhang
- Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University, New York, NY 10032, USA; Mortimer B. Zukerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Cheng Ding
- Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University, New York, NY 10032, USA; Mortimer B. Zukerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Sean O'Keeffe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Mingyu Ye
- Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University, New York, NY 10032, USA; Mortimer B. Zukerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Charles S Zuker
- Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University, New York, NY 10032, USA; Mortimer B. Zukerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA.
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30
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Nichols RG, Peters JM, Patterson AD. Interplay Between the Host, the Human Microbiome, and Drug Metabolism. Hum Genomics 2019; 13:27. [PMID: 31186074 PMCID: PMC6558703 DOI: 10.1186/s40246-019-0211-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/21/2019] [Indexed: 02/07/2023] Open
Abstract
The human microbiome is composed of four major areas including intestinal, skin, vaginal, and oral microbiomes, with each area containing unique species and unique functionalities. The human microbiome may be modulated with prebiotics, probiotics, and postbiotics to potentially aid in the treatment of diseases like irritable bowel syndrome, bacterial vaginosis, atopic dermatitis, gingivitis, obesity, or cancer. There is also potential for many of the inhabitants of the human microbiome to directly modulate host gene expression and modulate host detoxifying enzyme activity like cytochrome P450s (CYPs), dehydrogenases, and carboxylesterases. Therefore, the microbiome may be important to consider during drug discovery, risk assessment, and dosing regimens for various diseases given that the human microbiome has been shown to impact host detoxification processes.
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Affiliation(s)
- Robert G. Nichols
- Department of Veterinary and Biomedical Science, The Pennsylvania State University, University Park, PA 16802 USA
| | - Jeffrey M. Peters
- Department of Veterinary and Biomedical Science, The Pennsylvania State University, University Park, PA 16802 USA
| | - Andrew D. Patterson
- Department of Veterinary and Biomedical Science, The Pennsylvania State University, University Park, PA 16802 USA
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31
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Saotome K, Teng B, Tsui CCA, Lee WH, Tu YH, Kaplan JP, Sansom MSP, Liman ER, Ward AB. Structures of the otopetrin proton channels Otop1 and Otop3. Nat Struct Mol Biol 2019; 26:518-525. [PMID: 31160780 PMCID: PMC6564688 DOI: 10.1038/s41594-019-0235-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/26/2019] [Indexed: 01/08/2023]
Abstract
Otopetrins (Otop1-Otop3) comprise one of two known eukaryotic proton-selective channel families. Otop1 is required for otoconia formation and a candidate mammalian sour taste receptor. Here we report cryo-EM structures of zebrafish Otop1 and chicken Otop3 in lipid nanodiscs. The structures reveal a dimeric architecture, with each subunit forming 12 transmembrane helices divided into structurally similar amino (N) and carboxy (C) domains. Cholesterol-like molecules occupy various sites in Otop1 and Otop3 and occlude a central tunnel. In molecular dynamics simulations, hydrophilic vestibules formed by the N and C domains and in the intrasubunit interface between N and C domains form conduits for water entry into the membrane core, suggesting three potential proton conduction pathways. By mutagenesis, we tested the roles of charged residues in each putative permeation pathway. Our results provide a structural basis for understanding selective proton permeation and gating of this conserved family of proton channels.
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Affiliation(s)
- Kei Saotome
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Bochuan Teng
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Che Chun Alex Tsui
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Yu-Hsiang Tu
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Joshua P Kaplan
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Emily R Liman
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
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32
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Chen Q, Zeng W, She J, Bai XC, Jiang Y. Structural and functional characterization of an otopetrin family proton channel. eLife 2019; 8:46710. [PMID: 30973323 PMCID: PMC6483595 DOI: 10.7554/elife.46710] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022] Open
Abstract
The otopetrin (OTOP) proteins were recently characterized as proton channels. Here we present the cryo-EM structure of OTOP3 from Xenopus tropicalis (XtOTOP3) along with functional characterization of the channel. XtOTOP3 forms a homodimer with each subunit containing 12 transmembrane helices that can be divided into two structurally homologous halves; each half assembles as an α-helical barrel that could potentially serve as a proton conduction pore. Both pores open from the extracellular half before becoming occluded at a central constriction point consisting of three highly conserved residues - Gln232/585-Asp262/Asn623-Tyr322/666 (the constriction triads). Mutagenesis shows that the constriction triad from the second pore is less amenable to perturbation than that of the first pore, suggesting an unequal contribution between the two pores to proton transport. We also identified several key residues at the interface between the two pores that are functionally important, particularly Asp509, which confers intracellular pH-dependent desensitization to OTOP channels.
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Affiliation(s)
- Qingfeng Chen
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Weizhong Zeng
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ji She
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Youxing Jiang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
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33
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Thiessen KD, Grzegorski SJ, Chin Y, Higuchi LN, Wilkinson CJ, Shavit JA, Kramer KL. Zebrafish otolith biomineralization requires polyketide synthase. Mech Dev 2019; 157:1-9. [PMID: 30974150 PMCID: PMC6531356 DOI: 10.1016/j.mod.2019.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/12/2019] [Accepted: 04/01/2019] [Indexed: 11/20/2022]
Abstract
Deflecting biomineralized crystals attached to vestibular hair cells are necessary for maintaining balance. Zebrafish (Danio rerio) are useful organisms to study these biomineralized crystals called otoliths, as many required genes are homologous to human otoconial development. We sought to identify and characterize the causative gene in a trio of homozygous recessive mutants, no content (nco) and corkscrew (csr), and vanished (vns), which fail to develop otoliths during early ear development. We show that nco, csr, and vns have potentially deleterious mutations in polyketide synthase (pks1), a multi-modular protein that has been previously implicated in biomineralization events in chordates and echinoderms. We found that Otoconin-90 (Oc90) expression within the otocyst is diffuse in nco and csr; therefore, it is not sufficient for otolith biomineralization in zebrafish. Similarly, normal localization of Otogelin, a protein required for otolith tethering in the otolithic membrane, is not sufficient for Oc90 attachment. Furthermore, eNOS signaling and Endothelin-1 signaling were the most up- and down-regulated pathways during otolith agenesis in nco, respectively. Our results demonstrate distinct processes for otolith nucleation and biomineralization in vertebrates and will be a starting point for models that are independent of Oc90-mediated seeding. This study will serve as a basis for investigating the role of eNOS signaling and Endothelin-1 signaling during otolith formation.
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Affiliation(s)
- Kevin D Thiessen
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States
| | - Steven J Grzegorski
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, United States
| | - Yvonne Chin
- Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Lisa N Higuchi
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States
| | - Christopher J Wilkinson
- Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
| | - Jordan A Shavit
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, United States
| | - Kenneth L Kramer
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States.
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34
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Kompotis K, Hubbard J, Emmenegger Y, Perrault A, Mühlethaler M, Schwartz S, Bayer L, Franken P. Rocking Promotes Sleep in Mice through Rhythmic Stimulation of the Vestibular System. Curr Biol 2019; 29:392-401.e4. [DOI: 10.1016/j.cub.2018.12.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/29/2018] [Accepted: 12/06/2018] [Indexed: 10/27/2022]
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35
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Bioinstructive microparticles for self-assembly of mesenchymal stem Cell-3D tumor spheroids. Biomaterials 2018; 185:155-173. [DOI: 10.1016/j.biomaterials.2018.09.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 12/13/2022]
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36
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Ma Y, Huang Z, Zhou Z, He X, Wang Y, Meng C, Huang G, Fang N. A novel antioxidant Mito-Tempol inhibits ox-LDL-induced foam cell formation through restoration of autophagy flux. Free Radic Biol Med 2018; 129:463-472. [PMID: 30321700 DOI: 10.1016/j.freeradbiomed.2018.10.412] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/06/2018] [Accepted: 10/08/2018] [Indexed: 11/25/2022]
Abstract
A bulk of cholesteryl esters accumulation in macrophage foam cells drives the occurrence and development of atherosclerosis. Evidence now shows that autophagy plays key roles in the degradation of intracellular lipid droplets via autolysosome, and also in the release of intracellular lipids via cholesterol efflux. In this study, we identified that a mitochondria-targeted antioxidant, Mito-Tempol, has protective effects against cholesteryl esters accumulation by activating autophagy. Mito-Tempol was shown to ameliorate the lipid burden for atherosclerosis, both in vitro and in vivo. In the established in vitro foam cell formation system using oxidized low-density lipoprotein (ox-LDL)-loaded THP-1 macrophages, Mito-Tempol prevented intracellular oxidative stress and attenuated lipid accumulation. Mito-Tempol rescued ox-LDL-impaired autophagic flux, thereby facilitating autophagy-mediated lipid degradation in THP-1 macrophages. Meanwhile, Mito-Tempol also increased the efflux of cholesterol via autophagy-dependent ABCA1 and ABCG1 up-regulation. The classical autophagy pathway of mTOR may be one of the effector for the autophagy restoration of Mito-Tempol. Our findings give the first insight that cardiovascular system disease may benefits more from the treatment of Mito-Tempol for its impact of reversing atherosclerosis via autophagy.
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Affiliation(s)
- Ying Ma
- Department of Geriatrics, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhenyu Huang
- Department of Neurosurgery, Changzheng Hospital of Shanghai, Second Millitary Medical University, Shanghai 200003, China
| | - Zhaoli Zhou
- Shanghai Key Laboratory for Molecular Imaging, Collaborative Scientific Research Center. Shanghai University of Medicine & Health Science, Shanghai 200093, China; Department of Pharmacology, School of Pharmacy, Shanghai University of Medicine & Health Science, Shanghai 200093, China
| | - Xiaoyan He
- Shanghai Key Laboratory for Molecular Imaging, Collaborative Scientific Research Center. Shanghai University of Medicine & Health Science, Shanghai 200093, China; Department of Pharmacology, School of Pharmacy, Shanghai University of Medicine & Health Science, Shanghai 200093, China
| | - Ying Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chao Meng
- Department of Geriatrics, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Gang Huang
- Shanghai Key Laboratory for Molecular Imaging, Collaborative Scientific Research Center. Shanghai University of Medicine & Health Science, Shanghai 200093, China
| | - Ningyuan Fang
- Department of Geriatrics, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
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37
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Otani K, Yokoya M, Kodama T, Hori K, Matsumoto K, Okada M, Yamawaki H. Plasma exosomes regulate systemic blood pressure in rats. Biochem Biophys Res Commun 2018; 503:776-783. [DOI: 10.1016/j.bbrc.2018.06.075] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 06/14/2018] [Indexed: 12/21/2022]
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Coll-Lladó C, Giebichenstein J, Webb PB, Bridges CR, de la Serrana DG. Ocean acidification promotes otolith growth and calcite deposition in gilthead sea bream (Sparus aurata) larvae. Sci Rep 2018; 8:8384. [PMID: 29849112 PMCID: PMC5976741 DOI: 10.1038/s41598-018-26026-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 05/03/2018] [Indexed: 11/29/2022] Open
Abstract
The effects of ocean acidification on otolith crystallization and growth rates were investigated in gilthead sea bream (Sparus aurata) larvae. Larvae were exposed to three different pH levels: pH8.2, pH7.7 and pH7.3 for a period of 18 days post-fertilization. For the first time, we demonstrate that pH has a significant impact on the carbonate polymorph composition, showing calcite in a significant percentage of individuals at low pH. Around 21% of the larvae exposed to pH7.3 showed irregular calcitic otoliths rather than commonly found round aragonitic otoliths. Calcitic otoliths showed a moderate level of heritability suggesting an important role of genetic factors. We also observed significantly larger otoliths in larvae reared at pH7.7 and pH7.3 compared to pH8.2 in both sagittae and lapilli. Our results demonstrate that otolith growth rates in gilthead sea bream larvae increase at low pH while a significant proportion of larvae are prone to the formation of calcitic otoliths at pH7.3.
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Affiliation(s)
- Clara Coll-Lladó
- Gatty Marine Laboratory, Scottish Oceans Institute, School of Biology, University of St Andrews, Scotland, UK
- Xelect Ltd, Horizon House, St Andrews, Scotland, UK
| | - Jan Giebichenstein
- Institut für Stoffwechselphysiologie/AG Ecophysiology, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Paul B Webb
- School of Chemistry, University of St Andrews, Scotland, UK
| | - Christopher R Bridges
- Institut für Stoffwechselphysiologie/AG Ecophysiology, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Daniel Garcia de la Serrana
- Gatty Marine Laboratory, Scottish Oceans Institute, School of Biology, University of St Andrews, Scotland, UK.
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Krause G, Hinz KM. Thyroid hormone transport across L-type amino acid transporters: What can molecular modelling tell us? Mol Cell Endocrinol 2017; 458:68-75. [PMID: 28341457 DOI: 10.1016/j.mce.2017.03.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/20/2017] [Accepted: 03/20/2017] [Indexed: 12/15/2022]
Abstract
Thyroid hormones (THs) and their derivatives require transmembrane transporters (TTs) to mediate their translocation across the cell membrane. Among these TTs, the L-type amino acid transporters (LAT) not only transport amino acids (AAs) but also certain THs and their derivatives. This review summarizes available knowledge concerning structure function patterns of the TH transport by LAT1 and LAT2. For example, LAT2 imports 3,3'-T2 and T3, but not rT3 and T4. In contrast to amino acids, THs are not at all exported by LAT2. Homology modelling of LAT1 and LAT2 is based on available crystal structures from the same superfamily the amino acid/polyamine/organocation transporter (APC). Molecular model guided mutagenesis has been used to predict substrate interaction sites. A common recognition feature for amino acid- and TH-derivatives has been suggested in an interior cavity of LAT1 and LAT2. Therein additional distinct molecular determinants that are responsible for the bidirectional AA transport but allowing only unidirectional import of particular THs have been confirmed for LAT2 by mutagenesis. Characterized substrate features that are needed for TH translocation and distinct LAT2 properties will be highlighted to understand the molecular import and export mechanisms of this transporter in more detail.
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Affiliation(s)
- Gerd Krause
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany.
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Hołubowicz R, Wojtas M, Taube M, Kozak M, Ożyhar A, Dobryszycki P. Effect of calcium ions on structure and stability of the C1q-like domain of otolin-1 from human and zebrafish. FEBS J 2017; 284:4278-4297. [DOI: 10.1111/febs.14308] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 10/17/2017] [Accepted: 10/24/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Rafał Hołubowicz
- Department of Biochemistry; Faculty of Chemistry; Wroclaw University of Science and Technology; Poland
| | - Magdalena Wojtas
- Department of Biochemistry; Faculty of Chemistry; Wroclaw University of Science and Technology; Poland
| | - Michał Taube
- Department of Macromolecular Physics; Faculty of Physics; A. Mickiewicz University; Poznan Poland
| | - Maciej Kozak
- Department of Macromolecular Physics; Faculty of Physics; A. Mickiewicz University; Poznan Poland
| | - Andrzej Ożyhar
- Department of Biochemistry; Faculty of Chemistry; Wroclaw University of Science and Technology; Poland
| | - Piotr Dobryszycki
- Department of Biochemistry; Faculty of Chemistry; Wroclaw University of Science and Technology; Poland
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Partridge SW, Benning MJ, German MJ, Dalgarno KW. Development of an arthroscopically compatible polymer additive layer manufacture technique. Proc Inst Mech Eng H 2017. [PMID: 28639513 DOI: 10.1177/0954411917690560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This article describes a proof of concept study designed to evaluate the potential of an in vivo three-dimensional printing route to support minimally invasive repair of the musculoskeletal system. The study uses a photocurable material to additively manufacture in situ a model implant and demonstrates that this can be achieved effectively within a clinically relevant timescale. The approach has the potential to be applied with a wide range of light-curable materials and with development could be applied to create functionally gradient structures in vivo.
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Affiliation(s)
- Simon W Partridge
- 1 School of Mechanical and Systems Engineering, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew J Benning
- 1 School of Mechanical and Systems Engineering, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew J German
- 2 Centre for Oral Health Research, School of Dental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Kenneth W Dalgarno
- 1 School of Mechanical and Systems Engineering, Newcastle University, Newcastle upon Tyne, UK
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A transcriptomic survey of Migdolus fryanus (sugarcane rhizome borer) larvae. PLoS One 2017; 12:e0173059. [PMID: 28248990 PMCID: PMC5332103 DOI: 10.1371/journal.pone.0173059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/14/2017] [Indexed: 11/19/2022] Open
Abstract
Sugarcane, a major crop grown in the tropical and subtropical areas of the world, is produced mainly for sucrose, which is used as a sweetener or for the production of bioethanol. Among the numerous pests that significantly affect the yield of sugarcane, the sugarcane rhizome borer (Migdolus fryanus, a cerambycidae beetle) is known to cause severe damage to the crops in Brazil. The absence of molecular information about this insect reinforces the need for studies and an effective method to control this pest. In this study, RNA-Seq technology was employed to study different parts of M. fryanus larvae. The generated data will help in further investigations about the taxonomy, development, and adaptation of this insect. RNA was extracted from six different parts (head, fat body, integument, hindgut, midgut, and foregut) using Trizol methodology. Using Illumina paired-end sequencing technology and the Trinity platform, trimming and de novo assembly was performed, resulting in 44,567 contigs longer than 200 nt for a reunion of data from all transcriptomes, with a mean length of 1,095.27 nt. Transcripts were annotated using BLAST against different protein databanks (Uniprot/Swissprot, PFAM, KEEG, SignalP 4.1, Gene Ontology, and CAZY) and were compared for similarity using a Venn diagram. Differential expression patterns were studied for select genes through qPCR and FPKM comprising important protein families (digestive peptidases, glucosyl hydrolases, serine protease inhibitors and otopetrin), which allowed a better understanding of the insect’s digestion, immunity and gravity sensorial mechanisms.
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Sapudom J, Ullm F, Martin S, Kalbitzer L, Naab J, Möller S, Schnabelrauch M, Anderegg U, Schmidt S, Pompe T. Molecular weight specific impact of soluble and immobilized hyaluronan on CD44 expressing melanoma cells in 3D collagen matrices. Acta Biomater 2017; 50:259-270. [PMID: 27965172 DOI: 10.1016/j.actbio.2016.12.026] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 12/09/2016] [Accepted: 12/09/2016] [Indexed: 01/09/2023]
Abstract
Hyaluronan (HA) and its principal receptor CD44 are known to be involved in regulating tumor cell dissemination and metastasis. The direct correlation of CD44-HA interaction on proliferation and invasion of tumor cells in dependence on the molecular weight and the presentation form of HA is not fully understood because of lack of appropriate matrix models. To address this issue, we reconstituted 3D collagen (Coll I) matrices and functionalized them with HA of molecular weight of 30-50kDa (low molecular weight; LMW-HA) and 500-750kDa (high molecular weight; HMW-HA). A post-modification strategy was applied to covalently immobilize HA to reconstituted fibrillar Coll I matrices, resulting in a non-altered Coll I network microstructure and stable immobilization over days. Functionalized Coll I matrices were characterized regarding topological and mechanical characteristics as well as HA amount using confocal laser scanning microscopy, colloidal probe force spectroscopy and quantitative Alcian blue assay, respectively. To elucidate HA dependent tumor cell behavior, BRO melanoma cell lines with and without CD44 receptor expression were used for in vitro cell experiments. We demonstrated that only soluble LMW-HA promoted cell proliferation in a CD44 dependent manner, while HMW-HA and immobilized LMW-HA did not. Furthermore, an enhanced cell invasion was found only for immobilized LMW-HA. Both findings correlated with a very strong and specific adhesive interaction of LMW-HA and CD44+ cells quantified in single cell adhesion measurements using soft colloidal force spectroscopy. Overall, our results introduce an in vitro biomaterials model allowing to test presentation mode and molecular weight specificity of HA in a 3D fibrillar matrix thus mimicking important in vivo features of tumor microenvironments. STATEMENT OF SIGNIFICANCE Molecular weight and presentation form (bound vs. soluble) of hyaluronan (HA) are intensively discussed as key regulators in tumor progression and inflammation. We introduce 3D fibrillar collagen matrices with defined microstructure and stiffness allowing the presentation of specific molecular weight forms of HA in soluble and bound manner. Mimicking in that way important in vivo features of tumor microenvironments, we found that only low molecular weight HA (LMW-HA) in soluble form promoted proliferation of a melanoma cell line (BRO), while it enhanced cell invasion in bound form. The molecular weight specificity of LMW-HA was verified to be CD44 receptor dependent and was correlated to adhesive ligand-receptor interactions in quantitative colloidal force spectroscopy at single cell level.
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Affiliation(s)
- Jiranuwat Sapudom
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Universität Leipzig, Leipzig 04103, Germany
| | - Franziska Ullm
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Universität Leipzig, Leipzig 04103, Germany
| | - Steve Martin
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Universität Leipzig, Leipzig 04103, Germany
| | - Liv Kalbitzer
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Universität Leipzig, Leipzig 04103, Germany
| | - Johanna Naab
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Universität Leipzig, Leipzig 04103, Germany
| | - Stephanie Möller
- INNOVENT e. V., Biomaterials Department, Prüssingstraße 27B, 07745 Jena, Germany
| | | | - Ulf Anderegg
- Department of Dermatology, Venerology and Allergology, Universitätsklinikum Leipzig, Leipzig 04103, Germany
| | - Stephan Schmidt
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Universität Leipzig, Leipzig 04103, Germany; Heinrich-Heine-Universität, Institute for Organic and Macromolecular Chemistry, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Tilo Pompe
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Universität Leipzig, Leipzig 04103, Germany.
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Thomas ORB, Ganio K, Roberts BR, Swearer SE. Trace element–protein interactions in endolymph from the inner ear of fish: implications for environmental reconstructions using fish otolith chemistry. Metallomics 2017; 9:239-249. [DOI: 10.1039/c6mt00189k] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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45
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Kao WTK, Parnes LS, Chole RA. Otoconia and otolithic membrane fragments within the posterior semicircular canal in benign paroxysmal positional vertigo. Laryngoscope 2016; 127:709-714. [PMID: 27726156 DOI: 10.1002/lary.26115] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 04/27/2016] [Accepted: 05/02/2016] [Indexed: 11/07/2022]
Abstract
OBJECTIVES/HYPOTHESIS Benign paroxysmal positional vertigo (BPPV) is the most common vestibular disorder with an incidence between 10.7 and 17.3 per 100,000 persons per year. The mechanism for BPPV has been postulated to involve displaced otoconia resulting in canalithiasis. Although particulate matter has been observed in the endolymph of affected patients undergoing posterior canal occlusion surgery, an otoconial origin for the disease is still questioned. STUDY DESIGN In this study, particulate matter was extracted from the posterior semicircular canal of two patients and examined with scanning electron microscopy. METHODS The samples were obtained from two patients intraoperatively during posterior semicircular canal occlusion. The particles were fixed, stored in ethanol, and chemically dehydrated. The samples were sputter coated and viewed under a scanning electron microscope. Digital images were obtained. RESULTS Intact and degenerating otoconia with and without linking filaments were found attached to amorphous particulate matter. Many otoconia appeared to be partially embedded in a gel matrix, presumably that which encases and anchors the otoconia within the otolith membrane, whereas others stood alone with no attached filaments and matrix. The otoconia measured roughly 2 to 8 μm in length and displayed a uniform outer shape with a cylindrical bulbous body and a 3 + 3 rhombohedral plane at each end. CONCLUSIONS These findings suggest that the source of the particulate matter in the semicircular canals of patients with BPPV is broken off fragments of the utricular otolithic membrane with attached and detached otoconia. LEVEL OF EVIDENCE NA Laryngoscope, 127:709-714, 2017.
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Affiliation(s)
- Wee Tin K Kao
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, Missouri, U.S.A
| | - Lorne S Parnes
- Department of Otolaryngology-Head and Neck Surgery, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Richard A Chole
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, Missouri, U.S.A
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46
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Loewen TN, Carriere B, Reist JD, Halden NM, Anderson WG. Linking physiology and biomineralization processes to ecological inferences on the life history of fishes. Comp Biochem Physiol A Mol Integr Physiol 2016; 202:123-140. [PMID: 27328377 DOI: 10.1016/j.cbpa.2016.06.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/10/2016] [Accepted: 06/14/2016] [Indexed: 02/07/2023]
Abstract
Biomineral chemistry is frequently used to infer life history events and habitat use in fishes; however, significant gaps remain in our understanding of the underlying mechanisms. Here we have taken a multidisciplinary approach to review the current understanding of element incorporation into biomineralized structures in fishes. Biominerals are primarily composed of calcium-based derivatives such as calcium carbonate found in otoliths and calcium phosphates found in scales, fins and bones. By focusing on non-essential life elements (strontium and barium) and essential life elements (calcium, zinc and magnesium), we attempt to connect several fields of study to synergise how physiology may influence biomineralization and subsequent inference of life history. Data provided in this review indicate that the presence of non-essential elements in biominerals of fish is driven primarily by hypo- and hyper-calcemic environmental conditions. The uptake kinetics between environmental calcium and its competing mimics define what is ultimately incorporated in the biomineral structure. Conversely, circannual hormonally driven variations likely influence essential life elements like zinc that are known to associate with enzyme function. Environmental temperature and pH as well as uptake kinetics for strontium and barium isotopes demonstrate the role of mass fractionation in isotope selection for uptake into fish bony structures. In consideration of calcium mobilisation, the action of osteoclast-like cells on calcium phosphates of scales, fins and bones likely plays a role in fractionation along with transport kinetics. Additional investigations into calcium mobilisation are warranted to understand differing views of strontium, and barium isotope fractionation between calcium phosphates and calcium carbonate structures in fishes.
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Affiliation(s)
- T N Loewen
- Interdisciplinary Studies (Geological Sciences), University of Manitoba, Winnipeg, MB, Canada; Freshwater Institute, Fisheries & Oceans, Winnipeg, MB, Canada.
| | - B Carriere
- Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - J D Reist
- Freshwater Institute, Fisheries & Oceans, Winnipeg, MB, Canada
| | - N M Halden
- Geological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - W G Anderson
- Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
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Brosel S, Laub C, Averdam A, Bender A, Elstner M. Molecular aging of the mammalian vestibular system. Ageing Res Rev 2016; 26:72-80. [PMID: 26739358 DOI: 10.1016/j.arr.2015.12.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 12/16/2015] [Accepted: 12/21/2015] [Indexed: 12/18/2022]
Abstract
Dizziness and imbalance frequently affect the elderly and contribute to falls and frailty. In many geriatric patients, clinical testing uncovers a dysfunction of the vestibular system, but no specific etiology can be identified. Neuropathological studies have demonstrated age-related degeneration of peripheral and central vestibular neurons, but the molecular mechanisms are poorly understood. In contrast, recent studies into age-related hearing loss strongly implicate mitochondrial dysfunction, oxidative stress and apoptotic cell death of cochlear hair cells. While some data suggest that analogous biological pathomechanisms may underlie vestibular dysfunction, actual proof is missing. In this review, we summarize the available data on the molecular causes of vestibular dysfunction.
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Affiliation(s)
- Sonja Brosel
- German Center for Vertigo and Balance Disorders, Department of Neurology, Klinikum Grosshadern, Ludwig-Maximilians-University, Marchioninistr. 15, 81377 Munich, Germany.
| | - Christoph Laub
- Department of Neurology with Friedrich-Baur-Institute, Klinikum Grosshadern, Ludwig-Maximilians-University, Marchioninistr. 15, 81377 Munich, Germany
| | - Anne Averdam
- Department of Neurology with Friedrich-Baur-Institute, Klinikum Grosshadern, Ludwig-Maximilians-University, Marchioninistr. 15, 81377 Munich, Germany
| | - Andreas Bender
- Department of Neurology, Therapiezentrum Burgau, Kapuzinerstr.34, 89331 Burgau, Germany
| | - Matthias Elstner
- Department of Neurology with Friedrich-Baur-Institute, Klinikum Grosshadern, Ludwig-Maximilians-University, Marchioninistr. 15, 81377 Munich, Germany; Department of Neurology and Clinical Neurophysiology, Academic Hospital Munich-Bogenhausen, Technical University of Munich, Englschalkingerstr. 77, 81925 Munich, Germany
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48
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Stooke-Vaughan GA, Obholzer ND, Baxendale S, Megason SG, Whitfield TT. Otolith tethering in the zebrafish otic vesicle requires Otogelin and α-Tectorin. Development 2015; 142:1137-45. [PMID: 25758224 PMCID: PMC4360185 DOI: 10.1242/dev.116632] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Otoliths are biomineralised structures important for balance and hearing in fish. Their counterparts in the mammalian inner ear, otoconia, have a primarily vestibular function. Otoliths and otoconia form over sensory maculae and are attached to the otolithic membrane, a gelatinous extracellular matrix that provides a physical coupling between the otolith and the underlying sensory epithelium. In this study, we have identified two proteins required for otolith tethering in the zebrafish ear, and propose that there are at least two stages to this process: seeding and maintenance. The initial seeding step, in which otolith precursor particles tether directly to the tips of hair cell kinocilia, fails to occur in the einstein (eis) mutant. The gene disrupted in eis is otogelin (otog); mutations in the human OTOG gene have recently been identified as causative for deafness and vestibular dysfunction (DFNB18B). At later larval stages, maintenance of otolith tethering to the saccular macula is dependent on tectorin alpha (tecta) function, which is disrupted in the rolling stones (rst) mutant. α-Tectorin (Tecta) is a major constituent of the tectorial membrane in the mammalian cochlea. Mutations in the human TECTA gene can cause either dominant (DFNA8/12) or recessive (DFNB21) forms of deafness. Our findings indicate that the composition of extracellular otic membranes is highly conserved between mammals and fish, reinforcing the view that the zebrafish is an excellent model system for the study of deafness and vestibular disease.
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Affiliation(s)
| | - Nikolaus D Obholzer
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Sarah Baxendale
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Tanya T Whitfield
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
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49
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Lundberg YW, Xu Y, Thiessen KD, Kramer KL. Mechanisms of otoconia and otolith development. Dev Dyn 2014; 244:239-53. [PMID: 25255879 DOI: 10.1002/dvdy.24195] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 08/25/2014] [Accepted: 08/26/2014] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Otoconia are bio-crystals that couple mechanic forces to the sensory hair cells in the utricle and saccule, a process essential for us to sense linear acceleration and gravity for the purpose of maintaining bodily balance. In fish, structurally similar bio-crystals called otoliths mediate both balance and hearing. Otoconia abnormalities are common and can cause vertigo and imbalance in humans. However, the molecular etiology of these illnesses is unknown, as investigators have only begun to identify genes important for otoconia formation in recent years. RESULTS To date, in-depth studies of selected mouse otoconial proteins have been performed, and about 75 zebrafish genes have been identified to be important for otolith development. CONCLUSIONS This review will summarize recent findings as well as compare otoconia and otolith development. It will provide an updated brief review of otoconial proteins along with an overview of the cells and cellular processes involved. While continued efforts are needed to thoroughly understand the molecular mechanisms underlying otoconia and otolith development, it is clear that the process involves a series of temporally and spatially specific events that are tightly coordinated by numerous proteins. Such knowledge will serve as the foundation to uncover the molecular causes of human otoconia-related disorders.
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Affiliation(s)
- Yunxia Wang Lundberg
- Vestibular Genetics Laboratory, Boys Town National Research Hospital, Omaha, Nebraska
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50
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Lundberg YW, Xu Y, Thiessen KD, Kramer KL. Mechanisms of otoconia and otolith development. Dev Dyn 2014. [PMID: 25255879 DOI: 10.1002/dvdy.24195(2014)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Otoconia are bio-crystals that couple mechanic forces to the sensory hair cells in the utricle and saccule, a process essential for us to sense linear acceleration and gravity for the purpose of maintaining bodily balance. In fish, structurally similar bio-crystals called otoliths mediate both balance and hearing. Otoconia abnormalities are common and can cause vertigo and imbalance in humans. However, the molecular etiology of these illnesses is unknown, as investigators have only begun to identify genes important for otoconia formation in recent years. RESULTS To date, in-depth studies of selected mouse otoconial proteins have been performed, and about 75 zebrafish genes have been identified to be important for otolith development. CONCLUSIONS This review will summarize recent findings as well as compare otoconia and otolith development. It will provide an updated brief review of otoconial proteins along with an overview of the cells and cellular processes involved. While continued efforts are needed to thoroughly understand the molecular mechanisms underlying otoconia and otolith development, it is clear that the process involves a series of temporally and spatially specific events that are tightly coordinated by numerous proteins. Such knowledge will serve as the foundation to uncover the molecular causes of human otoconia-related disorders.
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Affiliation(s)
- Yunxia Wang Lundberg
- Vestibular Genetics Laboratory, Boys Town National Research Hospital, Omaha, Nebraska
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