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Baker MR, Fan G, Arige V, Yule DI, Serysheva II. Understanding IP 3R channels: From structural underpinnings to ligand-dependent conformational landscape. Cell Calcium 2023; 114:102770. [PMID: 37393815 PMCID: PMC10529787 DOI: 10.1016/j.ceca.2023.102770] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/04/2023]
Abstract
Inositol 1,4,5-trisphosphate receptors (IP3Rs) are ubiquitously expressed large-conductance Ca2+-permeable channels predominantly localized to the endoplasmic reticulum (ER) membranes of virtually all eukaryotic cell types. IP3Rs work as Ca2+ signaling hubs through which diverse extracellular stimuli and intracellular inputs are processed and then integrated to result in delivery of Ca2+ from the ER lumen to generate cytosolic Ca2+ signals with precise temporal and spatial properties. IP3R-mediated Ca2+ signals control a vast repertoire of cellular functions ranging from gene transcription and secretion to the more enigmatic brain activities such as learning and memory. IP3Rs open and release Ca2+ when they bind both IP3 and Ca2+, the primary channel agonists. Despite overwhelming evidence supporting functional interplay between IP3 and Ca2+ in activation and inhibition of IP3Rs, the mechanistic understanding of how IP3R channels convey their gating through the interplay of two primary agonists remains one of the major puzzles in the field. The last decade has seen much progress in the use of cryogenic electron microscopy to elucidate the molecular mechanisms of ligand binding, ion permeation, ion selectivity and gating of the IP3R channels. The results of these studies, summarized in this review, provide a prospective view of what the future holds in structural and functional research of IP3Rs.
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Affiliation(s)
- Mariah R Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Guizhen Fan
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Vikas Arige
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - David I Yule
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA.
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA.
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2
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Neumann J, Van Nieuwenhove E, Terry LE, Staels F, Knebel TR, Welkenhuyzen K, Ahmadzadeh K, Baker MR, Gerbaux M, Willemsen M, Barber JS, Serysheva II, De Waele L, Vermeulen F, Schlenner S, Meyts I, Yule DI, Bultynck G, Schrijvers R, Humblet-Baron S, Liston A. Author Correction: Disrupted Ca 2+ homeostasis and immunodeficiency in patients with functional IP 3 receptor subtype 3 defects. Cell Mol Immunol 2023; 20:114. [PMID: 36471115 PMCID: PMC9794697 DOI: 10.1038/s41423-022-00960-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Julika Neumann
- grid.511015.1VIB Center for Brain and Disease Research, Leuven, Belgium ,grid.5596.f0000 0001 0668 7884Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Erika Van Nieuwenhove
- grid.511015.1VIB Center for Brain and Disease Research, Leuven, Belgium ,grid.5596.f0000 0001 0668 7884Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium ,grid.410569.f0000 0004 0626 3338UZ Leuven, Leuven, Belgium
| | - Lara E. Terry
- grid.16416.340000 0004 1936 9174Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14526 USA
| | - Frederik Staels
- grid.5596.f0000 0001 0668 7884Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium ,grid.410569.f0000 0004 0626 3338UZ Leuven, Leuven, Belgium
| | - Taylor R. Knebel
- grid.16416.340000 0004 1936 9174Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14526 USA
| | - Kirsten Welkenhuyzen
- grid.5596.f0000 0001 0668 7884Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Leuven Kankerinstituut, KU Leuven, Leuven, Belgium
| | - Kourosh Ahmadzadeh
- grid.415751.3Laboratory of Immunobiology, Department Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Mariah R. Baker
- grid.267308.80000 0000 9206 2401Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Margaux Gerbaux
- grid.5596.f0000 0001 0668 7884Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium ,grid.4989.c0000 0001 2348 0746Pediatric Department, Academic Children Hospital Queen Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Mathijs Willemsen
- grid.511015.1VIB Center for Brain and Disease Research, Leuven, Belgium ,grid.5596.f0000 0001 0668 7884Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - John S. Barber
- grid.511015.1VIB Center for Brain and Disease Research, Leuven, Belgium ,grid.5596.f0000 0001 0668 7884Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Irina I. Serysheva
- grid.267308.80000 0000 9206 2401Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Liesbeth De Waele
- grid.410569.f0000 0004 0626 3338Department of Pediatric Neurology, University Hospitals Leuven, Leuven, Belgium
| | - François Vermeulen
- grid.410569.f0000 0004 0626 3338Department of Pulmonology, University Hospitals Leuven, Leuven, Belgium
| | - Susan Schlenner
- grid.5596.f0000 0001 0668 7884Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Isabelle Meyts
- grid.410569.f0000 0004 0626 3338UZ Leuven, Leuven, Belgium ,grid.5596.f0000 0001 0668 7884Laboratory for Inborn Errors of Immunity, Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium
| | - David I. Yule
- grid.16416.340000 0004 1936 9174Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14526 USA
| | - Geert Bultynck
- grid.5596.f0000 0001 0668 7884Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Leuven Kankerinstituut, KU Leuven, Leuven, Belgium
| | - Rik Schrijvers
- grid.410569.f0000 0004 0626 3338UZ Leuven, Leuven, Belgium ,grid.5596.f0000 0001 0668 7884Laboratory for Allergy and Clinical Immunology and Immunogenetics Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Stephanie Humblet-Baron
- grid.5596.f0000 0001 0668 7884Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Adrian Liston
- grid.511015.1VIB Center for Brain and Disease Research, Leuven, Belgium ,grid.5596.f0000 0001 0668 7884Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium ,grid.418195.00000 0001 0694 2777Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT UK
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3
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Neumann J, Van Nieuwenhove E, Terry LE, Staels F, Knebel TR, Welkenhuyzen K, Ahmadzadeh K, Baker MR, Gerbaux M, Willemsen M, Barber JS, Serysheva II, De Waele L, Vermeulen F, Schlenner S, Meyts I, Yule DI, Bultynck G, Schrijvers R, Humblet-Baron S, Liston A. Disrupted Ca 2+ homeostasis and immunodeficiency in patients with functional IP 3 receptor subtype 3 defects. Cell Mol Immunol 2023; 20:11-25. [PMID: 36302985 PMCID: PMC9794825 DOI: 10.1038/s41423-022-00928-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/12/2022] [Indexed: 11/27/2022] Open
Abstract
Calcium signaling is essential for lymphocyte activation, with genetic disruptions of store-operated calcium (Ca2+) entry resulting in severe immunodeficiency. The inositol 1,4,5-trisphosphate receptor (IP3R), a homo- or heterotetramer of the IP3R1-3 isoforms, amplifies lymphocyte signaling by releasing Ca2+ from endoplasmic reticulum stores following antigen stimulation. Although knockout of all IP3R isoforms in mice causes immunodeficiency, the seeming redundancy of the isoforms is thought to explain the absence of variants in human immunodeficiency. In this study, we identified compound heterozygous variants of ITPR3 (a gene encoding IP3R subtype 3) in two unrelated Caucasian patients presenting with immunodeficiency. To determine whether ITPR3 variants act in a nonredundant manner and disrupt human immune responses, we characterized the Ca2+ signaling capacity, the lymphocyte response, and the clinical phenotype of these patients. We observed disrupted Ca2+ signaling in patient-derived fibroblasts and immune cells, with abnormal proliferation and activation responses following T-cell receptor stimulation. Reconstitution of IP3R3 in IP3R knockout cell lines led to the identification of variants as functional hypomorphs that showed reduced ability to discriminate between homeostatic and induced states, validating a genotype-phenotype link. These results demonstrate a functional link between defective endoplasmic reticulum Ca2+ channels and immunodeficiency and identify IP3Rs as diagnostic targets for patients with specific inborn errors of immunity. These results also extend the known cause of Ca2+-associated immunodeficiency from store-operated entry to impaired Ca2+ mobilization from the endoplasmic reticulum, revealing a broad sensitivity of lymphocytes to genetic defects in Ca2+ signaling.
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Affiliation(s)
- Julika Neumann
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Erika Van Nieuwenhove
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- UZ Leuven, Leuven, Belgium
| | - Lara E Terry
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY, 14526, USA
| | - Frederik Staels
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- UZ Leuven, Leuven, Belgium
| | - Taylor R Knebel
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY, 14526, USA
| | - Kirsten Welkenhuyzen
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Leuven Kankerinstituut, KU Leuven, Leuven, Belgium
| | - Kourosh Ahmadzadeh
- Laboratory of Immunobiology, Department Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Mariah R Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Margaux Gerbaux
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- Pediatric Department, Academic Children Hospital Queen Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Mathijs Willemsen
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - John S Barber
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Liesbeth De Waele
- Department of Pediatric Neurology, University Hospitals Leuven, Leuven, Belgium
| | | | - Susan Schlenner
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Isabelle Meyts
- UZ Leuven, Leuven, Belgium.
- Laboratory for Inborn Errors of Immunity, Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium.
| | - David I Yule
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY, 14526, USA
| | - Geert Bultynck
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Leuven Kankerinstituut, KU Leuven, Leuven, Belgium
| | - Rik Schrijvers
- UZ Leuven, Leuven, Belgium.
- Laboratory for Allergy and Clinical Immunology and Immunogenetics Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium.
| | | | - Adrian Liston
- VIB Center for Brain and Disease Research, Leuven, Belgium.
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium.
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
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Fan G, Baker MR, Terry LE, Arige V, Chen M, Seryshev AB, Baker ML, Ludtke SJ, Yule DI, Serysheva II. Conformational motions and ligand-binding underlying gating and regulation in IP 3R channel. Nat Commun 2022; 13:6942. [PMID: 36376291 PMCID: PMC9663519 DOI: 10.1038/s41467-022-34574-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/28/2022] [Indexed: 11/16/2022] Open
Abstract
Inositol-1,4,5-trisphosphate receptors (IP3Rs) are activated by IP3 and Ca2+ and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IP3R1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP3, Ca2+ and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP3 binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IP3R channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel.
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Affiliation(s)
- Guizhen Fan
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431, Fannin Street, Houston, TX, USA
| | - Mariah R Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431, Fannin Street, Houston, TX, USA
| | - Lara E Terry
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Vikas Arige
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Muyuan Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Alexander B Seryshev
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431, Fannin Street, Houston, TX, USA
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431, Fannin Street, Houston, TX, USA
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - David I Yule
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431, Fannin Street, Houston, TX, USA.
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5
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Arige V, Terry LE, Wagner LE, Malik S, Baker MR, Fan G, Joseph SK, Serysheva II, Yule DI. Functional determination of calcium-binding sites required for the activation of inositol 1,4,5-trisphosphate receptors. Proc Natl Acad Sci U S A 2022; 119:e2209267119. [PMID: 36122240 PMCID: PMC9522344 DOI: 10.1073/pnas.2209267119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/23/2022] [Indexed: 01/25/2023] Open
Abstract
Inositol 1,4,5-trisphosphate receptors (IP3Rs) initiate a diverse array of physiological responses by carefully orchestrating intracellular calcium (Ca2+) signals in response to various external cues. Notably, IP3R channel activity is determined by several obligatory factors, including IP3, Ca2+, and ATP. The critical basic amino acid residues in the N-terminal IP3-binding core (IBC) region that facilitate IP3 binding are well characterized. In contrast, the residues conferring regulation by Ca2+ have yet to be ascertained. Using comparative structural analysis of Ca2+-binding sites identified in two main families of intracellular Ca2+-release channels, ryanodine receptors (RyRs) and IP3Rs, we identified putative acidic residues coordinating Ca2+ in the cytosolic calcium sensor region in IP3Rs. We determined the consequences of substituting putative Ca2+ binding, acidic residues in IP3R family members. We show that the agonist-induced Ca2+ release, single-channel open probability (P0), and Ca2+ sensitivities are markedly altered when the negative charge on the conserved acidic side chain residues is neutralized. Remarkably, neutralizing the negatively charged side chain on two of the residues individually in the putative Ca2+-binding pocket shifted the Ca2+ required to activate IP3R to higher concentrations, indicating that these residues likely are a component of the Ca2+ activation site in IP3R. Taken together, our findings indicate that Ca2+ binding to a well-conserved activation site is a common underlying mechanism resulting in increased channel activity shared by IP3Rs and RyRs.
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Affiliation(s)
- Vikas Arige
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642
| | - Lara E. Terry
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642
| | - Larry E. Wagner
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642
| | - Sundeep Malik
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642
| | - Mariah R. Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Guizhen Fan
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Suresh K. Joseph
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Irina I. Serysheva
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030
| | - David I. Yule
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642
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Ahmed N, Baker MR, Bashford J. The landscape of neurophysiological outcome measures in ALS interventional trials: A systematic review. Clin Neurophysiol 2022; 137:132-141. [PMID: 35313253 PMCID: PMC10166714 DOI: 10.1016/j.clinph.2022.02.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/11/2022] [Accepted: 02/18/2022] [Indexed: 12/28/2022]
Abstract
OBJECTIVE We collated all interventional clinical trials in amyotrophic lateral sclerosis (ALS), which utilised at least one neurophysiological technique as a primary or secondary outcome measure. By identifying the strengths and limitations of these studies, we aim to guide study design in future trials. METHODS We conducted and reported this systematic review according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Eight databases were searched from inception. In total, 703 studies were retrieved for screening and eligibility assessment. RESULTS Dating back to 1986, 32 eligible interventional clinical trials were identified, recruiting a median of 30 patients per completed trial. The most widely employed neurophysiological techniques were electromyography, motor unit number estimation (including motor unit number index), neurophysiological index and transcranial magnetic stimulation (including resting motor threshold and short-interval intracortical inhibition). Almost 40% of trials reported a positive outcome with respect to at least one neurophysiological measure. The interventions targeted either ion channels, immune mechanisms or neuronal metabolic pathways. CONCLUSIONS Neurophysiology offers many promising biomarkers that can be utilised as outcome measures in interventional clinical trials in ALS. When selecting the most appropriate technique, key considerations include methodological standardisation, target engagement and logistical burden. SIGNIFICANCE Future trial design in ALS would benefit from a standardised, updated and easily accessible repository of neurophysiological outcome measures.
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Affiliation(s)
- N Ahmed
- GKT School of Medical Education, Faculty of Life Sciences and Medicine, King's College London, UK
| | - M R Baker
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - J Bashford
- UK Dementia Research Institute, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK.
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Baker MR, Fan G, Seryshev AB, Agosto MA, Baker ML, Serysheva II. Cryo-EM structure of type 1 IP 3R channel in a lipid bilayer. Commun Biol 2021; 4:625. [PMID: 34035440 PMCID: PMC8149723 DOI: 10.1038/s42003-021-02156-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 04/26/2021] [Indexed: 12/11/2022] Open
Abstract
Type 1 inositol 1,4,5-trisphosphate receptor (IP3R1) is the predominant Ca2+-release channel in neurons. IP3R1 mediates Ca2+ release from the endoplasmic reticulum into the cytosol and thereby is involved in many physiological processes. Here, we present the cryo-EM structures of full-length rat IP3R1 reconstituted in lipid nanodisc and detergent solubilized in the presence of phosphatidylcholine determined in ligand-free, closed states by single-particle electron cryo-microscopy. Notably, both structures exhibit the well-established IP3R1 protein fold and reveal a nearly complete representation of lipids with similar locations of ordered lipids bound to the transmembrane domains. The lipid-bound structures show improved features that enabled us to unambiguously build atomic models of IP3R1 including two membrane associated helices that were not previously resolved in the TM region. Our findings suggest conserved locations of protein-bound lipids among homotetrameric ion channels that are critical for their structural and functional integrity despite the diversity of structural mechanisms for their gating. 3D structure of full-length rat type 1 inositol 1,4,5-trisphosphate receptor reconstituted in lipid nanodisc is determined using single-particle cryo-electron microscopy. The study suggests conserved locations of protein-bound lipids among structurally diverse, homo-tetrameric ion channels.
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Affiliation(s)
- Mariah R Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Guizhen Fan
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Alexander B Seryshev
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Melina A Agosto
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, USA.
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8
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Ivanova H, Vervliet T, Monaco G, Terry LE, Rosa N, Baker MR, Parys JB, Serysheva II, Yule DI, Bultynck G. Bcl-2-Protein Family as Modulators of IP 3 Receptors and Other Organellar Ca 2+ Channels. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035089. [PMID: 31501195 DOI: 10.1101/cshperspect.a035089] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The pro- and antiapoptotic proteins belonging to the B-cell lymphoma-2 (Bcl-2) family exert a critical control over cell-death processes by enabling or counteracting mitochondrial outer membrane permeabilization. Beyond this mitochondrial function, several Bcl-2 family members have emerged as critical modulators of intracellular Ca2+ homeostasis and dynamics, showing proapoptotic and antiapoptotic functions. Bcl-2 family proteins specifically target several intracellular Ca2+-transport systems, including organellar Ca2+ channels: inositol 1,4,5-trisphosphate receptors (IP3Rs) and ryanodine receptors (RyRs), Ca2+-release channels mediating Ca2+ flux from the endoplasmic reticulum, as well as voltage-dependent anion channels (VDACs), which mediate Ca2+ flux across the mitochondrial outer membrane into the mitochondria. Although the formation of protein complexes between Bcl-2 proteins and these channels has been extensively studied, a major advance during recent years has been elucidating the complex interaction of Bcl-2 proteins with IP3Rs. Distinct interaction sites for different Bcl-2 family members were identified in the primary structure of IP3Rs. The unique molecular profiles of these Bcl-2 proteins may account for their distinct functional outcomes when bound to IP3Rs. Furthermore, Bcl-2 inhibitors used in cancer therapy may affect IP3R function as part of their proapoptotic effect and/or as an adverse effect in healthy cells.
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Affiliation(s)
- Hristina Ivanova
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Tim Vervliet
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Giovanni Monaco
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Lara E Terry
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642
| | - Nicolas Rosa
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Mariah R Baker
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Structural Biology Imaging Center, Houston, Texas 77030
| | - Jan B Parys
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Structural Biology Imaging Center, Houston, Texas 77030
| | - David I Yule
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642
| | - Geert Bultynck
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
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Baker MR, Dharmadasa T, Jaiser SR, Kiernan MC. Amyotrophic lateral sclerosis - Time for beta testing? Clin Neurophysiol 2018; 129:1455-1456. [PMID: 29754830 DOI: 10.1016/j.clinph.2018.04.613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 04/18/2018] [Indexed: 11/29/2022]
Affiliation(s)
- M R Baker
- Institute of Neuroscience, The Medical School, Newcastle University, NE2 4HH, UK; Department of Neurology, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK; Department of Clinical Neurophysiology, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK.
| | - T Dharmadasa
- Brain and Mind Centre, The University of Sydney, Sydney, Australia
| | - S R Jaiser
- Institute of Neuroscience, The Medical School, Newcastle University, NE2 4HH, UK; Department of Clinical Neurophysiology, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK
| | - M C Kiernan
- Brain and Mind Centre, The University of Sydney, Sydney, Australia; Institute of Clinical Neurosciences, Royal Prince Alfred Hospital, Sydney, Australia
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Simpson AJ, Cunningham MO, Baker MR. Electrodiagnostic applications of somatosensory evoked high-frequency EEG oscillations: Technical considerations. Brain Res Bull 2018; 137:351-355. [PMID: 29366907 DOI: 10.1016/j.brainresbull.2018.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 01/02/2018] [Accepted: 01/15/2018] [Indexed: 10/18/2022]
Abstract
INTRODUCTION High frequency oscillations (HFOs) embedded within the somatosensory evoked potential (SEP) are not routinely recorded/measured as part of standard clinical SEPs. However, HFOs could provide important additional diagnostic/prognostic information in various patient groups in whom SEPs are tested routinely. One area is the management of patients with hypoxic ischaemic encephalopathy (HIE) in the intensive care unit (ICU). However, the sensitivity of standard clinical SEP recording techniques for detecting HFOs is unknown. METHODS SEPs were recorded using routine clinical methods in 17 healthy subjects (median nerve stimulation; 0.5 ms pulse width; 5 Hz; maximum 4000 stimuli) in an unshielded laboratory. Bipolar EEG recordings were acquired (gain 50 k; bandpass 3Hz-2 kHz; sampling rate 5 kHz; non-inverting electrode 2 cm anterior to C3/C4; inverting electrode 2 cm posterior to C3/C4). Data analysis was performed in MATLAB. RESULTS SEP-HFOs were detected in 65% of controls using standard clinical recording techniques. In 3 controls without significant HFOs, experiments were repeated using a linear electrode array with higher spatial sampling frequency. SEP-HFOs were observed in all 3 subjects. CONCLUSIONS Currently standard clinical methods of recording SEPs are not sufficiently sensitive to permit the inclusion of SEP-HFOs in routine clinical diagnostic/prognostic assessments. Whilst an increase in the number/density of EEG electrodes should improve the sensitivity for detecting SEP-HFOs, this requires confirmation. By improving and standardising clinical SEP recording protocols to permit the acquisition/analysis of SEP-HFOs, it should be possible to gain important insights into the pathophysiology of neurological disorders and refine the management of conditions such as HIE.
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Affiliation(s)
- A J Simpson
- Institute of Neuroscience, The Medical School, Newcastle University, NE2 4HH, UK
| | - M O Cunningham
- Institute of Neuroscience, The Medical School, Newcastle University, NE2 4HH, UK
| | - M R Baker
- Institute of Neuroscience, The Medical School, Newcastle University, NE2 4HH, UK; Department of Neurology, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK; Department of Clinical Neurophysiology, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK.
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Baker MR, Fan G, Serysheva II. Structure of IP 3R channel: high-resolution insights from cryo-EM. Curr Opin Struct Biol 2017; 46:38-47. [PMID: 28618351 PMCID: PMC5683905 DOI: 10.1016/j.sbi.2017.05.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 05/08/2017] [Accepted: 05/25/2017] [Indexed: 01/19/2023]
Abstract
Inositol 1,4,5-trisphosphate receptors (IP3Rs) are ubiquitously expressed intracellular Ca2+ channels and the major mediators of cellular Ca2+ signals generated by the release of Ca2+ ions from intracellular stores in response to a variety of extracellular stimuli. Despite established physiological significance and proven involvements of IP3R channels in many human diseases, detailed structural basis for signal detection by these ion channels and their gating remain obscure. Recently, single particle electron cryomicroscopy (cryo-EM) has yielded a long-awaited near-atomic resolution structure of the entire full-length type 1 IP3R. This structure provided exciting mechanistic insights into the molecular assembly of IP3R, revealing the pronounced structural conservation of Ca2+ release channels and raising many fundamental and controversial questions on their activation and gating. Here we summarize the major technological advances that propelled our cryo-EM analysis of IP3R to near-atomic resolution and discuss what the future holds for structural biology of Ca2+ release channels.
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Affiliation(s)
- Mariah R Baker
- Structural Biology Imaging Center, Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Guizhen Fan
- Structural Biology Imaging Center, Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Irina I Serysheva
- Structural Biology Imaging Center, Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA.
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Abstract
BACKGROUND Physicians can come across patients who are exposed to certain prescription drugs or toxins that can result in adverse effects and complications which have high rates of morbidity and mortality. OBJECTIVE To summarise the key clinical features and management of the common movement disorder toxidromes relevant to physicians (with an interest in neurology). METHODS We searched PUBMED from 1946 to 2016 for papers relating to movement toxidromes and their treatment. The findings from those studies were then summarised and are presented here. RESULTS The key features of 6 of the common movement disorder toxidromes and their treatment are tabulated and highlighted. The management of toxidromes with the highest mortality like neuroleptic malignant syndrome and serotonin syndrome are discussed in detail. CONCLUSION There are several toxidromes that have the potential to become a serious life-threatening emergency if there is a delay in recognition of key clinical features and instituting the appropriate treatment at the earliest is crucial.
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Affiliation(s)
- N Malek
- Department of Neurology, Ipswich Hospital NHS Trust, Ipswich, UK
| | - M R Baker
- Department of Neurology, Royal Victoria Infirmary, Newcastle-upon-Tyne, UK
- Department of Clinical Neurophysiology, Royal Victoria Infirmary, Newcastle -upon-Tyne, UK
- Institute of Neuroscience, The Medical School, Newcastle University, Newcastle-upon-Tyne, UK
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Fan G, Baker ML, Wang Z, Baker MR, Sinyagovskiy PA, Chiu W, Ludtke SJ, Serysheva II. Gating machinery of InsP3R channels revealed by electron cryomicroscopy. Nature 2015; 527:336-41. [PMID: 26458101 DOI: 10.1038/nature15249] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 07/24/2015] [Indexed: 12/12/2022]
Abstract
Inositol-1,4,5-trisphosphate receptors (InsP3Rs) are ubiquitous ion channels responsible for cytosolic Ca(2+) signalling and essential for a broad array of cellular processes ranging from contraction to secretion, and from proliferation to cell death. Despite decades of research on InsP3Rs, a mechanistic understanding of their structure-function relationship is lacking. Here we present the first, to our knowledge, near-atomic (4.7 Å) resolution electron cryomicroscopy structure of the tetrameric mammalian type 1 InsP3R channel in its apo-state. At this resolution, we are able to trace unambiguously ∼85% of the protein backbone, allowing us to identify the structural elements involved in gating and modulation of this 1.3-megadalton channel. Although the central Ca(2+)-conduction pathway is similar to other ion channels, including the closely related ryanodine receptor, the cytosolic carboxy termini are uniquely arranged in a left-handed α-helical bundle, directly interacting with the amino-terminal domains of adjacent subunits. This configuration suggests a molecular mechanism for allosteric regulation of channel gating by intracellular signals.
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Affiliation(s)
- Guizhen Fan
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, Texas 77030, USA
| | - Matthew L Baker
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Zhao Wang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Mariah R Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, Texas 77030, USA
| | - Pavel A Sinyagovskiy
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, Texas 77030, USA
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, Texas 77030, USA
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Baker MR, Fan G, Serysheva II. Single-Particle Cryo-EM of the Ryanodine Receptor Channel in an Aqueous Environment. Eur J Transl Myol 2015; 25:4803. [PMID: 26913144 PMCID: PMC4748972 DOI: 10.4081/ejtm.2015.4803] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/22/2014] [Accepted: 12/31/2014] [Indexed: 12/31/2022] Open
Abstract
Ryanodine receptors (RyRs) are tetrameric ligand-gated Ca2+ release channels that are responsible for the increase of cytosolic Ca2+ concentration leading to muscle contraction. Our current understanding of RyR channel gating and regulation is greatly limited due to the lack of a high-resolution structure of the channel protein. The enormous size and unwieldy shape of Ca2+ release channels make X-ray or NMR methods difficult to apply for high-resolution structural analysis of the full-length functional channel. Single-particle electron cryo-microscopy (cryo-EM) is one of the only effective techniques for the study of such a large integral membrane protein and its molecular interactions. Despite recent developments in cryo-EM technologies and break-through single-particle cryo-EM studies of ion channels, cryospecimen preparation, particularly the presence of detergent in the buffer, remains the main impediment to obtaining atomic-resolution structures of ion channels and a multitude of other integral membrane protein complexes. In this review we will discuss properties of several detergents that have been successfully utilized in cryo-EM studies of ion channels and the emergence of the detergent alternative amphipol to stabilize ion channels for structure-function characterization. Future structural studies of challenging specimen like ion channels are likely to be facilitated by cryo-EM amenable detergents or alternative surfactants.
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Affiliation(s)
- Mariah R Baker
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Guizhen Fan
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA
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Popova OB, Fan G, Baker MR, Jakana J, Chiu W, Ludtke SJ, Serysheva II. Cryo-EM Studies of RyR1 Channel in Detergent-Free Aqueous Environment. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Fisher KM, Chinnery PF, Baker SN, Baker MR. Enhanced reticulospinal output in patients with (REEP1) hereditary spastic paraplegia type 31. J Neurol 2013; 260:3182-4. [PMID: 24221643 PMCID: PMC3843367 DOI: 10.1007/s00415-013-7178-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/27/2013] [Accepted: 10/28/2013] [Indexed: 11/28/2022]
Affiliation(s)
- K M Fisher
- Institute of Neuroscience, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
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Lalani SR, Ware SM, Wang X, Zapata G, Tian Q, Franco LM, Jiang Z, Bucasas K, Scott DA, Campeau PM, Hanchard N, Umaña L, Cast A, Patel A, Cheung SW, McBride KL, Bray M, Craig Chinault A, Boggs BA, Huang M, Baker MR, Hamilton S, Towbin J, Jefferies JL, Fernbach SD, Potocki L, Belmont JW. MCTP2 is a dosage-sensitive gene required for cardiac outflow tract development. Hum Mol Genet 2013; 22:4339-48. [PMID: 23773997 DOI: 10.1093/hmg/ddt283] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Coarctation of the aorta (CoA) and hypoplastic left heart syndrome (HLHS) have been reported in rare individuals with large terminal deletions of chromosome 15q26. However, no single gene important for left ventricular outflow tract (LVOT) development has been identified in this region. Using array-comparative genomic hybridization, we identified two half-siblings with CoA with a 2.2 Mb deletion on 15q26.2, inherited from their mother, who was mosaic for this deletion. This interval contains an evolutionary conserved, protein-coding gene, MCTP2 (multiple C2-domains with two transmembrane regions 2). Using gene-specific array screening in 146 individuals with non-syndromic LVOT obstructive defects, another individual with HLHS and CoA was found to have a de novo 41 kb intragenic duplication within MCTP2, predicted to result in premature truncation, p.F697X. Alteration of Mctp2 gene expression in Xenopus laevis embryos by morpholino knockdown and mRNA overexpression resulted in the failure of proper OT development, confirming the functional importance of this dosage-sensitive gene for cardiogenesis. Our results identify MCTP2 as a novel genetic cause of CoA and related cardiac malformations.
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Abstract
ATP is an important modulator of gating in type 1 ryanodine receptor (RyR1), also known as a Ca2+ release channel in skeletal muscle cells. The activating effect of ATP on this channel is achieved by directly binding to one or more sites on the RyR1 protein. However, the number and location of these sites have yet to be determined. To identify the ATP-binding regions within RyR1 we used 2N3ATP-2′,3′-Biotin-LC-Hydrazone (BioATP-HDZ), a photo-reactive ATP analog to covalently label the channel. We found that BioATP-HDZ binds RyR1 specifically with an IC50 = 0.6±0.2 mM, comparable with the reported EC50 for activation of RyR1 with ATP. Controlled proteolysis of labeled RyR1 followed by sequence analysis revealed three fragments with apparent molecular masses of 95, 45 and 70 kDa that were crosslinked by BioATP-HDZ and identified as RyR1 sequences. Our analysis identified four glycine-rich consensus motifs that can potentially constitute ATP-binding sites and are located within the N-terminal 95-kDa fragment. These putative nucleotide-binding sequences include amino acids 699–704, 701–706, 1081–1084 and 1195–1200, which are conserved among the three RyR isoforms. Located next to the N-terminal disease hotspot region in RyR1, these sequences may communicate the effects of ATP-binding to channel function by tuning conformational motions within the neighboring cytoplasmic regulatory domains. Two other labeled fragments lack ATP-binding consensus motifs and may form non-canonical ATP-binding sites. Based on domain topology in the 3D structure of RyR1 it is also conceivable that the identified ATP-binding regions, despite their wide separation in the primary sequence, may actually constitute the same non-contiguous ATP-binding pocket within the channel tetramer.
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Affiliation(s)
- Olga B. Popova
- Department of Biochemistry and Molecular Biology, The University of Texas at Houston Medical School, Houston, Texas, United States of America
| | - Mariah R. Baker
- Department of Biochemistry and Molecular Biology, The University of Texas at Houston Medical School, Houston, Texas, United States of America
| | - Tina P. Tran
- Department of Biochemistry and Molecular Biology, The University of Texas at Houston Medical School, Houston, Texas, United States of America
| | - Tri Le
- Department of Biochemistry and Molecular Biology, The University of Texas at Houston Medical School, Houston, Texas, United States of America
| | - Irina I. Serysheva
- Department of Biochemistry and Molecular Biology, The University of Texas at Houston Medical School, Houston, Texas, United States of America
- * E-mail:
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Abstract
The complex interplay of proteins and other molecules, often in the form of large transitory assemblies, are critical to cellular function. Today, X-ray crystallography and electron cryo-microscopy (cryo-EM) are routinely used to image these macromolecular complexes, though often at limited resolutions. Despite the rapidly growing number of macromolecular structures, few tools exist for modeling and annotating structures in the range of 3-10 Å resolution. To address this need, we have developed a number of utilities specifically targeting subnanometer resolution density maps. As part of the 2010 Cryo-EM Modeling Challenge, we demonstrated two of our latest de novo modeling tools, Pathwalking and Gorgon, as well as a tool for secondary structure identification (SSEHunter) and a new rigid-body/flexible fitting tool in Gorgon. In total, we submitted 30 structural models from ten different subnanometer resolution data sets in four of the six challenge categories. Each of our utlities produced accurate structural models and annotations across the various density maps. In the end, the utilities that we present here offer users a robust toolkit for analyzing and modeling protein structure in macromolecular assemblies at non-atomic resolutions.
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Affiliation(s)
- Matthew L Baker
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA.
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Baker MR, Rees I, Ludtke SJ, Chiu W, Baker ML. Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking. Structure 2012; 20:450-63. [PMID: 22405004 DOI: 10.1016/j.str.2012.01.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 12/16/2011] [Accepted: 01/03/2012] [Indexed: 11/26/2022]
Abstract
A significant number of macromolecular structures solved by electron cryo-microscopy and X-ray crystallography obtain resolutions of 3.5-6Å, at which direct atomistic interpretation is difficult. To address this, we developed pathwalking, a semi-automated protocol to enumerate reasonable Cα models from near-atomic resolution density maps without a structural template or sequence-structure correspondence. Pathwalking uses an approach derived from the Traveling Salesman Problem to rapidly generate an ensemble of initial models for individual proteins, which can later be optimized to produce full atomic models. Pathwalking can also be used to validate and identify potential structural ambiguities in models generated from near-atomic resolution density maps. In this work, examples from the EMDB and PDB are used to assess the broad applicability and accuracy of our method. With the growing number of near-atomic resolution density maps from cryo-EM and X-ray crystallography, pathwalking can become an important tool in modeling protein structures.
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Affiliation(s)
- Mariah R Baker
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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Gillis VL, Senthinathan A, Dzingina M, Chamberlain K, Banks E, Baker MR, Longson D. Management of an acute painful sickle cell episode in hospital: summary of NICE guidance. BMJ 2012; 344:e4063. [PMID: 22740566 DOI: 10.1136/bmj.e4063] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- V L Gillis
- National Institute for Health and Clinical Excellence, Manchester M1 4BD, UK
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Jaiser S, Fisher KM, Zaaimi B, Seow H, Miller JAL, Chinnery PF, Williams TL, Baker SN, Baker MR. 161 15–30 Hz intermuscular coherence as a potential biomarker of upper motor neuron dysfunction in motor neuron disease. J Neurol Psychiatry 2012. [DOI: 10.1136/jnnp-2011-301993.203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Affiliation(s)
- K Chamberlain
- National Institute for Health and Clinical Excellence, Manchester M1 4BD, UK
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Baker MR, Fisher KM, Whittaker RG, Griffiths PG, Yu-Wai-Man P, Chinnery PF. Subclinical multisystem neurologic disease in "pure" OPA1 autosomal dominant optic atrophy. Neurology 2011; 77:1309-12. [PMID: 21917770 PMCID: PMC3179647 DOI: 10.1212/wnl.0b013e318230a15a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- M R Baker
- Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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Yu-Wai-Man P, Griffiths PG, Gorman GS, Lourenco CM, Wright AF, Auer-Grumbach M, Toscano A, Musumeci O, Valentino ML, Caporali L, Lamperti C, Tallaksen CM, Duffey P, Miller J, Whittaker RG, Baker MR, Jackson MJ, Clarke MP, Dhillon B, Czermin B, Stewart JD, Hudson G, Reynier P, Bonneau D, Marques W, Lenaers G, McFarland R, Taylor RW, Turnbull DM, Votruba M, Zeviani M, Carelli V, Bindoff LA, Horvath R, Amati-Bonneau P, Chinnery PF. Multi-system neurological disease is common in patients with OPA1 mutations. ACTA ACUST UNITED AC 2010; 133:771-86. [PMID: 20157015 PMCID: PMC2842512 DOI: 10.1093/brain/awq007] [Citation(s) in RCA: 314] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Additional neurological features have recently been described in seven families transmitting pathogenic mutations in OPA1, the most common cause of autosomal dominant optic atrophy. However, the frequency of these syndromal 'dominant optic atrophy plus' variants and the extent of neurological involvement have not been established. In this large multi-centre study of 104 patients from 45 independent families, including 60 new cases, we show that extra-ocular neurological complications are common in OPA1 disease, and affect up to 20% of all mutational carriers. Bilateral sensorineural deafness beginning in late childhood and early adulthood was a prominent manifestation, followed by a combination of ataxia, myopathy, peripheral neuropathy and progressive external ophthalmoplegia from the third decade of life onwards. We also identified novel clinical presentations with spastic paraparesis mimicking hereditary spastic paraplegia, and a multiple sclerosis-like illness. In contrast to initial reports, multi-system neurological disease was associated with all mutational subtypes, although there was an increased risk with missense mutations [odds ratio = 3.06, 95% confidence interval = 1.44-6.49; P = 0.0027], and mutations located within the guanosine triphosphate-ase region (odds ratio = 2.29, 95% confidence interval = 1.08-4.82; P = 0.0271). Histochemical and molecular characterization of skeletal muscle biopsies revealed the presence of cytochrome c oxidase-deficient fibres and multiple mitochondrial DNA deletions in the majority of patients harbouring OPA1 mutations, even in those with isolated optic nerve involvement. However, the cytochrome c oxidase-deficient load was over four times higher in the dominant optic atrophy + group compared to the pure optic neuropathy group, implicating a causal role for these secondary mitochondrial DNA defects in disease pathophysiology. Individuals with dominant optic atrophy plus phenotypes also had significantly worse visual outcomes, and careful surveillance is therefore mandatory to optimize the detection and management of neurological disability in a group of patients who already have significant visual impairment.
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Affiliation(s)
- P Yu-Wai-Man
- Mitochondrial Research Group, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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Lanner JT, Long C, Xu J, Baker MR, Hamilton S. AICAR Prevents Heat-Induced Death in Mice with Malignant Hyperthermia. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.2781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Abstract
Today, electron cryomicroscopy (cryo-EM) can routinely achieve subnanometer resolutions of complex macromolecular assemblies. From a density map, one can extract key structural and functional information using a variety of computational analysis tools. At subnanometer resolution, these tools make it possible to isolate individual subunits, identify secondary structures, and accurately fit atomic models. With several cryo-EM studies achieving resolutions beyond 5Å, computational modeling and feature recognition tools have been employed to construct backbone and atomic models of the protein components directly from a density map. In this chapter, we describe several common classes of computational tools that can be used to analyze and model subnanometer resolution reconstructions from cryo-EM. A general protocol for analyzing subnanometer resolution density maps is presented along with a full description of steps used in analyzing the 4.3Å resolution structure of Mm-cpn.
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Affiliation(s)
- Matthew L Baker
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
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Kennelly MM, Baker MR, Birchall D, Hanley JP, Turnbull DM, Loughney AD. Hyperemesis gravidarum and first trimester sagittal sinus thrombosis. J OBSTET GYNAECOL 2008; 28:453-4. [PMID: 18604696 DOI: 10.1080/01443610802131119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- M M Kennelly
- Department of Obstetrics and Gynaecology, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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Durham WJ, Aracena-Parks P, Long C, Rossi AE, Goonasekera SA, Boncompagni S, Galvan DL, Gilman CP, Baker MR, Shirokova N, Protasi F, Dirksen R, Hamilton SL. RyR1 S-nitrosylation underlies environmental heat stroke and sudden death in Y522S RyR1 knockin mice. Cell 2008; 133:53-65. [PMID: 18394989 DOI: 10.1016/j.cell.2008.02.042] [Citation(s) in RCA: 262] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Revised: 10/30/2007] [Accepted: 02/29/2008] [Indexed: 11/30/2022]
Abstract
Mice with a malignant hyperthermia mutation (Y522S) in the ryanodine receptor (RyR1) display muscle contractures, rhabdomyolysis, and death in response to elevated environmental temperatures. We demonstrate that this mutation in RyR1 causes Ca(2+) leak, which drives increased generation of reactive nitrogen species (RNS). Subsequent S-nitrosylation of the mutant RyR1 increases its temperature sensitivity for activation, producing muscle contractures upon exposure to elevated temperatures. The Y522S mutation in humans is associated with central core disease. Many mitochondria in the muscle of heterozygous Y522S mice are swollen and misshapen. The mutant muscle displays decreased force production and increased mitochondrial lipid peroxidation with aging. Chronic treatment with N-acetylcysteine protects against mitochondrial oxidative damage and the decline in force generation. We propose a feed-forward cyclic mechanism that increases the temperature sensitivity of RyR1 activation and underlies heat stroke and sudden death. The cycle eventually produces a myopathy with damaged mitochondria.
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Affiliation(s)
- William J Durham
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
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Abstract
It has been proposed that the conduction velocities of cerebellar climbing fibre (olivocerebellar) axons are tuned according to length, in order to precisely fix the conduction time between the inferior olive and cerebellar cortex. Some data conflict with this view. We have re-evaluated this issue using the climbing fibre reflex. The white matter of the tip of one folium in lobule VI or VII was stimulated electrically 0.5-1 mm below the surface and recordings were made from Purkinje cells in lobules VIII and IX. Reflex evoked climbing fibre (CF) responses (33 units) were recorded at different depths from Purkinje cells found in a narrow sagittal zone of cortex as complex spikes. The responses had latencies ranging from 4.3 ms to 11.3 ms. A consistent trend was that Purkinje cell responses recorded at greater depth had shorter CF reflex latencies than those recorded more superficially, both in individual experiments and in grouped data. These data show that the CF reflex latency is not constant, but is directly proportional to the distance an action potential has to travel along a CF. These data are not consistent with tuning of CF conduction velocities to normalize olivocerebellar conduction time, but are consistent with a CF conduction velocity in the cortex of approximately 0.6 m s-1. This suggests that climbing fibres projecting to different parts of the cerebellar cortex may have differences in spike conduction time of a few milliseconds, and that submillisecond precision is not an important element of the climbing fibre signal.
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Affiliation(s)
- M R Baker
- Department of Anatomy, Downing Street, Cambridge CB2 3DY, UK
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Abstract
This case report is about the novel use of the anti-CD20 antibody, rituximab, in the treatment of a 41 year old woman with stiff person syndrome. She was admitted to hospital as an emergency with prolonged and painful extensor spasms affecting the neck and back, arms, and legs. The disease had progressed despite a favourable initial response to conventional treatment with intravenous immunoglobulin and cytotoxics. Treatment with rituximab induced a lasting clinical remission.
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Affiliation(s)
- M R Baker
- Department of Neurology, Royal Victoria Infirmary Queen Victoria Road, Newcastle upon Tyne NE1 4LP, UK
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Serysheva II, Ludtke SJ, Baker MR, Chiu W, Hamilton SL. Structure of the voltage-gated L-type Ca2+ channel by electron cryomicroscopy. Proc Natl Acad Sci U S A 2002; 99:10370-5. [PMID: 12149473 PMCID: PMC124921 DOI: 10.1073/pnas.162363499] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2002] [Accepted: 06/18/2002] [Indexed: 11/18/2022] Open
Abstract
Voltage-dependent L-type Ca(2+) channels play important functional roles in many excitable cells. We present a three-dimensional structure of an L-type Ca(2+) channel. Electron cryomicroscopy in conjunction with single-particle processing was used to determine a 30-A resolution structure of the channel protein. The asymmetrical channel structure consists of two major regions: a heart-shaped region connected at its widest end with a handle-shaped region. A molecular model is proposed for the arrangement of this skeletal muscle L-type Ca(2+) channel structure with respect to the sarcoplasmic reticulum Ca(2+)-release channel, the physical partner of the L-type channel for signal transduction during the excitation-contraction coupling in muscle.
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Affiliation(s)
- I I Serysheva
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Baker MR, Javid M, Edgley SA. Activation of cerebellar climbing fibres to rat cerebellar posterior lobe from motor cortical output pathways. J Physiol 2001; 536:825-39. [PMID: 11691875 PMCID: PMC2278917 DOI: 10.1111/j.1469-7793.2001.00825.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2001] [Accepted: 06/11/2001] [Indexed: 11/28/2022] Open
Abstract
1. The activation of climbing fibres projecting to the posterior lobe cerebellar cortex by focal stimulation of the cerebral corticofugal pathway was investigated in anaesthetised rats. Large climbing fibre responses were evoked in parts of crus II and paramedian lobule by stimulation of corticofugal fibres. Lesions of the pyramidal tract just rostral to the inferior olive substantially reduced these responses, suggesting that they were not mediated by relays in the rostral brainstem. 2. By comparison of latencies of climbing fibre responses evoked from different locations in the corticofugal pathway, the conduction velocities of the corticofugal fibres that mediate the responses were estimated to be 1.9 +/- 0.3 m s(-1) (mean +/- S.E.M.). The fastest conducting corticofugal fibres were estimated to conduct significantly faster (18.7 +/- 2.3 m s(-1)). 3. Climbing fibre responses with similar form and cerebellar distribution were evoked from sites in the pyramidal tract rostral and caudal to the inferior olive. This suggests that at least a proportion of the fibres that activate climbing fibres are corticospinal fibres. 4. Lesions of the dorsal column nuclei did not affect the climbing fibre responses evoked in crus II, and produced a relatively small reduction of the responses in the paramedian lobule. This implies that the climbing fibre responses were not exclusively mediated via the dorsal column nuclei. 5. Corticofugal evoked climbing fibre responses were mapped across the cerebellar hemisphere. At some sites they were co-localised with responses evoked by limb afferents. On the basis of limb afferent inputs and other work, these zones were tentatively identified as being functionally equivalent to the c1, c2 and d zones described in the cat.
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Affiliation(s)
- M R Baker
- Department of Anatomy, Downing Street, Cambridge CB2 3DY, UK
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35
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Wright J, Baker MR. Sleep apnoea. J R Coll Physicians Lond 1999; 33:483-4. [PMID: 10624673 PMCID: PMC9665709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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Affiliation(s)
- J M Tiffany
- Nuffield Laboratory of Ophthalmology, University of Oxford, United Kingdom
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Wright WH, McCreery TP, Krupinski EA, Lund PJ, Smyth SH, Baker MR, Hulett RL, Unger EC. Evaluation of new thrombus-specific ultrasound contrast agent. Acad Radiol 1998; 5 Suppl 1:S240-2. [PMID: 9561090 DOI: 10.1016/s1076-6332(98)80117-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- W H Wright
- Department of Radiology, University of Arizona, Tucson 85724-5067, USA
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Baker MR, Henderson J, Hill A. Does Inverting Text Improve Reading Performance in Homonymous Hemianopes? Perception 1997. [DOI: 10.1068/v970039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Anecdotal information from rehabilitation practice of reading performance and low-vision practice suggests that where right homonymous parafoveal field loss impairs reading at the visual-sensory level, an improvement in reading speed can be achieved by inverting the text. This is because whilst left-field loss is considered to impair return eye movements to the beginning of a line, right-field loss is considered to reduce the spatial size of the perceptual window and increase its temporal extent by prolonging fixations times, reducing the amplitudes of saccades to the right, and introducing frequent regressive saccades. Inverting the text was thought to reverse these effects as the leading edge of the perceptual window is ‘returned’ to the sighted field so that in-line saccades can be visually guided. Here we report that this does not appear to be the case. In our study we measured the eye movements of patients with right homonymous hemianopia and others with peripheral loss due to retinitis pigmentosa as well as normal controls using an infrared video eye-tracker. All groups display a similar proportional prolongation of fixations times, reduction of saccadic amplitude, and proportion of regressive saccades when asked to read inverted text, which suggests a cognitive component of impairment independent of visual field loss in right homonymous hemianopes.
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Metzger-Rose C, Krupinski EA, Wright WH, Baker MR, McCreery TP, Barrette TR, Unger EC. Ultrasonographic detection of testicular ischemia in a canine model using phospholipid coated microbubbles (MRX-115). J Ultrasound Med 1997; 16:317-326. [PMID: 9315169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The purpose of this study was to determine if the sonographic contrast agent MRX-115 could improve the accuracy of Doppler ultrasonographic diagnosis of testicular ischemia. Testicular duplex ultrasonography was performed on six dogs before and after surgical ligation of the testicular artery, and before and after intravenous injection of MRX-115. Six radiologists blinded to experimental conditions rated the testicular blood flow. Receiver operating characteristics curves for conditions with and without administration of contrast agent were compared using Student's t-test for paired observations. Statistically significant differences were found both for the tests viewed individually (P = 0.003) and for the testes in comparison to the contralateral side (P = 0.0001). MRX-115 therefore is found to improve duplex sonographic evaluation of testicular ischemia.
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Affiliation(s)
- C Metzger-Rose
- Department of Radiology, University of Arizona, Tucson 85724-5067, USA
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Metzger-Rose C, Wright WH, Baker MR, Krupinski EA, McCreery TP, Barrette TR, Unger EC. Effect of phospholipid-coated microbubbles (MRX-115) on the detection of testicular ischemia in dogs. Acad Radiol 1996; 3 Suppl 2:S315-6. [PMID: 8796590 DOI: 10.1016/s1076-6332(96)80568-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- C Metzger-Rose
- Department of Radiology, University of Arizona, Tucson 85724, USA
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Abstract
PURPOSE Positional popliteal artery obstruction is believed to be an important factor contributing to popliteal artery entrapment syndromes. This study was undertaken to define the positional anatomy and physiologic condition of the vessels in the popliteal fossa in groups of highly trained and normally active young men and women. We postulate that at least some symptom-free individuals can occlude the popliteal artery with leg positioning. METHODS Seventy-two limbs were evaluated in 36 subjects. Symptom-free subjects were recruited in four groups: normally active men, normally active women, male competitive runners, and female competitive runners. All subjects underwent noninvasive testing that included resting segmental limb pressures and Doppler waveforms and color-flow duplex imaging with the leg in the neutral position and then with knee extension with active and passive dorsiflexion and plantar flexion of the foot. Subjects unable to occlude the popliteal artery with positioning were then exercised, and studies were repeated. Magnetic resonance imaging, with magnetic resonance angiography, was conducted on 14 subjects, with each leg studied in the neutral position and with active positioning. RESULTS Positional popliteal arterial occlusion occurred in 38 of 72 limbs (53%). No intergroup comparisons were statistically significant. The response of each leg was symmetric in 89% of subjects. No subject who could not occlude the popliteal artery at rest was able to do so with exercise. Magnetic resonance imaging disclosed normal anatomy in all subjects and showed the location of popliteal occlusion to be at the level of the soleal sling, with positional compression by the soleus muscle, the lateral head of the gastrocnemius, the plantaris, and popliteus muscles. CONCLUSION Popliteal arterial occlusion can be induced in 53% of subjects with simple leg positioning caused by myofascial compression. This must be considered when evaluating patients for intervention on the basis of physiologic testing of the popliteal vessels.
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Affiliation(s)
- L S Erdoes
- Section of Vascular Surgery, University of Arizona Health Sciences Center Tucson
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Katial RK, Hatch RM, Baker MR. Cardiac tamponade and recurrent upper respiratory tract infections in a 22-year-old woman. Ann Allergy 1994; 73:473-7. [PMID: 7998658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The association of IgA deficiency with SLE is clearly established but occurs in only a small percentage of patients. Several hypotheses address the relationship between the two disease processes but the common link remains undetermined. It is important to investigate the diagnosis of IgA deficiency in patients presenting with SLE in order to provide the most appropriate treatment. This patient not only represents a rare presentation of SLE but highlights the uncommon occurrence with IgA deficiency and brings forth valuable teaching points of both diseases.
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Affiliation(s)
- R K Katial
- Department of Medicine, Dwight David Eisenhower Army Medical Center, Augusta, Georgia
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Jarek MJ, West SG, Baker MR, Rak KM. Magnetic resonance imaging in systemic lupus erythematosus patients without a history of neuropsychiatric lupus erythematosus. Arthritis Rheum 1994; 37:1609-13. [PMID: 7980671 DOI: 10.1002/art.1780371108] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVE To determine the prevalence of magnetic resonance imaging (MRI) lesions in systemic lupus erythematosus (SLE) patients without a history of neuropsychiatric symptoms and to correlate any MRI abnormalities with the patient's other disease manifestations or treatment. METHODS Prospective study of 32 consecutive patients with SLE without a history of neuropsychiatric symptoms, from inpatient and outpatient rheumatology services, who underwent MRI scan during a 3-year period. RESULTS Five patients had MRI abnormalities consisting of white matter lesions or periventricular hyperintensities; this is similar to the prevalence of these abnormalities in the general population. CONCLUSION The prevalence of silent brain MRI abnormalities is not increased in SLE patients who do not have a history of neuropsychiatric manifestations.
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Affiliation(s)
- M J Jarek
- Department of Medicine, Fitzsimons Army Medical Center, Aurora, CO 80045-5001
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Abstract
METHODS All patients with rheumatoid arthritis (RA) attending an outpatient rheumatology clinic at a major military medical center over 6 years were included in follow-up for the development and subsequent course of sacral insufficiency fractures. RESULTS Sacral insufficiency fractures developed in 4 of 386 patients. Consistent with the literature, patients were female, elderly, and/or postmenopausal, had severe or long-standing disease, and were taking corticosteroids. The correct diagnosis was initially delayed because radiographs were normal but was later established with bone scan and sacral computerized tomography. Each patient improved with calcitonin and/or physical therapy over time. CONCLUSIONS Patients with RA represent a unique subgroup predisposed to insufficiency fractures because of multiple osteoporotic risk factors. Patients who have RA and acute low back or buttock pain should be evaluated aggressively for sacral insufficiency fractures with bone and/or computed tomography scans regardless of normal plain radiographs.
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Affiliation(s)
- S G West
- Rheumatology Service, Fitzsimons Army Medical Center, Aurora, Colorado
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Abstract
Fifteen presurgical patients with a history of ovarian carcinoma were evaluated with immunoscintigraphy using the In-111-labeled monoclonal antibody conjugate CYT-103. Twelve of these patients had residual neoplasia at time of laparotomy. A single intravenous dose of the radiolabeled monoclonal antibody was given to these patients before restaging laparotomy. All patients also underwent CT scanning of the abdomen and pelvis before laparotomy. Immunoscintigraphy detected the presence of disease in 10 of 12 patients before surgery, whereas CT scanning detected disease in only 6 of these 12 women. The results of this study indicate that immunoscintigraphy using In-111 CYT-103 is more sensitive than CT and may add useful information to the preoperative evaluation of women with ovarian carcinoma.
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Affiliation(s)
- C E Neal
- Department of Radiology, Memorial Medical Center, Springfield, Illinois 62781
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Knight T, Smith Z, Lockton JA, Sahota P, Bedford A, Toop M, Kernohan E, Baker MR. Ethnic differences in risk markers for heart disease in Bradford and implications for preventive strategies. J Epidemiol Community Health 1993; 47:89-95. [PMID: 8326279 PMCID: PMC1059734 DOI: 10.1136/jech.47.2.89] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
OBJECTIVES To assess and compare the prevalence of established risk markers for ischaemic heart disease in a sample of Asian and non-Asian men and to relate these observations to preventive strategies. SETTING Two factories in the textile industry in Bradford, West Yorkshire, UK. Subjects--288 male manual workers aged 20 to 65 years. DESIGN Cross sectional study within one occupational/social class stratum. MEASUREMENTS AND MAIN RESULTS Age, body mass index, plasma lipids, fibrinogen and serum insulin values, blood pressure, smoking habits, alcohol consumption, and exercise routines were recorded. Plasma total cholesterol concentrations were significantly lower in Asian than non-Asian men (5.3 mmol/l v 5.8 mmol/l respectively, p < 0.0001), as were low density lipoprotein cholesterol concentrations (3.4 mmol/l v 3.7 mmol/l, p = 0.0150), and high density lipoprotein (HDL) cholesterol (1.1 mmol/l v 1.3 mmol/l, p < 0.0001). Hypercholesterolaemia (concentration > 6.5mM) was present in nearly one quarter of non-Asians but less than one eighth of Asian men. Triglyceride values were not significantly higher in Asians. Smoking rates were high in non-Asians (43.8%) and only slightly lower in Asians (39.1%). Asian smokers smoked fewer cigarettes per day on average (9.3 v 16.1, p = 0.0001). Almost a quarter of non-Asian men (23.1%) and 26.6% of Asian men had raised blood pressure. Systolic pressures were higher in non-Asian men (138.3 mmHg v 133.0 mmHg, p = 0.0070), but diastolic pressures showed no ethnic differences. Diabetes was more prevalent in Asian men (10.9% v 4.4% p < 0.05), who also showed higher serum insulin concentrations after glucose loading (22.3 mU/l v 10.2 mU/l, p < 0.0001). Plasma fibrinogen values were higher in non-Asian men (2.9 g/l v 2.6 g/l, p < 0.0001) and these were associated with smoking. Nearly all non-Asians (92.5%) consumed alcohol at some time whereas 62.5% of Asians habitually abstained from alcohol consumption. Among the drinkers, non-Asian men consumed on average, 23.9 units per week and Asian men 18.4 units per week (p = 0.083). The mean body mass index for Asian men was 24.5 kg/m2 which was not significantly different to the mean in non-Asian men (25.2 kg/m2). The frequency of exercise in leisure time was low in both groups with 44.4% of non-Asian and 21.1% of Asian men taking moderate exercise weekly, and even fewer, regular strenuous exercise (16.3% and 8.6% respectively). CONCLUSIONS The plasma cholesterol and fibrinogen concentrations, prevalence of hypertension, smoking habits, alcohol intakes, and infrequency of exercise in leisure time in these non-Asian men in Bradford were consistent with an increased risk of heart disease. The pattern of risk markers was clearly different in Asian men. Only their lower HDL cholesterol concentrations, marginally higher triglyceride values, higher prevalence of diabetes, and very low frequency of exercise in leisure time would be consistent with a higher risk of heart disease compared with non-Asians. The implications of these observations for heart disease preventive strategies are discussed.
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Affiliation(s)
- T Knight
- University of Bradford, Clinical Epidemiology Research Unit
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Knight TM, Smith Z, Whittles A, Sahota P, Lockton JA, Hogg G, Bedford A, Toop M, Kernohan EE, Baker MR. Insulin resistance, diabetes, and risk markers for ischaemic heart disease in Asian men and non-Asian in Bradford. Heart 1992; 67:343-50. [PMID: 1389712 PMCID: PMC1024852 DOI: 10.1136/hrt.67.5.343] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVE To examine the hypothesis, in a community not studied before, that insulin resistance associated with centralised adiposity is the mechanism underlying the predisposition of Asian immigrant communities to both ischaemic heart disease and diabetes mellitus. DESIGN Cross sectional study within one socioeconomic stratum. SETTING Two factories in the textile sector in Bradford, West Yorkshire. SUBJECTS Male manual workers of Asian (110) and non-Asian origin (156) aged 20-65 years. RESULTS Diabetes was almost three times more prevalent in the Asian group. Two hours after an oral glucose load Asian men had double the serum insulin concentrations of non-Asian men (p < 0.0001). Asian men also had significantly lower concentrations of plasma total cholesterol (p < 0.03), high density lipoprotein cholesterol (HDL) (HDL2, p < 0.0001; HDL3, p < 0.0001), and apolipoprotein AI (p < 0.0001). Fasting plasma triglyceride concentrations were slightly higher (p = 0.072) in the Asian men; thus the ratio of triglyceride cholesterol was higher (p = 0.006). The inter-relation between serum insulin and plasma lipid concentrations indicated metabolic differences between the ethnic groups. Insulin concentrations were associated with cholesterol concentrations in the Asian men only and there was a lack of association between triglyceride, low density lipoprotein cholesterol, and HDL cholesterol in this group. The risk marker profile in the Asian men was therefore quite different to that of their non-Asian counterparts and was associated with a greater tendency to centralised adiposity. CONCLUSION These data support the insulin resistance hypothesis and thus have important implications for strategies for the prevention of heart disease in Asian communities in the United Kingdom.
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Affiliation(s)
- T M Knight
- Department of Public Health, Bradford Health Authority, West Yorkshire
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Baker MR. Role of the medical director. Br J Hosp Med (Lond) 1992; 47:111-4. [PMID: 1543957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The regulations establishing NHS trusts make specific provision for a medical director on the board of every trust, although no guidance is issued on the responsibilities associated with such a post. This paper explores the possible roles and relationships facing the medical director.
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Hanes PJ, O'Dell NL, Baker MR, Keagle JG, Davis HC. The effect of tensile strength on the clinical effectiveness and patient acceptance of dental floss. J Clin Periodontol 1992; 19:30-4. [PMID: 1732307 DOI: 10.1111/j.1600-051x.1992.tb01145.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This study compared the clinical effectiveness and subjective approval of 2 waxed dental flosses that differed significantly in tensile strength and wax content. At the initial appointment, subjects (20 1st-year dental students) were instructed to stop interproximal cleaning on 2 contralateral quadrants in order to allow plaque to accumulate on these surfaces for 1 week. 1 week later, subjects were instructed to begin flossing these 2 contralateral quadrants with 1 of the 2 types of floss for the next 1-week period, while withdrawing interproximal cleaning on the opposite 2 contralateral quadrants. After flossing these 2 quadrants for 1 week, the subjects began flossing the opposite 2 contralateral quadrants with the same floss. After 2 weeks of flossing contralateral quadrants, the 1st floss was withdrawn and replaced with the alternative floss for another similar 2-week trial period. At the end of each 2-week trial period, subjects completed subjective questionnaires concerning the floss they had used during the previous 2-week period. Pre- and post-flossing plaque indices were calculated for each week for both flosses, and compared statistically by a repeated measures analysis of variance. The results showed that both flosses significantly reduced interproximal plaque deposits, and had equal subjective approval. However, neither the greater-strength nor the lower-wax content of the experimental floss was associated with an increase in clinical effectiveness or with a change in subjective approval.
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Affiliation(s)
- P J Hanes
- Department of Periodontics, Medical College of Georgia, Augusta 30912
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