Necrox-5 Protects Mitochondrial Oxidative Phosphorylation Capacity
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The Heterotaxy Candidate Gene, TMEM195, Regulates Nuclear Localization of Beta-Catenin
Yale University EliScholar – A Digital Platform for Scholarly Publishing at Yale Yale Medicine Thesis Digital Library School of Medicine January 2015 The etH erotaxy Candidate Gene, Tmem195, Regulates Nuclear Localization Of Beta-Catenin Anna Ruth Duncan Yale School of Medicine, [email protected] Follow this and additional works at: http://elischolar.library.yale.edu/ymtdl Recommended Citation Duncan, Anna Ruth, "The eH terotaxy Candidate Gene, Tmem195, Regulates Nuclear Localization Of Beta-Catenin" (2015). Yale Medicine Thesis Digital Library. 1961. http://elischolar.library.yale.edu/ymtdl/1961 This Open Access Thesis is brought to you for free and open access by the School of Medicine at EliScholar – A Digital Platform for Scholarly Publishing at Yale. It has been accepted for inclusion in Yale Medicine Thesis Digital Library by an authorized administrator of EliScholar – A Digital Platform for Scholarly Publishing at Yale. For more information, please contact [email protected]. The Heterotaxy Candidate Gene, TMEM195, Regulates Nuclear Localization of Beta-catenin A Thesis Submitted to the Yale University School of Medicine in Partial Fulfillment of the Requirements for the Degree of Doctor of Medicine By Anna Ruth Duncan 2015 Abstract THE HETEROTAXY CANDIDATE GENE, TMEM195, REGULATES NUCLEAR LOCALIZATION OF BETA-CATENIN. Anna R. Duncan, John Griffin, Andrew Robson, and Mustafa K. Khokha. Department of Pediatrics, Yale University, School of Medicine, New Haven, CT. Congenital heart disease (CHD) affects 1 in every 130 newborns and is the leading cause of infant mortality (2). Heterotaxy (Htx), a disorder of left-right (LR) development, commonly leads to CHD. Despite aggressive surgical management, patients with Htx have poor survival rates and severe morbidity due to their complex CHD. -
Pathway and Gene-Set Activation Measurement from Mrna Expression Data
Open Access Research2006LevineetVolume al. 7, Issue 10, Article R93 Pathway and gene-set activation measurement from mRNA comment expression data: the tissue distribution of human pathways David M Levine*, David R Haynor†, John C Castle*, Sergey B Stepaniants*, Matteo Pellegrini‡, Mao Mao* and Jason M Johnson* Addresses: *Rosetta Inpharmatics LLC, a wholly owned subsidiary of Merck and Co., Inc., Terry Avenue North, Seattle, WA 98109, USA. †Department of Radiology, University of Washington, Seattle, WA 98195, USA. ‡Department of MCD Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA. reviews Correspondence: Jason M Johnson. Email: [email protected] Published: 17 October 2006 Received: 12 July 2006 Revised: 13 September 2006 Genome Biology 2006, 7:R93 (doi:10.1186/gb-2006-7-10-r93) Accepted: 17 October 2006 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2006/7/10/R93 reports © 2006 Levine et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The<p>Asented.</p> tissue comparison distribution of five of differenthuman pathways measures of pathway expression and a public map of pathway expression in human tissues are pre- deposited research Abstract Background: Interpretation of lists of genes or proteins with altered expression is a critical and time-consuming part of microarray and proteomics research, but relatively little attention has been paid to methods for extracting biological meaning from these output lists. -
Novel Gene Discovery in Primary Ciliary Dyskinesia
Novel Gene Discovery in Primary Ciliary Dyskinesia Mahmoud Raafat Fassad Genetics and Genomic Medicine Programme Great Ormond Street Institute of Child Health University College London A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy University College London 1 Declaration I, Mahmoud Raafat Fassad, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. 2 Abstract Primary Ciliary Dyskinesia (PCD) is one of the ‘ciliopathies’, genetic disorders affecting either cilia structure or function. PCD is a rare recessive disease caused by defective motile cilia. Affected individuals manifest with neonatal respiratory distress, chronic wet cough, upper respiratory tract problems, progressive lung disease resulting in bronchiectasis, laterality problems including heart defects and adult infertility. Early diagnosis and management are essential for better respiratory disease prognosis. PCD is a highly genetically heterogeneous disorder with causal mutations identified in 36 genes that account for the disease in about 70% of PCD cases, suggesting that additional genes remain to be discovered. Targeted next generation sequencing was used for genetic screening of a cohort of patients with confirmed or suggestive PCD diagnosis. The use of multi-gene panel sequencing yielded a high diagnostic output (> 70%) with mutations identified in known PCD genes. Over half of these mutations were novel alleles, expanding the mutation spectrum in PCD genes. The inclusion of patients from various ethnic backgrounds revealed a striking impact of ethnicity on the composition of disease alleles uncovering a significant genetic stratification of PCD in different populations. -
Identification, Tissue Specific Expression, and Chromosomal
European Journal of Human Genetics (2000) 8, 923–932 © 2000 Macmillan Publishers Ltd All rights reserved 1018–4813/00 $15.00 y www.nature.com/ejhg ARTICLE Identification, tissue specific expression, and chromosomal localisation of several human dynein heavy chain genes Amit K Maiti1, Marie-Genevi`eve Matt´ei2, Mark Jorissen3, Armin Volz4, Andreas Zeigler4 and Patrice Bouvagnet5 1Division of Medical Genetics, Geneva University School of Medicine, Geneva, Switzerland; 2INSERM U 406, Facult´e de M´edecine, Marseille, France; 3Centrum voor Menselijke Erfelijkheid, Campus Gasthuisberg, O & N, Leuven, Belgium; 4Institut f¨ur Immungenetik, Universit¨atsklinikum Charit´e, Humboldt-Universit¨at zu Berlin, Berlin, Germany; 5Laboratoire de G´en´etique Mol´eculaire Humaine, Facult´e de Pharmacie, Lyon, France Sliding between adjacent microtubules within the axonema gives rise to the motility of cilia and flagella. The driving force is produced by dynein complexes which are mainly composed of the axonemal dynein heavy chains. We used cells of human respiratory epithelium after in vitro ciliogenesis to clone cDNA fragments of nine dynein heavy chain genes, one of which had never been identified before. Dynein heavy chains are highly conserved from protozoa to human and the evolutionary ancestry of these dynein heavy chain cDNA fragments was deduced by phylogenetic analysis. These dynein heavy chain cDNAs are highly transcribed in human tissues containing axonema such as trachea, testis and brain, but not in adult heart or placenta. PAC clones containing dynein heavy chains were obtained and used to determine by FISH their chromosomal position in the human genome. They were mapped to 2p12–p11, 2q33, 3p21.2–p21.1, 13q14, 16p12 and 17p12. -
Cardiovascular Diseases Genetic Testing Program Information
Cardiovascular Diseases Genetic Testing Program Description: Congenital Heart Disease Panels We offer comprehensive gene panels designed to • Congenital Heart Disease Panel (187 genes) diagnose the most common genetic causes of hereditary • Heterotaxy Panel (114 genes) cardiovascular diseases. Testing is available for congenital • RASopathy/Noonan Spectrum Disorders Panel heart malformation, cardiomyopathy, arrythmia, thoracic (31 genes) aortic aneurysm, pulmonary arterial hypertension, Marfan Other Panels syndrome, and RASopathy/Noonan spectrum disorders. • Pulmonary Arterial Hypertension (PAH) Panel Hereditary cardiovascular disease is caused by variants in (20 genes) many different genes, and may be inherited in an autosomal dominant, autosomal recessive, or X-linked manner. Other Indications: than condition-specific panels, we also offer single gene Panels: sequencing for any gene on the panels, targeted variant • Confirmation of genetic diagnosis in a patient with analysis, and targeted deletion/duplication analysis. a clinical diagnosis of cardiovascular disease Tests Offered: • Carrier or pre-symptomatic diagnosis identification Arrythmia Panels in individuals with a family history of cardiovascular • Comprehensive Arrhythmia Panel (81 genes) disease of unknown genetic basis • Atrial Fibrillation (A Fib) Panel (28 genes) Gene Specific Sequencing: • Atrioventricular Block (AV Block) Panel (7 genes) • Confirmation of genetic diagnosis in a patient with • Brugada Syndrome Panel (21 genes) cardiovascular disease and in whom a specific -
Research Article Complex and Multidimensional Lipid Raft Alterations in a Murine Model of Alzheimer’S Disease
SAGE-Hindawi Access to Research International Journal of Alzheimer’s Disease Volume 2010, Article ID 604792, 56 pages doi:10.4061/2010/604792 Research Article Complex and Multidimensional Lipid Raft Alterations in a Murine Model of Alzheimer’s Disease Wayne Chadwick, 1 Randall Brenneman,1, 2 Bronwen Martin,3 and Stuart Maudsley1 1 Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA 2 Miller School of Medicine, University of Miami, Miami, FL 33124, USA 3 Metabolism Unit, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA Correspondence should be addressed to Stuart Maudsley, [email protected] Received 17 May 2010; Accepted 27 July 2010 Academic Editor: Gemma Casadesus Copyright © 2010 Wayne Chadwick et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Various animal models of Alzheimer’s disease (AD) have been created to assist our appreciation of AD pathophysiology, as well as aid development of novel therapeutic strategies. Despite the discovery of mutated proteins that predict the development of AD, there are likely to be many other proteins also involved in this disorder. Complex physiological processes are mediated by coherent interactions of clusters of functionally related proteins. Synaptic dysfunction is one of the hallmarks of AD. Synaptic proteins are organized into multiprotein complexes in high-density membrane structures, known as lipid rafts. These microdomains enable coherent clustering of synergistic signaling proteins. -
Program in Human Neutrophils Fails To
Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 is online at: average * The Journal of Immunology Anaplasma phagocytophilum , 20 of which you can access for free at: 2005; 174:6364-6372; ; from submission to initial decision 4 weeks from acceptance to publication J Immunol doi: 10.4049/jimmunol.174.10.6364 http://www.jimmunol.org/content/174/10/6364 Insights into Pathogen Immune Evasion Mechanisms: Fails to Induce an Apoptosis Differentiation Program in Human Neutrophils Dori L. Borjesson, Scott D. Kobayashi, Adeline R. Whitney, Jovanka M. Voyich, Cynthia M. Argue and Frank R. DeLeo cites 28 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2005/05/03/174.10.6364.DC1 This article http://www.jimmunol.org/content/174/10/6364.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* • Why • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2005 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Insights into Pathogen Immune Evasion Mechanisms: Anaplasma phagocytophilum Fails to Induce an Apoptosis Differentiation Program in Human Neutrophils1 Dori L. -
The Hypothalamus As a Hub for SARS-Cov-2 Brain Infection and Pathogenesis
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.139329; this version posted June 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. The hypothalamus as a hub for SARS-CoV-2 brain infection and pathogenesis Sreekala Nampoothiri1,2#, Florent Sauve1,2#, Gaëtan Ternier1,2ƒ, Daniela Fernandois1,2 ƒ, Caio Coelho1,2, Monica ImBernon1,2, Eleonora Deligia1,2, Romain PerBet1, Vincent Florent1,2,3, Marc Baroncini1,2, Florence Pasquier1,4, François Trottein5, Claude-Alain Maurage1,2, Virginie Mattot1,2‡, Paolo GiacoBini1,2‡, S. Rasika1,2‡*, Vincent Prevot1,2‡* 1 Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, DistAlz, UMR-S 1172, Lille, France 2 LaBoratorY of Development and PlasticitY of the Neuroendocrine Brain, FHU 1000 daYs for health, EGID, School of Medicine, Lille, France 3 Nutrition, Arras General Hospital, Arras, France 4 Centre mémoire ressources et recherche, CHU Lille, LiCEND, Lille, France 5 Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and ImmunitY of Lille (CIIL), Lille, France. # and ƒ These authors contriButed equallY to this work. ‡ These authors directed this work *Correspondence to: [email protected] and [email protected] Short title: Covid-19: the hypothalamic hypothesis 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.139329; this version posted June 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
The Role of Lamin Associated Domains in Global Chromatin Organization and Nuclear Architecture
THE ROLE OF LAMIN ASSOCIATED DOMAINS IN GLOBAL CHROMATIN ORGANIZATION AND NUCLEAR ARCHITECTURE By Teresa Romeo Luperchio A dissertation submitted to The Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland March 2016 © 2016 Teresa Romeo Luperchio All Rights Reserved ABSTRACT Nuclear structure and scaffolding have been implicated in expression and regulation of the genome (Elcock and Bridger 2010; Fedorova and Zink 2008; Ferrai et al. 2010; Li and Reinberg 2011; Austin and Bellini 2010). Discrete domains of chromatin exist within the nuclear volume, and are suggested to be organized by patterns of gene activity (Zhao, Bodnar, and Spector 2009). The nuclear periphery, which consists of the inner nuclear membrane and associated proteins, forms a sub- nuclear compartment that is mostly associated with transcriptionally repressed chromatin and low gene expression (Guelen et al. 2008). Previous studies from our lab and others have shown that repositioning genes to the nuclear periphery is sufficient to induce transcriptional repression (K L Reddy et al. 2008; Finlan et al. 2008). In addition, a number of studies have provided evidence that many tissue types, including muscle, brain and blood, use the nuclear periphery as a compartment during development to regulate expression of lineage specific genes (Meister et al. 2010; Szczerbal, Foster, and Bridger 2009; Yao et al. 2011; Kosak et al. 2002; Peric-Hupkes et al. 2010). These large regions of chromatin that come in molecular contact with the nuclear periphery are called Lamin Associated Domains (LADs). The studies described in this dissertation have furthered our understanding of maintenance and establishment of LADs as well as the relationship of LADs with the epigenome and other factors that influence three-dimensional chromatin structure. -
Astrocytes Close the Critical Period for Visual Plasticity
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.30.321497; this version posted October 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Astrocytes close the critical period for visual plasticity 2 3 Jérôme Ribot1‡, Rachel Breton1,2,3‡#, Charles-Félix Calvo1, Julien Moulard1,4, Pascal Ezan1, 4 Jonathan Zapata1, Kevin Samama1, Alexis-Pierre Bemelmans5, Valentin Sabatet6, Florent 5 Dingli6, Damarys Loew6, Chantal Milleret1, Pierre Billuart7, Glenn Dallérac1£#, Nathalie 6 Rouach1£* 7 8 1Neuroglial Interactions in Cerebral Physiology, Center for Interdisciplinary Research in 9 Biology, Collège de France, CNRS UMR 7241, INSERM U1050, Labex Memolife, PSL 10 Research University Paris, France 11 12 2Doctoral School N°568, Paris Saclay University, PSL Research University, Le Kremlin 13 Bicetre, France 14 15 3Astrocytes & Cognition, Paris-Saclay Institute for Neurosciences, CNRS UMR 9197, Paris- 16 Saclay University, Orsay, France 17 18 4Doctoral School N°158, Sorbonne University, Paris France 19 20 5Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Département de la 21 Recherche Fondamentale, Institut de biologie François Jacob, MIRCen, and CNRS UMR 22 9199, Université Paris-Saclay, Neurodegenerative Diseases Laboratory, Fontenay-aux-Roses, 23 France 24 25 6Institut Curie, PSL Research University, Mass Spectrometry and Proteomics Laboratory, 26 Paris, France 27 28 7Université de Paris, Institute of -
A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression
Supplementary Materials A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression Table S1. Statistically significant DEGs (Adj. p-value < 0.01) derived from meta-analysis for samples irradiated with high doses of HZE particles, collected 6-24 h post-IR not common with any other meta- analysis group. This meta-analysis group consists of 3 DEG lists obtained from DGEA, using a total of 11 control and 11 irradiated samples [Data Series: E-MTAB-5761 and E-MTAB-5754]. Ensembl ID Gene Symbol Gene Description Up-Regulated Genes ↑ (2425) ENSG00000000938 FGR FGR proto-oncogene, Src family tyrosine kinase ENSG00000001036 FUCA2 alpha-L-fucosidase 2 ENSG00000001084 GCLC glutamate-cysteine ligase catalytic subunit ENSG00000001631 KRIT1 KRIT1 ankyrin repeat containing ENSG00000002079 MYH16 myosin heavy chain 16 pseudogene ENSG00000002587 HS3ST1 heparan sulfate-glucosamine 3-sulfotransferase 1 ENSG00000003056 M6PR mannose-6-phosphate receptor, cation dependent ENSG00000004059 ARF5 ADP ribosylation factor 5 ENSG00000004777 ARHGAP33 Rho GTPase activating protein 33 ENSG00000004799 PDK4 pyruvate dehydrogenase kinase 4 ENSG00000004848 ARX aristaless related homeobox ENSG00000005022 SLC25A5 solute carrier family 25 member 5 ENSG00000005108 THSD7A thrombospondin type 1 domain containing 7A ENSG00000005194 CIAPIN1 cytokine induced apoptosis inhibitor 1 ENSG00000005381 MPO myeloperoxidase ENSG00000005486 RHBDD2 rhomboid domain containing 2 ENSG00000005884 ITGA3 integrin subunit alpha 3 ENSG00000006016 CRLF1 cytokine receptor like -
Molecular Architecture of the Chick Vestibular Hair Bundle
RE so UR c E Molecular architecture of the chick vestibular hair bundle Jung-Bum Shin1,2,8, Jocelyn F Krey2,8, Ahmed Hassan3, Zoltan Metlagel3, Andrew N Tauscher3, James M Pagana1,2, Nicholas E Sherman4, Erin D Jeffery4, Kateri J Spinelli2, Hongyu Zhao2, Phillip A Wilmarth5, Dongseok Choi6, Larry L David5, Manfred Auer3 & Peter G Barr-Gillespie2,7 Hair bundles of the inner ear have a specialized structure and protein composition that underlies their sensitivity to mechanical stimulation. Using mass spectrometry, we identified and quantified >1,100 proteins, present from a few to 400,000 copies per stereocilium, from purified chick bundles; 336 of these were significantly enriched in bundles. Bundle proteins that we detected have been shown to regulate cytoskeleton structure and dynamics, energy metabolism, phospholipid synthesis and cell signaling. Three-dimensional imaging using electron tomography allowed us to count the number of actin-actin cross-linkers and actin- membrane connectors; these values compared well to those obtained from mass spectrometry. Network analysis revealed several hub proteins, including RDX (radixin) and SLC9A3R2 (NHERF2), which interact with many bundle proteins and may perform functions essential for bundle structure and function. The quantitative mass spectrometry of bundle proteins reported here establishes a framework for future characterization of dynamic processes that shape bundle structure and function. An outstanding example of a specialized organelle devoted to a single identified those proteins selectively targeted to bundles. Many bundle- purpose, the vertebrate hair bundle transduces mechanical signals enriched proteins are expressed from deafness-associated genes, for the inner ear, converting sound and head movement to electrical confirming their essential function in the inner ear.