Cochlin in the Eye: Functional Implications
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Sequence Function Classification by Machine Learning Methods
From the Institute for Neuro- and Bioinformatics of the University of Lübeck Director: Prof. Dr. Thomas Martinetz Sequence function classification by machine learning methods Dissertation for Fulfillment of Requirements for the Doctoral Degree of the University of Lübeck from the Department of Computer Sciences/Engineering Submitted by Krishna Kumar Kandaswamy Born in Coimbatore - TN, India Lübeck, 2011 First referee: Prof. Thomas Martinetz Second referee: Prof. Enno Hartmann Date of oral examination: 18.04.2012 Approved for printing, Lübeck : 23.04.2012 Acknowledgements Many people contributed either directly or indirectly. It will be difficult to name all of them. To start, I express sincere gratitude to my thesis advisor Prof. Thomas Martinetz, I enjoyed every moment discussing many related things to my thesis. I always admired his perfect scientific judgment in solving problems, a clear wit and a rare ability to stay cool in the most critical situations. Despite his busy schedule, he was always there to advise and give support whenever required. I convey my thanks and gratitude to Prof. Enno Hartmann, who introduced me to the field of protein secretion and translocation. In a budding phase, we had many discussions and I used to wonder his ability to put in tireless efforts in reading and discussing things out (which helped in speeding up the things). I am very grateful to Dr. Kai-Uwe Kalies and Dr. Steffen Möller for an incalculable number of suggestions, critical talk and motivational sessions. A special thank you must go to Dr. Ganesan Pugalenthi for his valuable inputs in regards to the concept of sequence analysis. -
(12) Patent Application Publication (10) Pub. No.: US 2003/0198970 A1 Roberts (43) Pub
US 2003O19897OA1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2003/0198970 A1 Roberts (43) Pub. Date: Oct. 23, 2003 (54) GENOSTICS clinical trials on groups or cohorts of patients. This group data is used to derive a Standardised method of treatment (75) Inventor: Gareth Wyn Roberts, Cambs (GB) which is Subsequently applied on an individual basis. There is considerable evidence that a significant factor underlying Correspondence Address: the individual variability in response to disease, therapy and FINNEGAN, HENDERSON, FARABOW, prognosis lies in a person's genetic make-up. There have GARRETT & DUNNER been numerous examples relating that polymorphisms LLP within a given gene can alter the functionality of the protein 1300 ISTREET, NW encoded by that gene thus leading to a variable physiological WASHINGTON, DC 20005 (US) response. In order to bring about the integration of genomics into medical practice and enable design and building of a (73) Assignee: GENOSTIC PHARMA LIMITED technology platform which will enable the everyday practice (21) Appl. No.: 10/206,568 of molecular medicine a way must be invented for the DNA Sequence data to be aligned with the identification of genes (22) Filed: Jul. 29, 2002 central to the induction, development, progression and out come of disease or physiological States of interest. Accord Related U.S. Application Data ing to the invention, the number of genes and their configu rations (mutations and polymorphisms) needed to be (63) Continuation of application No. 09/325,123, filed on identified in order to provide critical clinical information Jun. 3, 1999, now abandoned. concerning individual prognosis is considerably less than the 100,000 thought to comprise the human genome. -
Uniprot Acceprotiens 121 113 Ratio(113/12 114 Ratio
Uniprot Acceprotiens 121 113 ratio(113/12 114 ratio(114/12 115 ratio(115/12 116 ratio(116/12 117 ratio(117/12 118 ratio(118/12 119 ratio(119/121) P02768 Serum albumin OS=Homo s666397.2 862466.6 1.29 593482.1 0.89 2220420.5 3.33 846469.3 1.27 634302.5 0.95 736961.1 1.11 842297.5 1.26 P02760 Protein AMBP OS=Homo s381627.7 294812.3 0.77 474165.8 1.24 203377.3 0.53 349197.6 0.92 346271.7 0.91 328356.1 0.86 411229.3 1.08 B4E1B2 cDNA FLJ53691, highly sim78511.8 107560.1 1.37 85218.8 1.09 199640.4 2.54 90022.3 1.15 73427.3 0.94 82722 1.05 102491.8 1.31 A0A0K0K1HEpididymis secretory sperm 3358.1 4584.8 1.37 4234.8 1.26 8496.1 2.53 4193.7 1.25 3507.1 1.04 3632.2 1.08 4873.3 1.45 D3DNU8 Kininogen 1, isoform CRA_302648.3 294936.6 0.97 257956.9 0.85 193831.3 0.64 290406.7 0.96 313453.3 1.04 279805.5 0.92 228883.9 0.76 B4E1C2 Kininogen 1, isoform CRA_167.9 229.7 1.37 263.2 1.57 278 1.66 326 1.94 265.5 1.58 290.3 1.73 341.5 2.03 O60494 Cubilin OS=Homo sapiens G40132.6 45037.5 1.12 38654.5 0.96 34055.8 0.85 39708.6 0.99 44702.9 1.11 45025.7 1.12 32701.3 0.81 P98164 Low-density lipoprotein rece40915.4 45344.8 1.11 35817.7 0.88 35721.8 0.87 42157.7 1.03 46693.4 1.14 48624 1.19 38847.7 0.95 A0A024RABHeparan sulfate proteoglyca46985.3 43536.1 0.93 49827.7 1.06 33964.3 0.72 44780.9 0.95 46858.6 1.00 47703.5 1.02 37785.7 0.80 P01133 Pro-epidermal growth factor 75270.8 73109.5 0.97 66336.1 0.88 56680.9 0.75 70877.8 0.94 76444.3 1.02 81110.3 1.08 65749.7 0.87 Q6N093 Putative uncharacterized pro47825.3 55632.5 1.16 48428.3 1.01 63601.5 1.33 65204.2 1.36 59384.5 -
Molecular Architecture Underlying Fluid Absorption by the Developing Inner
RESEARCH ARTICLE Molecular architecture underlying fluid absorption by the developing inner ear Keiji Honda1†, Sung Huhn Kim2‡, Michael C Kelly3, Joseph C Burns3§, Laura Constance2, Xiangming Li2#, Fei Zhou2, Michael Hoa4, Matthew W Kelley3, Philine Wangemann2*, Robert J Morell5, Andrew J Griffith1* 1Molecular Biology and Genetics Section, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, United States; 2Anatomy and Physiology Department, Kansas State University, Manhattan, United States; 3Developmental Neuroscience Section, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, United States; 4Auditory Development and Restoration Program, National Institute on *For correspondence: Deafness and Other Communication Disorders, National Institutes of Health, [email protected] (PW); Bethesda, United States; 5Genomics and Computational Biology Core, National [email protected] (AJG) Institute on Deafness and Other Communication Disorders, National Institutes of Present address: Health, Bethesda, United States †Otolaryngology Department, Tsuchiura Kyodo General Hospital, Tsuchiura, Japan; ‡Department of Abstract Mutations of SLC26A4 are a common cause of hearing loss associated with Otorhinolaryngology, Head and enlargement of the endolymphatic sac (EES). Slc26a4 expression in the developing mouse Neck Surgery, Yonsei University College of Medicine, Seoul, endolymphatic sac is required for acquisition of normal inner ear structure and function. Here, we Korea; §Decibel Therapeutics, show that the mouse endolymphatic sac absorbs fluid in an SLC26A4-dependent fashion. Fluid Cambridge, United States; absorption was sensitive to ouabain and gadolinium but insensitive to benzamil, bafilomycin and #Technique R and D-Drug S3226. Single-cell RNA-seq analysis of pre- and postnatal endolymphatic sacs demonstrates two Substance, GlaxoSmithKline types of differentiated cells. -
Investigating the Effect of Chronic Activation of AMP-Activated Protein
Investigating the effect of chronic activation of AMP-activated protein kinase in vivo Alice Pollard CASE Studentship Award A thesis submitted to Imperial College London for the degree of Doctor of Philosophy September 2017 Cellular Stress Group Medical Research Council London Institute of Medical Sciences Imperial College London 1 Declaration I declare that the work presented in this thesis is my own, and that where information has been derived from the published or unpublished work of others it has been acknowledged in the text and in the list of references. This work has not been submitted to any other university or institute of tertiary education in any form. Alice Pollard The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution Non-Commercial No Derivatives license. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, that they do not use it for commercial purposes and that they do not alter, transform or build upon it. For any reuse or redistribution, researchers must make clear to others the license terms of this work. 2 Abstract The prevalence of obesity and associated diseases has increased significantly in the last decade, and is now a major public health concern. It is a significant risk factor for many diseases, including cardiovascular disease (CVD) and type 2 diabetes. Characterised by excess lipid accumulation in the white adipose tissue, which drives many associated pathologies, obesity is caused by chronic, whole-organism energy imbalance; when caloric intake exceeds energy expenditure. Whilst lifestyle changes remain the most effective treatment for obesity and the associated metabolic syndrome, incidence continues to rise, particularly amongst children, placing significant strain on healthcare systems, as well as financial burden. -
Genome Folding in Evolution and Disease
Johannes Gutenberg University Mainz Faculty of Biology Institute of Organismic and Molecular Evolution Computational Biology and Data Mining Group Dissertation Genome folding in evolution and disease Jonas Ibn-Salem February, 2018 Jonas Ibn-Salem Genome folding in evolution and disease Dissertation, February, 2018 Johannes Gutenberg University Mainz Computational Biology and Data Mining Group Institute of Organismic and Molecular Evolution Faculty of Biology Ackermannweg 4 55128 and Mainz Contents Abstract 7 1 Introduction 9 1.1 Regulation of gene expression ...................... 9 1.2 Distal regulation by enhancers ...................... 10 1.3 Methods to probe the 3D chromatin architecture . 11 1.3.1 Microscopy-based techniques to visualize the genome in 3D . 11 1.3.2 Proximity-ligation based method to quantify chromatin inter- actions ............................... 11 1.4 Hierarchy of chromatin 3D structure . 13 1.4.1 Chromosomal territories and inter-chromosomal contacts . 13 1.4.2 A/B compartments ........................ 15 1.4.3 Topologically associating domains (TADs) . 15 1.4.4 Hierarchy of domain structures across genomic length scales . 17 1.4.5 Chromatin looping interactions . 17 1.4.6 TAD and loop formation by architectural proteins . 18 1.5 Dynamics of chromatin structure .................... 20 1.5.1 Dynamics across the cell cycle . 20 1.5.2 Dynamics across cell types and differntiation . 20 1.6 Evolution of chromatin organization . 21 1.7 Disruption of chromatin architecture in disease . 23 1.8 Aims of this thesis ............................ 24 1.9 Structure of this thesis .......................... 27 2 Paralog genes in the 3D genome architecture 29 Preamble ................................. 29 Abstract .................................. 29 2.1 Introduction ................................ 30 2.2 Materials and methods ......................... -
Overview of the Matrisome—An Inventory of Extracellular Matrix Constituents and Functions
Downloaded from http://cshperspectives.cshlp.org/ on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Overview of the Matrisome—An Inventory of Extracellular Matrix Constituents and Functions Richard O. Hynes and Alexandra Naba Howard Hughes Medical Institute, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 Correspondence: [email protected] Completion of genome sequences for many organisms allows a reasonably complete definition of the complement of extracellular matrix (ECM) proteins. In mammals this “core matrisome” comprises 300 proteins. In addition there are large numbers of ECM- modifying enzymes, ECM-binding growth factors, and other ECM-associated proteins. These different categories of ECM and ECM-associated proteins cooperate to assemble and remodel extracellular matrices and bind to cells through ECM receptors. Togetherwith recep- tors for ECM-bound growth factors, they provide multiple inputs into cells to control survival, proliferation, differentiation, shape, polarity, and motility of cells. The evolution of ECM pro- teins was key in the transition to multicellularity, the arrangement of cells into tissue layers, and the elaboration of novel structures during vertebrate evolution. This key role of ECM is reflected in the diversity of ECM proteins and the modular domain structures of ECM proteins both allow their multiple interactions and, during evolution, development of novel protein architectures. he term extracellular matrix (ECM) means make up basement membranes. Biochemistry Tsomewhat different things to different of native ECM was, and still is, impeded by people (Hay 1981, 1991; Mecham 2011). Light the fact that the ECM is, by its very nature, and electron microscopy show that extracellular insoluble and is frequently cross-linked. -
A Novel COCH Mutation, V104del, Impairs Folding of the LCCL Domain
1of3 J Med Genet: first published as 10.1136/jmg.2003.012286 on 16 January 2004. Downloaded from ONLINE MUTATION REPORT A novel COCH mutation, V104del, impairs folding of the LCCL domain of cochlin and causes progressive hearing loss I Nagy, M Horva´th, M Trexler, G Re´pa´ssy, L Patthy ............................................................................................................................... J Med Genet 2004;41:e9 (http://www.jmedgenet.com/cgi/content/full/41/1/e9) ecently the causative gene of autosomal dominant sensorineural nonsyndromic late onset hearing loss Key points R(DFNA9) has been identified as the COCH gene, which lies in the DFNA9 region of human chromosome 14 (gene N Autosomal dominant nonsyndromic sensorineural map locus 14q12–q13). Molecular analysis of cases of DFNA9 deafness 9 (DFNA9, OMIM #601369) is a rare, late have identified several families with five different mutations onset hearing loss. In DFNA9 patients, hearing loss in this gene.1–5 usually begins in the third decade of life as a high The cochlin protein encoded by COCH is an extracellular frequency loss with concomitant vestibular dysfunction. matrix protein that contains an LCCL domain and two von N 1 DFNA9 is caused by mutations in the COCH gene, Willebrand type A domains. Interestingly, all mutations which encodes cochlin, an extracellular matrix protein causing DFNA9 type deafness disorder affect the LCCL that contains an LCCL domain and two von Willebrand domain of cochlin. In view of the central role of this domain type A domains. in the DFNA9 disorder, we initiated studies on it to explore the molecular basis of the disease.6 We found that most N Molecular analysis of cases of DFNA9 has identified DFNA9 mutations affected conserved structural elements of five different mutations in this gene. -
Absence of COCH Mutations in Patients with Meniere Disease
European Journal of Human Genetics (2004) 12, 75–78 & 2004 Nature Publishing Group All rights reserved 1018-4813/04 $25.00 www.nature.com/ejhg SHORT REPORT Absence of COCH mutations in patients with Meniere disease Elena Sanchez1, Jose A Lo´pez-Esca´mez2,*, Miguel A Lo´pez-Nevot3, Alicia Lo´pez-Nevot4, Rosario Cortes4 and Javier Martin1 1Instituto de Parasitologı´a y Biomedicina ‘Lopez-Neyra’, CSIC, Granada, Spain; 2Department of Surgery, Division of Otorhinolaryngology, Hospital de Poniente, El Ejido, Almerı´a, Spain; 3Department of Immunology, Hospital Universitario Virgen de las Nieves, Granada, Spain; 4Department of Otolaryngology, Hospital Universitario Virgen de las Nieves, Granada, Spain Missense mutations in the coagulation factor C homology (COCH) gene (14q12–q13) cause the autosomal dominant sensorineural hearing loss and vestibular disorder DFNA9 (OMIM 603196), and a high prevalence of symptoms of Meniere disease (MD) has been described in families with a mutation in the COCH gene. In this study, we search for mutations in the COCH gene in peripheral blood from patients with definite MD. DNA was extracted from peripheral blood cells of 30 individuals with MD and 30 controls. Exons 4 and 5 of the COCH gene were amplified by PCR reaction, using primer pairs flanking both exons. Sequences were analysed by a DNA sequencing system and compared with the published COCH cDNA sequence. No differences were found in the nucleotide sequences of exons 4 and 5 in the COCH gene in patients with definite sporadic MD when they were compared with the control group. Patients with definite MD have a low prevalence of mutations in exons 4 and 5 of the COCH gene. -
Physico-Chemical Characterization of the Native and Mutant Protein
Physico-Chemical characterization of the native and mutant protein cochlin, and its role in adult-onset hearing and balance loss MASSACHUSETTS INSTIE OF TECHNOLOGY by JUL 0 7 2009 Benjamin L. Grannan LIBRARIES Submitted to the Department of Physics in partial fulfillment of the requirements for the degree of Bachelor of Science in Physics at the MASSACHUSETTS INSTITUTE OF TECHNOLOGY June 2009 ( Massachusetts Institute of Technology 2009. All rights reserved. A/ Author ......... V Department of Physics May 8, 2009 -1) -t-b Certified by ...... , -- --- George B. Benedek Alfred H. Caspary Professor of Physics and Biological Physics Thesis Supervisor Accepted by............ ..... ... ........... David E. Pritchard Senior Thesis Coordinator, Department of Physics ARCHIVES Physico-Chemical characterization of the native and mutant protein cochlin, and its role in adult-onset hearing and balance loss by Benjamin L. Grannan Submitted to the Department of Physics on May 8, 2009, in partial fulfillment of the requirements for the degree of Bachelor of Science in Physics Abstract This thesis investigates the role of the protein cochlin and its isoforms in DFNA9 au- tosomal dominant late onset senorineural loss and vestibular disorder by quantifying the concentration of cochlin in the inner fluid called perilymph. Through the use of affinity chromatography, high performance liquid chromatography, the Bradford as- say, western blot analysis, and proteomics analysis by mass spectroscopy, I acquired data which suggests that the concentration of cochlin in the perilymph of bovine calf ears is at most on the order of 10- mg/ml. I also determined the total protein con- centration of native bovine perilymph to be 2.1+0.2 mg/ml. -
Neonatal Growth Measurements, Umbilical Concentrations, And
Clemson University TigerPrints All Theses Theses 12-2017 Neonatal Growth Measurements, Umbilical Concentrations, and Differential Gene Expression in the Placenta of Swine in Relation to Placental Efficiency Shanice Katelin Krombeen Clemson University Follow this and additional works at: https://tigerprints.clemson.edu/all_theses Recommended Citation Krombeen, Shanice Katelin, "Neonatal Growth Measurements, Umbilical Concentrations, and Differential Gene Expression in the Placenta of Swine in Relation to Placental Efficiency" (2017). All Theses. 2789. https://tigerprints.clemson.edu/all_theses/2789 This Thesis is brought to you for free and open access by the Theses at TigerPrints. It has been accepted for inclusion in All Theses by an authorized administrator of TigerPrints. For more information, please contact [email protected]. NEONATAL GROWTH MEASUREMENTS, UMBILICAL CONCENTRATIONS, AND DIFFERENTIAL GENE EXPRESSION IN THE PLACENTA OF SWINE IN RELATION TO PLACENTAL EFFICIENCY A Thesis Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Master of Science Animal and Veterinary Science by Shanice Katelin Krombeen December 2017 Accepted by: Dr. Tiffany A. Wilmoth, Committee Chair Dr. Julia L. Sharp Dr. Christopher A. Saski i ABSTRACT Placental efficiency (PE) describes the relationship between placental and fetal weights and is defined as fetal weight divided by placental weight. Within pig litters, PE can vary drastically, resulting in similarly sized pigs associated with very different placenta, up to a 50% weight difference. However, the means enabling the smaller placenta to grow a similarly sized littermate is unknown. The main objectives of this study were to (1) determine the concentration of glucose and cortisol in venous umbilical blood of pigs at birth and evaluate if a relationship existed between concentration and PE, and (2) determine the expression level of genes in placental and associated endometrial tissues of high PE and low PE feto-placental units. -
Gene List.Pdf
Gene symbol EntrezID Gene description Target tissue specimen Specimen type A2M 2 alpha-2-macroglobulin Hippocampus, Amygdala, Ventral striatum, Medial prefrontal cortex, Visual cortex Adult ABAT 18 4-aminobutyrate aminotransferase Hippocampus, Amygdala, Ventral striatum, Medial prefrontal cortex, Visual cortex Adult ACE 1636 angiotensin I converting enzyme (peptidyl-dipeptidase A) 1 Hippocampus, Amygdala, Ventral striatum, Medial prefrontal cortex, Visual cortex Adult ADORA2A 135 adenosine A2a receptor Hippocampus, Amygdala, Ventral striatum, Medial prefrontal cortex, Visual cortex Adult ADRA1B 147 adrenergic, alpha-1B-, receptor Hippocampus, Amygdala, Ventral striatum, Medial prefrontal cortex, Visual cortex Adult ADRBK2 157 adrenergic, beta, receptor kinase 2 Hippocampus, Amygdala, Ventral striatum, Medial prefrontal cortex, Visual cortex Adult AHI1 54806 Abelson helper integration site 1 Hippocampus, Amygdala, Ventral striatum, Medial prefrontal cortex, Visual cortex Adult AKT1 207 v-akt murine thymoma viral oncogene homolog 1 Hippocampus, Amygdala, Ventral striatum, Medial prefrontal cortex, Visual cortex Adult ALDH2 217 aldehyde dehydrogenase 2 family (mitochondrial) Hippocampus, Amygdala, Ventral striatum, Medial prefrontal cortex, Visual cortex Adult AMBRA1 55626 autophagy/beclin-1 regulator 1 Hippocampus, Amygdala, Ventral striatum, Medial prefrontal cortex, Visual cortex Adult ANK3 288 ankyrin 3, node of Ranvier (ankyrin G) Hippocampus, Amygdala, Ventral striatum, Medial prefrontal cortex, Visual cortex Adult APBB2 323 amyloid