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Comprehensive Sequence Analysis of Nine Usher Syndrome Genes in The
Genotype-phenotype correlations J Med Genet: first published as 10.1136/jmedgenet-2011-100468 on 1 December 2011. Downloaded from ORIGINAL ARTICLE Comprehensive sequence analysis of nine Usher syndrome genes in the UK National Collaborative Usher Study Polona Le Quesne Stabej,1 Zubin Saihan,2,3 Nell Rangesh,4 Heather B Steele-Stallard,1 John Ambrose,5 Alison Coffey,5 Jenny Emmerson,5 Elene Haralambous,1 Yasmin Hughes,1 Karen P Steel,5 Linda M Luxon,4,6 Andrew R Webster,2,3 Maria Bitner-Glindzicz1,6 < Additional materials are ABSTRACT characterised by congenital, moderate to severe published online only. To view Background Usher syndrome (USH) is an autosomal hearing loss, with normal vestibular function and these files please visit the recessive disorder comprising retinitis pigmentosa, onset of RP around or after puberty; and type III journal online (http://jmg.bmj. fi com/content/49/1.toc). hearing loss and, in some cases, vestibular dysfunction. (USH3), de ned by postlingual progressive hearing 1 It is clinically and genetically heterogeneous with three loss and variable vestibular response together with Clinical and Molecular e 1 2 Genetics, Institute of Child distinctive clinical types (I III) and nine Usher genes RP. In addition there remain patients whose Health, UCL, London, UK identified. This study is a comprehensive clinical and disease does not fit into any of these three 2Institute of Ophthalmology, genetic analysis of 172 Usher patients and evaluates the subtypes, because of atypical audiovestibular or UCL, London, UK fi ‘ 3 contribution of digenic inheritance. retinal ndings, who are said to have atypical Moorfields Eye Hospital, Methods The genes MYO7A, USH1C, CDH23, PCDH15, ’ London, UK Usher syndrome . -
Diversity of the Genes Implicated in Algerian Patients Affected by Usher Syndrome
RESEARCH ARTICLE Diversity of the Genes Implicated in Algerian Patients Affected by Usher Syndrome Samia Abdi1,2,3, Amel Bahloul4, Asma Behlouli1,5, Jean-Pierre Hardelin4, Mohamed Makrelouf1, Kamel Boudjelida3,6, Malek Louha7, Ahmed Cheknene3,8, Rachid Belouni2,3, Yahia Rous3,8, Zahida Merad3,6, Djamel Selmane9, Mokhtar Hasbelaoui10, Crystel Bonnet11, Akila Zenati1, Christine Petit4,11,12* 1 Laboratoire de biochimie génétique, Service de biologie - CHU de Bab El Oued, Université d'Alger 1, 16 Alger, Algérie, 2 Laboratoire central de biologie, CHU Frantz Fanon, 09 Blida, Algérie, 3 Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie, 4 Unité de génétique et physiologie de l’audition, INSERM UMRS1120, Institut Pasteur, 75015, Paris, France, 5 Faculté des sciences biologiques, Université des sciences et de la technologie Houari Boumédiène, 16 Alger, Algérie, 6 Service d’ophtalmologie, CHU Frantz Fanon, 09 Blida, Algérie, 7 Service de biochimie et de biologie moléculaire, Hôpital Armand Trousseau, APHP, 75012, Paris, France, 8 Service d’ORL, CHU Frantz Fanon, 09 Blida, Algérie, 9 Service a11111 d’ORL, CHU Bab el Oued, 16 Alger, Algérie, 10 Service d’ORL, CHU Tizi Ouzou, 15 Tizi-Ouzou, Algérie, 11 INSERM UMRS 1120, Institut de la vision, Université Pierre et Marie Curie, 75005, Paris, France, 12 Collège de France, 75005, Paris, France * [email protected] OPEN ACCESS Abstract Citation: Abdi S, Bahloul A, Behlouli A, Hardelin J-P, Usher syndrome (USH) is an autosomal recessive disorder characterized by a dual sensory Makrelouf M, Boudjelida K, et al. (2016) Diversity of the Genes Implicated in Algerian Patients Affected by impairment affecting hearing and vision. -
Impact of a Diet and Activity Health Promotion Intervention on Regional
Hibler et al. Clinical Epigenetics (2019) 11:133 https://doi.org/10.1186/s13148-019-0707-0 RESEARCH Open Access Impact of a diet and activity health promotion intervention on regional patterns of DNA methylation Elizabeth Hibler1* , Lei Huang2, Jorge Andrade2,3 and Bonnie Spring1 Abstract Background: Studies demonstrate the impact of diet and physical activity on epigenetic biomarkers, specifically DNA methylation. However, no intervention studies have examined the combined impact of dietary and activity changes on the blood epigenome. The objective of this study was to examine the impact of the Make Better Choices 2 (MBC2) healthy diet and activity intervention on patterns of epigenome-wide DNA methylation. The MBC2 study was a 9-month randomized controlled trial among adults aged 18–65 with non-optimal levels of health behaviors. The study compared three 12-week interventions to (1) simultaneously increase exercise and fruit/ vegetable intake, while decreasing sedentary leisure screen time; (2) sequentially increase fruit/vegetable intake and decrease leisure screen time first, then increase exercise; (3) increase sleep and decrease stress (control). We collected blood samples at baseline, 3 and 9 months, and measured DNA methylation using the Illumina EPIC (850 k) BeadChip. We examined region-based differential methylation patterns using linear regression models with the false discovery rate of 0.05. We also conducted pathway analysis using gene ontology (GO), KEGG, and IPA canonical pathway databases. Results: We found no differences between the MBC2 population (n = 340) and the subsample with DNA methylation measured (n = 68) on baseline characteristics or the impact of the intervention on behavior change. -
Supplementary Materials
Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine -
Homology Modeling and Global Computational Mutagenesis of Human Myosin Viia
Journal of Analytical & Pharmaceutical Research Research Article Open Access Homology modeling and global computational mutagenesis of human myosin VIIa Abstract Volume 10 Issue 1 - 2021 Usher syndrome type 1B (USH1B) is a genetic disorder caused by mutations in the Annapurna Kuppa, Yuri V Sergeev unconventional Myosin VIIa (MYO7A) protein. USH1B is characterized by hearing loss Ophthalmic Genetics and Visual Function Branch, National Eye due to abnormalities in the inner ear and vision loss due to retinitis pigmentosa. Here, Institute, National Institutes of Health, Bethesda, United States we present the model of human MYO7A homodimer, built using homology modeling, and refined using 5 ns molecular dynamics in water. Global computational mutagenesis Correspondence: Yuri V. Sergeev, Ophthalmic Genetics was applied to evaluate the effect of missense mutations that are critical for maintaining and Visual Function Branch, National Eye Institute, National protein structure and stability of MYO7A in inherited eye disease. We found that 43.26% Institutes of Health, Bethesda, MD, United States, (77 out of 178 in HGMD) and 41.9% (221 out of 528 in ClinVar) of the disease-related Email missense mutations were associated with higher protein structure destabilizing effects. Overall, most mutations destabilizing the MYO7A protein were found to associate with Received: February 20, 2021 | Published: March 04, 2021 USH1 and USH1B. Particularly, motor domain and MyTH4 domains were found to be most susceptible to mutations causing the USH1B phenotype. Our work contributes to the understanding of inherited disease from the atomic level of protein structure and analysis of the impact of genetic mutations on protein stability and genotype-to-phenotype relationships in human disease. -
Foraging Shifts and Visual Pre Adaptation in Ecologically Diverse Bats
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/340654059 Foraging shifts and visual preadaptation in ecologically diverse bats Article in Molecular Ecology · April 2020 DOI: 10.1111/mec.15445 CITATIONS READS 0 153 9 authors, including: Kalina T. J. Davies Laurel R Yohe Queen Mary, University of London Yale University 40 PUBLICATIONS 254 CITATIONS 24 PUBLICATIONS 93 CITATIONS SEE PROFILE SEE PROFILE Edgardo M. Rengifo Elizabeth R Dumont University of São Paulo University of California, Merced 13 PUBLICATIONS 28 CITATIONS 115 PUBLICATIONS 3,143 CITATIONS SEE PROFILE SEE PROFILE Some of the authors of this publication are also working on these related projects: Ecology of the Greater horseshoe bat View project BAT 1K View project All content following this page was uploaded by Liliana M. Davalos on 14 May 2020. The user has requested enhancement of the downloaded file. Received: 17 October 2019 | Revised: 28 February 2020 | Accepted: 31 March 2020 DOI: 10.1111/mec.15445 ORIGINAL ARTICLE Foraging shifts and visual pre adaptation in ecologically diverse bats Kalina T. J. Davies1 | Laurel R. Yohe2,3 | Jesus Almonte4 | Miluska K. R. Sánchez5 | Edgardo M. Rengifo6,7 | Elizabeth R. Dumont8 | Karen E. Sears9 | Liliana M. Dávalos2,10 | Stephen J. Rossiter1 1School of Biological and Chemical Sciences, Queen Mary University of London, London, UK 2Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, USA 3Department of Geology & Geophysics, Yale University, -
A Locus on Distal Chromosome 11 (Ahl8) and Its Interaction with Cdh23ahl Underlie the Early Onset, Age-Related Hearing Loss of DBA/2J Mice
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Genomics 92 (2008) 219–225 Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno A locus on distal chromosome 11 (ahl8) and its interaction with Cdh23ahl underlie the early onset, age-related hearing loss of DBA/2J mice Kenneth R. Johnson a,⁎, Chantal Longo-Guess a, Leona H. Gagnon a, Heping Yu b, Qing Yin Zheng b a The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA b Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University, University Hospitals-Case Medical Center, 11100 Euclid Avenue, Cleveland, OH 44106, USA article info abstract Article history: The DBA/2J inbred strain of mice is used extensively in hearing research, yet little is known about the genetic Received 7 April 2008 basis for its early onset, progressive hearing loss. To map underlying genetic factors we analyzed recombinant Accepted 23 June 2008 inbred strains and linkage backcrosses. Analysis of 213 mice from 31 BXD recombinant inbred strains Available online 15 August 2008 detected linkage of auditory brain-stem response thresholds with a locus on distal chromosome 11, which we designate ahl8. Analysis of 225 N2 mice from a backcross of (C57BL/6J×DBA/2J) F1 hybrids to DBA/2J mice Keywords: confirmed this linkage (LODN50) and refined the ahl8 candidate gene interval. Analysis of 214 mice from a Presbycusis Ahl+ Age-related hearing loss backcross of (B6.CAST-Cdh23 ×DBA/2J) F1 hybrids to DBA/2J mice demonstrated a genetic interaction of Progressive hearing loss Cdh23 with ahl8. -
Novel Mutations in the USH1C Gene in Usher Syndrome Patients
Molecular Vision 2010; 16:2948-2954 <http://www.molvis.org/molvis/v16/a317> © 2010 Molecular Vision Received 30 September 2010 | Accepted 26 December 2010 | Published 31 December 2010 Novel mutations in the USH1C gene in Usher syndrome patients María José Aparisi,1 Gema García-García,1 Teresa Jaijo,1,2 Regina Rodrigo,1 Claudio Graziano,3 Marco Seri,3 Tulay Simsek,4 Enver Simsek,5 Sara Bernal,2,6 Montserrat Baiget,2,6 Herminio Pérez-Garrigues,2,7 Elena Aller,1,2 José María Millán1,2,8 1Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria IIS-La Fe, Valencia, Spain; 2CIBER de Enfermedades Raras (CIBERER), Valencia, Spain; 3U.O. Genetica Medica, Policlinico S. Orsola-Malpighi, Università di Bologna, Italy; 4Ulucanlar Training and Research Eye Hospital, Ankara, Turkey; 5Department of Pediatric Endocrinology, Ankara Training and Research Hospital, Ankara, Turkey; 6Servicio de Genética, Hospital de la Santa Creu y Sant Pau. Barcelona, Spain; 7Servicio de Otorrinolaringología, Hospital Universitario La Fe, Valencia, Spain; 8Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario La Fe, Valencia, Spain Purpose: Usher syndrome type I (USH1) is an autosomal recessive disorder characterized by severe-profound sensorineural hearing loss, retinitis pigmentosa, and vestibular areflexia. To date, five USH1 genes have been identified. One of these genes is Usher syndrome 1C (USH1C), which encodes a protein, harmonin, containing PDZ domains. The aim of the present work was the mutation screening of the USH1C gene in a cohort of 33 Usher syndrome patients, to identify the genetic cause of the disease and to determine the relative involvement of this gene in USH1 pathogenesis in the Spanish population. -
NIDCD Fact Sheet Usher Syndrome Hearing Balance U.S
NIDCD Fact Sheet Usher Syndrome hearing balance U.S. DEPARTMENT OF HEALTH & HUMAN SERVICES ∙ NATIONAL INSTITUTES OF HEALTH ∙ NATIONAL INSTITUTE ON DEAFNESS AND OTHER COMMUNICATION DISORDERS What is Usher syndrome? Who is affected by Usher syndrome? Usher syndrome is the most common condition that Approximately 3 to 6 percent of all children who are affects both hearing and vision. A syndrome is a deaf and another 3 to 6 percent of children who are disease or disorder that has more than one feature or hard-of-hearing have Usher syndrome. In developed symptom. The major symptoms of Usher syndrome countries such as the United States, about four babies are hearing loss and an eye disorder called retinitis in every 100,000 births have Usher syndrome. pigmentosa, or RP. RP causes night-blindness and a loss of peripheral vision (side vision) through the What causes Usher syndrome? progressive degeneration of the retina. The retina is Usher syndrome is inherited, which means that it is a light-sensitive tissue at the back of the eye and is passed from parents to their children through genes. crucial for vision (see photograph). As RP progresses, Genes are located in almost every cell of the body. the field of vision narrows—a condition known as Genes contain instructions that tell cells what to do. “tunnel vision”—until only central vision (the ability to Every person inherits two copies of each gene, one see straight ahead) remains. Many people with Usher from each parent. Sometimes genes are altered, syndrome also have severe balance problems. or mutated. -
Deafblind Cajuns* by Phyllis Baudoin Grifard, Department of Biology, University of Louisiana at Lafayette
NATIONAL CENTER FOR CASE STUDY TEACHING IN SCIENCE DeafBlind Cajuns* by Phyllis Baudoin Grifard, Department of Biology, University of Louisiana at Lafayette Part I – Meet Dan and Annie Annie pulled a chair for me at their dining room table and brought out snacks while her husband Dan made his way from the back of the house with his new diploma. Dan did not need to use his white cane inside their home. Since I am not fuent in American Sign Language (ASL), Annie ofered me a blank, boldly lined tablet labeled “low- vision notebook” and a thick black marker. I wrote “Congratulations!” when Dan proudly showed me his diploma from Gallaudet University (Figure 2), the only deaf-serving university in the world. He recently completed a BA degree in psychology and now is back home in Louisiana working as a case manager for deaf and deafblind residents at a local nursing home (Figure 3). Since Dan’s vision has deteriorated more than Annie’s, she used a tactile form of American Sign Language (tactile ASL) to convey what I wrote by signing into Dan’s hands. Figure 1. Dan and Annie. Dan and Annie are deafblind. Tey were born profoundly deaf and began to lose their peripheral and night vision in their late teens. Dan, now in his 50s, has only a small part of his central vision left. He uses adaptive technologies that magnify printed text and a white cane for mobility. Annie, who is in her 40s, has not lost as much of her peripheral vision yet, but navigating in low light, such as in dark restaurants, is becoming more difcult. -
Mouse Models of Inherited Retinal Degeneration with Photoreceptor Cell Loss
cells Review Mouse Models of Inherited Retinal Degeneration with Photoreceptor Cell Loss 1, 1, 1 1,2,3 1 Gayle B. Collin y, Navdeep Gogna y, Bo Chang , Nattaya Damkham , Jai Pinkney , Lillian F. Hyde 1, Lisa Stone 1 , Jürgen K. Naggert 1 , Patsy M. Nishina 1,* and Mark P. Krebs 1,* 1 The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; [email protected] (G.B.C.); [email protected] (N.G.); [email protected] (B.C.); [email protected] (N.D.); [email protected] (J.P.); [email protected] (L.F.H.); [email protected] (L.S.); [email protected] (J.K.N.) 2 Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand 3 Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand * Correspondence: [email protected] (P.M.N.); [email protected] (M.P.K.); Tel.: +1-207-2886-383 (P.M.N.); +1-207-2886-000 (M.P.K.) These authors contributed equally to this work. y Received: 29 February 2020; Accepted: 7 April 2020; Published: 10 April 2020 Abstract: Inherited retinal degeneration (RD) leads to the impairment or loss of vision in millions of individuals worldwide, most frequently due to the loss of photoreceptor (PR) cells. Animal models, particularly the laboratory mouse, have been used to understand the pathogenic mechanisms that underlie PR cell loss and to explore therapies that may prevent, delay, or reverse RD. Here, we reviewed entries in the Mouse Genome Informatics and PubMed databases to compile a comprehensive list of monogenic mouse models in which PR cell loss is demonstrated. -
Analysis and Functional Evaluation of the Hair-Cell Transcriptome
Analysis and functional evaluation of the hair-cell transcriptome Brian M. McDermott, Jr.*, Jessica M. Baucom, and A. J. Hudspeth† Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 Contributed by A. J. Hudspeth, May 17, 2007 (sent for review March 31, 2007) An understanding of the molecular bases of the morphogenesis, ciated from the lagena, a receptor organ of the zebrafish’s ear. organization, and functioning of hair cells requires that the genes Linear amplification of the RNA from 200 hair cells yielded Ϸ40 expressed in these cells be identified and their functions ascer- g of aRNA, an enhancement of Ϸ1 millionfold. The resultant tained. After purifying zebrafish hair cells and detecting mRNAs labeled aRNA was hybridized to an Affymetrix microarray with oligonucleotide microarrays, we developed a subtractive (Affymetrix, Santa Clara, CA) containing Ϸ15,000 oligonucle- strategy that identified 1,037 hair cell-expressed genes whose otide probe sets. Averaging the outcomes of three experiments cognate proteins subserve functions including membrane trans- (SI Data Set 1) resulted in the identification of 6,472 transcripts port, synaptic transmission, transcriptional control, cellular adhe- scored as ‘‘present’’ (SI Data Set 2). sion and signal transduction, and cytoskeletal organization. To In the second step, we defined the transcriptome from cells of assess the validity of the subtracted hair-cell data set, we verified a nonsensory organ, the liver (SI Data Set 1). Hepatocytes were the presence of 11 transcripts in inner-ear tissue. Functional eval- selected for the subtraction process for three reasons: they are uation of two genes from the subtracted data set revealed their nonneuronal and thus unlikely to express synaptic factors; they importance in hair bundles: zebrafish larvae bearing the seahorse lack cilia (http://members.global2000.net/bowser/cilialist.html) and ift 172 mutations display specific kinociliary defects.