Calpain-10 Regulates Actin Dynamics by Proteolysis of Microtubule-Associated Protein 1B
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Reconstructability Analysis As a Tool for Identifying Gene-Gene Interactions in Studies of Human Diseases
Portland State University PDXScholar Systems Science Faculty Publications and Presentations Systems Science 3-2010 Reconstructability Analysis As A Tool For Identifying Gene-Gene Interactions In Studies Of Human Diseases Stephen Shervais Eastern Washington University Patricia L. Kramer Oregon Health & Science University Shawn K. Westaway Oregon Health & Science University Nancy J. Cox University of Chicago Martin Zwick Portland State University, [email protected] Follow this and additional works at: https://pdxscholar.library.pdx.edu/sysc_fac Part of the Bioinformatics Commons, Diseases Commons, and the Genomics Commons Let us know how access to this document benefits ou.y Citation Details Shervais, S., Kramer, P. L., Westaway, S. K., Cox, N. J., & Zwick, M. (2010). Reconstructability Analysis as a Tool for Identifying Gene-Gene Interactions in Studies of Human Diseases. Statistical Applications In Genetics & Molecular Biology, 9(1), 1-25. This Article is brought to you for free and open access. It has been accepted for inclusion in Systems Science Faculty Publications and Presentations by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. Statistical Applications in Genetics and Molecular Biology Volume 9, Issue 1 2010 Article 18 Reconstructability Analysis as a Tool for Identifying Gene-Gene Interactions in Studies of Human Diseases Stephen Shervais∗ Patricia L. Kramery Shawn K. Westawayz Nancy J. Cox∗∗ Martin Zwickyy ∗Eastern Washington University, [email protected] yOregon Health & Science University, [email protected] zOregon Health & Science University, [email protected] ∗∗University of Chicago, [email protected] yyPortland State University, [email protected] Copyright c 2010 The Berkeley Electronic Press. -
Evaluation of the Genetic Susceptibility to the Metabolic Syndrome by the CAPN10 SNP19 Gene in the Population of South Benin
International Journal of Molecular Biology: Open Access Research Article Open Access Evaluation of the genetic susceptibility to the metabolic syndrome by the CAPN10 SNP19 gene in the population of South Benin Abstract Volume 4 Issue 6 - 2019 Metabolic syndrome is a multifactorial disorder whose etiology is resulting from the Nicodème Worou Chabi,1,2 Basile G interaction between genetic and environmental factors. Calpain 10 (CAPN10) is the first Sognigbé,1 Esther Duéguénon,1 Véronique BT gene associated with type 2 diabetes that has been identified by positional cloning with 1 1 sequencing method. This gene codes for cysteine protease; ubiquitously expressed in all Tinéponanti, Arnaud N Kohonou, Victorien 2 1 tissues, it is involved in the fundamental physiopathological aspects of insulin resistance T Dougnon, Lamine Baba Moussa and insulin secretion of type 2 diabetes. The goal of this study was to evaluate the genetic 1Department of Biochemistry and Cell Biology, University of susceptibility to the metabolic syndrome by the CAPN10 gene in the population of southern Abomey-Calavi, Benin 2 Benin. This study involved apparently healthy individuals’ aged 18 to 80 in four ethnic Laboratory of Research in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Benin groups in southern Benin. It included 74 subjects with metabolic syndrome and 323 non- metabolic syndrome patients who served as controls, with 222 women versus 175 men Correspondence: Nicodème Worou Chabi, Laboratory with an average age of 40.58 ± 14.03 years old. All subjects were genotyped for the SNP of Biochemistry and Molecular Biology, Department of 19 polymorphism of the CAPN10 gene with the PCR method in order to find associations Biochemistry and Cell Biology, Faculty of Science and between this polymorphism and the metabolic syndrome. -
Calpain-10 and Adiponectin Gene Polymorphisms in Korean Type 2 Diabetes Patients
Original Endocrinol Metab 2018;33:364-371 https://doi.org/10.3803/EnM.2018.33.3.364 Article pISSN 2093-596X · eISSN 2093-5978 Calpain-10 and Adiponectin Gene Polymorphisms in Korean Type 2 Diabetes Patients Ji Sun Nam1,2, Jung Woo Han1, Sang Bae Lee1, Ji Hong You1, Min Jin Kim1, Shinae Kang1,2, Jong Suk Park1,2, Chul Woo Ahn1,2 1Department of Internal Medicine, 2Severance Institute for Vascular and Metabolic Research, Yonsei University College of Medicine, Seoul, Korea Background: Genetic variations in calpain-10 and adiponectin gene are known to influence insulin secretion and resistance in type 2 diabetes mellitus. Recently, several single nucleotide polymorphisms (SNPs) in calpain-10 and adiponectin gene have been report- ed to be associated with type 2 diabetes and various metabolic derangements. We investigated the associations between specific cal- pain-10 and adiponectin gene polymorphisms and Korean type 2 diabetes patients. Methods: Overall, 249 type 2 diabetes patients and 131 non-diabetic control subjects were enrolled in this study. All the subjects were genotyped for SNP-43 and -63 of calpain-10 gene and G276T and T45G frequencies of the adiponectin gene. The clinical char- acteristics and measure of glucose metabolism were compared within these genotypes. Results: Among calpain-10 polymorphisms, SNP-63 T/T were more frequent in diabetes patients, and single SNP-63 increases the susceptibility to type 2 diabetes. However, SNP-43 in calpain-10 and T45G and intron G276T in adiponectin gene were not signifi- cantly associated with diabetes, insulin resistance, nor insulin secretion. Conclusion: Variations in calpain-10, SNP-63 seems to increase the susceptibility to type 2 diabetes in Koreans while SNP-43 and adiponectin SNP-45, -276 are not associated with impaired glucose metabolism. -
Splicing Impact of Deep Exonic Missense Variants in CAPN3 Explored Systematically by Minigene Functional Assay
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.26.009332; this version posted March 26, 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 4.0 International license. Splicing impact of deep exonic missense variants in CAPN3 explored systematically by minigene functional assay Eugénie Dionnet*1, Aurélia Defour*1, Nathalie Da Silva1, Alexandra Salvi1, Nicolas Lévy1,2, Martin Krahn1,2, Marc Bartoli1, Francesca Puppo#1 and Svetlana Gorokhova#1,2 1 Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France. 2 Service de génétique Médicale, Hôpital de la Timone, APHM, Marseille, France * both authors should be considered as co-first authors # both authors should be considered as co-last authors Corresponding authors: Francesca Puppo and Svetlana Gorokhova Corresponding authors’ postal address: Marseille Medical Genetics, U 1251, Aix Marseille Université, Faculté des Sciences Médicales et Paramédicales, 27 bd Jean Moulin 13385 Marseille, France. Corresponding authors’ phone: +33 4 91 32 49 06, fax +33 4 91 80 43 19 Corresponding authors’ e-mail addresses: [email protected], [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.26.009332; this version posted March 26, 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 4.0 International license. -
Influenza Virus Infection Modulates the Death Receptor Pathway During Early Stages of Infection in Human Bronchial Epithelial Cells
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Physiol Manuscript Author Genomics. Author Manuscript Author manuscript; available in PMC 2019 September 01. Published in final edited form as: Physiol Genomics. 2018 September 01; 50(9): 770–779. doi:10.1152/physiolgenomics.00051.2018. Influenza virus infection modulates the death receptor pathway during early stages of infection in human bronchial epithelial cells Sreekumar Othumpangat, Donald H. Beezhold, and John D. Noti Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, West Virginia Abstract Host-viral interaction occurring throughout the infection process between the influenza A virus (IAV) and bronchial cells determines the success of infection. Our previous studies showed that the apoptotic pathway triggered by the host cells was repressed by IAV facilitating prolonged survival of infected cells. A detailed understanding on the role of IAV in altering the cell death pathway during early-stage infection of human bronchial epithelial cells (HBEpCs) is still unclear. We investigated the gene expression profiles of IAV-infected vs. mock-infected cells at the early stage of infection with a PCR array for death receptor (DR) pathway. At early stages infection (2 h) with IAV significantly upregulated DR pathway genes in HBEpCs, whereas 6 h exposure to IAV resulted in down-regulation of the same genes. IAV replication in HBEpCs decreased the levels of DR pathway genes including TNF-receptor superfamily 1, Fas-associated death domain, caspase-8, and caspase-3 by 6 h, resulting in increased survival of cells. -
Limb Girdle Muscular Dystrophy in The
Limb Girdle Muscular Dystrophy in the Hutterite Population of North America by Patrick Flosk A Thesis Submitted to the Faculty of Gmduate Studies in Fulhlment of the Requirements for the Degree of Doctor of Philosophy Deparlrnent of Biochemistry and Medical Genetics University of Manitoba WiIuripeg, Manitoba OPatrick Frosk, April 2005 THE UNI\'ERSITY OF MANITOBA FACULTY OF G.RÄDUATE STUDMS COPYRIGHT PERI{ISSION PAGE Limb Girdle Muscular Dystrophy in the Hutterite Population of North Anrerica BY Patrick Frosk A Thesis/Practicum submitted to the Faculfy of Graduate Studies ofThe University of Manitoba in partial fulfìllnlent of the requir.ements of the degree of DOCTOR OF PHILOSOPHY PATRICK FROSK @2005 Permission has been granted to the Library ofrhe university of Manitoba to Iend or sell copies of this thesis/¡rracticum, to the National Library of Canada to microfilm this thesis and to lend or sell copies of the fìlm, and to university Microfilm Inc. to publish a¡l âbstrâct of this thesis/practicun. The author reserves other publication rights, and neither this thesis/practícum nor extensive extracts from it may be printed or othelrvise reproduced \yithout the author's n'ritten permission. Table of Contents Table of Contents i Abstract iv Acknorvledgements vi List of Figures v l List of Tables ix List of Abbreviations x List of Manufacturers x Chapter 1: Introduction I Chapter 2: Revierv of Limb Girdle Muscular Dystrophies J 2,1 General Features of LGMD 3 2.2 Dominant Forms 6 (A) LGMDlA 6 (B) LGMDIB 9 (c) LGMDlC 18 (D) LGMDID 24 (E) LGMD1E -
Calcium Mechanisms in Limb-Girdle Muscular Dystrophy with CAPN3 Mutations
International Journal of Molecular Sciences Review Calcium Mechanisms in Limb-Girdle Muscular Dystrophy with CAPN3 Mutations Jaione Lasa-Elgarresta 1,2, Laura Mosqueira-Martín 1,2, Neia Naldaiz-Gastesi 1,2, Amets Sáenz 1,2, Adolfo López de Munain 1,2,3,4,* and Ainara Vallejo-Illarramendi 1,2,5,* 1 Biodonostia, Neurosciences Area, Group of Neuromuscular Diseases, 20014 San Sebastian, Spain; [email protected] (J.L.-E.); [email protected] (L.M.-M.); [email protected] (N.N.-G.); [email protected] (A.S.) 2 CIBERNED, Instituto de Salud Carlos III, Ministry of Science, Innovation and Universities, 28031 Madrid, Spain 3 Departmento de Neurosciencias, Universidad del País Vasco UPV/EHU, 20014 San Sebastian, Spain 4 Osakidetza Basque Health Service, Donostialdea Integrated Health Organisation, Neurology Department, 20014 San Sebastian, Spain 5 Grupo Neurociencias, Departmento de Pediatría, Hospital Universitario Donostia, UPV/EHU, 20014 San Sebastian, Spain * Correspondence: [email protected] (A.L.d.M.); [email protected] (A.V.-I.); Tel.: +34-943-006294 (A.L.d.M.); +34-943-006128 (A.V.-I.) Received: 4 August 2019; Accepted: 11 September 2019; Published: 13 September 2019 Abstract: Limb-girdle muscular dystrophy recessive 1 (LGMDR1), previously known as LGMD2A, is a rare disease caused by mutations in the CAPN3 gene. It is characterized by progressive weakness of shoulder, pelvic, and proximal limb muscles that usually appears in children and young adults and results in loss of ambulation within 20 years after disease onset in most patients. The pathophysiological mechanisms involved in LGMDR1 remain mostly unknown, and to date, there is no effective treatment for this disease. -
ADCY5, CAPN10 and JAZF1 Gene Polymorphisms and Placental Expression in Women with Gestational Diabetes
life Article ADCY5, CAPN10 and JAZF1 Gene Polymorphisms and Placental Expression in Women with Gestational Diabetes Przemysław Ustianowski 1 , Damian Malinowski 2 , Patrycja Kopytko 3, Michał Czerewaty 3, Maciej Tarnowski 3 , Violetta Dziedziejko 4 , Krzysztof Safranow 4 and Andrzej Pawlik 3,* 1 Department of Obstetrics and Gynecology, Pomeranian Medical University, 70-111 Szczecin, Poland; [email protected] 2 Department of Experimental and Clinical Pharmacology, Pomeranian Medical University, 70-111 Szczecin, Poland; [email protected] 3 Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; [email protected] (P.K.); [email protected] (M.C.); [email protected] (M.T.) 4 Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, 70-111 Szczecin, Poland; [email protected] (V.D.); [email protected] (K.S.) * Correspondence: [email protected] Abstract: Gestational diabetes mellitus (GDM) is carbohydrate intolerance that occurs during preg- nancy. This disease may lead to various maternal and neonatal complications; therefore, early diagnosis is very important. Because of the similarity in pathogenesis of type 2 diabetes and GDM, Citation: Ustianowski, P.; the genetic variants associated with type 2 diabetes are commonly investigated in GDM. The aim Malinowski, D.; Kopytko, P.; of the present study was to examine the associations between the polymorphisms in the ADCY5 Czerewaty, M.; Tarnowski, M.; (rs11708067, rs2877716), CAPN10 (rs2975760, rs3792267), and JAZF1 (rs864745) genes and GDM as Dziedziejko, V.; Safranow, K.; Pawlik, well as to determine the expression of these genes in the placenta. This study included 272 pregnant A. ADCY5, CAPN10 and JAZF1 Gene women with GDM and 348 pregnant women with normal glucose tolerance. -
Magnesium Deficiency Alters Expression of Genes Critical For
nutrients Article Magnesium Deficiency Alters Expression of Genes Critical for Muscle Magnesium Homeostasis and Physiology in Mice Dominique Bayle 1,Cécile Coudy-Gandilhon 1, Marine Gueugneau 1, Sara Castiglioni 2 , Monica Zocchi 2 , Magdalena Maj-Zurawska 3,4 , Adriana Palinska-Saadi 3,4, André Mazur 1, Daniel Béchet 1,* and Jeanette A. Maier 2,5 1 UNH, Unité de Nutrition Humaine, Université Clermont Auvergne, INRAE, F-63000 Clermont-Ferrand, France; [email protected] (D.B.); [email protected] (C.C.-G.); [email protected] (M.G.); [email protected] (A.M.) 2 Department of Biomedical and Clinical Sciences Luigi Sacco, Università di Milano, 20157 Milano, Italy; [email protected] (S.C.); [email protected] (M.Z.); [email protected] (J.A.M.) 3 Biological and Chemical Research Centre, University of Warsaw, PL-02-089 Warsaw, Poland; [email protected] (M.M.-Z.); [email protected] (A.P.-S.) 4 Faculty of Chemistry, University of Warsaw, PL-02-093 Warsaw, Poland 5 Interdisciplinary Centre for Nanostructured Materials and Interfaces (CIMaINa), Università di Milano, 20133 Milano, Italy * Correspondence: [email protected] Abstract: Chronic Mg2+ deficiency is the underlying cause of a broad range of health dysfunctions. Citation: Bayle, D.; As 25% of body Mg2+ is located in the skeletal muscle, Mg2+ transport and homeostasis systems Coudy-Gandilhon, C.; Gueugneau, (MgTHs) in the muscle are critical for whole-body Mg2+ homeostasis. In the present study, we as- M.; Castiglioni, S.; Zocchi, M.; sessed whether Mg2+ deficiency alters muscle fiber characteristics and major pathways regulating Maj-Zurawska, M.; Palinska-Saadi, muscle physiology. -
The Potential Role of Environmental Exposures and Genomic Signaling
Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 11-14-2011 The otP ential Role of Environmental Exposures and Genomic Signaling in Development of Central Nervous System Tumors Brian W. Kunkle Florida International University, [email protected] DOI: 10.25148/etd.FI11120809 Follow this and additional works at: https://digitalcommons.fiu.edu/etd Recommended Citation Kunkle, Brian W., "The otP ential Role of Environmental Exposures and Genomic Signaling in Development of Central Nervous System Tumors" (2011). FIU Electronic Theses and Dissertations. 524. https://digitalcommons.fiu.edu/etd/524 This work is brought to you for free and open access by the University Graduate School at FIU Digital Commons. It has been accepted for inclusion in FIU Electronic Theses and Dissertations by an authorized administrator of FIU Digital Commons. For more information, please contact [email protected]. FLORIDA INTERNATIONAL UNIVERSITY Miami, Florida THE POTENTIAL ROLE OF ENVIRONMENTAL EXPOSURES AND GENOMIC SIGNALING IN DEVELOPMENT OF CENTRAL NERVOUS SYSTEM TUMORS A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in PUBLIC HEALTH by Brian William Kunkle 2011 To: Interim Dean Michelle Cicazzo Robert Stempel College of Public Health and Social Work This dissertation written by Brian William Kunkle, and entitled The Potential Role of Environmental Exposures and Genomic Signaling in Development of Central Nervous System Tumors, having been approved in respect to style and intellectual content, is referred to you for judgment. We have read this dissertation and recommend that it be approved. ____________________________________ Changwon Yoo ____________________________________ Quentin Felty ____________________________________ Nasar Ahmed ____________________________________ Deodutta Roy, Major Professor Date of Defense: November 14, 2011 The dissertation of Brian William Kunkle is approved. -
Elevated Levels of Calpain 14 in Nasal Tissue in Chronic Rhinosinusitis
ORIGINAL RESEARCH LETTER Elevated levels of calpain 14 in nasal tissue in chronic rhinosinusitis To the Editor: Recently, calpain (CAPN) 14 was identified by a genome-wide genetic association study to play a role in eosinophilic oesophagitis [1]. CAPN14 expression is also linked with asthma and allergy sensitivity [2]. The overexpression of CAPN14 impairs epithelial barrier function and CAPN14 expression is triggered by Th2-associated signalling, such as interleukin (IL)-13 and IL-4 [3]. CAPNs are intracellular regulatory proteases, and there are 16 members of the human CAPN family. CAPNs perform a number of functions, including cytoskeletal and membrane proteins restructuring, signal transduction and inactivating enzymes involved in cell cycle progression, gene expression and apoptosis [4]. Therefore, our group performed a small pilot study to investigate CAPN gene expression profiles in tissue from another disease associated with eosinophilia and epithelial barrier function, chronic rhinosinusitis (CRS) [5]. Sinusitis is a condition associated with inflammation in the paranasal sinuses and contiguous nasal mucosa and ∼30 million adults report sinusitis symptoms annually in the United States [6]. Sinusitis is deemed chronic if symptoms persist more than 3 months, with most episodes of sinusitis associated with viral upper respiratory tract infections, asthma, allergic rhinitis and exposure to environmental factors, such as cigarette smoke [7]. Steroids are effective in treating sinusitis, thereby underlining the importance of inflammation in disease pathophysiology, with inflammatory cells such as eosinophils linked to nasal polyps formation that contribute to nasal obstruction [8]. Here, we investigated nasal tissue samples collected from patients with documented CRS, who met diagnostic criteria set forth by the Adult Sinusitis Clinical Practice Guideline [9]. -
The Pennsylvania State University the Graduate School Department of Biology CONTRIBUTION of TRANSPOSABLE ELEMENTS to GENOMIC
The Pennsylvania State University The Graduate School Department of Biology CONTRIBUTION OF TRANSPOSABLE ELEMENTS TO GENOMIC NOVELTY: A COMPUTATIONAL APPROACH A Thesis in Biology by Valer Gotea © 2007 Valer Gotea Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy August 2007 The thesis of Valer Gotea was reviewed and approved* by the following: Wojciech Makałowski Associate Professor of Biology Thesis Advisor Chair of Committee Stephen W. Schaeffer Associate Professor of Biology Kateryna D. Makova Assistant Professor of Biology Piotr Berman Associate Professor of Computer Science and Engineering Douglas R. Cavener Professor of Biology Head of the Department of Biology *Signatures are on file in the Graduate School iii ABSTRACT Transposable elements (TEs) are DNA entities that have the ability to move and multiply within genomes, and thus have the ability to influence their function and evolution. Their impact on the genomes of different species varies greatly, yet they made an important contribution to eukaryotic genomes, including to those of vertebrate and mammalian species. Almost half of the human genome itself originated from various TEs, few of them still being active. Often times, TEs can disrupt the function of certain genes and generate disease phenotypes, but over long evolutionary times they can also offer evolutionary advantages to their host genome. For example, they can serve as recombination hotspots, they can influence gene regulation, or they can even contribute to the sequence of protein coding genes. Here I made use of multiple computational tools to investigate in more detail a few of these aspects. Starting with a set of well characterized proteins to complement inferences made at the level of transcripts, I investigated the contribution of TEs to protein coding sequences.