Genes Involved in Amelogenesis Imperfecta. Part II*
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Dynamic Regulation of FGF23 by Fam20c Phosphorylation, Galnac-T3 Glycosylation, and Furin Proteolysis
Dynamic regulation of FGF23 by Fam20C phosphorylation, GalNAc-T3 glycosylation, and furin proteolysis Vincent S. Tagliabraccia, James L. Engela,1, Sandra E. Wileya, Junyu Xiaoa, David J. Gonzaleza,b, Hitesh Nidumanda Appaiahc, Antonius Kollerd, Victor Nizetb,e, Kenneth E. Whitec, and Jack E. Dixona,f,g,2 Departments of aPharmacology, bPediatrics, fCellular and Molecular Medicine, and gChemistry and Biochemistry and eSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093; cDepartment of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202; and dStony Brook University Proteomics Center, School of Medicine, Stony Brook University, Stony Brook, NY 11794 Contributed by Jack E. Dixon, February 8, 2014 (sent for review January 23, 2014) The family with sequence similarity 20, member C (Fam20C) has life. Nonlethal cases have also been reported, and these patients recently been identified as the Golgi casein kinase. Fam20C phosphor- develop hypophosphatemia as a result of elevated levels of the ylates secreted proteins on Ser-x-Glu/pSer motifs and loss-of-function phosphate-regulating hormone fibroblast growth factor 23 (FGF23) mutations in the kinase cause Raine syndrome, an often-fatal osteo- (12). Additionally, Fam20C knockout (KO) mice develop renal sclerotic bone dysplasia. Fam20C is potentially an upstream regulator phosphate wasting due to an increase in circulating bioactive of the phosphate-regulating hormone fibroblast growth factor 23 FGF23 as well as severe hypophosphatemic rickets (13, 14). (FGF23), because humans with FAM20C mutations and Fam20C KO Thus, Fam20C has been proposed to be a regulator of FGF23; mice develop hypophosphatemia due to an increase in full-length, bi- however, the molecular mechanisms underlying the control of ologically active FGF23. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Genome-Wide Screen of Otosclerosis in Population Biobanks
medRxiv preprint doi: https://doi.org/10.1101/2020.11.15.20227868; this version posted November 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . 1 Genome-wide Screen of Otosclerosis in 2 Population Biobanks: 18 Loci and Shared 3 Heritability with Skeletal Structure 4 Joel T. Rämö1, Tuomo Kiiskinen1, Juha Karjalainen1,2,3,4, Kristi Krebs5, Mitja Kurki1,2,3,4, Aki S. 5 Havulinna6, Eija Hämäläinen1, Paavo Häppölä1, Heidi Hautakangas1, FinnGen, Konrad J. 6 Karczewski1,2,3,4, Masahiro Kanai1,2,3,4, Reedik Mägi5, Priit Palta1,5, Tõnu Esko5, Andres Metspalu5, 7 Matti Pirinen1,7,8, Samuli Ripatti1,2,7, Lili Milani5, Antti Mäkitie9, Mark J. Daly1,2,3,4,10, and Aarno 8 Palotie1,2,3,4 9 1. Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of 10 Helsinki, Helsinki, Finland 11 2. Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, 12 Massachusetts, USA 13 3. Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 14 USA 15 4. Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA 16 5. Estonian Genome Center, University of Tartu, Tartu, Estonia, Institute of Molecular and Cell Biology, 17 University of Tartu, Tartu, Estonia 18 6. Finnish Institute for Health and Welfare, Helsinki, Finland 19 7. Department of Public Health, Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland 20 8. -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
Supporting Online Material
1 Conserved Transcriptomic Profiles Underpin Monogamy across 2 Vertebrates 3 4 Rebecca L. Younga,b,1, Michael H. Ferkinc, Nina F. Ockendon-Powelld, Veronica N. Orre, 5 Steven M. Phelpsa,f, Ákos Pogányg, Corinne L. Richards-Zawackih, Kyle Summersi, 6 Tamás Székelyd,j,k, Brian C. Trainore, Araxi O. Urrutiaj,l, Gergely Zacharm, Lauren A. 7 O’Connelln, and Hans A. Hofmanna,b,f,1 8 9 1correspondence to: [email protected]; [email protected] 10 1 www .pnas.org/cgi/doi/10.1073/pnas.1813775115 11 Materials and Methods 12 Sample collection and RNA extraction 13 Reproductive males of each focal species were sacrificed and brains were rapidly 14 dissected and stored to preserve RNA (species-specific details provided below). All animal 15 care and use practices were approved by the respective institutions. For each species, 16 RNA from three individuals was pooled to create an aggregate sample for transcriptome 17 comparison. The focus of this study is to characterize similarity among species with 18 independent species-level transitions to a monogamous mating system rather than to 19 characterize individual-level variation in gene expression. Pooled samples are reflective 20 of species-level gene expression variation of each species and limit potentially 21 confounding individual variation for species-level comparisons (1, 2). While exploration of 22 individual variation is critical to identify mechanisms underlying differences in behavioral 23 expression, high levels of variation between two pooled samples of conspecifics could 24 obscure more general species-specific gene expression patterns. Note that two pooled 25 replicates per species would not be sufficiently large for estimating within species 26 variance, and the effect of an outlier within a pool of two individuals would be considerable. -
Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing -
( 12 ) United States Patent
US010428349B2 (12 ) United States Patent ( 10 ) Patent No. : US 10 , 428 ,349 B2 DeRosa et al . (45 ) Date of Patent: Oct . 1 , 2019 ( 54 ) MULTIMERIC CODING NUCLEIC ACID C12N 2830 / 50 ; C12N 9 / 1018 ; A61K AND USES THEREOF 38 / 1816 ; A61K 38 /45 ; A61K 38/ 44 ; ( 71 ) Applicant: Translate Bio , Inc ., Lexington , MA A61K 38 / 177 ; A61K 48 /005 (US ) See application file for complete search history . (72 ) Inventors : Frank DeRosa , Lexington , MA (US ) ; Michael Heartlein , Lexington , MA (56 ) References Cited (US ) ; Daniel Crawford , Lexington , U . S . PATENT DOCUMENTS MA (US ) ; Shrirang Karve , Lexington , 5 , 705 , 385 A 1 / 1998 Bally et al. MA (US ) 5 ,976 , 567 A 11/ 1999 Wheeler ( 73 ) Assignee : Translate Bio , Inc ., Lexington , MA 5 , 981, 501 A 11/ 1999 Wheeler et al. 6 ,489 ,464 B1 12 /2002 Agrawal et al. (US ) 6 ,534 ,484 B13 / 2003 Wheeler et al. ( * ) Notice : Subject to any disclaimer , the term of this 6 , 815 ,432 B2 11/ 2004 Wheeler et al. patent is extended or adjusted under 35 7 , 422 , 902 B1 9 /2008 Wheeler et al . 7 , 745 ,651 B2 6 / 2010 Heyes et al . U . S . C . 154 ( b ) by 0 days. 7 , 799 , 565 B2 9 / 2010 MacLachlan et al. (21 ) Appl. No. : 16 / 280, 772 7 , 803 , 397 B2 9 / 2010 Heyes et al . 7 , 901, 708 B2 3 / 2011 MacLachlan et al. ( 22 ) Filed : Feb . 20 , 2019 8 , 101 ,741 B2 1 / 2012 MacLachlan et al . 8 , 188 , 263 B2 5 /2012 MacLachlan et al . (65 ) Prior Publication Data 8 , 236 , 943 B2 8 /2012 Lee et al . -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in -
Gene Regulation Underlies Environmental Adaptation in House Mice
Downloaded from genome.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Research Gene regulation underlies environmental adaptation in house mice Katya L. Mack,1 Mallory A. Ballinger,1 Megan Phifer-Rixey,2 and Michael W. Nachman1 1Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California 94720, USA; 2Department of Biology, Monmouth University, West Long Branch, New Jersey 07764, USA Changes in cis-regulatory regions are thought to play a major role in the genetic basis of adaptation. However, few studies have linked cis-regulatory variation with adaptation in natural populations. Here, using a combination of exome and RNA- seq data, we performed expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses to study the genetic architecture of regulatory variation in wild house mice (Mus musculus domesticus) using individuals from five pop- ulations collected along a latitudinal cline in eastern North America. Mice in this transect showed clinal patterns of variation in several traits, including body mass. Mice were larger in more northern latitudes, in accordance with Bergmann’s rule. We identified 17 genes where cis-eQTLs were clinal outliers and for which expression level was correlated with latitude. Among these clinal outliers, we identified two genes (Adam17 and Bcat2) with cis-eQTLs that were associated with adaptive body mass variation and for which expression is correlated with body mass both within and between populations. Finally, we per- formed a weighted gene co-expression network analysis (WGCNA) to identify expression modules associated with measures of body size variation in these mice. -
PDF Hosted at the Radboud Repository of the Radboud University Nijmegen
PDF hosted at the Radboud Repository of the Radboud University Nijmegen The following full text is a publisher's version. For additional information about this publication click this link. http://hdl.handle.net/2066/194292 Please be advised that this information was generated on 2021-10-04 and may be subject to change. Unlocking the doors of transcription of doors the Unlocking Uitnodiging voor het bijwonen van Unlocking the doors de openbare verdediging of transcription: van mijn proefschrift Unlocking the doors Key transcriptional regulators of transcription: in calcium and magnesium reabsorption Key transcriptional regulators in calcium and magnesium reabsorption op woensdag 12 september 2018 om 16.30 uur precies in de aula van de Radboud Universiteit Nijmegen, Comeniuslaan 2 te Nijmegen. U bent van harte welkom bij deze plechtigheid AndreasKompatscher en de aansluitende receptie. Andreas Kompatscher [email protected] Paranimfen Steef Kurstjens Andreas Kompatscher [email protected] 2018-11 RIMLS Karin Kompatscher [email protected] Unlocking the doors of transcription: Key transcriptional regulators in calcium and magnesium reabsorption Andreas Kompatscher 521424-L-sub01-bw-Kompatscher Processed on: 24-7-2018 PDF page: 1 The research presented in this thesis was performed at the department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud university medical center, The Netherlands and financially supported by grant from the Netherlands Organization for Scientific Research, grant NWO VICI 016.130.668 -
Functional Interpretation of Gene Lists
Functional interpretation of gene lists Bing Zhang Department of Biomedical Informatics Vanderbilt University [email protected] Microarray data analysis workflow log2(ratio) 92546_r_at 92545_f_at 96055_at 102105_f_at 102700_at -log10(p value) 161361_s_at Microarray data Differential 92202_g_at expression 103548_at 100947_at 101869_s_at 102727_at 160708_at …... Normalization Clustering Lists of genes with potential biological interest 2 Applied Bioinformatics, Spring 2013 Omics studies generate gene/protein lists n Genomics q Genome Wide Association Study (GWAS) q Next generation sequencing (NGS) n Transcriptomics q mRNA profiling ……….. n Microarrays ……….. ……….. n Serial analysis of gene expression (SAGE) ……….. n RNA-Seq ………. q Protein-DNA interaction ………. n Chromatin immunoprecipitation ………. n Proteomics ………. ……… q Protein profiling n LC-MS/MS ……… ……… q Protein-protein interaction n Yeast two hybrid n Affinity pull-down/LC-MS/MS 3 Applied Bioinformatics, Spring 2013 Microarray experiment comparing metastatic and non- metastatic colon cancer cell lines Parental cell line Affymetrix RNA Mouse430_2 Metastatic cell line Smith et al., Gastroenterology, 138:958-968, 2010 4 Applied Bioinformatics, Spring 2013 Data matrix and differential expression analysis 863 significant probe set IDs (adjp<0.01 and fold-change>2), out of 45,101 probe sets *because the data are log2 based, fold-change>2 means abs(logFC)>1 5 Applied Bioinformatics, Spring 2013 Understanding a gene list n Level I 1451263_a_at 1436486_x_at q What are the genes behind the IDs and 1451780_at what do we know about the function of the 1438237_at 1417023_a_at genes? 1441054_at 1416203_at 1416295_a_at 1435012_x_at 1416069_at 1436485_s_at 1438148_at 1452740_at 1422184_a_at …… 6 Applied Bioinformatics, Spring 2013 One-gene-at-a-time information systems 7 Applied Bioinformatics, Spring 2013 Biomart: a batch information retrieval system n In contrast to the “one-gene-at-a-time” systems, e.g. -
Transdifferentiation of Human Mesenchymal Stem Cells
Transdifferentiation of Human Mesenchymal Stem Cells Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Julius-Maximilians-Universität Würzburg vorgelegt von Tatjana Schilling aus San Miguel de Tucuman, Argentinien Würzburg, 2007 Eingereicht am: Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Martin J. Müller Gutachter: PD Dr. Norbert Schütze Gutachter: Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am: Hiermit erkläre ich ehrenwörtlich, dass ich die vorliegende Dissertation selbstständig angefertigt und keine anderen als die von mir angegebenen Hilfsmittel und Quellen verwendet habe. Des Weiteren erkläre ich, dass diese Arbeit weder in gleicher noch in ähnlicher Form in einem Prüfungsverfahren vorgelegen hat und ich noch keinen Promotionsversuch unternommen habe. Gerbrunn, 4. Mai 2007 Tatjana Schilling Table of contents i Table of contents 1 Summary ........................................................................................................................ 1 1.1 Summary.................................................................................................................... 1 1.2 Zusammenfassung..................................................................................................... 2 2 Introduction.................................................................................................................... 4 2.1 Osteoporosis and the fatty degeneration of the bone marrow..................................... 4 2.2 Adipose and bone