Activation of NF

Total Page:16

File Type:pdf, Size:1020Kb

Activation of NF Downloaded from http://www.jbc.org/ at Murdoch University (CAUL) on March 7, 2016 sox9 , and , ‡1 dead end B activation , ␬ ) Department ¶ cyp19a1a , foxl2 NOVEMBER 2, 2012 Department of ʈ sox9 , Marie Karlsson ) (7–10). Nr5a or steroido- ), anti-Müllerian hormone ‡1 ␣ fig ( sox9 ␣ nuclear receptor subfamily 5, group ). Earlier, neither cytogenetic studies b), VOLUME 287•NUMBER 45• and ), forkhead box protein L2 ( , Jarno Koskinen b ‡3 Danio rerio ¶1,2 Department of Animal Science and Breeding, and ** cyp19a1a leads to lack of its transcription and development of and factor in germ line (11). In mice, homozygous mutation of Sox9 binding site , ), cytochrome P450, family 19, subfamily A, polypeptide 4 (7, 10). In mammals, SOX9 is involved in the regulation of ) THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 287, NO. 45, pp. 37926–37938, November 2, 2012 nr5a1 a Amh © 2012 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. The molecular mechanism of sex determination is unknown Zebrafish gonadal differentiation starts with the formation of On the other hand, a number of candidate genes with poten- apoptosis protein; DOC, sodium deoxycholate; NAI, NF- inhibitor; qRT-PCR, quantitative RT-PCR; I, intermediate;CF, CM, control control females. male; The abbreviations used are: AMH, anti-Müllerian hormone; IAP, inhibitor of amh dnd 4 in zebrafish ( zebrafish and represents an important step toward theunderstanding complete of the complicated process of sexin differentiation this species and possibly other cyprinid teleosts as well. in pseudohermaphrodites (12), whereasgene mutations result in in sex reversal in the (13). XY campomelic dysplasia patients a juvenile ovarian structure that eitherries or matures transforms into into adult testes ova- (14, 15).process The testis has transformation been suggested to depend on apoptosis (16). This genic factor-1 controls theamh expression of Amh A( (1, 2) nor comparative analysis ofthe recombination two rates sexes between (3) nor an array-basedto genome screen the (4) identification have of led sexgenetic chromosomes. Recently, linkage analysis of mapsassociated have with sex revealed determination on the fourindicating chromosomes presence (5, polygenic 6), sex of determination in regions zebrafish (4–7). tial role in sexual developmentSry-related have HMG been identified, box including gene( 9 ( 1a and b ( ( Published, JBC Papers in Press, September 17, 2012, DOI 10.1074/jbc.M112.386284 , and Per-Erik Olsson , Rajini Sreenivasan ** B-me- ʈ §1 ␬ ¶ B in zebrafish ␬ B pathways and ␬ , László Orbán § B Protein Prevents the Transition from B using NAI resulted in a ␬ B-regulated genes. To con- , Scott A. Ochsner ␬ ␬ ‡1 B in gonadal differentiation of B-induced anti-apoptotic effects, ␬ ␬ S □ B activation inhibitor (NAI). Sodium activated the NF- * ␬ B is a key regulator of anti-apoptotic processes and plays a role in gonad formation in mammals. ␬ , Neil J. McKenna supplemental Tables 1–3. B activation leads to female-biased sex differentiation in zebrafish. NF- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, Unraveling the regulation of apoptotic processes during gonadal transformation will facilitate understanding the ‡1 , Hazem Khalaf Anti-apoptotic signaling during the juvenile ovary stage is needed for the maintenance of oocytes in zebrafish. § ␬ BorNF- ‡1 ␬ —Final version full access. NF- B is activated at an early stage of development and ␬ Department of Biology, Örebro Life Science Center, School of Science and Technology, Örebro University, SE-701 82 ‡ JOURNAL OF BIOLOGICAL CHEMISTRY Escherichia coli ) gene expression. Because steroidogenic factor-1 and Background: molecular mechanism of zebrafish sex differentiation. Conclusion: Significance: Results: ry’s Institute of Medical Research, Monash Medical Centre,3168, Clayton, Victoria Australia. 46-19-303566; E-mail: [email protected]. edge Foundation, Sweden, and ÖrebroAgri-Food University and (to Veterinary P. Authority E.-O.) asoratory, well and Singapore as by (to Temasek the L. Life O.). Sciences Lab- under the accession number E-MEXP-3249. Testis differentiation in zebrafish involves juvenile ovary to This article contains Author’s Choice Author’s Choice This research was financed by the Swedish Research Council, the Knowl- Present address: Molecular Genetics and Development Division, Prince Hen- To whom correspondence should be addressed. Tel.: 46-19-301244; Fax: These authors have contributed equally. Amh S in Zebrafish Juvenile Ovary to Testis and Promotes Ovarian Development gonad differentiation. Exposure ofkilled juvenile zebrafish to heat- decrease in females from 45for to 20%. an This essential study provides role proof of NF- Jesper Karlsson 37926 2 3 □ 1 * resulted in anMicroarray and increased quantitative ratio real-time-PCR analysisshowed of of elevated expression gonads females of NF- from 30 to 85%. diated induction of anti-apoptotic genesplay could, a therefore, role also instudy zebrafish was gonad to differentiation. examine The the aim potential of role this of NF- Ajay Pradhan From the Received for publication, June 20, 2012, and in revised form, September 14, 2012 Activation of NF- firm the involvement of NF- has been shown to interact with steroidogenicmals, factor-1 in leading mam- to( the suppression ofAmh anti-Müllerian are hormone important for proper testis development, NF- Biological Sciences, National University of Singapore, SingaporeGeorgikon 117543, Faculty, and University of Pannonia, Keszthely, H-8360 Hungary of Reproductive Genomics, Strategic Research Program, Temasek Life Sciences Laboratory, Singapore 117604, deoxycholate treatment mimicked the effect ofteria heat-killed and bac- resulted in an increased proportionto of 45%, females whereas from the 25 inhibition of NF- The full set of microarray expression data has been deposited in ArrayExpress Örebro, Sweden, zebrafish were treatedinducer of with NF- sodium deoxycholate, a known testis transformation initiated by an apoptotic wave. Theular molec- regulation of this transformation process is notstood. fully NF- under- NF-␬B Activation Causes Female Bias in Zebrafish was further supported by a recent study where mutations in the EXPERIMENTAL PROCEDURES Fanconi anemia, complementation group L (fancl) gene led to Breeding—Adult zebrafish were maintained in a recirculat- germ cell apoptosis and consequently activated the testis devel- ing system (Aquaneering) with a 14-h light/10-h dark cycle. opment pathway (17). Introducing mutations in the tumor pro- The fish were fed twice a day with newly hatched Artemia tein p53 (tp53) gene counteracted the effect of the fancl muta- salina nauplii and commercial flake food (Tetrarubin). The tions (17), suggesting a role for apoptosis in this process. In line male and female brooders were kept in separate aquaria at with this, germ cell numbers are also important for ovarian 26–27 °C, and they were allowed to breed once a week. The fish development and complete absence of germ cells results in handling procedures were approved by the Swedish Ethical development of sterile males (9, 18). Committee in Linköping (Permit 32-10). Nuclear factor ␬-light-chain-enhancer of activated B cells Preparation of Heat-killed Bacteria—E. coli MG1655 was (NF-␬B) is involved in regulation of inflammation, apoptosis, grown on Luria-Bertani (LB) agar and incubated at 37 °C over- cell growth, and differentiation and can be activated by various night. One colony was inoculated into 10 ml of LB broth and physical and chemical factors (19). NF-␬B is a protein complex incubated on a shaker (200 rpm) at 37 °C overnight. The bacte- composed of homo- or heterodimers of five members of the Rel ria were then centrifuged and washed with 5 ml of phosphate- family including NF-␬B1 (p50), NF-␬B2 (p52), Rel A (p65), Rel buffered saline (Sigma). The bacterial pellet was resuspended in B, and c-Rel. These proteins are capable of binding one another 2 ml of PBS and killed by heating to 70 °C for 1 h. To ensure Downloaded from with different binding specificities resulting in different DNA 100% bacteria death, 10 ␮l of the heat-killed suspension was binding properties. The p65/p50 dimer is the most abundant plated and incubated overnight at 37 °C. heterodimeric form present in cells and is involved in transcrip- NF␬B-pGL4 Plasmid Construction—The pGL4 plasmid with tion activation of a multitude of genes (19, 20). NF-␬B subunits promoter-less Luciferase gene and neomycin selection marker ␬ are generally sequestered in the cytoplasm by the inhibitor pro- was purchased from Promega, and the NF B cis-element insert http://www.jbc.org/ ␬ tein I␬B. Numerous factors including UV irradiation, stress, was obtained from commercially available pNF B-Luc plasmid ␬ cytokine, and free radicals can promote I␬B degradation of the (BD Biosciences). The pGL4 luciferase plasmid and the pNF B- I␬B/NF-␬B complex, allowing the translocation of NF-␬Bto Luc plasmid were cut with HindIII and KpnI (Fermentas) and the nucleus resulting in subsequent induction of the transcrip- gel-purified by using Wizard SV Gel and PCR Clean-Up System (Promega). The NF␬B cis-element and the pGL4 luciferase tion of its target genes (20–22). at Murdoch University (CAUL) on March 7, 2016 NF-␬B activation blocks apoptotic processes and promotes plasmid were ligated using T4 DNA ligase (Fermentas). cell survival by interacting with the inhibitor of apoptosis pro- Cell Culture and Development of Stably
Recommended publications
  • 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.
    [Show full text]
  • Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights Into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle
    animals Article Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle Masoumeh Naserkheil 1 , Abolfazl Bahrami 1 , Deukhwan Lee 2,* and Hossein Mehrban 3 1 Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; [email protected] (M.N.); [email protected] (A.B.) 2 Department of Animal Life and Environment Sciences, Hankyong National University, Jungang-ro 327, Anseong-si, Gyeonggi-do 17579, Korea 3 Department of Animal Science, Shahrekord University, Shahrekord 88186-34141, Iran; [email protected] * Correspondence: [email protected]; Tel.: +82-31-670-5091 Received: 25 August 2020; Accepted: 6 October 2020; Published: 9 October 2020 Simple Summary: Hanwoo is an indigenous cattle breed in Korea and popular for meat production owing to its rapid growth and high-quality meat. Its yearling weight and carcass traits (backfat thickness, carcass weight, eye muscle area, and marbling score) are economically important for the selection of young and proven bulls. In recent decades, the advent of high throughput genotyping technologies has made it possible to perform genome-wide association studies (GWAS) for the detection of genomic regions associated with traits of economic interest in different species. In this study, we conducted a weighted single-step genome-wide association study which combines all genotypes, phenotypes and pedigree data in one step (ssGBLUP). It allows for the use of all SNPs simultaneously along with all phenotypes from genotyped and ungenotyped animals. Our results revealed 33 relevant genomic regions related to the traits of interest.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Elabscience.Com ® E-Mail:[email protected] Elabscience Elabscience Biotechnology Inc
    Produktinformation Diagnostik & molekulare Diagnostik Laborgeräte & Service Zellkultur & Verbrauchsmaterial Forschungsprodukte & Biochemikalien Weitere Information auf den folgenden Seiten! See the following pages for more information! Lieferung & Zahlungsart Lieferung: frei Haus Bestellung auf Rechnung SZABO-SCANDIC Lieferung: € 10,- HandelsgmbH & Co KG Erstbestellung Vorauskassa Quellenstraße 110, A-1100 Wien T. +43(0)1 489 3961-0 Zuschläge F. +43(0)1 489 3961-7 [email protected] • Mindermengenzuschlag www.szabo-scandic.com • Trockeneiszuschlag • Gefahrgutzuschlag linkedin.com/company/szaboscandic • Expressversand facebook.com/szaboscandic Tel:240-252-7368(USA) Fax:240-252-7376(USA) www.elabscience.com ® E-mail:[email protected] Elabscience Elabscience Biotechnology Inc. RMND5B Polyclonal Antibody Catalog No. E-AB-52625 Reactivity H,M Storage Store at -20℃. Avoid freeze / thaw cycles. Host Rabbit Applications IHC,ELISA Isotype IgG Note: Centrifuge before opening to ensure complete recovery of vial contents. Images Immunogen Information Immunogen Fusion protein of human RMND5B Gene Accession BC009911 Swissprot Q96G75 Synonyms FLJ22318,MGC112682,Protein RMD5 homolog B,Required for meiotic nuclear division 5 homolog B (S. cerevisiae),RP23-79E13.4 Immunohistochemistry of paraffin- Product Information embedded Human esophagus cancer Buffer PBS with 0.05% NaN3 and 40% Glycerol,pH7.4 tissue using RMND5B Polyclonal Purify Antigen affinity purification Antibody at dilution of 1:50(×200) Dilution IHC 1:50-1:300, ELISA 1:5000-1:10000 Background The function of this protein remains unknown. For Research Use Only Focus on your research Thank you for your recent purchase. If you would like to learn more about antibodies,please visit www.elabscience.com. Service for life science Applications:WB-Western Blot IHC-Immunohistochemistry IF-Immunofluorescence IP-Immunoprecipitation FC-Flow cytometry ChIP- Chromatin Immunoprecipitation Reactivity: H-Human R-Rat M-Mouse Mk-Monkey Dg-Dog Ch-Chicken Hm-Hamster Rb-Rabbit Sh- Sheep Pg-Pig Z-Zebrafish X-Xenopus C-Cow.
    [Show full text]
  • Meta-Analysis of Gene Expression in Individuals with Autism Spectrum Disorders
    Meta-analysis of Gene Expression in Individuals with Autism Spectrum Disorders by Carolyn Lin Wei Ch’ng BSc., University of Michigan Ann Arbor, 2011 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Master of Science in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Bioinformatics) The University of British Columbia (Vancouver) August 2013 c Carolyn Lin Wei Ch’ng, 2013 Abstract Autism spectrum disorders (ASD) are clinically heterogeneous and biologically complex. State of the art genetics research has unveiled a large number of variants linked to ASD. But in general it remains unclear, what biological factors lead to changes in the brains of autistic individuals. We build on the premise that these heterogeneous genetic or genomic aberra- tions will converge towards a common impact downstream, which might be reflected in the transcriptomes of individuals with ASD. Similarly, a considerable number of transcriptome analyses have been performed in attempts to address this question, but their findings lack a clear consensus. As a result, each of these individual studies has not led to any significant advance in understanding the autistic phenotype as a whole. The goal of this research is to comprehensively re-evaluate these expression profiling studies by conducting a systematic meta-analysis. Here, we report a meta-analysis of over 1000 microarrays across twelve independent studies on expression changes in ASD compared to unaffected individuals, in blood and brain. We identified a number of genes that are consistently differentially expressed across studies of the brain, suggestive of effects on mitochondrial function. In blood, consistent changes were more difficult to identify, despite individual studies tending to exhibit larger effects than the brain studies.
    [Show full text]
  • Identification of Genomic Targets of Krüppel-Like Factor 9 in Mouse Hippocampal
    Identification of Genomic Targets of Krüppel-like Factor 9 in Mouse Hippocampal Neurons: Evidence for a role in modulating peripheral circadian clocks by Joseph R. Knoedler A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Neuroscience) in the University of Michigan 2016 Doctoral Committee: Professor Robert J. Denver, Chair Professor Daniel Goldman Professor Diane Robins Professor Audrey Seasholtz Associate Professor Bing Ye ©Joseph R. Knoedler All Rights Reserved 2016 To my parents, who never once questioned my decision to become the other kind of doctor, And to Lucy, who has pushed me to be a better person from day one. ii Acknowledgements I have a huge number of people to thank for having made it to this point, so in no particular order: -I would like to thank my adviser, Dr. Robert J. Denver, for his guidance, encouragement, and patience over the last seven years; his mentorship has been indispensable for my growth as a scientist -I would also like to thank my committee members, Drs. Audrey Seasholtz, Dan Goldman, Diane Robins and Bing Ye, for their constructive feedback and their willingness to meet in a frequently cold, windowless room across campus from where they work -I am hugely indebted to Pia Bagamasbad and Yasuhiro Kyono for teaching me almost everything I know about molecular biology and bioinformatics, and to Arasakumar Subramani for his tireless work during the home stretch to my dissertation -I am grateful for the Neuroscience Program leadership and staff, in particular
    [Show full text]
  • An Integrated Analysis of Cashmere Fineness Lncrnas in Cashmere Goats
    G C A T T A C G G C A T genes Article An Integrated Analysis of Cashmere Fineness lncRNAs in Cashmere Goats Yuan Y. Zheng 1 , Sheng D. Sheng 1, Tai Y. Hui 1, Chang Yue 1, Jia M. Sun 1, Dan Guo 2, Su L. Guo 3, Bo J. Li 1, Hui L. Xue 1, Ze Y. Wang 1,* and Wen L. Bai 1,* 1 College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China; [email protected] (Y.Y.Z.); [email protected] (S.D.S.); [email protected] (T.Y.H.); [email protected] (C.Y.); [email protected] (J.M.S.); [email protected] (B.J.L.); [email protected] (H.L.X.) 2 Animal Genetic Breeding, Academy of Animal Husbandry Science of Liaoning Province, Liaoyang 130062, China; [email protected] 3 Prosperous Community, Changshun Town, Huade 013350, China; [email protected] * Correspondence: [email protected] (Z.Y.W.); [email protected] (W.L.B.); Tel.: +86-15998362195 (Z.Y.W.) Received: 29 January 2019; Accepted: 28 March 2019; Published: 2 April 2019 Abstract: Animal growth and development are regulated by long non-coding RNAs (lncRNAs). However, the functions of lncRNAs in regulating cashmere fineness are poorly understood. To identify the key lncRNAs that are related to cashmere fineness in skin, we have collected skin samples of Liaoning cashmere goats (LCG) and Inner Mongolia cashmere goats (MCG) in the anagen phase, and have performed RNA sequencing (RNA-seq) approach on these samples. The high-throughput sequencing and bioinformatics analyses identified 437 novel lncRNAs, including 93 differentially expressed lncRNAs.
    [Show full text]
  • Of the T Cell by G-CSF and IL-10 Cell Mobilization Requires Direct
    Downloaded from http://www.jimmunol.org/ by guest on October 1, 2021 is online at: average * The Journal of Immunology , 26 of which you can access for free at: 2014; 192:3180-3189; Prepublished online 28 from submission to initial decision 4 weeks from acceptance to publication February 2014; doi: 10.4049/jimmunol.1302315 http://www.jimmunol.org/content/192/7/3180 Modification of T Cell Responses by Stem Cell Mobilization Requires Direct Signaling of the T Cell by G-CSF and IL-10 Kelli P. A. MacDonald, Laetitia Le Texier, Ping Zhang, Helen Morris, Rachel D. Kuns, Katie E. Lineburg, Lucie Leveque, Alistair L. Don, Kate A. Markey, Slavica Vuckovic, Frederik O. Bagger, Glen M. Boyle, Bruce R. Blazar and Geoffrey R. Hill J Immunol cites 45 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription http://www.jimmunol.org/content/suppl/2014/02/28/jimmunol.130231 5.DCSupplemental This article http://www.jimmunol.org/content/192/7/3180.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 © 2014 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606.
    [Show full text]
  • Supplemental Material
    Supplemental Material Methods Laboratory Analyses We measured levels of serum and urine electrolytes and creatinine in samples obtained from all patients using routine methods. Intact parathyroid hormone (iPTH) levels were measured by chemiluminescent immunoassay (CLIA Immulite 2000XP, Siemens, Germany), FGF-23 plasma concentrations were determined by ELISA (Human FGF23 C-terminal Elisa kit, Immutopics International, San Clemente, CA, USA) (reference range 26-110 kRU/mL)(for details see below), 25-OH-D3 was measured by a direct competitive chemiluminescent immunoassay (CLIA, Liaison Analyzer, Diasorin S.p.A.), and 1,25-(OH)2D3 was measured after purification by radioimmunoassay (IDS kit, Immunodiagnostic Systems, Germany). Tubular phosphate reabsorption Renal phosphate handling was assessed according to Stark et al. as TmP/GFR = SPO4 – (UPO4 x 1 1,2 SCr / UCr) . For SPO4 and TmP/GFR, age dependent reference values were used . Mean and SD for TmP/GFR were converted to mmol/L GFR resulting in the following reference ranges (mean ±2SD): Newborn=1.4-3.0mmol/l; 1month to 2years = 0.9-2.1mmol/l, 2-12years = 1.0- 1.8mmol/l, 12-16years = 0.9-1.7mmol/l, >16years = 0.8-1.2mmol/l. Genome wide linkage / LOD score calculation DNA of four affected individuals shown in the pedigrees F1, F2, F3 (Figure S1) was used to map the disease locus. Individuals F1.1, F1.2 and F2.1 were analyzed using Illumina Human660W-Quad BeadChips, individual F3.1 was run on a Human OmniExpress BeadChip. For combined analysis only those SNPs present on both chip types were used where a genotype was obtained for all four individuals (about 239.000 SNPs).
    [Show full text]
  • Autocrine IFN Signaling Inducing Profibrotic Fibroblast Responses by a Synthetic TLR3 Ligand Mitigates
    Downloaded from http://www.jimmunol.org/ by guest on September 28, 2021 Inducing is online at: average * The Journal of Immunology published online 16 August 2013 from submission to initial decision 4 weeks from acceptance to publication http://www.jimmunol.org/content/early/2013/08/16/jimmun ol.1300376 A Synthetic TLR3 Ligand Mitigates Profibrotic Fibroblast Responses by Autocrine IFN Signaling Feng Fang, Kohtaro Ooka, Xiaoyong Sun, Ruchi Shah, Swati Bhattacharyya, Jun Wei and John Varga J Immunol Submit online. Every submission reviewed by practicing scientists ? is published twice each month by http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://www.jimmunol.org/content/suppl/2013/08/20/jimmunol.130037 6.DC1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 28, 2021. Published August 16, 2013, doi:10.4049/jimmunol.1300376 The Journal of Immunology A Synthetic TLR3 Ligand Mitigates Profibrotic Fibroblast Responses by Inducing Autocrine IFN Signaling Feng Fang,* Kohtaro Ooka,* Xiaoyong Sun,† Ruchi Shah,* Swati Bhattacharyya,* Jun Wei,* and John Varga* Activation of TLR3 by exogenous microbial ligands or endogenous injury-associated ligands leads to production of type I IFN.
    [Show full text]
  • Mycobacterium Tuberculosis Induced Transcription in Macrophages: the Role of TPL2/ERK Signalling in the Negative Regulation of T
    Mycobacterium tuberculosis induced transcription in macrophages: the role of TPL2/ERK signalling in the negative regulation of type I interferon production and implications for control of tuberculosis John Benson Ewbank August 2012 Division of Immunoregulation MRC National Institute for Medical Research The Ridgeway, Mill Hill London NW7 1AA Submitted to University College London for the Degree of Doctor of Philosophy I, John Benson Ewbank, 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 Abstract Abstract Mycobacterium tuberculosis is an important global cause of mortality and morbidity. The major host cell of Mycobacterium tuberculosis is the macrophage, and Mycobacterium tuberculosis is able to subvert the macrophage response in order to survive and replicate. The majority of infected individuals mount an immune response capable of controlling Mycobacterium tuberculosis infection. This requires the cytokines IL-12, TNFα, IL-1 and IFNγ, which promote eradication or control of infection. However, other immune factors, including IL-10 and type I IFN, can inhibit this protective response. In this study we have used microarray analysis to study the temporal response of macrophages to Mycobacterium tuberculosis infection, in an unbiased fashion. In response to Mycobacterium tuberculosis infection, macrophages produced cytokines and chemokines, upregulated genes involved with major histocompatability class I antigen presentation, activated both pro- and anti-apoptotic genes and downregulated many genes involved in cell-division and metabolism. We also observed the early induction of genes regulated by the extracellular-regulated kinase (ERK) MAP kinase pathway, and the upregulation of genes known to be induced by type I IFN, leading us to further investigate the role of these pathways in the macrophage response to Mycobacterium tuberculosis.
    [Show full text]
  • A Biochemical Landscape of A-To-I RNA Editing in the Human Brain Transcriptome
    Downloaded from genome.cshlp.org on October 3, 2021 - Published by Cold Spring Harbor Laboratory Press Resource A biochemical landscape of A-to-I RNA editing in the human brain transcriptome Masayuki Sakurai,1,4 Hiroki Ueda,1,4 Takanori Yano,1 Shunpei Okada,1 Hideki Terajima,1 Toutai Mitsuyama,2 Atsushi Toyoda,3 Asao Fujiyama,3 Hitomi Kawabata,1 and Tsutomu Suzuki1,5 1Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan; 2Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan; 3Comparative Genomics Laboratory, Center for Genetic Resource Information, National Institute of Genetics, Shizuoka 411-8540, Japan Inosine is an abundant RNA modification in the human transcriptome and is essential for many biological processes in modulating gene expression at the post-transcriptional level. Adenosine deaminases acting on RNA (ADARs) catalyze the hydrolytic deamination of adenosines to inosines (A-to-I editing) in double-stranded regions. We previously established a biochemical method called ‘‘inosine chemical erasing’’ (ICE) to directly identify inosines on RNA strands with high reliability. Here, we have applied the ICE method combined with deep sequencing (ICE-seq) to conduct an unbiased genome-wide screening of A-to-I editing sites in the transcriptome of human adult brain. Taken together with the sites identified by the conventional ICE method, we mapped 19,791 novel sites and newly found 1258 edited mRNAs, including 66 novel sites in coding regions, 41 of which cause altered amino acid assignment. ICE-seq detected novel editing sites in various repeat elements as well as in short hairpins.
    [Show full text]