DOCSLIB.ORG

Proquest Dissertations

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Proquest Dissertations INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. Each original is also photographed in one exposure and is included in reduced form at the back of the book. Photographs included in the original manuscript have been reproduced xerographically in this copy. Higher quality 6” x 9” black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMI directly to order. UMI Bell & Howell Information and Learning 300 North Zeeb Road, Ann Arbor, Ml 48106-1346 USA 800-521-0600 NOTE TO USERS Page(s) missing in number only; text follows. Microfilmed as received. 222-229 This reproduction is the best copy available. UMI MOLECULAR GENETIC AND BIOCHEMICAL STUDIES OF THE HUMAN AND MOUSE MHC COMPLEMENT GENE CLUSTERS DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Zhenyu Yang, M.S. ***** The Ohio State Univeristy 1999 Dissertation Committee: Approved by Chack Yung Yu, D.Phil., Adviser % - Adviser George A. Marzluf, Ph.D. Molecular, Cellular and Gail D. Wenger, Ph.D. Developmental Biology Program Arthur H. M. Burghes, Ph.D. UMI Number: 9931705 UMI Microform 9931705 Copyright 1999, by UMI Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. UMI 300 North Zeeb Road Ann Arbor, MI 48103 Copyright by Zhenyu Yang 1999 ABSTRACT The major histocompatibility complex (MHC) is associated with more than 70 diseases. The goals of this study are to investigate the mechanisms of diseases associated with the MHC class HI region. As shown by definitive restriction fragment length polymorphisms, the four tandemly arranged genes serine/threonine kinase RP, complement component C4, steroid 21-hydroylase CYP21, and tenascin TNX are organized as a genetic unit designated as the RCCX module. Variations in the number and size of the RCCX modules can promote unequal crossover, leading to gene duplications and deletions. A TNXB-XA recombinant resulted from an unequal crossover between a monomodular and a bimodular RCCX was observed in a patient with congenital adrenal hyperplasia. Elucidation of the DNA sequence for the recombination breakpoint region enabled the designation of a diagnostic technique to detect the presence of TNXB-XA hybrids concurrent with deletions of CYP21B and C4B. Since the major genetic factor(s) for insulin dependent diabetes mellitus (IDDM) reside in the MHC, EDDM patients were investigated for specific patterns of the RCCX modular structures. The frequency of monomodular RCCX structures is found significantly higher in the diabetic population than in the normal. A novel gene, DOM3Z, was discovered in the intergenic region between SKI2W and RPl. The cDNA sequence and the exon-intron structure of D0M 3Z were determined. Immunochemical and transient expression experiments revealed that human Dom3z is a nuclear protein. Z)OMiZ-related genes are present in simple and complex eukaryotes. Located between the complement factor B and C4 genes are the four ubiquitously expressed genes, RD-SKI2W-DOM3Z-RP1. These four genes are configured as two head-to-head orientated gene pairs. The presence of unmethylated CpG sequences at the 5' regulatory regions of each gene pair indicates that they may be housekeeping genes. RD, Ski2w, DomSz, and RP probably have concerted functions related to RNA transcription, translation and turnover. The organization of the mouse MHC complement gene cluster (MCGC) is similar to that of human's. However, the duplication of mouse RCCX modules is markedly different from human as the mouse gene fragments RP2 and TNXA are larger and less conserved, suggesting an independent gene duplication event during evolution. Ill Dedicated to My Parents IV ACKNOWLEGMENTS First and foremost, I am grateful to my adviser. Dr. Chack Yung Yu, for all his understanding and support during my graudate studies; for his patience in correcting my scientific errors; and for his encouragement and enthusiasm, which made my research and eventually, this thesis, possible. I want to thank Dr. George A. Marzluf, a real gentleman, for the chance he provided for me to do my first rotation (during which I ran the very first sequencing gel in my life); for sparing time and offering encouragement; and for being there whenever I need help. I want to express my appreciation to Dr. Gail D. Wenger, for teaching me the FISH technique, the result of which inspired me to discover my gene DOM3Z\ and for bringing the toothbrush back from Baltimore for a "night person"©. Thank-you also goes to Dr. Arthur H. M. Burghes, for showing me how to search the databases. I wish to thank Dr. M. Sue O'Dorisio for being my cheerleader, offering the support and encouragement I needed. It is still fresh in my memory that despite of her busy schedule, she c aie fully reviewed my first first-author paper. I want to thank Dr. William B. Zipf and the nurses in the Department of Endocrinology at Columbus Children's Hospital for recruiting IDDM and CAR patients, which makes the genetic analysis possible. I also appreciate all the patients who volunteered for the study. They are the real heroes whose belief in science will eventually benefit millions of other patients. A special thank-you goes to Professor Manfred P. Dierich at University Innsbruck, Austria. His personal acknowledgment has enabled me to be more confident in myself. His graciousness has set a perfect example for me to be a decent person. I also wish to thank Dr. Joann Moulds from The University of Texas at Houston, not only for her help in setting up C4 allotyping experiments, but also for offering support and being a friend. I want to thank Jan Zinaich, manager of MCDB Program, for keeping me informed of all opportunities, and for ensuring me happiness is the most important part of life (This is more than an appreciation between Gemini's). I am grateful to members of Dr. Yu's laboratory: Brad Baker, Andrew Dan gel, Anna Mendoza, Xiaodong Qu, Kristi Rupert (my English teacher), Shanxiang Zhang, and Bi Zhou. They are the people who have watched me through the ups and downs, shared my happiness and pain. They are the ones who helped me in dealing with various problems. I also thank Monica Summers and Doug Balster for sharing cell lines, and for being friends. Thank you to all my friends, for their love, which holds me through hard times. VI Finally, I thank the Presidential Fellowship from The Ohio State University for the financial support. VITA June 2, 1971 ......................................... Bom - P.R.China 1992 ..................................................... B.S., Biology, Beijing Normal University 1992-1994............................................ Research Associate, Institute of Genetics, Chinese Academy of Sciences, Beijing, P.R.China 1994-1998 ............................................Graduate Teaching and Research Associate, The Ohio State University 1998 ...................................................... M.S., Molecular, Cellular and Developmental Biology The Ohio State University 1998-present .........................................Presidential Research Fellow, The Ohio State University VIII PUBLICATIONS Original Research Articles 1. Qu, X. ,Yang.Z„ Zhang,S., Shen, L., Dangel,A.W., Hughes, J., Redman, K.L., Wu, L.-C. and Yu, C.Y. (1998) The human DEVH-box protein Ski2w from the HLA is localized in nucleoli and ribosomes. Nucleic Acids Res. 26: 4068-4077. 2. Yang Z., Shen L., Wu L.C., Dangel A.W., and Yu C.Y. (1998) Four ubiquitously expressed genes, RD-SKI2W-DOM3Z-RP1, are present between complement component genes factor B and C4 in the class EH region of the HLA. Genomics 53: 338-347. 3. Yang, Z„ Mendoza, A.R., Welch, T.R., Zipf W.B., and Yu, C.Y. (1999) Modular variations of the human MHC class EH genes for serine/threonine kinase RP, complement component C4, steroid 21-hydroxylase CYP21 and tenascin TNX (RCCX): a mechanism for gene deletions and disease associations. J. Biol. Chem. 274: 12147-12156. 4. Yang. Z. and Yu, C.Y. (1999) Organizations and gene duplications of the human and mouse MHC complement gene clusters. Exp. Clin. Immunogenet. (in press). Peer-Reviewed Abstracts 1. Yang. Z., Wenger, G., Labanowska, J., Mendoza, A., and Yu, C.Y. (1996) The putative human helicase gene KIAA0052 that is evolutionally related to the yeast antiviral gene SKI2 and to the human HLA class EH gene SKI2W maps to chromosome 9qter and chromosome 5ql 1.2. Am. J. Hum. Genet. 59: A408. 2. Yang. Z.. Wenger, G., and Yu, C.Y. (1997) Ski2k, a putative RNA helicase involved in RNA transport, is conserved from yeast to human. Am. J. Hum. Genet. 61: A 186. 3. Yang. Z.. Mendoza, A.R., Welch, T.R., Zipf W.B., and Yu, C.Y. (1999) Frequent and concurrent duplication and deletion of four consecutive genes in the human MHC class EH region: a mechanism for disease associations. FASEB J. 13: A1472. IX Electronic publications 1.
Load more

Recommended publications
  • Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
    Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement.
    [Show full text]
  • Datasheet Blank Template
    SAN TA C RUZ BI OTEC HNOL OG Y, INC . DOM3Z (B-12): sc-393141 BACKGROUND APPLICATIONS DOM3Z (dom-3 homolog Z), also known as NG6 or DOM3L, is a 396 amino DOM3Z (B-12) is recommended for detection of DOM3Z of mouse, rat and acid ubiquitously expressed protein belonging to the DOM3Z family. The gene human origin by Western Blotting (starting dilution 1:100, dilution range encoding DOM3Z maps to human chromosome 6 in the major histocompati - 1:100-1:1000), immunoprecipitation [1-2 µg per 100-500 µg of total protein bility complex (MHC) class III region. Chromosome 6 contains 170 million base (1 ml of cell lysate)], immunofluorescence (starting dilution 1:50, dilution pairs and comprises nearly 6% of the human genome. Deletion of a portion range 1:50-1:500), immunohistochemistry (including paraffin-embedded of the q arm of chromosome 6 is associated with early onset intestinal can - sections) (starting dilution 1:50, dilution range 1:50-1:500) and solid phase cer, suggesting the presence of a cancer susceptibility locus. Additionally, ELISA (starting dilution 1:30, dilution range 1:30-1:3000). Porphyria cutanea tarda, Parkinson’s disease and Stickler syndrome are all Suitable for use as control antibody for DOM3Z siRNA (h): sc-95321, DOM3Z associated with genes that map to chromosome 6. siRNA (m): sc-143143, DOM3Z shRNA Plasmid (h): sc-95321-SH, DOM3Z shRNA Plasmid (m): sc-143143-SH, DOM3Z shRNA (h) Lentiviral Particles: REFERENCES sc-95321-V and DOM3Z shRNA (m) Lentiviral Particles: sc-143143-V. 1. Brunner, H.G., et al .
    [Show full text]
  • DNA Methylation Alterations in Blood Cells of Toddlers with Down Syndrome
    G C A T T A C G G C A T genes Article DNA Methylation Alterations in Blood Cells of Toddlers with Down Syndrome Oxana Yu. Naumova 1,2,* , Rebecca Lipschutz 2, Sergey Yu. Rychkov 1, Olga V. Zhukova 1 and Elena L. Grigorenko 2,3,4,* 1 Vavilov Institute of General Genetics RAS, 119991 Moscow, Russia; [email protected] (S.Y.R.); [email protected] (O.V.Z.) 2 Department of Psychology, University of Houston, Houston, TX 77204, USA; [email protected] 3 Department of Psychology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia 4 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA * Correspondence: [email protected] or [email protected] (O.Y.N.); [email protected] (E.L.G.) Abstract: Recent research has provided evidence on genome-wide alterations in DNA methylation patterns due to trisomy 21, which have been detected in various tissues of individuals with Down syndrome (DS) across different developmental stages. Here, we report new data on the systematic genome-wide DNA methylation perturbations in blood cells of individuals with DS from a previously understudied age group—young children. We show that the study findings are highly consistent with those from the prior literature. In addition, utilizing relevant published data from two other developmental stages, neonatal and adult, we track a quasi-longitudinal trend in the DS-associated DNA methylation patterns as a systematic epigenomic destabilization with age. Citation: Naumova, O.Y.; Lipschutz, R.; Rychkov, S.Y.; Keywords: Down syndrome; infants and toddlers; trisomy 21; DNA methylation; Illumina 450K Zhukova, O.V.; Grigorenko, E.L.
    [Show full text]
  • UNIVERSITY of CALIFORNIA Los Angeles the Subproteome Of
    UNIVERSITY OF CALIFORNIA Los Angeles The subproteome of mitoBKCa channels from cardiomyocytes reveals novel insights into its mitochondrial import mechanism and function A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Molecular and Medical Pharmacology by Jin Zhang 2016 © Copyright by Jin Zhang 2016 ABSTRACT OF DISSERTATION The subproteome of mitoBKCa channels from cardiomyocytes reveals novel insights into its mitochondrial import mechanism and function by Jin Zhang Doctor of Philosophy in Molecular and Medical Pharmacology University of California, Los Angeles, 2016 Professor Ligia G Toro De Stefani, CO-Chair Professor Riccardo Olcese, CO-Chair BKCa channels are widely expressed ion channels and characterized by their large conductance to potassium and sensitivity to calcium and voltage. It is typically observed at the plasma membrane in the majority of cell types, with adult cardiomyocytes being an exception. Previously, both electrophysiological and immunological studies have detected BKCa channels in + cardiomyocytes mitoplasts, confirming the presence of this K channel (mitoBKCa); however, its physiological functions have not yet fully understood. This work is the first one to examine the interactome of mitoBKCa channels in adult heart (isolated cardiomyocytes and whole ventricle). We used a directed proteomic approach aided by co-immunoprecipitation with BKCa antibodies and pull-down with recombinant DEC sequences. ii As a result, we identified an extensive network of the mitoBKCa, channel and overall, a total of 1079 different proteins were identified as partners of the BKCa channel in cardiomyocytes and left ventricle, including 151 mitochondrial proteins. Two putative protein partners were selected to validate and further examine the associations with BKCa channels: i) the Tom22 from the mitochondrial import system, and ii) the adenine nucleotide translocator (ANT), which is linked to oxidative phosphorylation and the regulation of mPTP.
    [Show full text]
  • Supporting Information
    Supporting Information Poulogiannis et al. 10.1073/pnas.1009941107 SI Materials and Methods Loss of Heterozygosity (LOH) Analysis of PARK2. Seven microsatellite Bioinformatic Analysis of Genome and Transcriptome Data. The markers (D6S1550, D6S253, D6S305, D6S955, D6S980, D6S1599, aCGH package in R was used to identify significant DNA copy and D6S396) were amplified for LOH analysis within the PARK2 number (DCN) changes in our collection of 100 sporadic CRCs locus using primers that were previously described (8). (1) (Gene Expression Omnibus, accession no. GSE12520). The MSP of the PARK2 Promoter. CpG sites within the PARK2 promoter aCGH analysis of cell lines and liver metastases was derived region were detected using the Methprimer software (http://www. from published data (2, 3). Chromosome 6 tiling-path array- urogene.org/methprimer/index.html). Methylation-specificand CGH was used to identify the smallest and most frequently al- control primers were designed using the Primo MSP software tered regions of DNA copy number change on chromosome 6. (http://www.changbioscience.com/primo/primom.html); bisulfite An integrative approach was used to correlate expression pro- modification of genomic DNA was performed as described pre- files with genomic copy number data from a SNP array from the viously (9). All tumor DNA samples from primary CRC tumors same tumors (n = 48) (4) (GSE16125), using Pearson’s corre- (n = 100) and CRC lines (n = 5), as well as those from the leukemia lation coefficient analysis to identify the relationships between cell lines KG-1a (acute myeloid leukemia, AML), U937 (acute DNA copy number changes and gene expression of those genes lymphoblastic leukemia, ALL), and Raji (Burkitt lymphoma, BL) SssI located within the small frequently altered regions of DCN were screened as part of this analysis.
    [Show full text]
  • DOM3Z (DXO) (NM 005510) Human Recombinant Protein Product Data
    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TP305657 DOM3Z (DXO) (NM_005510) Human Recombinant Protein Product data: Product Type: Recombinant Proteins Description: Recombinant protein of human dom-3 homolog Z (C. elegans) (DOM3Z) Species: Human Expression Host: HEK293T Tag: C-Myc/DDK Predicted MW: 44.7 kDa Concentration: >50 ug/mL as determined by microplate BCA method Purity: > 80% as determined by SDS-PAGE and Coomassie blue staining Buffer: 25 mM Tris.HCl, pH 7.3, 100 mM glycine, 10% glycerol Preparation: Recombinant protein was captured through anti-DDK affinity column followed by conventional chromatography steps. Storage: Store at -80°C. Stability: Stable for 12 months from the date of receipt of the product under proper storage and handling conditions. Avoid repeated freeze-thaw cycles. RefSeq: NP_005501 Locus ID: 1797 UniProt ID: O77932, A0A024RCW8 RefSeq Size: 1590 Cytogenetics: 6p21.33 RefSeq ORF: 1188 Synonyms: DOM3L; DOM3Z; NG6; RAI1 Summary: This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. The function of its protein product is unknown, but its ubiquitous expression and conservation in both simple and complex eukaryotes suggests that this may be a housekeeping gene. [provided by RefSeq, Jul 2008] This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 DOM3Z (DXO) (NM_005510) Human Recombinant Protein – TP305657 Product images: Coomassie blue staining of purified DXO protein (Cat# TP305657).
    [Show full text]
  • Predict AID Targeting in Non-Ig Genes Multiple Transcription Factor
    Downloaded from http://www.jimmunol.org/ by guest on September 26, 2021 is online at: average * The Journal of Immunology published online 20 March 2013 from submission to initial decision 4 weeks from acceptance to publication Multiple Transcription Factor Binding Sites Predict AID Targeting in Non-Ig Genes Jamie L. Duke, Man Liu, Gur Yaari, Ashraf M. Khalil, Mary M. Tomayko, Mark J. Shlomchik, David G. Schatz and Steven H. Kleinstein J Immunol http://www.jimmunol.org/content/early/2013/03/20/jimmun ol.1202547 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/2013/03/20/jimmunol.120254 7.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 26, 2021. Published March 20, 2013, doi:10.4049/jimmunol.1202547 The Journal of Immunology Multiple Transcription Factor Binding Sites Predict AID Targeting in Non-Ig Genes Jamie L. Duke,* Man Liu,†,1 Gur Yaari,‡ Ashraf M. Khalil,x Mary M. Tomayko,{ Mark J. Shlomchik,†,x David G.
    [Show full text]
  • A Comprehensive Reference Genome Representation And
    UNIVERSITY OF CALIFORNIA SANTA CRUZ ADDRESSING THE OMICS DATA EXPLOSION: A COMPREHENSIVE REFERENCE GENOME REPRESENTATION AND THE DEMOCRATIZATION OF COMPARATIVE GENOMICS AND IMMUNOGENOMICS A dissertation submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in BIOMOLECULAR ENGINEERING AND BIOINFORMATICS by Ngan K. Nguyen June 2014 The Dissertation of Ngan K. Nguyen is approved: Professor David Haussler, Chair Professor Joshua Stuart Dietlind L. Gerloff, PhD Professor Martha Zuniga Dean Tyrus Miller Vice Provost and Dean of Graduate Studies Copyright c by Ngan K. Nguyen 2014 Table of Contents List of Figures vi List of Tables x Abstract xii Dedication xiv Acknowledgments xv 1 Introduction 1 1.1 Reexamine the Reference Genome . .2 1.2 The Decentralization of Comparative Genomic Resources . .3 1.2.1 The Comparative Assembly Hub (CAH) Pipeline . .4 1.2.2 The Adaptive Immunosequencing Toolkit (aimseqtk) Pipeline . .5 2 Building a Pan-genome Reference for a Population 6 2.1 Overview . .7 2.2 Introduction . .8 2.2.1 Reference Genome, Utilities and Limitations . .8 2.2.2 The Human Major Histocompatability Complex Reference . 11 2.2.3 Background of the Pan-genome Reference Problem . 12 2.3 Results . 15 2.3.1 The Pan-genome Reference Problem . 15 2.3.2 NP-hardness of the Pan-genome Reference Problem . 21 2.3.3 Algorithms for the Pan-genome Reference Problem . 21 2.3.4 Simulation Experiments . 24 2.3.5 Creating a Pan-genome Reference for the Human Major Histo- compatibility Complex (MHC) . 29 2.4 Discussion . 57 2.5 Materials and Methods .
    [Show full text]
  • For Personal Use. Only Reproduce with Permission from the Lancet Publishing Group
    Acc Number Symbol Gene name Gene ontology function U50648 PRKR protein kinase, interferon-inducible double stranded RNA dependent U37055 MST1 macrophage stimulating 1 (hepatocyte growth factor-like) K03183 CGB7 chorionic gonadotropin, beta polypeptide 7 J03069 MYCL2 v-myc myelocytomatosis viral oncogene homolog 2 (avian) M36711 TFAP2A transcription factor AP-2 alpha (activating enhancer binding Signal transduction, developmental processes, protein 2 alpha) transcription regulation from Pol II promoter, oncogenesis, ectoderm development X69699 PAX8 paired box gene 8 histogenesis and organogenesis, embryogenesis and morphogenesis L38929 PTPRD protein tyrosine phosphatase, receptor type, D protein dephosphorylation, transmembrane receptor protein tyrosine phosphatase signalling, phosphate metabolism L76568 ERCC4 excision repair cross-complementing rodent repair deficiency, complementation group 4 U11870 IL8RA interleukin 8 receptor, alpha M36067 LIG1 ligase I, DNA, ATP-dependent DNA repair, embryogenesis and morphogenesis, DNA metabolism D16105 LTK leukocyte tyrosine kinase Signal transduction, protein phosphorylation U12779 MAPKAPK2 mitogen-activated protein kinase-activated protein kinase 2 protein phosphorylation, MAPKKK cascade L34059 CDH4 cadherin 4, type 1, R-cadherin (retinal) cell adhesion U22028 CYP2A13 cytochrome P450, subfamily IIA (phenobarbital-inducible), complementation group 4polypeptide 13 U27193 DUSP8 dual specificity phosphatase 8 protein dephosphorylation, inactiviation of MAPK L24559 POLA2 polymerase (DNA-directed), alpha
    [Show full text]
  • Evaluation of Proteomic and Transcriptomic Biomarker Discovery
    EVALUATION OF PROTEOMIC AND TRANSCRIPTOMIC BIOMARKER DISCOVERY TECHNOLOGIES IN OVARIAN CANCER. CLARE RITA ELIZABETH COVENEY A thesis submitted in partial fulfilment of the requirements of the Nottingham Trent University for the degree of Doctor of Philosophy October 2016 Copyright Statement “This work is the intellectual property of the author. You may copy up to 5% of this work for private study, or personal, non-commercial research. Any re-use of the information contained within this document should be fully referenced, quoting the author, title, university, degree level and pagination. Queries or requests for any other use, or if a more substantial copy is required, should be directed in the owner(s) of the Intellectual Property Rights.” Acknowledgments This work was funded by The John Lucille van Geest Foundation and undertaken at the John van Geest Cancer Research Centre, at Nottingham Trent University. I would like to extend my foremost gratitude to my supervisory team Professor Graham Ball, Dr David Boocock, Professor Robert Rees for their guidance, knowledge and advice throughout the course of this project. I would also like to show my appreciation of the hard work of Mr Ian Scott, Professor Bob Shaw and Dr Matharoo-Ball, Dr Suman Malhi and later Mr Viren Asher who alongside colleagues at The Nottingham University Medical School and Derby City General Hospital initiated the ovarian serum collection project that lead to this work. I also would like to acknowledge the work of Dr Suha Deen at Queen’s Medical Centre and Professor Andrew Green and Christopher Nolan of the Cancer & Stem Cells Division of the School of Medicine, University of Nottingham for support with the immunohistochemistry.
    [Show full text]
  • Biomarkers for Lupus
    (19) TZZ ¥ _T (11) EP 2 375 252 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 12.10.2011 Bulletin 2011/41 G01N 33/564 (2006.01) (21) Application number: 11158716.8 (22) Date of filing: 11.06.2009 (84) Designated Contracting States: • Fallon, Rachel, Alison AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Maidenhead, Berkshire SL6 7RJ (GB) HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL • Joyce, Sarah, Paula PT RO SE SI SK TR Maidenhead, Berkshire SL6 7RJ (GB) • Koopman, Jens-Oliver (30) Priority: 11.06.2008 GB 0810709 Maidenhead, Berkshire SL6 7RJ (GB) • McAndrew, Michael, Bernard (62) Document number(s) of the earlier application(s) in Maidenhead, Berkshire SL6 7RJ (GB) accordance with Art. 76 EPC: • Workman,, Nicholas, Ian 09761971.2 / 2 300 826 Maidenhead, Berkshire SL6 7RJ (GB) (71) Applicant: SENSE PROTEOMIC LIMITED (74) Representative: Marshall, Cameron John Yarnton Carpmaels & Ransford Oxford One Southampton Row Oxfordshire OX5 1PF (GB) London WC1B 5HA (GB) (72) Inventors: Remarks: • Ebner, Martin Johannes This application was filed on 17-03-2011 as a Maidenhead, Berkshire SL6 7RJ (GB) divisional application to the application mentioned • Wheeler, Colin, Henry under INID code 62. Maiadenhead, Berkshire SL6 7RJ (GB) (54) Biomarkers for lupus (57) The present invention provides biomarkers val- the progression or regression of lupus, or monitoring the uable in diagnosing or detecting a susceptibility to lupus. progression to a flare of the disease or transition from a The present invention also provides panels of biomarkers flare into remission or monitoring the efficacy of a thera- valuable in diagnosing or detecting a susceptibility to lu- peutic agent to lupus.
    [Show full text]
  • Sequence Tags for Camelus Dromedarius
    Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus dromedarius Abdulaziz M. Al-Swailem1, Maher M. Shehata1, Faisel M. Abu-Duhier1, Essam J. Al-Yamani1, Khalid A. Al-Busadah2, Mohammed S. Al-Arawi1, Ali Y. Al-Khider1, Abdullah N. Al-Muhaimeed1, Fahad H. Al-Qahtani1, Manee M. Manee1, Badr M. Al-Shomrani1, Saad M. Al-Qhtani1, Amer S. Al-Harthi1, Kadir C. Akdemir3, Mehmet S. Inan1{, Hasan H. Otu1,3* 1 Biotechnology Research Center, Natural Resources and Environment Research Institute, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia, 2 Faculty of Veterinary Medicine and Animal Resources, King Faisal University, Al-Hassa, Saudi Arabia, 3 Department of Medicine, BIDMC Genomics Center, Harvard Medical School, Boston, Massachusetts, United States of America Abstract Despite its economical, cultural, and biological importance, there has not been a large scale sequencing project to date for Camelus dromedarius. With the goal of sequencing complete DNA of the organism, we first established and sequenced camel EST libraries, generating 70,272 reads. Following trimming, chimera check, repeat masking, cluster and assembly, we obtained 23,602 putative gene sequences, out of which over 4,500 potentially novel or fast evolving gene sequences do not carry any homology to other available genomes. Functional annotation of sequences with similarities in nucleotide and protein databases has been obtained using Gene Ontology classification. Comparison to available full length cDNA sequences and Open Reading Frame (ORF) analysis of camel sequences that exhibit homology to known genes show more than 80% of the contigs with an ORF.300 bp and ,40% hits extending to the start codons of full length cDNAs suggesting successful characterization of camel genes.
    [Show full text]