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Contig Protein Description Symbol Anterior Posterior Ratio
Table S2. List of proteins detected in anterior and posterior intestine pooled samples. Data on protein expression are mean ± SEM of 4 pools fed the experimental diets. The number of the contig in the Sea Bream Database (http://nutrigroup-iats.org/seabreamdb) is indicated. Contig Protein Description Symbol Anterior Posterior Ratio Ant/Pos C2_6629 1,4-alpha-glucan-branching enzyme GBE1 0.88±0.1 0.91±0.03 0.98 C2_4764 116 kDa U5 small nuclear ribonucleoprotein component EFTUD2 0.74±0.09 0.71±0.05 1.03 C2_299 14-3-3 protein beta/alpha-1 YWHAB 1.45±0.23 2.18±0.09 0.67 C2_268 14-3-3 protein epsilon YWHAE 1.28±0.2 2.01±0.13 0.63 C2_2474 14-3-3 protein gamma-1 YWHAG 1.8±0.41 2.72±0.09 0.66 C2_1017 14-3-3 protein zeta YWHAZ 1.33±0.14 4.41±0.38 0.30 C2_34474 14-3-3-like protein 2 YWHAQ 1.3±0.11 1.85±0.13 0.70 C2_4902 17-beta-hydroxysteroid dehydrogenase 14 HSD17B14 0.93±0.05 2.33±0.09 0.40 C2_3100 1-acylglycerol-3-phosphate O-acyltransferase ABHD5 ABHD5 0.85±0.07 0.78±0.13 1.10 C2_15440 1-phosphatidylinositol phosphodiesterase PLCD1 0.65±0.12 0.4±0.06 1.65 C2_12986 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta-1 PLCD1 0.76±0.08 1.15±0.16 0.66 C2_4412 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-2 PLCG2 1.13±0.08 2.08±0.27 0.54 C2_3170 2,4-dienoyl-CoA reductase, mitochondrial DECR1 1.16±0.1 0.83±0.03 1.39 C2_1520 26S protease regulatory subunit 10B PSMC6 1.37±0.21 1.43±0.04 0.96 C2_4264 26S protease regulatory subunit 4 PSMC1 1.2±0.2 1.78±0.08 0.68 C2_1666 26S protease regulatory subunit 6A PSMC3 1.44±0.24 1.61±0.08 -
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. -
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. -
UGT1A7 and UGT1A9 Polymorphisms Predict Response and Toxicity in Colorectal Cancer Patients Treated with Capecitabine/Irinotecan
1226 Vol. 11, 1226–1236, February 1, 2005 Clinical Cancer Research UGT1A7 and UGT1A9 Polymorphisms Predict Response and Toxicity in Colorectal Cancer Patients Treated with Capecitabine/Irinotecan Leslie E. Carlini,1 Neal J. Meropol,1 John Bever,2 irinotecan. Specifically, patients with genotypes conferring Michael L. Andria,2 Todd Hill,2 Philip Gold,3 low UGT1A7 activity and/or the UGT1A9 (dT)9/9 genotype may be particularly likely to exhibit greater antitumor Andre Rogatko,1 Hao Wang,1 and response with little toxicity. Rebecca L. Blanchard1 1 2 Fox Chase Cancer Center, Philadelphia, Pennsylvania; Roche INTRODUCTION Laboratories, Inc., Nutley, New Jersey; and 3Swedish Cancer Institute, Seattle, Washington Colorectal cancer (CRC) is the third most common cancer in both men and women and the third most prevalent cause of cancer-related death (1). A common approach to the systemic ABSTRACT management of metastatic colorectal cancer is a combination Purpose: Capecitabine and irinotecan are commonly of fluoropyrimidine (e.g., 5-fluorouracil or capecitabine) used in the treatment of metastatic colorectal cancer (CRC). and irinotecan (reviewed in ref. 2). Fluoropyrimidines act We hypothesized that germline polymorphisms within genes primarily through the inhibition of thymidylate synthase (TS), related to drug target (thymidylate synthase) or metabolizing resulting in impaired DNA synthesis and cell death. Irinotecan is enzymes (UDP-glucuronosyltransferase, UGT) would impact a camptothecin compound that inhibits DNA topoisomerase I, response and toxicity to the combination of capecitabine plus resulting in an accumulation of DNA damage and cell death. irinotecan (CPT-11). Irinotecan is a prodrug that undergoes conversion by liver Experimental Design: Sixty-seven patients with measur- carboxylesterases to form the active compound SN-38, 7-ethyl- able CRC were treated with irinotecan i.v. -
Toxicogenomic Approach to Impact Assessment of Whole Wastewater Effluents and Development of Effluent- Title Responsive Biomarker
Toxicogenomic Approach to Impact Assessment of Whole Wastewater Effluents and Development of Effluent- Title Responsive Biomarker Author(s) 山村, 宏江 Citation 北海道大学. 博士(工学) 甲第11137号 Issue Date 2013-09-25 DOI 10.14943/doctoral.k11137 Doc URL http://hdl.handle.net/2115/77180 Type theses (doctoral) File Information Hiroe_Yamamura.pdf Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP Doctoral Thesis Toxicogenomic Approach to Impact Assessment of Whole Wastewater Effluents and Development of Effluent-Responsive Biomarker Hiroe Hara-Yamamura Acknowledgement My doctoral research works presented here cannot be completed without a numerous number of tangible and intangible supports from my peers, my supervisor, instructors, friends, and family. I would first express my deepest gratitude to Prof. Satoshi OKABE for his technical advices and crisp ideas which often came to break the deadlock of my research progress, and for continued provision of another chance to me, even in the least fruitful season. Indeed, my three years in Prof. OKABE’s lab was “luxuri- ous” time in my life with a lot of supports, encouragements, and chances. In addition, I appreciate both Prof. Daisuke SANO and Dr. Satoshi ISHII for offering their insights on my experimental design and data analysis as well as giving me words of encouragements from time to time. Also, thank you to Prof. Takashi KUSUI from Toyama Prefectural University for his assistance to bioassay techniques and valuable discussion dur- ing my 1st year and 2nd year evaluation presentations. Furthermore, I would like to express my gratitude to specific efforts kindly provide by: Mr. Kenzo Kudo, Prof. -
Novel Copy-Number Variations in Pharmacogenes Contribute to Interindividual Differences in Drug Pharmacokinetics
ORIGINAL RESEARCH ARTICLE © American College of Medical Genetics and Genomics Novel copy-number variations in pharmacogenes contribute to interindividual differences in drug pharmacokinetics María Santos, MSc1, Mikko Niemi, PhD2, Masahiro Hiratsuka, PhD3, Masaki Kumondai, BSc3, Magnus Ingelman-Sundberg, PhD4, Volker M. Lauschke, PhD4 and Cristina Rodríguez-Antona, PhD1,5 Purpose: Variability in pharmacokinetics and drug response is of the genes studied. We experimentally confirmed novel deletions shaped by single-nucleotide variants (SNVs) as well as copy- in CYP2C19, CYP4F2, and SLCO1B3 by Sanger sequencing and number variants (CNVs) in genes with importance for drug validated their allelic frequencies in selected populations. absorption, distribution, metabolism, and excretion (ADME). Conclusion: CNVs are an additional source of pharmacogenetic While SNVs have been extensively studied, a systematic assessment variability with important implications for drug response and of the CNV landscape in ADME genes is lacking. personalized therapy. This, together with the important contribu- Methods: We integrated data from 2,504 whole genomes from the tion of rare alleles to the variability of pharmacogenes, emphasizes 1000 Genomes Project and 59,898 exomes from the Exome the necessity of comprehensive next-generation sequencing–based Aggregation Consortium to identify CNVs in 208 relevant genotype identification for an accurate prediction of the genetic pharmacogenes. variability of drug pharmacokinetics. Results: We describe novel exonic deletions -
Endogenous Protein Interactome of Human UDP-Glucuronosyltransferases Exposed by Untargeted Proteomics
ORIGINAL RESEARCH published: 03 February 2017 doi: 10.3389/fphar.2017.00023 Endogenous Protein Interactome of Human UDP-Glucuronosyltransferases Exposed by Untargeted Proteomics Michèle Rouleau, Yannick Audet-Delage, Sylvie Desjardins, Mélanie Rouleau, Camille Girard-Bock and Chantal Guillemette * Pharmacogenomics Laboratory, Canada Research Chair in Pharmacogenomics, Faculty of Pharmacy, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec, QC, Canada The conjugative metabolism mediated by UDP-glucuronosyltransferase enzymes (UGTs) significantly influences the bioavailability and biological responses of endogenous molecule substrates and xenobiotics including drugs. UGTs participate in the regulation of cellular homeostasis by limiting stress induced by toxic molecules, and by Edited by: controlling hormonal signaling networks. Glucuronidation is highly regulated at genomic, Yuji Ishii, transcriptional, post-transcriptional and post-translational levels. However, the UGT Kyushu University, Japan protein interaction network, which is likely to influence glucuronidation, has received Reviewed by: little attention. We investigated the endogenous protein interactome of human UGT1A Ben Lewis, Flinders University, Australia enzymes in main drug metabolizing non-malignant tissues where UGT expression is Shinichi Ikushiro, most prevalent, using an unbiased proteomics approach. Mass spectrometry analysis Toyama Prefectural University, Japan of affinity-purified UGT1A enzymes and associated protein complexes in liver, -
Flavolignans from Silymarin As Nrf2 Bioactivators and Their Therapeutic Applications
biomedicines Review Flavolignans from Silymarin as Nrf2 Bioactivators and Their Therapeutic Applications 1, 2, 3 Nancy Vargas-Mendoza y , Ángel Morales-González y , Mauricio Morales-Martínez , Marvin A. Soriano-Ursúa 4, Luis Delgado-Olivares 5 , Eli Mireya Sandoval-Gallegos 5, Eduardo Madrigal-Bujaidar 6, Isela Álvarez-González 6 , Eduardo Madrigal-Santillán 1,* and José A. Morales-Gonzalez 1,* 1 Laboratorio de Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México Escuela Superior de Medicina, Plan de San Luis y Díaz Mirón, Col. Casco de Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico; [email protected] 2 Escuela Superior de Cómputo, Instituto Politécnico Nacional, Av. Juan de Dios Bátiz s/n esquina Miguel Othón de Mendizabal, Unidad Profesional Adolfo López Mateos, Mexico City CP 07738, Mexico; [email protected] 3 Licenciatura en Nutrición, Universidad Intercontinental, Insurgentes Sur 4303, Santa Úrsula Xitla, Alcaldía Tlalpan, Mexico City CP 14420, Mexico; [email protected] 4 Academia de Fisiología Humana, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Col. Casco de Santo Tomás, Del. Miguel Hidalgo, Mexico City 11340, Mexico; [email protected] 5 Centro de Investigación Interdisciplinario, Área Académica de Nutrición, Instituto de Ciencias de la Salud. Universidad Autónoma del Estado de Hidalgo. Circuito Actopan-Tilcuauttla, s/n, Ex hacienda La Concepción, San Agustín Tlaxiaca, Hidalgo CP 42160, Mexico; [email protected] (L.D.-O.); [email protected] (E.M.S.-G.) 6 Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, “Unidad Profesional A. López Mateos”. Av. Wilfrido Massieu. Col., Zacatenco, Mexico City 07738, Mexico; [email protected] (E.M.-B.); [email protected] (I.Á.-G.) * Correspondence: [email protected] (E.M.-S.); [email protected] (J.A.M.-G.); Tel.: +52-55-5729-6300 (E.M.-S. -
Nº Ref Uniprot Proteína Péptidos Identificados Por MS/MS 1 P01024
Document downloaded from http://www.elsevier.es, day 26/09/2021. This copy is for personal use. Any transmission of this document by any media or format is strictly prohibited. Nº Ref Uniprot Proteína Péptidos identificados 1 P01024 CO3_HUMAN Complement C3 OS=Homo sapiens GN=C3 PE=1 SV=2 por 162MS/MS 2 P02751 FINC_HUMAN Fibronectin OS=Homo sapiens GN=FN1 PE=1 SV=4 131 3 P01023 A2MG_HUMAN Alpha-2-macroglobulin OS=Homo sapiens GN=A2M PE=1 SV=3 128 4 P0C0L4 CO4A_HUMAN Complement C4-A OS=Homo sapiens GN=C4A PE=1 SV=1 95 5 P04275 VWF_HUMAN von Willebrand factor OS=Homo sapiens GN=VWF PE=1 SV=4 81 6 P02675 FIBB_HUMAN Fibrinogen beta chain OS=Homo sapiens GN=FGB PE=1 SV=2 78 7 P01031 CO5_HUMAN Complement C5 OS=Homo sapiens GN=C5 PE=1 SV=4 66 8 P02768 ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2 66 9 P00450 CERU_HUMAN Ceruloplasmin OS=Homo sapiens GN=CP PE=1 SV=1 64 10 P02671 FIBA_HUMAN Fibrinogen alpha chain OS=Homo sapiens GN=FGA PE=1 SV=2 58 11 P08603 CFAH_HUMAN Complement factor H OS=Homo sapiens GN=CFH PE=1 SV=4 56 12 P02787 TRFE_HUMAN Serotransferrin OS=Homo sapiens GN=TF PE=1 SV=3 54 13 P00747 PLMN_HUMAN Plasminogen OS=Homo sapiens GN=PLG PE=1 SV=2 48 14 P02679 FIBG_HUMAN Fibrinogen gamma chain OS=Homo sapiens GN=FGG PE=1 SV=3 47 15 P01871 IGHM_HUMAN Ig mu chain C region OS=Homo sapiens GN=IGHM PE=1 SV=3 41 16 P04003 C4BPA_HUMAN C4b-binding protein alpha chain OS=Homo sapiens GN=C4BPA PE=1 SV=2 37 17 Q9Y6R7 FCGBP_HUMAN IgGFc-binding protein OS=Homo sapiens GN=FCGBP PE=1 SV=3 30 18 O43866 CD5L_HUMAN CD5 antigen-like OS=Homo -
Linkage Disequilibrium of UGT1A1*6 and UGT1A1*28 in Relation to UGT1A6 and UGT1A7 Polymorphisms
801-806 11/9/06 12:25 Page 801 ONCOLOGY REPORTS 16: 801-806, 2006 801 Linkage disequilibrium of UGT1A1*6 and UGT1A1*28 in relation to UGT1A6 and UGT1A7 polymorphisms NAOHITO URAWA, YOSHINAO KOBAYASHI, JUN ARAKI, RYOSUKE SUGIMOTO, MOTOH IWASA, MASAHIKO KAITO and YUKIHKO ADACHI Division of Clinical Medicine and Biomedical Sciences, Department of Gastroenterology and Hepatology, Institute of Medical Science, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie 514-8507, Japan Received April 17, 2006; Accepted May 17, 2006 Abstract. UDP-glucuronosyltransferase (UGT) enzymes are first time that the LD of UGT1A1*6 in relation to UGT1A6 responsible for the glucuronidation and detoxification of many and 1A7 polymorphisms is far stronger than UGT1A1*28. endogenous or exogenous xenobiotics. Gilbert's syndrome The UGT1A1*6 allele appears to be independent of the (GS) and Crigler Najjar syndrome type 2 (CNS-II) are UGT1A1*28 allele. Although patients with GS and CNS-II characterized by unconjugated hyperbilirubinemia due to are believed to have good prognosis, a subgroup of GS or reduced enzymatic activity of UGT1A1. Recent studies have CNS-II patients with the UGT1A1*6 polymorphism might be demonstrated the frequent co-existence of UGT1A1*28 (-53 at risk of abnormal drug metabolism and of developing [TA]6>7) with other polymorphisms of UGT1A6 and malignant disease. UGT1A7. This finding suggests the occurrence of linkage disequilibrium (LD) among UGT1A1, UGT1A6 and UGT1A7 Introduction polymorphisms. UGT1A1*6 (211G>A, G71R) and UGT1A1*28 are common in Asian populations. In the present study, we UDP-glucuronosyltransferase (UGT) enzymes are responsible investigated the LD of UGT1A1*6 and UGT1A1*28 in for the glucuronidation and detoxification of many xenobiotics relation to UGT1A6 and UGT1A7 polymorphisms. -
Strand Breaks for P53 Exon 6 and 8 Among Different Time Course of Folate Depletion Or Repletion in the Rectosigmoid Mucosa
SUPPLEMENTAL FIGURE COLON p53 EXONIC STRAND BREAKS DURING FOLATE DEPLETION-REPLETION INTERVENTION Supplemental Figure Legend Strand breaks for p53 exon 6 and 8 among different time course of folate depletion or repletion in the rectosigmoid mucosa. The input of DNA was controlled by GAPDH. The data is shown as ΔCt after normalized to GAPDH. The higher ΔCt the more strand breaks. The P value is shown in the figure. SUPPLEMENT S1 Genes that were significantly UPREGULATED after folate intervention (by unadjusted paired t-test), list is sorted by P value Gene Symbol Nucleotide P VALUE Description OLFM4 NM_006418 0.0000 Homo sapiens differentially expressed in hematopoietic lineages (GW112) mRNA. FMR1NB NM_152578 0.0000 Homo sapiens hypothetical protein FLJ25736 (FLJ25736) mRNA. IFI6 NM_002038 0.0001 Homo sapiens interferon alpha-inducible protein (clone IFI-6-16) (G1P3) transcript variant 1 mRNA. Homo sapiens UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15 GALNTL5 NM_145292 0.0001 (GALNT15) mRNA. STIM2 NM_020860 0.0001 Homo sapiens stromal interaction molecule 2 (STIM2) mRNA. ZNF645 NM_152577 0.0002 Homo sapiens hypothetical protein FLJ25735 (FLJ25735) mRNA. ATP12A NM_001676 0.0002 Homo sapiens ATPase H+/K+ transporting nongastric alpha polypeptide (ATP12A) mRNA. U1SNRNPBP NM_007020 0.0003 Homo sapiens U1-snRNP binding protein homolog (U1SNRNPBP) transcript variant 1 mRNA. RNF125 NM_017831 0.0004 Homo sapiens ring finger protein 125 (RNF125) mRNA. FMNL1 NM_005892 0.0004 Homo sapiens formin-like (FMNL) mRNA. ISG15 NM_005101 0.0005 Homo sapiens interferon alpha-inducible protein (clone IFI-15K) (G1P2) mRNA. SLC6A14 NM_007231 0.0005 Homo sapiens solute carrier family 6 (neurotransmitter transporter) member 14 (SLC6A14) mRNA. -
IRIS Toxicological Review of Benzo[A]Pyrene
EPA/635/R-10/006 DRAFT - DO NOT CITE OR QUOTE www.epa.gov/iris TOXICOLOGICAL REVIEW OF BENZO[a]PYRENE (CAS No. 50-32-8) In Support of Summary Information on the Integrated Risk Information System (IRIS) June 2011 NOTICE This document is an Interagency Science Consultation draft. This information is distributed solely for the purpose of pre-dissemination peer review under applicable information quality guidelines. It has not been formally disseminated by EPA. It does not represent and should not be construed to represent any Agency determination or policy. It is being circulated for review of its technical accuracy and science policy implications. U.S. Environmental Protection Agency Washington, DC DISCLAIMER This document is a preliminary draft for review purposes only. This information is distributed solely for the purpose of pre-dissemination peer review under applicable information quality guidelines. It has not been formally disseminated by EPA. It does not represent and should not be construed to represent any Agency determination or policy. Mention of trade names or commercial products does not constitute endorsement or recommendation for use. ii DRAFT - DO NOT CITE OR QUOTE 1 CONTENTS TOXICOLOGICAL REVIEW OF BENZO[a]PYRENE (CAS No. 50-32-8) 2 3 4 LIST OF TABLES ....................................................................................................................... VII 5 LIST OF FIGURES ....................................................................................................................... X 6 LIST