Zinc As a Gatekeeper of Immune Function
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The Significance of the Evolutionary Relationship of Prion Proteins and ZIP Transporters in Health and Disease
The Significance of the Evolutionary Relationship of Prion Proteins and ZIP Transporters in Health and Disease by Sepehr Ehsani A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Laboratory Medicine and Pathobiology University of Toronto © Copyright by Sepehr Ehsani 2012 The Significance of the Evolutionary Relationship of Prion Proteins and ZIP Transporters in Health and Disease Sepehr Ehsani Doctor of Philosophy Department of Laboratory Medicine and Pathobiology University of Toronto 2012 Abstract The cellular prion protein (PrPC) is unique amongst mammalian proteins in that it not only has the capacity to aggregate (in the form of scrapie PrP; PrPSc) and cause neuronal degeneration, but can also act as an independent vector for the transmission of disease from one individual to another of the same or, in some instances, other species. Since the discovery of PrPC nearly thirty years ago, two salient questions have remained largely unanswered, namely, (i) what is the normal function of the cellular protein in the central nervous system, and (ii) what is/are the factor(s) involved in the misfolding of PrPC into PrPSc? To shed light on aspects of these questions, we undertook a discovery-based interactome investigation of PrPC in mouse neuroblastoma cells (Chapter 2), and among the candidate interactors, identified two members of the ZIP family of zinc transporters (ZIP6 and ZIP10) as possessing a PrP-like domain. Detailed analyses revealed that the LIV-1 subfamily of ZIP transporters (to which ZIPs 6 and 10 belong) are in fact the evolutionary ancestors of prions (Chapter 3). -
Loss of the Dermis Zinc Transporter ZIP13 Promotes the Mildness Of
www.nature.com/scientificreports OPEN Loss of the dermis zinc transporter ZIP13 promotes the mildness of fbrosarcoma by inhibiting autophagy Mi-Gi Lee1,8, Min-Ah Choi2,8, Sehyun Chae3,8, Mi-Ae Kang4, Hantae Jo4, Jin-myoung Baek4, Kyu-Ree In4, Hyein Park4, Hyojin Heo4, Dongmin Jang5, Sofa Brito4, Sung Tae Kim6, Dae-Ok Kim 1,7, Jong-Soo Lee4, Jae-Ryong Kim2* & Bum-Ho Bin 4* Fibrosarcoma is a skin tumor that is frequently observed in humans, dogs, and cats. Despite unsightly appearance, studies on fbrosarcoma have not signifcantly progressed, due to a relatively mild tumor severity and a lower incidence than that of other epithelial tumors. Here, we focused on the role of a recently-found dermis zinc transporter, ZIP13, in fbrosarcoma progression. We generated two transformed cell lines from wild-type and ZIP13-KO mice-derived dermal fbroblasts by stably expressing the Simian Virus (SV) 40-T antigen. The ZIP13−/− cell line exhibited an impairment in autophagy, followed by hypersensitivity to nutrient defciency. The autophagy impairment in the ZIP13−/− cell line was due to the low expression of LC3 gene and protein, and was restored by the DNA demethylating agent, 5-aza-2’-deoxycytidine (5-aza) treatment. Moreover, the DNA methyltransferase activity was signifcantly increased in the ZIP13−/− cell line, indicating the disturbance of epigenetic regulations. Autophagy inhibitors efectively inhibited the growth of fbrosarcoma with relatively minor damages to normal cells in xenograft assay. Our data show that proper control over autophagy and zinc homeostasis could allow for the development of a new therapeutic strategy to treat fbrosarcoma. -
Protein Identities in Evs Isolated from U87-MG GBM Cells As Determined by NG LC-MS/MS
Protein identities in EVs isolated from U87-MG GBM cells as determined by NG LC-MS/MS. No. Accession Description Σ Coverage Σ# Proteins Σ# Unique Peptides Σ# Peptides Σ# PSMs # AAs MW [kDa] calc. pI 1 A8MS94 Putative golgin subfamily A member 2-like protein 5 OS=Homo sapiens PE=5 SV=2 - [GG2L5_HUMAN] 100 1 1 7 88 110 12,03704523 5,681152344 2 P60660 Myosin light polypeptide 6 OS=Homo sapiens GN=MYL6 PE=1 SV=2 - [MYL6_HUMAN] 100 3 5 17 173 151 16,91913397 4,652832031 3 Q6ZYL4 General transcription factor IIH subunit 5 OS=Homo sapiens GN=GTF2H5 PE=1 SV=1 - [TF2H5_HUMAN] 98,59 1 1 4 13 71 8,048185945 4,652832031 4 P60709 Actin, cytoplasmic 1 OS=Homo sapiens GN=ACTB PE=1 SV=1 - [ACTB_HUMAN] 97,6 5 5 35 917 375 41,70973209 5,478027344 5 P13489 Ribonuclease inhibitor OS=Homo sapiens GN=RNH1 PE=1 SV=2 - [RINI_HUMAN] 96,75 1 12 37 173 461 49,94108966 4,817871094 6 P09382 Galectin-1 OS=Homo sapiens GN=LGALS1 PE=1 SV=2 - [LEG1_HUMAN] 96,3 1 7 14 283 135 14,70620005 5,503417969 7 P60174 Triosephosphate isomerase OS=Homo sapiens GN=TPI1 PE=1 SV=3 - [TPIS_HUMAN] 95,1 3 16 25 375 286 30,77169764 5,922363281 8 P04406 Glyceraldehyde-3-phosphate dehydrogenase OS=Homo sapiens GN=GAPDH PE=1 SV=3 - [G3P_HUMAN] 94,63 2 13 31 509 335 36,03039959 8,455566406 9 Q15185 Prostaglandin E synthase 3 OS=Homo sapiens GN=PTGES3 PE=1 SV=1 - [TEBP_HUMAN] 93,13 1 5 12 74 160 18,68541938 4,538574219 10 P09417 Dihydropteridine reductase OS=Homo sapiens GN=QDPR PE=1 SV=2 - [DHPR_HUMAN] 93,03 1 1 17 69 244 25,77302971 7,371582031 11 P01911 HLA class II histocompatibility antigen, -
MA Identifier Upordown LFC Avgexpr T P Value P Corrected
MA_Identifier UpOrDown LFC AvgExpr t p_value p_corrected mRNA_Accession mRNA_Name AGT_Accession GD214292.1 Up 2.09674838 10.60378749 30.17940104 1.3532E-12 4.15339E-08 No Good Match No Good Match TR73477|c2_g4_i1 EB253690.1 Up 1.42056324 8.629454582 16.9400776 8.61647E-10 4.15339E-08 No Good Match No Good Match TR114624|c0_g1_i1 EB324506.1 Up 1.714877372 11.7626061 29.56600148 1.62329E-12 4.15339E-08 XM_013079935 uncharacterized LOC101862711, transcript variant X2 TR105757|c1_g1_i3 EB244298.1 Up 1.504941765 13.13555745 25.49705172 8.54949E-12 6.17912E-08 XM_005093725 uncharacterized LOC101862711, transcript variant X3 TR105757|c1_g1_i1 EB350631.1 Up 1.951725495 13.11211692 23.57801356 2.22739E-11 1.45399E-07 No Good Match No Good Match TR674|c0_g1_i1 EB250403.1 Up 2.236254197 12.79847784 21.59049993 6.28948E-11 3.48034E-07 No Good Match No Good Match TR107643|c0_g1_i1 EB229658.1 Up 1.196239323 12.26876042 18.23277846 3.64746E-10 5.66891E-07 No Good Match No Good Match CL455Contig2 EB349970.1 Up 0.915715907 13.66977042 17.25614464 6.50486E-10 8.43055E-07 No Good Match No Good Match TR112158|c9_g9_i1 EB215450.1 Down -0.779710678 9.573335222 -15.07554052 2.88601E-09 1.03781E-06 No Good Match No Good Match TR81289|c1_g1_i5 EB256532.1 Up 0.957584438 12.63905003 15.56227553 2.07024E-09 1.19669E-06 No Good Match No Good Match TR64854|c4_g1_i2 EB261386.1 Up 0.771865585 7.532393475 13.39242509 1.06221E-08 1.19669E-06 No Good Match No Good Match TR87266|c0_g1_i1 EB323709.1 Up 0.993428329 8.843840926 14.33197647 5.17673E-09 1.19669E-06 XM_013085446 -
Secreted Proteins in Microsporidian Parasites: a Functional and Evolutionary Perspective on Host-Parasite Interactions
Secreted proteins in microsporidian parasites: a functional and evolutionary perspective on host-parasite interactions. Submitted by Scott Edward Campbell to the University of Exeter as a thesis for the degree of Doctor of Philosophy in Biological Science. In September 2013 This thesis is available for Library use on the understanding that it is copyright material and that no quotation from this thesis may be published without proper acknowledgment. I certify that all material in this thesis which is not my own work has been identified and that no material has previously been submitted and approved for the award of a degree by this or any other University. Signature ……………………………………. Page| 1 Abstract The Microsporidia form a phylum of obligate intracellular parasites known to cause disease in humans and a diverse range of economically important animal species. Once classified as ‘primitive’ eukaryotes, it is now recognised that the peculiarities of microsporidian genomics and cell biology are, in fact, the consequence of extreme reduction allowed by an intimate relationship with the host cell. Excluding survival as an extracellular spore, microsporidia are in direct contact with the host throughout their developmental lifecycle, from entry to egress. Host cell manipulations have been described in morphological terms, but despite this, characterisation of such processes at the molecular level remains challenging. The logistics of the microsporidian lifecycle suggest secreted proteins and membrane proteins with extracellular domains may be involved in virulence and implicated in host cell manipulation. This study employs bioinformatic tools to predict secreted proteins in diverse microsporidia and comparative genomics to identify conserved proteins which may be required for host cell manipulation, pathogenicity and lifecycle progression. -
The Atiregs – Characterization of a New Family of Metal Transporters in Arabidopsis Thaliana
Silvia Kirchner The AtIREGs – Characterization of a new family of metal transporters in Arabidopsis thaliana Institute of Plant Nutrition University of Hohenheim Prof. Dr. N. von Wirén The AtIREGs - Characterization of a new family of metal transporters in Arabidopsis thaliana Dissertation Submitted in fulfilment of the requirements for the degree „Doktor der Agrarwissenschaften“ (Dr. Sc. Agr. / Ph. D. in Agricultural Sciences) to the Faculty Agricultural Sciences of the University of Hohenheim presented by Silvia Kirchner from Neu-Ulm 2009 This thesis was accepted as a doctoral dissertation in fulfilment of the requirements for the degree “Doktor der Agrarwissenschaften” by the Faculty of Agricultural Sciences at the University of Hohenheim. Date of oral examination: 3rd March 2009 Examination Committee Supervisor and reviewer Prof. Dr. Nicolaus von Wirén Co-reviewer Prof. Dr. Gerd Weber Additional examiner Prof. Dr. Wolfgang Hanke Vice dean and head of the committee Prof. Dr. Werner Bessei Table of contents 1 Summary – Zusammenfassung ………………………......................………………………...….... 1 1.1 Summary ……………………………...........................………………………………………........ 1 1.2 Zusammenfassung ……………………........................…………………………………….......... 3 2 Introduction ………………………………………………………...…............................................... 5 2.1 Heavy metals: definition and terminology ……...………………..........……....................... 5 2.2 Metal homeostasis in higher plants: dealing with deficiency and toxicity ........................ 5 2.2.1 The physiological -
9-Azido Analogs of Three Sialic Acid Forms for Metabolic Remodeling Of
Supporting Information 9-Azido Analogs of Three Sialic Acid Forms for Metabolic Remodeling of Cell-Surface Sialoglycans Bo Cheng,†,‡ Lu Dong,†,§ Yuntao Zhu,†,‡ Rongbing Huang,†,‡ Yuting Sun,†,‖ Qiancheng You,†,‡ Qitao Song,†,§ James C. Paton, ∇ Adrienne W. Paton,∇ and Xing Chen*,†,‡,§,⊥,# †College of Chemistry and Molecular Engineering, ‡Beijing National Laboratory for Molecular Sciences, §Peking−Tsinghua Center for Life Sciences,‖Academy for Advanced Interdisciplinary Studies, ⊥Synthetic and Functional Biomolecules Center, and #Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China ∇Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide SA 5005, Australia Page S1 Table of Contents: Scheme S1.……………………………………………………….........……………. S3 Figure S1……………………………………………………..………..……………. S3 Figure S2……………………………………………………..………..…………… S4 Figure S3……………………………………………………..………..…………… S4 Figure S4……………………………………………………..………..…………… S5 Figure S5……………………………………………………..………..…………… S6 Figure S6……………………………………………………..………..…………….S7 Figure S7……………………………………………………..………..…………….S8 Figure S8……………………………………………………..………..…………….S9 Experimental Procedures……………………………….…........…………....S10-S27 Table S1………………………………………………..………..…………….S28-S48 Supporting Reference……………………………………………….......………...S49 Page S2 Scheme S1. Synthesis of 9AzNeu5Gc Figure S1: a, b, c, d) Representative scatter plots (FSC vs. SSC) and histograms of flow cytometry analysis -
The Role of Zip Superfamily of Metal Transporters in Chronic Diseases, Purification & Characterization of a Bacterial Zip Tr
Wayne State University Wayne State University Theses 1-1-2011 The Role Of Zip Superfamily Of Metal Transporters In Chronic Diseases, Purification & Characterization Of A Bacterial Zip Transporter: Zupt. Iryna King Wayne State University Follow this and additional works at: http://digitalcommons.wayne.edu/oa_theses Part of the Biochemistry Commons, and the Molecular Biology Commons Recommended Citation King, Iryna, "The Role Of Zip Superfamily Of Metal Transporters In Chronic Diseases, Purification & Characterization Of A Bacterial Zip Transporter: Zupt." (2011). Wayne State University Theses. Paper 63. This Open Access Thesis is brought to you for free and open access by DigitalCommons@WayneState. It has been accepted for inclusion in Wayne State University Theses by an authorized administrator of DigitalCommons@WayneState. THE ROLE OF ZIP SUPERFAMILY OF METAL TRANSPORTERS IN CHRONIC DISEASES, PURIFICATION & CHARACTERIZATION OF A BACTERIAL ZIP TRANSPORTER: ZUPT by IRYNA KING THESIS Submitted to the Graduate School of Wayne State University, Detroit, Michigan in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE 2011 MAJOR: BIOCHEMISTRY & MOLECULAR BIOLOGY Approved by: ___________________________________ Advisor Date © COPYRIGHT BY IRYNA KING 2011 All Rights Reserved DEDICATION I dedicate this work to my father, Julian Banas, whose footsteps I indisputably followed into science & my every day inspiration, my son, William Peter King ii ACKNOWLEDGMENTS First and foremost I would like to thank the department of Biochemistry & Molecular Biology at Wayne State University School of Medicine for giving me an opportunity to conduct my research and be a part of their family. I would like to thank my advisor Dr. Bharati Mitra for taking me into the program and nurturing a biochemist in me. -
Transcriptomic and Proteomic Profiling Provides Insight Into
BASIC RESEARCH www.jasn.org Transcriptomic and Proteomic Profiling Provides Insight into Mesangial Cell Function in IgA Nephropathy † † ‡ Peidi Liu,* Emelie Lassén,* Viji Nair, Celine C. Berthier, Miyuki Suguro, Carina Sihlbom,§ † | † Matthias Kretzler, Christer Betsholtz, ¶ Börje Haraldsson,* Wenjun Ju, Kerstin Ebefors,* and Jenny Nyström* *Department of Physiology, Institute of Neuroscience and Physiology, §Proteomics Core Facility at University of Gothenburg, University of Gothenburg, Gothenburg, Sweden; †Division of Nephrology, Department of Internal Medicine and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan; ‡Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan; |Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; and ¶Integrated Cardio Metabolic Centre, Karolinska Institutet Novum, Huddinge, Sweden ABSTRACT IgA nephropathy (IgAN), the most common GN worldwide, is characterized by circulating galactose-deficient IgA (gd-IgA) that forms immune complexes. The immune complexes are deposited in the glomerular mesangium, leading to inflammation and loss of renal function, but the complete pathophysiology of the disease is not understood. Using an integrated global transcriptomic and proteomic profiling approach, we investigated the role of the mesangium in the onset and progression of IgAN. Global gene expression was investigated by microarray analysis of the glomerular compartment of renal biopsy specimens from patients with IgAN (n=19) and controls (n=22). Using curated glomerular cell type–specific genes from the published literature, we found differential expression of a much higher percentage of mesangial cell–positive standard genes than podocyte-positive standard genes in IgAN. Principal coordinate analysis of expression data revealed clear separation of patient and control samples on the basis of mesangial but not podocyte cell–positive standard genes. -
Insulin Action/Molecular Metabolism
INSULIN ACTION—ADIPOCYTECATEGORY BIOLOGY 1692-P 1694-P Stress in Beta Cells Obtained with Laser Capture Microdissection Biopsy-Proven Insulitis of Clinical Islet Transplantation Is Not from Cadaver Pancreases of Brain Dead Donors Reversed by Steroid Therapy AREF EBRAHIMI, MIN-HO JUNG, JONATHAN M. DREYFUSS, HUI PAN, DENNIS ANNA LAM, BEHRUZ RAHIMI, SHARLEEN IMES, KIM SOLEZ, JAMES SHAPIRO, C. SGROI, SUSAN BONNER-WEIR, GORDON C. WEIR, Boston, MA PETER A. SENIOR, Edmonton, AB, Canada Brain death of pancreas donors is thought to lead to the expression of Gradual decline in islet function remains a challenge in clinical islet infl ammatory, stress and apoptotic pathways in isolated islets resulting in transplantation (CIT), but acute graft loss is relatively uncommon. Here we poor clinical outcomes. To test this hypothesis we obtained cadaveric pan- describe a case of acute decline in graft function with histology suggesting creases from brain dead pancreatic donors (n=7, mean age 5011) and normal an immune mechanism. A 49 year old female (BMI 24.4 kg/m2, insulin 0.3 pancreatic tissue obtained at surgery done for pancreatic neoplasms (n=7, U/kg) with type 1 diabetes for 37 years underwent two CIT (6071 and 6827 age 699). Frozen sections were subjected to laser capture microdissection islet equivalents/kg) following alemtuzumab induction with tacrolimus (TAC, to obtain beta-cell rich islet tissue, from which extracted RNA was analyzed mean 8 ug/L) and mycophenolate mofetil for maintenance. Initial engraft- with Affymetrix arrays. Gene expression of the two groups was evaluated ment was reasonable (β2 score of 12 at 1 week), but β2 score gradually with principle component analysis (PCA), and differential expression anal- declined (Figure 1) rising to 19 after the second CIT. -
Identification of Biomarker Responses in Humans Under Experimentally Induced Zinc Depletion
IDENTIFICATION OF BIOMARKER RESPONSES IN HUMANS UNDER EXPERIMENTALLY INDUCED ZINC DEPLETION By MOON-SUHN RYU A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2011 1 © 2011 Moon-Suhn Ryu 2 To my parents, Ji-Chul Ryu and Soon-Young Park, and my grandmother, Jung-Seo Seo 3 ACKNOWLEDGMENTS The achievements from the past years in my life as a doctoral student would not exist without the presence of the support and love from my family far way in South Korea. I thank my parents for their love and belief in me which have been the greatest motivation for me to pursue accomplishments and success with my best efforts. I also render my gratefulness to my younger sister, Jin-Suhn Ryu, for being the best supporter in all aspects of my life. Additionally, I thank everyone with whom I shared the moments in the lab, especially, Dr. Juan P. Liuzzi, Dr. Louis A. Lichten, Dr. Liang Guo, Dr. Shou- mei Chang, Tolunay Beker Aydemir, for their invaluable advices and help. The excitement from our findings was always the greatest motivation for me to stay in progress. I also thank Gregory Guthrie, Alyssa Maki, Luisa Rios and Vanessa Da Silva for their cheer and support, particularly, during the last year of my doctoral research. I thank Meena Shankar and the staff members at the General Clinical Research Center for their advices and assistance during the phases of study design and implementation of the dietary regimen. -
The Effect of Acid on the Dynamics of Intracellular Zinc and the Marker Expressions Of
The Effect of Acid on the Dynamics of Intracellular Zinc and the Marker Expressions of Pluripotency in Somatic Cells A thesis presented to the faculty of the College of Arts and Sciences of Ohio University In partial fulfillment of the requirements for the degree Master of Science Yuli Hu April 2021 © 2021 Yuli Hu. All Rights Reserved. 2 This thesis titled The Effect of Acid on the Dynamics of Intracellular Zinc and the Marker Expressions of Pluripotency in Somatic Cells by YULI HU has been approved for the Department of Biological Sciences and the College of Arts and Sciences by Yang V. Li Professor of Biomedical Sciences Florenz Plassmann Dean, College of Arts and Sciences 3 Abstract YULI HU, M.S., April 2021, Biological Sciences The Effect of Acid on the Dynamics of Intracellular Zinc and the Marker Expressions of Pluripotency in Somatic Cells Director of Thesis: Yang V. Li Microenvironmental pH is one of the factors that affect the stability of zinc- protein binding. The tight binding between zinc and proteins is favored by the basic pH, whereas acidic pH favors a loose bound, and treatment of strong acid results in the dissociation of zinc. Physiologically, the stomach uses a very acidic pH to digest food which results in a high amount of soluble zinc in the stomach. Whether or not zinc co- present with acid and the effect of zinc on the gastric lining has rarely been discussed. In my experiments, acidic treatment induced the expression of a pluripotent marker in primary cultured gastric cells. It also stimulated the release of intracellular zinc, suggesting that acidic pH supported protein expression through dynamic zinc regulation.