The Effects of Estrogen in Atrazine-Mediated Foxp3 Induction and Inhibition of Cd4+ T Effector Cells
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The Title of the Dissertation
UNIVERSITY OF CALIFORNIA SAN DIEGO Novel network-based integrated analyses of multi-omics data reveal new insights into CD8+ T cell differentiation and mouse embryogenesis A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Biology by Kai Zhang Committee in charge: Professor Wei Wang, Chair Professor Pavel Arkadjevich Pevzner, Co-Chair Professor Vineet Bafna Professor Cornelis Murre Professor Bing Ren 2018 Copyright Kai Zhang, 2018 All rights reserved. The dissertation of Kai Zhang is approved, and it is accept- able in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California San Diego 2018 iii EPIGRAPH The only true wisdom is in knowing you know nothing. —Socrates iv TABLE OF CONTENTS Signature Page ....................................... iii Epigraph ........................................... iv Table of Contents ...................................... v List of Figures ........................................ viii List of Tables ........................................ ix Acknowledgements ..................................... x Vita ............................................. xi Abstract of the Dissertation ................................. xii Chapter 1 General introduction ............................ 1 1.1 The applications of graph theory in bioinformatics ......... 1 1.2 Leveraging graphs to conduct integrated analyses .......... 4 1.3 References .............................. 6 Chapter 2 Systematic -
Acute Toxicity of Atrazine, Endosulfan Sulphate and Chlorpyrifos
Bull Environ Contam Toxicol (2008) 81:485–489 DOI 10.1007/s00128-008-9517-3 Acute Toxicity of Atrazine, Endosulfan Sulphate and Chlorpyrifos to Vibrio fischeri, Thamnocephalus platyurus and Daphnia magna, Relative to Their Concentrations in Surface Waters from the Alentejo Region of Portugal P. Palma Æ V. L. Palma Æ R. M. Fernandes Æ A. M. V. M. Soares Æ I. R. Barbosa Received: 28 September 2007 / Accepted: 20 August 2008 / Published online: 8 September 2008 Ó Springer Science+Business Media, LLC 2008 Abstract Ecotoxicological effects of the herbicide atra- the herbicide atrazine are three of the pesticides most fre- zine and the insecticides endosulfan sulphate and chlor- quently used in Alentejo region crops. These compounds pyrifos were evaluated using a test battery comprising were chosen taking in account their concentration in the aquatic organisms from different trophic levels. According surface water of Alentejo region, mainly in Guadiana River, to the categories established in the EU legislation, atrazine and their environmental significance. The herbicide atrazine can be considered non-harmful for the species tested, while may reach values above maximum admissible concentration the insecticides can be considered very toxic for the crus- (MAC) allowed by Portuguese Legislation for surface taceans. The results of acute toxicity tests showed that the waters (Decreto-Lei n8236/98 1998). Despite that, atrazine sensitivity of organisms were as follows: Thamnocephalus did not pose a significant threat to the aquatic environment. platyurus [ Daphnia magna [ Vibrio fischeri. Chlorpyri- However, Solomon et al. (1996) cautioned that, when atra- fos may act as a toxic compound in the aquatic environment zine is retained in small, standing-water reservoirs or has of Guadiana River, as it may be detected in water at levels repeated inputs to a reservoir, damage can occur in the that promote toxic effects. -
What's the Deal with Andropause?
What’sF.A.Q. the Deal Troches and Bio-Identical With HormonesAndropause? Compounding Without WrittenWritten and Edited ByBy CompromiseCompounding Since Without 1962 LisaLisa Everett Everett Andersen, Andersen, B.Sc B.Sc Pharm, Pharm, CCN, CCN, FACA, FACA FIACP Compromise Since 1962 and Shana Curtis Webb, Pharm Tech In the beginning, it can be difficult to recognize and easily and Dobs of Johns Hopkins University recommend that dismissed. It might start with lowered immune function, elderly men with symptoms of hypogonadism and a total Whatmaybe aIs little a Troche irritability? and unexplainable fatigue, or perhaps testosteroneOther Dosage level of Forms 300ng/dl or less should start hormone difficulty sleeping. Slowly, the symptoms can increase and A troche is a French dosage form that dissolves between the replacement.Besides troches, But dosagewhat about forms young for hormones men with include those sameoral others appear, including hair loss, depression, the typical levels? They are also being told by their physicians that upper cheek and gum, allowing the medication to absorb tablets and capsules, sublingual lozenges, topical creams and actions of a “mid-life crisis,” and erectile dysfunction. This their lab values are in range and therefore just fine. After directly into the blood stream. Born out of the need to address ointments, suppositories, pessaries, injections, implanted cascade of events is often due to andropause (AKA the “male all, testosterone is now a controlled substance and some the problems associated with other dosage forms, troches pellets, and patches. menopause” or hypogonadism). It is the decline of androgens, practitioners don’t want to go there unless they have to. -
The Transcription Factors Blimp-1 and IRF4 Jointly Control the Differentiation and Function of Effector Regulatory T Cells
ARTICLES The transcription factors Blimp-1 and IRF4 jointly control the differentiation and function of effector regulatory T cells Erika Cretney1,2,6, Annie Xin1,2,6, Wei Shi1,3, Martina Minnich4, Frederick Masson1,2, Maria Miasari1,2, Gabrielle T Belz1,2, Gordon K Smyth1,5, Meinrad Busslinger4, Stephen L Nutt1,2 & Axel Kallies1,2 Regulatory T cells (Treg cells) are required for peripheral tolerance. Evidence indicates that Treg cells can adopt specialized differentiation programs in the periphery that are controlled by transcription factors usually associated with helper T cell differentiation. Here we demonstrate that expression of the transcription factor Blimp-1 defined a population of Treg cells that localized mainly to mucosal sites and produced IL-10. Blimp-1 was required for IL-10 production by these cells and for their tissue homeostasis. We provide evidence that the transcription factor IRF4, but not the transcription factor T-bet, was essential for Blimp-1 expression and for the differentiation of all effector Treg cells. Thus, our study defines a differentiation pathway that leads to the acquisition of Treg cell effector functions and requires both IRF4 and Blimp-1. + + Naturally occurring CD4 Foxp3 regulatory T cells (Treg cells) are Foxp3. The transcription factor IRF4 acts downstream of Foxp3, which derived from the thymus and are essential for the preservation of suggests that Treg cells use the transcriptional machinery of T helper 1,2 immune homeostasis and suppression of autoimmune pathology . type 2 (TH2) effector cells to specifically control this subset of helper 17 Treg cells depend on interleukin 2 (IL-2) for their maintenance and T cells . -
Impact of Atrazine on Organophosphate Insecticide Toxicity
Environmental Toxicology and Chemistry, Vol. 19, No. 9, pp. 2266±2274, 2000 q 2000 SETAC Printed in the USA 0730-7268/00 $9.00 1 .00 IMPACT OF ATRAZINE ON ORGANOPHOSPHATE INSECTICIDE TOXICITY JASON B. BELDEN and MICHAEL J. LYDY* Department of Biological Sciences, 1845 N Fairmount, Wichita State University, Wichita, Kansas 67260-0026, USA (Received 9 August 1999; Accepted 24 January 2000) AbstractÐAcute toxicity of selected organophosphorus insecticides (OPs; chlorpyrifos, methyl parathion, diazinon, and malathion) was determined for individual OPs and binary combinations of the OPs with atrazine to larvae of the midge Chironomus tentans. Atrazine individually was not acutely toxic even at high concentrations (10,000 mg/L); however, the presence of atrazine at much lower concentrations (40±200 mg/L) increased the toxicity of chlorpyrifos, methyl parathion, and diazinon. Atrazine did not increase the toxicity of malathion. Possible mechanisms for the synergistic toxicity found between atrazine and chlorpyrifos were investigated, including increased uptake rate and increased biotransformation into a more toxic metabolite. Although the uptake rate was increased by more than 40%, the resulting increase in toxicity would be minimal as compared to the 400% decrease estimated to occur in EC50 values for the same atrazine exposure (200 mg/L). Body residue analysis of midges exposed in vivo to atrazine and chlorpyrifos mixtures for 96 h indicated that a larger amount of metabolites was generated in atrazine treatments as compared to controls. Additionally, in vitro assays of microsomal proteins obtained from treated and control midges indicated that an increase in toxic metabolite (chlorpyrifos-O-analog) was generated in atrazine-treated midges. -
Escape from X Chromosome Inactivation and the Female Predominance in Autoimmune Diseases
International Journal of Molecular Sciences Review Escape from X Chromosome Inactivation and the Female Predominance in Autoimmune Diseases Ali Youness 1,†, Charles-Henry Miquel 1,2,† and Jean-Charles Guéry 1,* 1 Infinity-Toulouse Institute for Infectious and Inflammatory Diseases, University of Toulouse, INSERM, CNRS, UPS, 31300 Toulouse, France; [email protected] (A.Y.); [email protected] (C.-H.M.) 2 Arthritis R&D, 92200 Neuilly-Sur-Seine, France * Correspondence: [email protected]; Tel.: +33-5-62-74-83-78; Fax: +33-5-62-74-45-58 † These authors contributed equally to this work. Abstract: Women represent 80% of people affected by autoimmune diseases. Although, many studies have demonstrated a role for sex hormone receptor signaling, particularly estrogens, in the direct regulation of innate and adaptive components of the immune system, recent data suggest that female sex hormones are not the only cause of the female predisposition to autoimmunity. Besides sex steroid hormones, growing evidence points towards the role of X-linked genetic factors. In female mammals, one of the two X chromosomes is randomly inactivated during embryonic development, resulting in a cellular mosaicism, where about one-half of the cells in a given tissue express either the maternal X chromosome or the paternal one. X chromosome inactivation (XCI) is however not complete and 15 to 23% of genes from the inactive X chromosome (Xi) escape XCI, thereby contributing to the emergence of a female-specific heterogeneous population of cells with bi-allelic expression of some X-linked genes. Although the direct contribution of this genetic mechanism in the female susceptibility to autoimmunity still remains to be established, the cellular mosaicism resulting from XCI escape is likely to create a unique functional plasticity within female immune cells. -
Effects of the Pesticides Atrazine, Metoachlor and Diazinon and Binary Mixtures on Proliferation of Human Fibroblasts
CORE Metadata, citation and similar papers at core.ac.uk Provided by University of Northern Iowa International Journal of Global Health Volume 2 Number 2 Article 3 2003 Effects of the Pesticides Atrazine, Metoachlor and Diazinon and Binary Mixtures on Proliferation of Human Fibroblasts Kavita R. Dhanwada University of Northern Iowa Yijun Deng University of Northern Iowa Maureen E. Clayton University of Northern Iowa Follow this and additional works at: https://scholarworks.uni.edu/ijgh Part of the Public Health Commons Recommended Citation Dhanwada, Kavita R.; Deng, Yijun; and Clayton, Maureen E. (2003) "Effects of the Pesticides Atrazine, Metoachlor and Diazinon and Binary Mixtures on Proliferation of Human Fibroblasts," International Journal of Global Health, 2(2), 21-36. Available at: https://scholarworks.uni.edu/ijgh/vol2/iss2/3 This Research is brought to you for free and open access by the Journals at UNI ScholarWorks. It has been accepted for inclusion in International Journal of Global Health by an authorized editor of UNI ScholarWorks. For more information, please contact [email protected]. EFFECTS OF THE PESTICIDES ATRAZINE, METOACHLOR AND DIAZINON AND BINARY MIXTURES ON PROLIFERATION OF HUMAN FIBROBLASTS Kavita R. Dhanwada, Ph.D. Department of Biology, University of Northern Iowa Cedar Falls, IA 50614-0421 Yijun Deng, M.S . Environmental Programs, University of Northern Iowa Maureen E. Clayton, Ph.D . Department of Biology and Environmental Programs, University of Northern Iowa ABSTRACT The frequent and heavy use of pesticides in agriculture has led to the contamina tion of surface and ground waters worldwide. Many questions have arisen about the human health effects of exposure to these pesticides and their mixtures. -
Robust Nanocatalyst Membranes for Degradation of Atrazine in Water T ⁎ H
Journal of Water Process Engineering 25 (2018) 15–21 Contents lists available at ScienceDirect Journal of Water Process Engineering journal homepage: www.elsevier.com/locate/jwpe Robust nanocatalyst membranes for degradation of atrazine in water T ⁎ H. Vijwani, M.N. Nadagouda, S.M. Mukhopadhyay Center for Nanoscale Multifunctional Materials, Mechanical & Materials Engineering, Wright State University, Dayton, OH 45435, United States ARTICLE INFO ABSTRACT Keywords: Solid membranes for degradation of emerging contaminants such as atrazine is of significant interest for water Hierarchical hybrid surfaces as catalyst support engineering applications. In this study, nanocatalyst particles have been anchored on vertically-aligned carpet- Carbon nanotube carpets on porous membranes like arrays of carbon nanotubes (CNT) grown on porous carbon foams. This hierarchical architecture combines Palladium nano-particles the advantages of highly surface-active nanoparticles with the robust and reusable structural advantage of Atrazine degradation porous solid membranes suitable for water treatment devices. Three types of palladium-based nano-catalytic Surface chemical states surfaces have been investigated: metallic palladium (Pd), Pd nanoparticle with a layer of oxide (PdO-coated Pd), Nano-catalysts and Pd nanoparticle coated with thin film of silver (Ag-Pd). Their catalytic activities have been compared by analysing the degradation rate of atrazine in water. It is noted that all three catalysts show high levels of atrazine degradation, with the PdO-coated nanoparticles showing the highest kinetics. These results demonstrate that hierarchical hybrid architectures can provide compact and powerful surface-active materials such as adsorbents and catalytic degradation devices in future water treatment applications. 1. Introduction significantly constrained by the morphology of the underlying solid. -
Sex Differences in Immune Responses
REVIEWS Sex differences in immune responses Sabra L. Klein1 and Katie L. Flanagan2 Abstract | Males and females differ in their immunological responses to foreign and self-antigens and show distinctions in innate and adaptive immune responses. Certain immunological sex differences are present throughout life, whereas others are only apparent after puberty and before reproductive senescence, suggesting that both genes and hormones are involved. Furthermore, early environmental exposures influence the microbiome and have sex-dependent effects on immune function. Importantly, these sex-based immunological differences contribute to variations in the incidence of autoimmune diseases and malignancies, susceptibility to infectious diseases and responses to vaccines in males and females. Here, we discuss these differences and emphasize that sex is a biological variable that should be considered in immunological studies. Sex is a biological variable that affects immune responses have 40% less viral RNA in their blood than men, men to both self and foreign antigens (for example, those show an almost twofold higher risk of death from from fungi, viruses, bacteria, parasites and allergens). malignant cancer than women and antibody responses The sex of an individual is defined by the differential to seasonal influenza vaccines are consistently at least organization of chromosomes, reproductive organs, twice as strong in women than men. Generally, adult and sex steroid levels; it is distinct from gender, which females mount stronger innate and adaptive immune includes behaviours and activities that are determined responses than males. This results in faster clearance of by society or culture in humans. Male and female differ pathogens and greater vaccine efficacy in females than ences in immunological responses may be influenced by in males but also contributes to their increased suscepti both sex and gender, with sex contributing to physiologi bility to inflammatory and autoimmune diseases. -
Role of Estrogen Receptor in Breast Cancer Cell Gene Expression
4046 MOLECULAR MEDICINE REPORTS 13: 4046-4050, 2016 Role of estrogen receptor in breast cancer cell gene expression YABING ZHENG1, XIYING SHAO1, YUAN HUANG1, LEI SHI1, BO CHEN2, XIAOJIA WANG1, HONGJIAN YANG3, ZHANHONG CHEN1 and XIPING ZHANG3 Departments of 1Medical Oncology (Breast), 2Pathology and 3Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China Received April 28, 2015; Accepted February 23, 2016 DOI: 10.3892/mmr.2016.5018 Abstract. The aim of the present study was to establish the Europe in 2012, and the number of breast cancer-associated underlying regulatory mechanism of estrogen receptor (ER) mortalities is 131,000 (6). Furthermore, breast cancer is in breast cancer cell gene expression. A gene expression the most common cause of cancer-associated mortality in profile accession( no. GSE11324) was downloaded from the females. Therefore, it is essential to understand its molecular Gene Expression Omnibus (GEO) database. Differentially mechanism and develop more effective therapeutic methods expressed genes (DEGs) from an estrogen treatment group and for breast cancer treatment. a control group were identified. Chromatin immunoprecipita- The estrogen receptor (ER) is critical in determining the tion with high-throughput sequencing data (series GSE25710) phenotype of human breast cancers and is one of the most was obtained from the GEO for the ER binding sites, and important therapeutic targets (7). Furthermore, certain studies binding and expression target analysis was performed. A total have suggested that activation of ER is responsible for various of 3,122 DEGs were obtained and ER was demonstrated to biological processes, including cell growth and differentia- exhibit inhibition and activation roles during the regulation tion, and programmed cell death (8,9). -
Promoter Through Interaction with the FOXP3 RORC2 Is Involved in T Cell Polarization
RORC2 Is Involved in T Cell Polarization through Interaction with the FOXP3 Promoter This information is current as Simone Burgler, Pierre-Yves Mantel, Claudio Bassin, Nadia of September 28, 2021. Ouaked, Cezmi A. Akdis and Carsten B. Schmidt-Weber J Immunol 2010; 184:6161-6169; Prepublished online 28 April 2010; doi: 10.4049/jimmunol.0903243 http://www.jimmunol.org/content/184/11/6161 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2010/04/28/jimmunol.090324 Material 3.DC1 http://www.jimmunol.org/ References This article cites 64 articles, 27 of which you can access for free at: http://www.jimmunol.org/content/184/11/6161.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 28, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2010 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology RORC2 Is Involved in T Cell Polarization through Interaction with the FOXP3 Promoter Simone Burgler,* Pierre-Yves Mantel,*,† Claudio Bassin,* Nadia Ouaked,* Cezmi A. -
Development, Maintenance and Functions of CD8+ T-Regulatory Cells
Chakraborty S, Sa G. J Immunol Sci. (2018); 2(2): 8-12 Journal of Immunological Sciences Minireview Open Access Development, maintenance and functions of CD8+ T-regulatory cells: Molecular orchestration of FOXP3 transcription Sreeparna Chakraborty1 & Gaurisankar Sa1* 1Division of Molecular Medicine, Bose Institute, P-1/12, Calcutta Improvement Trust Scheme VII M, Kolkata 700054, India Article Info ABSTRACT Article Notes Modulation of immune cells to rejuvenate the immune responses Received: January 10, 2018 against cancer becomes a promising strategy for cancer therapy. T-regulatory Accepted: March 23, 2018 cells are one of the major hurdles in successful cancer immunotherapy. Recent + + *Correspondence: studies discovered that apart from CD4 Treg cells, CD8 Tregs also play roles in Prof. Gaurisankar Sa, Division of Molecular Medicine, Bose tumor immune evasion. Moreover, CD8+ Tregs shows synergistic immunosup- Institute, P-1/12, Calcutta Improvement Trust Scheme VII M, pression with CD4+ Treg cells in tumor microenvironment. Several phenotypic Kolkata 700 054, India; markers have been described for peripherally induced CD8+ Treg cells, but Tel: +91-33-2569-3258; till now no universal phenotypic signature has yet established. FOXP3 is the Fax: +91-33-2355-3886, E-mail: [email protected] master regulator of Treg cells and its transcription is critically regulated by pro- © 2018 Sa G. This article is distributed under the terms of the moter region as well as three intronic conserved non-coding regions, viz; CNS Creative Commons Attribution 4.0 International License. 1, 2 and 3. In this review, we have described the transcriptional networking associated with the regulation of FOXP3 in tumor-CD8+ Treg cells along with Keywords: CD4+ nTreg and iTreg cells.