Isolating the Role of Corticosterone in the Hypothalamic-Pituitary-Gonadal Genomic Stress Response
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Bioinformatics Approach for Pattern of Myelin-Specific Proteins And
CORE Metadata, citation and similar papers at core.ac.uk Provided by Qazvin University of Medical Sciences Repository Biotech Health Sci. 2016 November; 3(4):e38278. doi: 10.17795/bhs-38278. Published online 2016 August 16. Research Article Bioinformatics Approach for Pattern of Myelin-Specific Proteins and Related Human Disorders Samiie Pouragahi,1,2,3 Mohammad Hossein Sanati,4 Mehdi Sadeghi,2 and Marjan Nassiri-Asl3,* 1Department of Molecular Medicine, School of Medicine, Qazvin university of Medical Sciences, Qazvin, IR Iran 2Department of Bioinformatics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, IR Iran 3Department of Pharmacology, Cellular and Molecular Research Center, School of Medicine, Qazvin university of Medical Sciences, Qazvin, IR Iran 4Department of Molecular Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, IR Iran *Corresponding author: Marjan Nassiri-Asl, School of Medicine, Qazvin University of Medical Sciences, Qazvin, IR Iran. Tel: +98-2833336001, Fax: +98-2833324971, E-mail: [email protected] Received 2016 April 06; Revised 2016 May 30; Accepted 2016 June 22. Abstract Background: Recent neuroinformatic studies, on the structure-function interaction of proteins, causative agents basis of human disease have implied that dysfunction or defect of different protein classes could be associated with several related diseases. Objectives: The aim of this study was the use of bioinformatics approaches for understanding the structure, function and relation- ship of myelin protein 2 (PMP2), a myelin-basic protein in the basis of neuronal disorders. Methods: A collection of databases for exploiting classification information systematically, including, protein structure, protein family and classification of human disease, based on a new approach was used. -
A Genome-Wide Study of Blood Pressure in African Americans Accounting for Gene-Smoking Interaction Jacquelyn Y
A Genome-wide study of blood pressure in African Americans accounting for gene-smoking interaction Jacquelyn Y. Taylor, Yale University Karen Schwander, Washington University in St. Louis Sharon L. R. Kardia, University of Michigan Donna Arnett, University of Alabama, Birmingham Jingjing Liang, Case Western Reserve University Steven C. Hunt, University of Utah D.C. Rao, Washington University in St. Louis Yan Sun, Emory University Journal Title: Scientific Reports Volume: Volume 6 Publisher: Nature Publishing Group | 2016-01-11, Pages 18812-18812 Type of Work: Article | Final Publisher PDF Publisher DOI: 10.1038/srep18812 Permanent URL: https://pid.emory.edu/ark:/25593/rhb37 Final published version: http://dx.doi.org/10.1038/srep18812 Copyright information: © 2016, Macmillan Publishers Limited This is an Open Access work distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/). Accessed September 29, 2021 11:39 AM EDT www.nature.com/scientificreports OPEN A Genome-wide study of blood pressure in African Americans accounting for gene-smoking Received: 15 January 2015 Accepted: 09 November 2015 interaction Published: 11 January 2016 Jacquelyn Y. Taylor1, Karen Schwander2, Sharon L. R. Kardia3 & Donna Arnett4, Jingjing Liang5 Steven C. Hunt6, D.C. Rao2 & Yan V. Sun7,8 Cigarette smoking has been shown to be a health hazard. In addition to being considered a negative lifestyle behavior, studies have shown that cigarette smoking has been linked to genetic underpinnings of hypertension. Because African Americans have the highest incidence and prevalence of hypertension, we examined the joint effect of genetics and cigarette smoking on health among this understudied population. -
Supplementary Table 1. Down-Regulation of Oligodendrocyte Genes in Schizophrenia
Supplementary Table 1. Down-regulation of oligodendrocyte genes in schizophrenia Schizophrenia ID Accession Symbol product fold change P value oligodendrocyte transcription factors 36018_at AJ001183 SOX10 SRY (sex determining region Y)-box 10 -1.60 0.001 40624_at U48250 OLIG2 oligodendrocyte lineage transcription factor 2 -1.30 0.019 32187_at AB028973 MYT1 myelin transcription factor 1 1.12 0.571 33539_at W28567 MYEF2 myelin expression factor 2 -1.04 0.887 oligodendrocyte-expressed genes 38558_at M29273 MAG myelin associated glycoprotein -1.76 0.004 41158_at M54927 PLP1 proteolipid protein 1 -1.50 0.011 38499_s_at D28113 MOBP myelin-associated oligodendrocyte basic protein -1.59 0.017 35903_at M63623 OMG oligodendrocyte myelin glycoprotein -1.15 0.022 38653_at D11428 PMP22 peripheral myelin protein 22 -1.28 0.058 38051_at X76220 MAL mal, T-cell differentiation protein -1.11 0.065 612_s_at M19650 CNP 2',3'-cyclic nucleotide 3' phosphodiesterase -1.17 0.072 32538_at S95936 TF transferrin -1.48 0.098 32612_at X04412 GSN gelsolin (amyloidosis, Finnish type) -1.23 0.118 39598_at X04325 GJB1 gap junction protein, beta 1, 32kDa -1.10 0.416 37867_at Z48051 MOG myelin oligodendrocyte glycoprotein 1.39 0.600 35328_at AF055023 NF1 neurofibromin 1 -1.03 0.973 35817_at M13577 MBP myelin basic protein 1.02 1 other oligodendrocyte-related genes 41346_at AJ007583 LARGE like-glycosyltransferase -1.02 0.786 32719_at L41827 NRG1 neuregulin 1 1.07 0.792 1585_at M34309 ERBB3 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 -1.10 0.294 40387_at U80811 -
Surfactant Protein-C in the Maintenance of Lung Integrity and Function Stephan W
erg All y & of T l h a e n r r a Glasser, et al. J Aller Ther 2011, S7 p u y o J Journal of Allergy & Therapy DOI: 10.4172/2155-6121.S7-001 ISSN: 2155-6121 Review Article Open Access Surfactant Protein-C in the Maintenance of Lung Integrity and Function Stephan W. Glasser1*, John E. Baatz2 and Thomas R. Korfhagen1 1Department of Pediatrics, Cincinnati Children’s Hospital Medical Center , University of Cincinnati College of Medicine, Cincinnati, Ohio, USA 2Department of Pediatrics, Medical University of South Carolina and MUSC Children’s Hospital; Charleston, South Carolina, USA Abstract Surfactant protein-C (SP-C) is a lung cell specific protein whose expression is identified from the earliest stages of mammalian lung development in a subset of developing epithelial cells and in the alveolar type II cell in the mature lung. Although SP-C gene expression is not critical and protein function is not necessary for the normal developing morphological patterning of the lung, studies of SP-C protein mutations and SP-C deficiency have revealed critical roles of SP-C in the maintenance and function of the preterm and mature lung during various forms of intrinsic or extrinsic lung injury. This review summarizes studies using in vitro experimental approaches, in vivo modeling in transgenic mice, and analysis of human disease pathogenesis. Collected data reveal an essential role for SP-C singly and in combination with other lung proteins, in maintenance of lung structure and pulmonary function of the immature and mature lung. Introduction regulating lung development, function, and recovery from injury. -
Basic Protein Detect Circulating Antibodies in Ataxic Horses Siobhan P Ellison Tom J Kennedy Austin Li
Neuritogenic Peptides Derived from Equine Myelin P2 Basic Protein Detect Circulating Antibodies in Ataxic Horses Siobhan P Ellison Tom J Kennedy Austin Li Corresponding Author: Siobhan P. Ellison, DVM PhD 15471 NW 112th Ave Reddick, Fl 32686 Phone: 352-591-3221 Fax: 352-591-4318 e-mail: [email protected] KEY WORDS: Need Keywords nosis of EPM. No cross-reactivity between the antigens was observed. An evaluation of the agreement between the assays (McNe- ABSTRACT mar’s test) suggests as CRP values increase, the likelihood of a positive MPP ELISA also Polyneuritis equi is an immune-mediated increases. Clinical signs of EPM may be neurodegenerative condition in horses that is due to an immune-mediated polyneuropathy related to circulating demyelinating anti- that involves complex in vivo interactions bodies against equine myelin basic protein with the IL6 pathway because MPP antibod- 2 (MP ). The present study examined the 2 ies and elevated CRP concentrations were presence of circulating demyelinating anti- detected in some horses with S. neurona bodies against neuritogenic peptides of MP 2 sarcocystosis. in sera from horses suspected of equine pro- tozoal encephalomyelitis (EPM), a neurode- INTRODUCTION generative condition in horses that may be Polyneuritis equi is a neurodegenerative immune-mediated. The goals of this study condition in horses that is related to circulat- were to develop serum ELISA tests that may ing demyelinating antibodies against equine identify neuroinflammatory conditions in myelin basic protein 2 (MP2). The clinical horses with EPM and indirectly relate the signs of polyneuritis equi (PE) are simi- pathogenesis of inflammation to IL6 by se- lar to equine protozoal myeloencephalitis rum C-reactive protein (CRP) concentration. -
Primate Specific Retrotransposons, Svas, in the Evolution of Networks That Alter Brain Function
Title: Primate specific retrotransposons, SVAs, in the evolution of networks that alter brain function. Olga Vasieva1*, Sultan Cetiner1, Abigail Savage2, Gerald G. Schumann3, Vivien J Bubb2, John P Quinn2*, 1 Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, U.K 2 Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK 3 Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, D-63225 Germany *. Corresponding author Olga Vasieva: Institute of Integrative Biology, Department of Comparative genomics, University of Liverpool, Liverpool, L69 7ZB, [email protected] ; Tel: (+44) 151 795 4456; FAX:(+44) 151 795 4406 John Quinn: Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK, [email protected]; Tel: (+44) 151 794 5498. Key words: SVA, trans-mobilisation, behaviour, brain, evolution, psychiatric disorders 1 Abstract The hominid-specific non-LTR retrotransposon termed SINE–VNTR–Alu (SVA) is the youngest of the transposable elements in the human genome. The propagation of the most ancient SVA type A took place about 13.5 Myrs ago, and the youngest SVA types appeared in the human genome after the chimpanzee divergence. Functional enrichment analysis of genes associated with SVA insertions demonstrated their strong link to multiple ontological categories attributed to brain function and the disorders. SVA types that expanded their presence in the human genome at different stages of hominoid life history were also associated with progressively evolving behavioural features that indicated a potential impact of SVA propagation on a cognitive ability of a modern human. -
Supporting Information
Supporting Information Figure S1. The functionality of the tagged Arp6 and Swr1 was confirmed by monitoring cell growth and sensitivity to hydeoxyurea (HU). Five-fold serial dilutions of each strain were plated on YPD with or without 50 mM HU and incubated at 30°C or 37°C for 3 days. Figure S2. Localization of Arp6 and Swr1 on chromosome 3. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 3L, Tel 3R, CEN3, and the RP gene are shown under the panels. Figure S3. Localization of Arp6 and Swr1 on chromosome 4. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) in the whole chromosome region are compared. The position of Tel 4L, Tel 4R, CEN4, SWR1, and RP genes are shown under the panels. Figure S4. Localization of Arp6 and Swr1 on the region including the SWR1 gene of chromosome 4. The binding of Arp6- FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position and orientation of the SWR1 gene is shown. Figure S5. Localization of Arp6 and Swr1 on chromosome 5. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 5L, Tel 5R, CEN5, and the RP genes are shown under the panels. Figure S6. Preferential localization of Arp6 and Swr1 in the 5′ end of genes. Vertical bars represent the binding ratio of proteins in each locus. -
Investigation of Candidate Genes and Mechanisms Underlying Obesity
Prashanth et al. BMC Endocrine Disorders (2021) 21:80 https://doi.org/10.1186/s12902-021-00718-5 RESEARCH ARTICLE Open Access Investigation of candidate genes and mechanisms underlying obesity associated type 2 diabetes mellitus using bioinformatics analysis and screening of small drug molecules G. Prashanth1 , Basavaraj Vastrad2 , Anandkumar Tengli3 , Chanabasayya Vastrad4* and Iranna Kotturshetti5 Abstract Background: Obesity associated type 2 diabetes mellitus is a metabolic disorder ; however, the etiology of obesity associated type 2 diabetes mellitus remains largely unknown. There is an urgent need to further broaden the understanding of the molecular mechanism associated in obesity associated type 2 diabetes mellitus. Methods: To screen the differentially expressed genes (DEGs) that might play essential roles in obesity associated type 2 diabetes mellitus, the publicly available expression profiling by high throughput sequencing data (GSE143319) was downloaded and screened for DEGs. Then, Gene Ontology (GO) and REACTOME pathway enrichment analysis were performed. The protein - protein interaction network, miRNA - target genes regulatory network and TF-target gene regulatory network were constructed and analyzed for identification of hub and target genes. The hub genes were validated by receiver operating characteristic (ROC) curve analysis and RT- PCR analysis. Finally, a molecular docking study was performed on over expressed proteins to predict the target small drug molecules. Results: A total of 820 DEGs were identified between -
Cell Reprogramming Technologies for Treatment And
CELL REPROGRAMMING TECHNOLOGIES FOR TREATMENT AND UNDERSTANDING OF GENETIC DISORDERS OF MYELIN by ANGELA MARIE LAGER Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Thesis advisor: Paul J Tesar, PhD Department of Genetics and Genome Sciences CASE WESTERN RESERVE UNIVERSITY May 2015 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of Angela Marie Lager Candidate for the Doctor of Philosophy degree*. (signed) Ronald A Conlon, PhD (Committee Chair) Paul J Tesar, PhD (Advisor) Craig A Hodges, PhD Warren J Alilain, PhD (date) 31 March 2015 *We also certify that written approval has been obtained from any proprietary material contained therein. TABLE OF CONTENTS Table of Contents……………………………………………………………………….1 List of Figures……………………………………………………………………………4 Acknowledgements……………………………………………………………………..7 Abstract…………………………………………………………………………………..8 Chapter 1: Introduction and Background………………………………………..11 1.1 Overview of mammalian oligodendrocyte development in the spinal cord and myelination of the central nervous system…………………..11 1.1.1 Introduction……………………………………………………..11 1.1.2 The establishment of the neuroectoderm and ventral formation of the neural tube…………………………………..12 1.1.3 Ventral patterning of the neural tube and specification of the pMN domain in the spinal cord……………………………….15 1.1.4 Oligodendrocyte progenitor cell production through the process of gliogenesis ………………………………………..16 1.1.5 Oligodendrocyte progenitor cell to oligodendrocyte differentiation…………………………………………………...22 -
Single-Cell Transcriptomics Identifies Dysregulated Metabolic Programs of Aging Alveolar Progenitor Cells in Lung Fibrosis
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.30.227892; this version posted July 30, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Single-Cell Transcriptomics Identifies Dysregulated Metabolic Programs of Aging Alveolar Progenitor Cells in Lung Fibrosis Jiurong Liang1,6, Guanling Huang1,6, Xue Liu1, Forough Taghavifar1, Ningshan Liu1, Changfu Yao1, Nan Deng2, Yizhou Wang3, Ankita Burman1, Ting Xie1, Simon Rowan1, 5 Peter Chen1, Cory Hogaboam1, Barry Stripp1, S. Samuel Weigt5, John Belperio5, William C. Parks1,4, Paul W. Noble1, and Dianhua Jiang1,4 1Department of Medicine and Women’s Guild Lung Institute, 2Samuel Oschin Comprehensive Cancer Institute, 3Genomics Core, 4Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA. 5Department of Medicine 10 University of California, Los Angeles (UCLA), Los Angeles, CA 90048, USA. 6These authors contributed equally. Correspondence and requests for materials should be addressed to P.W.N. ([email protected]), D.J. ([email protected]). Running title: Metabolic defect of aging alveolar progenitor 15 One sentence summary: Metabolic defects of alveolar progenitors in aging and during lung injury impair their renewal. Data availability: The single cell RNA-seq are deposited Funding statement: This work was supported by NIH grants R35-HL150829, R01- HL060539, R01-AI052201, R01-HL077291, and R01-HL122068, and P01-HL108793. 20 Conflict of interest: The authors declare that there is no conflict of interest. Ethics approval statement: All mouse experimens were under the guidance of the IACUC008529 in accordance with institutional and regulatory guidelines. -
Identification and Characterization of Tissue-Resident Memory T Cells in Humans Brahma Vencel Kumar
Identification and characterization of tissue-resident memory T cells in humans Brahma Vencel Kumar Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2018 ©2017 Brahma Vencel Kumar All rights reserved ABSTRACT Identification and characterization of tissue-resident memory T cells in humans Brahma Vencel Kumar Memory T cells are critical for maintaining lifelong immunity by protecting against reinfection with previously encountered pathogens. In recent years, a subset of memory T cells termed tissue-resident memory T cells (TRM) has emerged as the primary mediator of protection at many tissue sites. Numerous studies in mice have demonstrated that TRM accelerate pathogen clearance compared with other subsets of memory T cells. The defining characteristic of TRM is that they are retained within tissues and do not circulate in the blood. The lack of TRM in blood has proved to be a barrier for investigating the role of TRM in healthy humans. As a result, there are many outstanding questions about TRM biology in humans, including which phenotypic markers identify TRM, if TRM represent a unique memory subset, as well as defining transcriptional and functional characteristics of this subset. Through a unique collaboration with the local organ procurement agency, we obtained samples from >15 tissue sites from healthy organ donors of all ages. We found that the surface marker CD69 was expressed by memory CD4 + and CD8 + T cells in multiple tissues including spleen and other lymphoid tissues, lung, and intestines, but not in blood, suggesting that this marker may identify TRM in human tissues. -
Cellular and Molecular Signatures in the Disease Tissue of Early
Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of