Transposable Elements As Sensors of SARS-Cov-2 Infection
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Gene Expression Atlas.Pptx
ArrayExpress Gene Expression Atlas Investigating gene expression patterns The Bioinformatics Roadshow – Rotterdam Erasmus Postgraduate school Molecular Medicine Ibrahim Emam Functional Genomics Group European Bioinformatics Institute ArrayExpress – two databases May 2, 2012 2 How we view experiments… • Given one experiment where the effect of a particular compound treatment is assayed from two different strains in four different tissue types. 02/05/2012 3 Examine profile of Saa4 in one experiment • With respect to Compound Treatment 02/05/2012 4 Examine profile of Saa4 in one experiment • With respect to Genotype 02/05/2012 5 Examine profile of Saa4 in one experiment • With respect to Organism Part (Tissue) 02/05/2012 6 Atlas construction Atlas construction - example Meta-analysis framework • For each experiment: • Identify differentially expressed genes between groups of samples • A gene is significantly differentially expressed if the combined F- statistic derived from all pairwise comparisons of the means of a gene's expression levels across factors has a sufficiently small adjusted p-value. • Score every condition/gene/experiment triplet – this score gives us the likelihood that this gene is differentially expressed for this condition in the given experiment • Correct these scores for multiple testing and make a cut-off – differentially expressed: yes/no • Repeat for all experiments 02/05/20129 Meta-analysis framework-cont’d • For every condition-gene pair count in how many experiments it is differentially expressed • The result is -
Discovery of Screening Biomarkers for Major Depressive Disorder in Remission by Proteomic Approach
Article Discovery of Screening Biomarkers for Major Depressive Disorder in Remission by Proteomic Approach Hyebin Choi 1, Sora Mun 1, Eun-Jeong Joo 2,3, Kyu Young Lee 2,4, Hee-Gyoo Kang 1,5,* and Jiyeong Lee 6,* 1 Department of Senior Healthcare, Graduate School, Eulji University, Seongnam 13135, Korea; [email protected] (H.C.); [email protected] (S.M.) 2 Department of Neuropsychiatry, School of Medicine, Eulji University, Daejeon 34824, Korea; [email protected] (E.-J.J.); [email protected] (K.Y.L.) 3 Department of Psychiatry, Uijeongbu Eulji Medical Center, Eulji University, Gyeonggi 11759, Korea 4 Department of Psychiatry, Eulji General Hospital, Seoul 01830, Korea 5 Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Seongnam 13135, Korea 6 Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Uijeongbu 11759, Korea * Correspondence: [email protected] (H.-G.K.); [email protected] (J.L.); Tel.: +82-31-740-7315 (H.-G.K.); +82-42-259-1752 (J.L.) Abstract: Major depressive disorder (MDD) is a common disorder involving depressive mood and decreased motivation. Due to its high heterogeneity, novel biomarkers are required to diagnose MDD. In this study, a proteomic method was used to identify a new MDD biomarker. Using sequential window acquisition of all theoretical mass spectra acquisitions and multiple reaction monitoring analysis via mass spectrometry, relative and absolute quantification of proteins in the sera was per- formed. The results of the relative quantitation by sequential window acquisition for all theoretical mass spectra data showed that seven proteins were significantly differently expressed between MDD Citation: Choi, H.; Mun, S.; Joo, E.-J.; Lee, K.Y.; Kang, H.-G.; Lee, J. -
The Structure, Function and Evolution of the Extracellular Matrix: a Systems-Level Analysis
The Structure, Function and Evolution of the Extracellular Matrix: A Systems-Level Analysis by Graham L. Cromar A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Molecular Genetics University of Toronto © Copyright by Graham L. Cromar 2014 ii The Structure, Function and Evolution of the Extracellular Matrix: A Systems-Level Analysis Graham L. Cromar Doctor of Philosophy Department of Molecular Genetics University of Toronto 2014 Abstract The extracellular matrix (ECM) is a three-dimensional meshwork of proteins, proteoglycans and polysaccharides imparting structure and mechanical stability to tissues. ECM dysfunction has been implicated in a number of debilitating conditions including cancer, atherosclerosis, asthma, fibrosis and arthritis. Identifying the components that comprise the ECM and understanding how they are organised within the matrix is key to uncovering its role in health and disease. This study defines a rigorous protocol for the rapid categorization of proteins comprising a biological system. Beginning with over 2000 candidate extracellular proteins, 357 core ECM genes and 524 functionally related (non-ECM) genes are identified. A network of high quality protein-protein interactions constructed from these core genes reveals the ECM is organised into biologically relevant functional modules whose components exhibit a mosaic of expression and conservation patterns. This suggests module innovations were widespread and evolved in parallel to convey tissue specific functionality on otherwise broadly expressed modules. Phylogenetic profiles of ECM proteins highlight components restricted and/or expanded in metazoans, vertebrates and mammals, indicating taxon-specific tissue innovations. Modules enriched for medical subject headings illustrate the potential for systems based analyses to predict new functional and disease associations on the basis of network topology. -
Evolution of Gene Regulation in Ruminants Differs Between Evolutionary Breakpoint Regions and Homologous Synteny Blocks
Downloaded from genome.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press Research Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks Marta Farré,1,18 Jaebum Kim,2,18 Anastasia A. Proskuryakova,3,4 Yang Zhang,5 Anastasia I. Kulemzina,3 Qiye Li,6 Yang Zhou,6 Yingqi Xiong,6 Jennifer L. Johnson,7 Polina L. Perelman,3,4 Warren E. Johnson,8,9 Wesley C. Warren,10 Anna V. Kukekova,7 Guojie Zhang,6,11,12 Stephen J. O’Brien,13,14 Oliver A. Ryder,15 Alexander S. Graphodatsky,3,4 Jian Ma,5 Harris A. Lewin,16 and Denis M. Larkin1,17 1Royal Veterinary College, University of London, London NW1 0TU, United Kingdom; 2Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea; 3Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk 630090, Russia; 4Synthetic Biology Unit, Novosibirsk State University, Novosibirsk 630090, Russia; 5Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA; 6China National GeneBank, BGI- Shenzhen, Shenzhen 518083, China; 7Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA; 8Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia 22630, USA; 9Walter Reed Biosystematics Unit, Museum Support Center, Smithsonian Institution, Suitland, Maryland 20746, USA; 10Bond Life Sciences Center, University of Missouri, Columbia, Missouri 63201, USA; 11State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; 12Centre for Social Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; 13Theodosius Dobzhansky Center for Genome Bioinformatics, St. -
(12) United States Patent (10) Patent No.: US 7,662,389 B2 Clark Et Al
USOO7662389B2 (12) United States Patent (10) Patent No.: US 7,662,389 B2 Clark et al. (45) Date of Patent: Feb. 16, 2010 (54) USE OF SERUM AMYLOIDA GENE IN Cotton et al., Proc. Natl. Acad. Sci. USA 85.4397 (1988): “Reactivity DAGNOSIS AND TREATMENT OF of cytosine and thymine in single-base-pair mismatches with GLAUCOMIA AND IDENTIFICATION OF hydroxylamine and osmium tetroxide and its application to the study ANT-GLAUCOMAAGENTS of mutations'. Cotton, Mutat. Res. 285:125-144 (1993); "Current methods of muta tion detection'. (75) Inventors: Abbot F. Clark, Arlington, TX (US); Croninet al., Human Mutation 7:244-255 (1996); "Cystic Fibrosis Wan-Heng Wang, Grapevine, TX (US); Mutation Detection by Hybridization to Light-Generated DNA Loretta Graves McNatt, Hurst, TX Probe Arrays”. (US) Ermilov et al. (1993); Arkh Patol.; “Senile amyloidosis of the eye as a manifestation of senile cerebral amyloidosis' abstract with article (73) Assignee: Alcon, Inc., Hunenberg (CH) in Russian 55(6):43-45. Furlenato, CJ, and Campa A, Biochem. Biophys. Res. Commun 268:405-408 (2002), “A novel function of serum amyloid A. apotent (*) Notice: Subject to any disclaimer, the term of this stimulus for the release of tumor necrosis factor-alpha, interleukin-1 patent is extended or adjusted under 35 beta, and interleukin-8 by human blood neutrophil”. U.S.C. 154(b) by 130 days. Gasparini et al., Mol. Cell Probes 6:1-7 (1992); "Restriction site generating-polymerase chain reaction (RG-PCR) for the probeless (21) Appl. No.: 11/615.454 detection of hidden genetic variation: application to the study of some common cystic fibrosis mutations'. -
(SAA) Gene Cluster: Isoform Specific Responses to Bacterial Infection
Organization and Biology of the Porcine Serum Amyloid A (SAA) Gene Cluster: Isoform Specific Responses to Bacterial Infection Helle G. Olsen1, Kerstin Skovgaard2, Ole L. Nielsen1,Pa´ll S. Leifsson1, Henrik E. Jensen1, Tine Iburg1¤, Peter M. H. Heegaard2* 1 Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark, 2 Innate Immunology Group, National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark Abstract Serum amyloid A (SAA) is a prominent acute phase protein. Although its biological functions are debated, the wide species distribution of highly homologous SAA proteins and their uniform behavior in response to injury or inflammation in itself suggests a significant role for this protein. The pig is increasingly being used as a model for the study of inflammatory reactions, yet only little is known about how specific SAA genes are regulated in the pig during acute phase responses and other responses induced by pro-inflammatory host mediators. We designed SAA gene specific primers and quantified the gene expression of porcine SAA1, SAA2, SAA3, and SAA4 by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) in liver, spleen, and lung tissue from pigs experimentally infected with the Gram-negative swine specific bacterium Actinobacillus pleuropneumoniae, as well as from pigs experimentally infected with the Gram-positive bacterium Staphylococcus aureus. Our results show that: 1) SAA1 may be a pseudogene in pigs; 2) we were able to detect two previously uncharacterized SAA transcripts, namely SAA2 and SAA4, of which the SAA2 transcript is primarily induced in the liver during acute infection and presumably contributes to circulating SAA in pigs; 3) Porcine SAA3 transcription is induced both hepatically and extrahepatically during acute infection, and may be correlated to local organ affection; 4) Hepatic transcription of SAA4 is markedly induced in pigs infected with A. -
Cycles of Gene Expression and Genome Response During
Rib et al. Epigenetics & Chromatin (2018) 11:52 https://doi.org/10.1186/s13072-018-0222-0 Epigenetics & Chromatin RESEARCH Open Access Cycles of gene expression and genome response during mammalian tissue regeneration Leonor Rib1,2,3, Dominic Villeneuve1, Shilpi Minocha1, Viviane Praz1,2, Nouria Hernandez1, Nicolas Guex2*, Winship Herr1* and The CycliX Consortium Abstract Background: Compensatory liver hyperplasia—or regeneration—induced by two-thirds partial hepatectomy (PH) permits the study of synchronized activation of mammalian gene expression, particularly in relation to cell prolifera- tion. Here, we measured genomic transcriptional responses and mRNA accumulation changes after PH and sham surgeries. Results: During the frst 10–20 h, the PH- and sham-surgery responses were very similar, including parallel early activation of cell-division-cycle genes. After 20 h, however, whereas post-PH livers continued with a robust and coor- dinate cell-division-cycle gene-expression response before returning to the resting state by 1 week, sham-surgery livers returned directly to a resting gene-expression state. Localization of RNA polymerase II (Pol II), and trimethylated histone H3 lysine 4 (H3K4me3) and 36 (H3K36me3) on genes dormant in the resting liver and activated during the PH response revealed a general de novo promoter Pol II recruitment and H3K4me3 increase during the early 10–20 h phase followed by Pol II elongation and H3K36me3 accumulation in gene bodies during the later proliferation phase. H3K36me3, generally appearing at the frst internal exon, was preceded 5′ by H3K36me2; 3′ of the frst internal exon, in about half of genes H3K36me3 predominated and in the other half H3K36me2 and H3K36me3 co-existed. -
Bioinformatics Analysis of Differentially Expressed Proteins in Alcoholic Fatty Liver Disease Treated with Recombinant Human Cytoglobin
MOLECULAR MEDICINE REPORTS 23: 289, 2021 Bioinformatics analysis of differentially expressed proteins in alcoholic fatty liver disease treated with recombinant human cytoglobin ZI‑RONG ZHANG1*, ZHENG‑GEN YANG2*, YAN‑MEI XU1, ZHE‑YAN WANG1, JIAN WEN1, BO‑HONG CHEN1, PING WANG1, WEI WEI1, ZHEN LI1 and WEN‑QI DONG1 1Department of Biopharmacy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515; 2Guangzhou Koncen BioScience Co., Ltd., Guangzhou, Guangdong 510530, P.R. China Received February 29, 2020; Accepted June 26, 2020 DOI: 10.3892/mmr.2021.11929 Abstract. Cytoglobin (Cygb) is a globin molecule that is Introduction ubiquitously expressed in all tissues and has a protective role under oxidative stress. It has also been demonstrated to Alcoholic fatty liver disease (AFLD) is a disease of the liver be effective in the treatment of alcoholic fatty liver disease caused by long‑term heavy drinking. Over 90% of long‑term (AFLD). In order to study the molecular mechanisms under‑ alcoholics suffer from AFLD (1). Without proper treatment, lying its beneficial effects for the treatment of alcoholic liver, AFLD continues to deteriorate and develops into inflamma‑ two‑dimensional electrophoresis and mass spectrometric tion, fibrosis and cirrhosis, eventually leading to hepatocellular analysis were performed on serum and liver tissues from carcinoma. Fatty liver is usually accompanied by insulin an in vivo rat model of AFLD. A total of 26 differentially resistance (2), obesity (3) and dyslipidemia (4). AFLD is a expressed proteins were identified in the serum and 20 differ‑ worldwide medical problem associated with high morbidity entially expressed proteins were identified in liver specimens. -
Mouse Anti-Human Serum Amyloid a Monoclonal Antibody, Clone 4I84 (DCABH-6007) This Product Is for Research Use Only and Is Not Intended for Diagnostic Use
Mouse Anti-Human Serum Amyloid A Monoclonal Antibody, clone 4I84 (DCABH-6007) This product is for research use only and is not intended for diagnostic use. PRODUCT INFORMATION Specificity Recognize human SAA1. Do not recognize human SAA2, human SAA4, feline, canine, equine or bovine SAA. Immunogen Human serum amyloid A (SAA) Isotype IgG1 Source/Host Mouse Species Reactivity Human Clone 4I84 Purity Protein G purified Purification Purity≥ 95 % Conjugate Unconjugated Applications ELISA(Cap), ELISA(Det), LFIA We recommend the following for sandwich ELISA (Capture - Detection): DMAB8184 - DCABH-6007; DMAB8186 - DCABH-6007; DCABH-6007 - CABT-54364MH; CABT-54364MH - DCABH-6007 Epitope Recognizes aa 64-71 but also reacts with aa 28-38 indicating that the epitope may be partly conformational. Format Liquid Concentration Lot specific Size 1 mg Buffer 50 mM Na-citrate, pH 6.0, 0.9 % NaCI, 0.095 % NaN3 as a preservative. Preservative 0.095% sodium azide Storage Store at 2-8℃. 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 1 © Creative Diagnostics All Rights Reserved Ship Wet ice Warnings This product is for research use only and is not intended for diagnostic use. BACKGROUND Introduction Serum amyloid A (SAA) proteins are a family of apolipoproteins associated with high-density lipoprotein (HDL) in plasma. Different isoforms of SAA are expressed constitutively (constitutive SAAs) at different levels or in response to inflammatory stimuli (acute phase SAAs). These proteins are produced predominantly by the liver. The conservation of these proteins throughout invertebrates and vertebrates suggests that SAAs play a highly essential role in all animals. -
HDL Subclass Proteomic Analysis and Functional Implication of Protein Dynamic Change During HDL Maturation Yuling Zhang Sun Yat-Sen University, China
University of Kentucky UKnowledge Saha Cardiovascular Research Center Faculty Cardiovascular Research Publications 6-2019 HDL Subclass Proteomic Analysis and Functional Implication of Protein Dynamic Change During HDL Maturation Yuling Zhang Sun Yat-sen University, China Scott M. Gordon University of Kentucky, [email protected] Hang Xi Temple University Seungbum Choi Temple University Merlin Abner Paz Temple University See next page for additional authors RFoigllohtw c licthiks t aond ope addn ait feionedalba wckork fosr mat :inh att nps://uknoew tab to lewtle usdg kne.ukowy .hedu/cow thivrsc_fa documcpubent benefits oy u. Part of the Biology Commons, Cardiology Commons, and the Circulatory and Respiratory Physiology Commons Repository Citation Zhang, Yuling; Gordon, Scott M.; Xi, Hang; Choi, Seungbum; Paz, Merlin Abner; Sun, Runlu; Yang, William; Saredy, Jason; Khan, Mohsin; Remaley, Alan Thomas; Wang, Jing-Feng; Yang, Xiaofeng; and Wang, Hong, "HDL Subclass Proteomic Analysis and Functional Implication of Protein Dynamic Change During HDL Maturation" (2019). Saha Cardiovascular Research Center Faculty Publications. 42. https://uknowledge.uky.edu/cvrc_facpub/42 This Article is brought to you for free and open access by the Cardiovascular Research at UKnowledge. It has been accepted for inclusion in Saha Cardiovascular Research Center Faculty Publications by an authorized administrator of UKnowledge. For more information, please contact [email protected]. Authors Yuling Zhang, Scott M. Gordon, Hang Xi, Seungbum Choi, Merlin Abner Paz, Runlu Sun, William Yang, Jason Saredy, Mohsin Khan, Alan Thomas Remaley, Jing-Feng Wang, Xiaofeng Yang, and Hong Wang HDL Subclass Proteomic Analysis and Functional Implication of Protein Dynamic Change During HDL Maturation Notes/Citation Information Published in Redox Biology, v. -
Communication in Asthmatic Airways Inflammation and Intercellular Gene
Downloaded from http://www.jimmunol.org/ by guest on October 2, 2021 is online at: average * The Journal of Immunology , 10 of which you can access for free at: 2011; 186:1861-1869; Prepublished online 27 from submission to initial decision 4 weeks from acceptance to publication December 2010; doi: 10.4049/jimmunol.1002568 http://www.jimmunol.org/content/186/3/1861 Gene Expression Patterns of Th2 Inflammation and Intercellular Communication in Asthmatic Airways David F. Choy, Barmak Modrek, Alexander R. Abbas, Sarah Kummerfeld, Hilary F. Clark, Lawren C. Wu, Grazyna Fedorowicz, Zora Modrusan, John V. Fahy, Prescott G. Woodruff and Joseph R. Arron J Immunol cites 63 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by 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://jimmunol.org/subscription http://www.jimmunol.org/content/suppl/2010/12/27/jimmunol.100256 8.DC1 This article http://www.jimmunol.org/content/186/3/1861.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2011 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of October 2, 2021. The Journal of Immunology Gene Expression Patterns of Th2 Inflammation and Intercellular Communication in Asthmatic Airways David F. -
SAA1 Polymorphisms Are Associated with Variation in Antiangiogenic and Tumor-Suppressive Activities in Nasopharyngeal Carcinoma
Oncogene (2015) 34, 878–889 © 2015 Macmillan Publishers Limited All rights reserved 0950-9232/15 www.nature.com/onc ORIGINAL ARTICLE SAA1 polymorphisms are associated with variation in antiangiogenic and tumor-suppressive activities in nasopharyngeal carcinoma HL Lung1, OY Man1, MC Yeung1, JMY Ko1, AKL Cheung1, EWL Law1,ZYu1, WH Shuen1, E Tung1,2, SHK Chan1, DK Bangarusamy3,8, Y Cheng1, X Yang1,RKan1, Y Phoon1, KC Chan1, D Chua1,2,4, DL Kwong1,2, AWM Lee2,5,6,MFJi7 and ML Lung1,2 Nasopharyngeal carcinoma (NPC) is a cancer that occurs in high frequency in Southern China. A previous functional complementation approach and the subsequent cDNA microarray analysis have identified that serum amyloid A1 (SAA1) is an NPC candidate tumor suppressor gene. SAA1 belongs to a family of acute-phase proteins that are encoded by five polymorphic coding alleles. The SAA1 genotyping results showed that only three SAA1 isoforms (SAA1.1, 1.3 and 1.5) were observed in both Hong Kong NPC patients and healthy individuals. This study aims to determine the functional role of SAA1 polymorphisms in tumor progression and to investigate the relationship between SAA1 polymorphisms and NPC risk. Indeed, we have shown that restoration of SAA1.1 and 1.3 in the SAA1-deficient NPC cell lines could suppress tumor formation and angiogenesis in vitro and in vivo. The secreted SAA1.1 and SAA1.3 proteins can block cell adhesion and induce apoptosis in the vascular endothelial cells. In contrast, the SAA1.5 cannot induce apoptosis or inhibit angiogenesis because of its weaker binding affinity to αVβ3 integrin.