The Role of Sp140 Revealed in Ige and Mast Cell Responses in Collaborative Cross Mice
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DEPs in osteosarcoma cells comparing to osteoblastic cells Biological Process Protein Percentage of Hits metabolic process (GO:0008152) 29.3 29.3% cellular process (GO:0009987) 20.2 20.2% localization (GO:0051179) 9.4 9.4% biological regulation (GO:0065007) 8 8.0% developmental process (GO:0032502) 7.8 7.8% response to stimulus (GO:0050896) 5.6 5.6% cellular component organization (GO:0071840) 5.6 5.6% multicellular organismal process (GO:0032501) 4.4 4.4% immune system process (GO:0002376) 4.2 4.2% biological adhesion (GO:0022610) 2.7 2.7% apoptotic process (GO:0006915) 1.6 1.6% reproduction (GO:0000003) 0.8 0.8% locomotion (GO:0040011) 0.4 0.4% cell killing (GO:0001906) 0.1 0.1% 100.1% Genes 2179Hits 3870 biological adhesion apoptotic process … reproduction (GO:0000003) , 0.8% (GO:0022610) , 2.7% locomotion (GO:0040011) ,… immune system process cell killing (GO:0001906) , 0.1% (GO:0002376) , 4.2% multicellular organismal process (GO:0032501) , metabolic process 4.4% (GO:0008152) , 29.3% cellular component organization (GO:0071840) , 5.6% response to stimulus (GO:0050896), 5.6% developmental process (GO:0032502) , 7.8% biological regulation (GO:0065007) , 8.0% cellular process (GO:0009987) , 20.2% localization (GO:0051179) , 9. -
CD56+ T-Cells in Relation to Cytomegalovirus in Healthy Subjects and Kidney Transplant Patients
CD56+ T-cells in Relation to Cytomegalovirus in Healthy Subjects and Kidney Transplant Patients Institute of Infection and Global Health Department of Clinical Infection, Microbiology and Immunology Thesis submitted in accordance with the requirements of the University of Liverpool for the degree of Doctor in Philosophy by Mazen Mohammed Almehmadi December 2014 - 1 - Abstract Human T cells expressing CD56 are capable of tumour cell lysis following activation with interleukin-2 but their role in viral immunity has been less well studied. The work described in this thesis aimed to investigate CD56+ T-cells in relation to cytomegalovirus infection in healthy subjects and kidney transplant patients (KTPs). Proportions of CD56+ T cells were found to be highly significantly increased in healthy cytomegalovirus-seropositive (CMV+) compared to cytomegalovirus-seronegative (CMV-) subjects (8.38% ± 0.33 versus 3.29%± 0.33; P < 0.0001). In donor CMV-/recipient CMV- (D-/R-)- KTPs levels of CD56+ T cells were 1.9% ±0.35 versus 5.42% ±1.01 in D+/R- patients and 5.11% ±0.69 in R+ patients (P 0.0247 and < 0.0001 respectively). CD56+ T cells in both healthy CMV+ subjects and KTPs expressed markers of effector memory- RA T-cells (TEMRA) while in healthy CMV- subjects and D-/R- KTPs the phenotype was predominantly that of naïve T-cells. Other surface markers, CD8, CD4, CD58, CD57, CD94 and NKG2C were expressed by a significantly higher proportion of CD56+ T-cells in healthy CMV+ than CMV- subjects. Functional studies showed levels of pro-inflammatory cytokines IFN-γ and TNF-α, as well as granzyme B and CD107a were significantly higher in CD56+ T-cells from CMV+ than CMV- subjects following stimulation with CMV antigens. -
The Conserved Structure of Plant Telomerase RNA Provides the Missing Link for an Evolutionary Pathway from Ciliates to Humans
The conserved structure of plant telomerase RNA provides the missing link for an evolutionary pathway from ciliates to humans Jiarui Songa, Dhenugen Logeswaranb,1, Claudia Castillo-Gonzáleza,1, Yang Lib, Sreyashree Bosea, Behailu Birhanu Aklilua, Zeyang Mac,d, Alexander Polkhovskiya,e, Julian J.-L. Chenb,2, and Dorothy E. Shippena,2 aDepartment of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843; bSchool of Molecular Sciences, Arizona State University, Tempe, AZ 85287; cNational Maize Improvement Center of China, China Agricultural University, 100193 Beijing, China; dCollege of Agronomy and Biotechnology, China Agricultural University, 100193 Beijing, China; and eCenter of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russian Federation Edited by Thomas R. Cech, University of Colorado Boulder, Boulder, CO, and approved October 24, 2019 (received for review September 4, 2019) Telomerase is essential for maintaining telomere integrity. Although transcribed by RNA polymerase III (Pol III) (6, 7). The La-related telomerase function is widely conserved, the integral telomerase protein P65 in Tetrahymena recognizes the 3′ poly-U tail of TR RNA (TR) that provides a template for telomeric DNA synthesis has and bends the RNA to facilitate telomerase RNP assembly (8, 9). diverged dramatically. Nevertheless, TR molecules retain 2 highly In contrast, fungi maintain much larger TR molecules (900 to conserved structural domains critical for catalysis: a template- 2,400 nt) that are transcribed by RNA polymerase II (Pol II) (3). proximal pseudoknot (PK) structure and a downstream stem-loop The 3′ end maturation of fungal TRs requires components of the structure. Here we introduce the authentic TR from the plant canonical snRNA biogenesis pathway and results in RNP assembly Arabidopsis thaliana, called AtTR, identified through next-generation sequencing of RNAs copurifying with Arabidopsis TERT. -
Role of the Transcriptional Regulator SP140 in Resistance
RESEARCH ARTICLE Role of the transcriptional regulator SP140 in resistance to bacterial infections via repression of type I interferons Daisy X Ji1†, Kristen C Witt1†, Dmitri I Kotov1,2, Shally R Margolis1, Alexander Louie1, Victoria Cheve´ e1, Katherine J Chen1,2, Moritz M Gaidt1, Harmandeep S Dhaliwal3, Angus Y Lee3, Stephen L Nishimura4, Dario S Zamboni5, Igor Kramnik6, Daniel A Portnoy1,7,8, K Heran Darwin9, Russell E Vance1,2,3* 1Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States; 2Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States; 3Cancer Research Laboratory, University of California, Berkeley, Berkeley, United States; 4Department of Pathology, University of California, San Francisco, San Francisco, United States; 5Department of Cell Biology, Ribeira˜ o Preto Medical School, University of Sa˜ o Paulo, Sa˜ o Paulo, Brazil; 6The National Emerging Infectious Diseases Laboratory, Department of Medicine (Pulmonary Center), and Department of Microbiology, Boston University School of Medicine, Boston, United States; 7Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States; 8Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States; 9Department of Microbiology, New York University Grossman School of Medicine, New York, United States *For correspondence: [email protected] Abstract Type I interferons (IFNs) are essential for anti-viral immunity, but often impair †These authors contributed protective immune responses during bacterial infections. An important question is how type I IFNs equally to this work are strongly induced during viral infections, and yet are appropriately restrained during bacterial infections. -
Análise Integrativa De Perfis Transcricionais De Pacientes Com
UNIVERSIDADE DE SÃO PAULO FACULDADE DE MEDICINA DE RIBEIRÃO PRETO PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Ribeirão Preto – 2012 ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Tese apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo para obtenção do título de Doutor em Ciências. Área de Concentração: Genética Orientador: Prof. Dr. Eduardo Antonio Donadi Co-orientador: Prof. Dr. Geraldo A. S. Passos Ribeirão Preto – 2012 AUTORIZO A REPRODUÇÃO E DIVULGAÇÃO TOTAL OU PARCIAL DESTE TRABALHO, POR QUALQUER MEIO CONVENCIONAL OU ELETRÔNICO, PARA FINS DE ESTUDO E PESQUISA, DESDE QUE CITADA A FONTE. FICHA CATALOGRÁFICA Evangelista, Adriane Feijó Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. Ribeirão Preto, 2012 192p. Tese de Doutorado apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo. Área de Concentração: Genética. Orientador: Donadi, Eduardo Antonio Co-orientador: Passos, Geraldo A. 1. Expressão gênica – microarrays 2. Análise bioinformática por module maps 3. Diabetes mellitus tipo 1 4. Diabetes mellitus tipo 2 5. Diabetes mellitus gestacional FOLHA DE APROVAÇÃO ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. -
(P -Value<0.05, Fold Change≥1.4), 4 Vs. 0 Gy Irradiation
Table S1: Significant differentially expressed genes (P -Value<0.05, Fold Change≥1.4), 4 vs. 0 Gy irradiation Genbank Fold Change P -Value Gene Symbol Description Accession Q9F8M7_CARHY (Q9F8M7) DTDP-glucose 4,6-dehydratase (Fragment), partial (9%) 6.70 0.017399678 THC2699065 [THC2719287] 5.53 0.003379195 BC013657 BC013657 Homo sapiens cDNA clone IMAGE:4152983, partial cds. [BC013657] 5.10 0.024641735 THC2750781 Ciliary dynein heavy chain 5 (Axonemal beta dynein heavy chain 5) (HL1). 4.07 0.04353262 DNAH5 [Source:Uniprot/SWISSPROT;Acc:Q8TE73] [ENST00000382416] 3.81 0.002855909 NM_145263 SPATA18 Homo sapiens spermatogenesis associated 18 homolog (rat) (SPATA18), mRNA [NM_145263] AA418814 zw01a02.s1 Soares_NhHMPu_S1 Homo sapiens cDNA clone IMAGE:767978 3', 3.69 0.03203913 AA418814 AA418814 mRNA sequence [AA418814] AL356953 leucine-rich repeat-containing G protein-coupled receptor 6 {Homo sapiens} (exp=0; 3.63 0.0277936 THC2705989 wgp=1; cg=0), partial (4%) [THC2752981] AA484677 ne64a07.s1 NCI_CGAP_Alv1 Homo sapiens cDNA clone IMAGE:909012, mRNA 3.63 0.027098073 AA484677 AA484677 sequence [AA484677] oe06h09.s1 NCI_CGAP_Ov2 Homo sapiens cDNA clone IMAGE:1385153, mRNA sequence 3.48 0.04468495 AA837799 AA837799 [AA837799] Homo sapiens hypothetical protein LOC340109, mRNA (cDNA clone IMAGE:5578073), partial 3.27 0.031178378 BC039509 LOC643401 cds. [BC039509] Homo sapiens Fas (TNF receptor superfamily, member 6) (FAS), transcript variant 1, mRNA 3.24 0.022156298 NM_000043 FAS [NM_000043] 3.20 0.021043295 A_32_P125056 BF803942 CM2-CI0135-021100-477-g08 CI0135 Homo sapiens cDNA, mRNA sequence 3.04 0.043389246 BF803942 BF803942 [BF803942] 3.03 0.002430239 NM_015920 RPS27L Homo sapiens ribosomal protein S27-like (RPS27L), mRNA [NM_015920] Homo sapiens tumor necrosis factor receptor superfamily, member 10c, decoy without an 2.98 0.021202829 NM_003841 TNFRSF10C intracellular domain (TNFRSF10C), mRNA [NM_003841] 2.97 0.03243901 AB002384 C6orf32 Homo sapiens mRNA for KIAA0386 gene, partial cds. -
Supplementary Material Computational Prediction of SARS
Supplementary_Material Computational prediction of SARS-CoV-2 encoded miRNAs and their putative host targets Sheet_1 List of potential stem-loop structures in SARS-CoV-2 genome as predicted by VMir. Rank Name Start Apex Size Score Window Count (Absolute) Direct Orientation 1 MD13 2801 2864 125 243.8 61 2 MD62 11234 11286 101 211.4 49 4 MD136 27666 27721 104 205.6 119 5 MD108 21131 21184 110 204.7 210 9 MD132 26743 26801 119 188.9 252 19 MD56 9797 9858 128 179.1 59 26 MD139 28196 28233 72 170.4 133 28 MD16 2934 2974 76 169.9 71 43 MD103 20002 20042 80 159.3 403 46 MD6 1489 1531 86 156.7 171 51 MD17 2981 3047 131 152.8 38 87 MD4 651 692 75 140.3 46 95 MD7 1810 1872 121 137.4 58 116 MD140 28217 28252 72 133.8 62 122 MD55 9712 9758 96 132.5 49 135 MD70 13171 13219 93 130.2 131 164 MD95 18782 18820 79 124.7 184 173 MD121 24086 24135 99 123.1 45 176 MD96 19046 19086 75 123.1 179 196 MD19 3197 3236 76 120.4 49 200 MD86 17048 17083 73 119.8 428 223 MD75 14534 14600 137 117 51 228 MD50 8824 8870 94 115.8 79 234 MD129 25598 25642 89 115.6 354 Reverse Orientation 6 MR61 19088 19132 88 197.8 271 10 MR72 23563 23636 148 188.8 286 11 MR11 3775 3844 136 185.1 116 12 MR94 29532 29582 94 184.6 271 15 MR43 14973 15028 109 183.9 226 27 MR14 4160 4206 89 170 241 34 MR35 11734 11792 111 164.2 37 52 MR5 1603 1652 89 152.7 118 53 MR57 18089 18132 101 152.7 139 94 MR8 2804 2864 122 137.4 38 107 MR58 18474 18508 72 134.9 237 117 MR16 4506 4540 72 133.8 311 120 MR34 10010 10048 82 132.7 245 133 MR7 2534 2578 90 130.4 75 146 MR79 24766 24808 75 127.9 59 150 MR65 21528 21576 99 127.4 83 180 MR60 19016 19049 70 122.5 72 187 MR51 16450 16482 75 121 363 190 MR80 25687 25734 96 120.6 75 198 MR64 21507 21544 70 120.3 35 206 MR41 14500 14542 84 119.2 94 218 MR84 26840 26894 108 117.6 94 Sheet_2 List of stable stem-loop structures based on MFE. -
Termination of RNA Polymerase II Transcription by the 5’-3’ Exonuclease Xrn2
TERMINATION OF RNA POLYMERASE II TRANSCRIPTION BY THE 5’-3’ EXONUCLEASE XRN2 by MICHAEL ANDRES CORTAZAR OSORIO B.S., Universidad del Valle – Colombia, 2011 A thesis submitted to the Faculty of the Graduate School of the University of Colorado in partial fulfillment of the requirements for the degree of Doctor of Philosophy Molecular Biology Program 2018 This thesis for the Doctor of Philosophy degree by Michael Andrés Cortázar Osorio has been approved for the Molecular Biology Program by Mair Churchill, Chair Richard Davis Jay Hesselberth Thomas Blumenthal James Goodrich David Bentley, Advisor Date: Aug 17, 2018 ii Cortázar Osorio, Michael Andrés (Ph.D., Molecular Biology) Termination of RNA polymerase II transcription by the 5’-3’ exonuclease Xrn2 Thesis directed by Professor David L. Bentley ABSTRACT Termination of transcription occurs when RNA polymerase (pol) II dissociates from the DNA template and releases a newly-made mRNA molecule. Interestingly, an active debate fueled by conflicting reports over the last three decades is still open on which of the two main models of termination of RNA polymerase II transcription does in fact operate at 3’ ends of genes. The torpedo model indicates that the 5’-3’ exonuclease Xrn2 targets the nascent transcript for degradation after cleavage at the polyA site and chases pol II for termination. In contrast, the allosteric model asserts that transcription through the polyA signal induces a conformational change of the elongation complex and converts it into a termination-competent complex. In this thesis, I propose a unified allosteric-torpedo mechanism. Consistent with a polyA site-dependent conformational change of the elongation complex, I found that pol II transitions at the polyA site into a mode of slow transcription elongation that is accompanied by loss of Spt5 phosphorylation in the elongation complex. -
RNA Polymerase III Interferes with Ty3 Integration
FEBS 18345 FEBS Letters 405 (1997) 305-311 RNA polymerase III interferes with Ty3 integration Charles M. Connolly1, Suzanne B. Sandmeyer* Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, CA 92697-4025, USA Received 8 January 1997; revised version received 12 February 1997 verse transcription of Ty3 RNA in association with the VLP, Abstract Ty3, a gypsylike retrotransposon of budding yeast, integrates at the transcription initiation site of genes transcribed the DNA copy is integrated into the host genome in a process by RNA polymerase III (pol III). It was previously shown that mediated by Ty3 integrase (IN) [12]. Ty3 IN is a homologue integration in vitro requires intact promoter elements and the pol of retroviral IN. Recombinant retroviral IN has been demon- III transcription factors TFIIIB and TFIIIC. In order to test the strated to have in vitro 3'-end processing and strand-transfer effect of pol III on integration, increasing amounts of a pol Ill- activities (reviewed in [13]). Although Ty3 IN has been dem- containing fraction were added to Ty3 in vitro integration onstrated to be required in vivo for 3'-end processing and reactions. The pol Ill-containing fraction was inhibitory to integration of Ty3 DNA, integration activity has only been integration. These results are consistent with a model where the observed in vitro in association with a VLP fraction [14]. Ty3 integration complex and pol III recognize similar features of the stable transcription complex and compete with each other for Despite the many similarities between retroviruses and Ty3 access to the transcription initiation site. -
Ncrna Synthesis Ny RNA Polymerase
“The functional characterization of mammalian non-coding Y RNAs” Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) der Naturwissenschaftlichen Fakultät I – Biowissenschaften – der Martin-Luther-Universität Halle-Wittenberg, vorgelegt von Herrn Marcel Köhn geb. am 04.01.1983 in Wolgast Öffentlich verteidigt am 30.10.2015 Gutachter: Prof. Dr. Stefan Hüttelmaier (Halle, Deutschland) Prof. Dr. Elmar Wahle (Halle, Deutschland) Prof. Dr. Daniel Zenklusen (Montreal, Kanada) Contents Abstract 1. Non-coding RNAs (ncRNAs) 2. NcRNA synthesis by RNA polymerase III 2.1. NcRNAs transcribed from type I and II POLIII-genes 2.2. NcRNAs transcribed from type III POLIII-genes 3. The non-coding Y RNAs 3.1. Evolution of Y RNAs 3.2. Y RNA genes and expression patterns 3.3. Processing of Y RNAs 3.4. Subcellular localization of Y RNAs 3.5. Y RNA-associated proteins 3.6. The Y RNA core proteins – La and Ro60 3.7. A paradigm of accessory Y RNA-binding proteins – IGF2BPs 3.8. The characterization of Y RNPs 3.9. The association of Y3/Y3** with mRNA 3’-end processing factors 4. Y RNA functions 4.1. The role of Y RNAs in DNA replication and cell growth 4.2. Y RNAs as modulators of Ro60 function and cellular stress 5. The role of Y3/Y3** in the 3’-end processing of histone mRNAs 5.1. The depletion of Y RNAs and their impact on pre-mRNA processing 5.2. The evolutionary conservation of Y3’s role in histone mRNA processing 5.3. Y3** ncRNA is essential for histone mRNA processing 5.4. -
Variants Within the SP110 Nuclear Body Protein Modify Risk of Canine
Variants within the SP110 nuclear body protein modify PNAS PLUS risk of canine degenerative myelopathy Emma L. Ivanssona,b,1,2, Kate Megquiera,b, Sergey V. Kozyreva, Eva Muréna, Izabella Baranowska Körbergc,3, Ross Swoffordb, Michele Koltookianb, Noriko Tonomurab,d, Rong Zenge, Ana L. Kolicheskie, Liz Hansene, Martin L. Katzf, Gayle C. Johnsone, Gary S. Johnsone, Joan R. Coatesg, and Kerstin Lindblad-Toha,b,1 aScience for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden; bBroad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142; cDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden; dDepartment of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA 01536; eDepartment of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211; fMason Eye Institute, School of Medicine, University of Missouri, Columbia, MO 65201; and gDepartment of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211 Edited by Stephen T. Warren, Emory University School of Medicine, Atlanta, GA, and approved April 15, 2016 (received for review January 7, 2016) Canine degenerative myelopathy (DM) is a naturally occurring several clinical subtypes with variable phenotypic presentation and neurodegenerative disease with similarities to some forms of prognosis. amyotrophic lateral sclerosis (ALS). Most dogs that develop DM Over 20 y ago, a mutation in the superoxide dismutase 1 gene are homozygous for a common superoxide dismutase 1 gene (SOD1) was the first genetic risk factor to be identified (4). To (SOD1) mutation. However, not all dogs homozygous for this date, more than 160 SOD1 mutations involving all five exons mutation develop disease. -
RNA Polymerase III Subunit Architecture and Implications for Open Promoter Complex Formation
RNA polymerase III subunit architecture and implications for open promoter complex formation Chih-Chien Wua,b, Franz Herzogc, Stefan Jennebachd, Yu-Chun Lina, Chih-Yu Paia, Ruedi Aebersoldc,e, Patrick Cramerd, and Hung-Ta Chena,1 aInstitute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China; bDepartment of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan 112, Republic of China; cDepartment of Biology, Institute of Molecular Systems Biology, Eidgenössiche Technische Hochschule Zurich, CH-8093 Zurich, Switzerland; dGene Center and Department of Biochemistry, Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany; and eFaculty of Science, University of Zurich, CH-8006 Zurich, Switzerland Edited by E. Peter Geiduschek, University of California at San Diego, La Jolla, CA, and approved October 3, 2012 (received for review July 11, 2012) Transcription initiation by eukaryotic RNA polymerase (Pol) III relies subcomplexes and their contacts with the 12-subunit polymerase on the TFIIE-related subcomplex C82/34/31. Here we combine cross- core. The C37/53 dimerization module was positioned into the linking and hydroxyl radical probing to position the C82/34/31 electron density adjacent to the lobe domain of the C128 subunit subcomplex around the Pol III active center cleft. The extended on one side of the polymerase cleft, similar to the localization of winged helix (WH) domains 1 and 4 of C82 localize to the polymerase the TFIIF dimerization module and the A49/34.5 dimerization domains clamp head and clamp core, respectively, and the two WH module on Pol II and Pol I, respectively (23–25).