DOCSLIB.ORG

Key Virus-Host Interactions Required for Arenavirus Particle Assembly and Release Christopher Michael Ziegler University of Vermont

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Key Virus-Host Interactions Required for Arenavirus Particle Assembly and Release Christopher Michael Ziegler University of Vermont University of Vermont ScholarWorks @ UVM Graduate College Dissertations and Theses Dissertations and Theses 2017 Key Virus-Host Interactions Required For Arenavirus Particle Assembly And Release Christopher Michael Ziegler University of Vermont Follow this and additional works at: https://scholarworks.uvm.edu/graddis Part of the Cell Biology Commons, and the Virology Commons Recommended Citation Ziegler, Christopher Michael, "Key Virus-Host Interactions Required For Arenavirus Particle Assembly And Release" (2017). Graduate College Dissertations and Theses. 755. https://scholarworks.uvm.edu/graddis/755 This Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks @ UVM. It has been accepted for inclusion in Graduate College Dissertations and Theses by an authorized administrator of ScholarWorks @ UVM. For more information, please contact [email protected]. KEY VIRUS-HOST INTERACTIONS REQUIRED FOR ARENAVIRUS PARTICLE ASSEMBLY AND RELEASE A Dissertation Presented by Christopher Michael Ziegler to The Faculty of the Graduate College of The University of Vermont In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Specializing in Cellular, Molecular and Biomedical Sciences May, 2017 Defense Date: March 24th, 2017 Dissertation Examination Committee: Jason W. Botten, Ph.D., Advisor Bryan A. Ballif, Ph.D., Chairperson Christopher D. Huston, Ph.D. Dimitry Krementsov, Ph.D. Cynthia J. Forehand, Ph.D., Dean of the Graduate College ABSTRACT Viruses are infectious agents that must infect the cells of living organisms in order to reproduce. They have relatively simple genomes which encode few proteins but can compensate for their simplicity by hijacking components of their cellular hosts. Arenaviruses, a family of zoonotic viruses carried by rodents, encode only 4 proteins. One of these proteins, Z, is responsible for several functions during the virus life cycle including driving the formation and release of new virus particles at the plasma membrane of infected cells. Relatively little is known about how this viral protein is regulated or the complement of host proteins it engages in order to produce new virus particles or augment Z’s other functions. To address this gap in knowledge, mass spectrometry was used to identify phosphorylation sites in the Old World arenavirus, lymphocytic choriomeningitis virus (LCMV) Z protein. Phosphorylation sites were identified at serine 41 (S41) and tyrosine 88 (Y88). Functional studies using recombinant (r)LCMV containing mutations at these phosphorylation sites revealed that both were important for the production of defective interfering (DI) particles. DI particles are replication-incompetent virus particles that interfere with the production of infectious virus and mitigate its cytopathic effect. While a mutation that mimics phosphorylation at S41 reduced LCMV’s ability to produce both infectious and DI particles, this mutation had a much stronger impact on DI particles. Production of DI particles in Y88-mutant rLCMV was drastically reduced while the impact on infectious virus was minimal. Y88 lies within a type of viral late domain (PPXY) also found in matrix proteins of several disparate virus families where it has been shown to drive infectious virus release by recruiting the membrane scission machinery of the cellular endosomal sorting complex required for transport (ESCRT). Inhibition of the ESCRT pathway drastically reduced LCMV DI particle but not infectious virus release indicating that Z’s PPXY late domain and the cellular ESCRT complex are required specifically for the production of DI particles. Mass spectrometry was also used to identify host protein partners of Z as well as the host proteins recruited into virus particles for the New World arenavirus, Junín (JUNV). ESCRT complex proteins were enriched in JUNV virus-like particles (VLPs) and bona fide virions. In contrast to LCMV, inhibition of the ESCRT complex resulted in significantly less infectious JUNV release. This indicates that the ultimate role of ESCRT engagement by the Old World arenavirus, LCMV, differs from that of New World, JUNV. This work represents the first demonstration that a viral protein motif and the host machinery it engages selectively drive DI particle production independently of infectious virus. It also suggests that host cell kinases can dynamically regulate the production of DI particles through phosphorylation of Z. Finally, the late domain-mutant rLCMV generated in these studies represents the first LCMV strain known to produce undetectable levels of DI particles which provides the opportunity to assess the impact that a loss of DI particles has on the ability of LCMV to establish or maintain a persistent infection. CITATIONS Material from this dissertation has been published in the following form: Ziegler, C.M., Eisenhauer, P., Bruce, E.A., Weir, M.E., King, B.R., Klaus, J.P., Krementsov, D.N., Shirley, D.J., Ballif, B.A., Botten, J.. (2016). The Lymphocytic Choriomeningitis Virus Matrix Protein PPXY Late Domain Drives the Production of Defective Interfering Particles. PLoS Pathogens, 12:e1005501. Ziegler, C.M., Eisenhauer, P., Bruce, E.A., Beganovic, V., King, B.R., Weir, M.E., Ballif, B.A., Botten, J.. (2016). A novel phosphoserine motif in the LCMV matrix protein Z regulates the release of infectious virus and defective interfering particles. Journal of General Virology, doi:doi:10.1099/jgv.0.000550. ii ACKNOWLEDGEMENTS I would like to thank my advisor, Jason Botten, for giving me this opportunity and for being such a positive and professional role model. It has been great to work with a fellow Minnesotan and I have really enjoyed my time in your lab. I would like to thank my colleagues in the Botten lab for all the support and advice over the years and for making the lab such a positive and enjoyable place to work. I would especially like to thank Phil Eisenhauer for all of the hours he put in to support this work. I have had the pleasure of working with several undergraduate students over the last few years including Vedran Beganovic, Loan Dang, and Jamie Kelly. I would like to thank them for all of their hard work and recognize their significant contributions to these projects. I would also like to thank them for giving me the opportunity to guide them through their research projects. Lastly, I would like to thank Terri Messier and Barry Finette for giving me a start in science. Terri took me under her wing when I was a young student and I will not forget the impact that she has had in getting me to where I am today. I would like to also thank my friends and family who have provided the support that has allowed me to reach this point. My parents, who imparted on me a work ethic that has driven me to achievement in many aspects of my life, but while also teaching me to stop and smell the roses once in a while. My two brothers, Matt and Jesse, who have always kept me motivated and provided support in many ways when I needed iii it. My older brother Jesse has been a role model for me in more ways than he probably realizes throughout my life. And finally, I would like to thank my girlfriend and best friend Catherine for all the support and encouragement through this endeavor. It wouldn’t have been nearly as great without you in my life. iv TABLE OF CONTENTS Page CITATIONS ....................................................................................................................... ii ACKNOWLEDGEMENTS ............................................................................................... iii LIST OF TABLES ........................................................................................................... viii LIST OF FIGURES ........................................................................................................... ix CHAPTER 1: COMPREHENSIVE LITERATURE REVIEW ......................................... 1 1.1. Introduction .............................................................................................................. 1 1.2. Arenaviruses ............................................................................................................ 3 1.3. The Z Matrix Protein ............................................................................................... 8 1.4. Defective Interfering Particles ............................................................................... 14 1.5. The ESCRT Pathway and Late Domains ............................................................... 21 1.6. Summary ................................................................................................................ 30 References ..................................................................................................................... 32 CHAPTER 2: THE LYMPHOCYTIC CHORIOMENINGITIS VIRUS MATRIX PROTEIN PPXY LATE DOMAIN DRIVES THE PRODUCTION OF DEFECTIVE INTERFERING PARTICLES .......................................................................................... 52 Abstract ......................................................................................................................... 53 Author Summary ........................................................................................................... 54 Introduction ................................................................................................................... 55 Results ..........................................................................................................................
Load more

Recommended publications
  • Anti-Rab11 Antibody (ARG41900)
    Product datasheet [email protected] ARG41900 Package: 100 μg anti-Rab11 antibody Store at: -20°C Summary Product Description Goat Polyclonal antibody recognizes Rab11 Tested Reactivity Hu, Ms, Rat, Dog, Mk Tested Application IHC-Fr, IHC-P, WB Host Goat Clonality Polyclonal Isotype IgG Target Name Rab11 Antigen Species Mouse Immunogen Purified recombinant peptides within aa. 110 to the C-terminus of Mouse Rab11a, Rab11b and Rab11c (Rab25). Conjugation Un-conjugated Alternate Names RAB11A: Rab-11; Ras-related protein Rab-11A; YL8 RAB11B: GTP-binding protein YPT3; H-YPT3; Ras-related protein Rab-11B RAB25: RAB11C; CATX-8; Ras-related protein Rab-25 Application Instructions Application table Application Dilution IHC-Fr 1:100 - 1:400 IHC-P 1:100 - 1:400 WB 1:250 - 1:2000 Application Note IHC-P: Antigen Retrieval: Heat mediation was recommended. * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Positive Control Hepa cell lysate Calculated Mw 24 kDa Observed Size ~ 26 kDa Properties Form Liquid Purification Affinity purification with immunogen. Buffer PBS, 0.05% Sodium azide and 20% Glycerol. Preservative 0.05% Sodium azide www.arigobio.com 1/3 Stabilizer 20% Glycerol Concentration 3 mg/ml Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. Note For laboratory research only, not for drug, diagnostic or other use.
    [Show full text]
  • Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma
    Anatomy and Pathology Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma Sarah L. Lake,1 Sarah E. Coupland,1 Azzam F. G. Taktak,2 and Bertil E. Damato3 PURPOSE. To detect deletions and loss of heterozygosity of disease is fatal in 92% of patients within 2 years of diagnosis. chromosome 3 in a rare subset of fatal, disomy 3 uveal mela- Clinical and histopathologic risk factors for UM metastasis noma (UM), undetectable by fluorescence in situ hybridization include large basal tumor diameter (LBD), ciliary body involve- (FISH). ment, epithelioid cytomorphology, extracellular matrix peri- ϩ ETHODS odic acid-Schiff-positive (PAS ) loops, and high mitotic M . Multiplex ligation-dependent probe amplification 3,4 5 (MLPA) with the P027 UM assay was performed on formalin- count. Prescher et al. showed that a nonrandom genetic fixed, paraffin-embedded (FFPE) whole tumor sections from 19 change, monosomy 3, correlates strongly with metastatic death, and the correlation has since been confirmed by several disomy 3 metastasizing UMs. Whole-genome microarray analy- 3,6–10 ses using a single-nucleotide polymorphism microarray (aSNP) groups. Consequently, fluorescence in situ hybridization were performed on frozen tissue samples from four fatal dis- (FISH) detection of chromosome 3 using a centromeric probe omy 3 metastasizing UMs and three disomy 3 tumors with Ͼ5 became routine practice for UM prognostication; however, 5% years’ metastasis-free survival. to 20% of disomy 3 UM patients unexpectedly develop metas- tases.11 Attempts have therefore been made to identify the RESULTS. Two metastasizing UMs that had been classified as minimal region(s) of deletion on chromosome 3.12–15 Despite disomy 3 by FISH analysis of a small tumor sample were found these studies, little progress has been made in defining the key on MLPA analysis to show monosomy 3.
    [Show full text]
  • Membrane Tension Buffering by Caveolae: a Role in Cancer?
    Cancer and Metastasis Reviews (2020) 39:505–517 https://doi.org/10.1007/s10555-020-09899-2 Membrane tension buffering by caveolae: a role in cancer? Vibha Singh1 & Christophe Lamaze1 Published online: 30 May 2020 # Springer Science+Business Media, LLC, part of Springer Nature 2020 Abstract Caveolae are bulb-like invaginations made up of two essential structural proteins, caveolin-1 and cavins, which are abundantly present at the plasma membrane of vertebrate cells. Since their discovery more than 60 years ago, the function of caveolae has been mired in controversy. The last decade has seen the characterization of new caveolae components and regulators together with the discovery of additional cellular functions that have shed new light on these enigmatic structures. Early on, caveolae and/ or caveolin-1 have been involved in the regulation of several parameters associated with cancer progression such as cell migration, metastasis, angiogenesis, or cell growth. These studies have revealed that caveolin-1 and more recently cavin-1 have a dual role with either a negative or a positive effect on most of these parameters. The recent discovery that caveolae can act as mechanosensors has sparked an array of new studies that have addressed the mechanobiology of caveolae in various cellular functions. This review summarizes the current knowledge on caveolae and their role in cancer development through their activity in membrane tension buffering. We propose that the role of caveolae in cancer has to be revisited through their response to the mechanical forces encountered by cancer cells during tumor mass development. Keywords Caveolae . Cancer . Mechanosensing . Mechanotransdcution . Membrane tension .
    [Show full text]
  • An Order Estimation Based Approach to Identify Response Genes
    AN ORDER ESTIMATION BASED APPROACH TO IDENTIFY RESPONSE GENES FOR MICRO ARRAY TIME COURSE DATA A Thesis Presented to The Faculty of Graduate Studies of The University of Guelph by ZHIHENG LU In partial fulfilment of requirements for the degree of Doctor of Philosophy September, 2008 © Zhiheng Lu, 2008 Library and Bibliotheque et 1*1 Archives Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington Ottawa ON K1A0N4 Ottawa ON K1A0N4 Canada Canada Your file Votre reference ISBN: 978-0-494-47605-5 Our file Notre reference ISBN: 978-0-494-47605-5 NOTICE: AVIS: The author has granted a non­ L'auteur a accorde une licence non exclusive exclusive license allowing Library permettant a la Bibliotheque et Archives and Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par Plntemet, prefer, telecommunication or on the Internet, distribuer et vendre des theses partout dans loan, distribute and sell theses le monde, a des fins commerciales ou autres, worldwide, for commercial or non­ sur support microforme, papier, electronique commercial purposes, in microform, et/ou autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in et des droits moraux qui protege cette these. this thesis. Neither the thesis Ni la these ni des extraits substantiels de nor substantial extracts from it celle-ci ne doivent etre imprimes ou autrement may be printed or otherwise reproduits sans son autorisation.
    [Show full text]
  • Identification of Novel Pathways That Promote Anoikis Through Genome-Wide Screens
    University of Massachusetts Medical School eScholarship@UMMS GSBS Dissertations and Theses Graduate School of Biomedical Sciences 2016-10-14 Identification of Novel Pathways that Promote Anoikis through Genome-wide Screens Victoria E. Pedanou University of Massachusetts Medical School Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/gsbs_diss Part of the Biology Commons, and the Cancer Biology Commons Repository Citation Pedanou VE. (2016). Identification of Novel Pathways that Promote Anoikis through Genome-wide Screens. GSBS Dissertations and Theses. https://doi.org/10.13028/M27G6D. Retrieved from https://escholarship.umassmed.edu/gsbs_diss/889 This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in GSBS Dissertations and Theses by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. i TITLE PAGE IDENTIFICATION OF NOVEL PATHWAYS THAT PROMOTE ANOIKIS THROUGH GENOME-WIDE SCREENS A Dissertation Presented By VICTORIA ELIZABETH PEDANOU Submitted to the Faculty of the University of Massachusetts Graduate School of Biomedical Sciences, Worcester in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY OCTOBER 14TH, 2016 CANCER BIOLOGY ii SIGNATURE PAGE IDENTIFICATION OF NOVEL PATHWAYS THAT PROMOTE ANOIKIS THROUGH GENOME-WIDE SCREENS A Dissertation Presented By VICTORIA ELIZABETH PEDANOU This work was undertaken in the Graduate School of Biomedical Sciences Cancer Biology The signature of the Thesis Advisor signifies validation of Dissertation content ___________________________ Michael R. Green, Thesis Advisor The signatures of the Dissertation Defense Committee signify completion and approval as to style and content of the Dissertation __________________________________ Eric H.
    [Show full text]
  • Protein Prenylation Reactions As Tools for Site-Specific Protein Labeling and Identification of Prenylation Substrates
    Protein prenylation reactions as tools for site-specific protein labeling and identification of prenylation substrates Dissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) des Fachbereichs Chemie der Technischen Universität Dortmund Angefertigt am Max-Planck-Institut für molekulare Physiologie in Dortmund Vorgelegt von Dipl.-Chemikerin Thi Thanh Uyen Nguyen aus Jülich Dortmund, April 2009 Die vorliegende Arbeit wurde in der Zeit von Oktober 2005 bis April 2009 am Max-Planck- Institut für molekulare Physiologie in Dortmund unter der Anleitung von Prof. Dr. Roger S. Goody, Prof. Dr. Kirill Alexandrov und Prof. Dr. Herbert Waldmann durchgeführt. 1. Gutachter : Prof. Dr. R. S. Goody 2. Gutachter : Prof. Dr. H. Waldmann The results of this work were published in the following journals: “Exploiting the substrate tolerance of farnesyltransferase for site-selective protein derivatization” U.T.T. Nguyen, J. Cramer, J. Gomis, R. Reents, M. Gutierrez-Rodriguez, R.S. Goody, K. Alexandrov, H. Waldmann, Chembiochem 2007, 8 (4), 408-23. “Development of selective RabGGTase inhibitors and crystal structure of a RabGGTase- inhibitor complex” Z. Guo, Y.W. Wu, K.T. Tan, R.S. Bon, E. Guiu-Rozas, C. Delon, U.T.T. Nguyen, S. Wetzel,S. Arndt, R.S. Goody, W. Blankenfeldt, K. Alexandrov, H. Waldmann, Angew Chem Int Ed Engl 2008, 47 (20), 3747-50. “Analysis of the eukaryotic prenylome by isoprenoid affinity tagging” U.T.T. Nguyen, Z. Guo, C. Delon, Y.W. Wu, C. Deraeve, B. Franzel, R.S. Bon, W. Blankenfeldt, R.S. Goody, H. Waldmann, D. Wolters, K. Alexandrov, Nat Chem Biol 2009, 5 (4), 227-35.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Evidence for Differential Alternative Splicing in Blood of Young Boys With
    Stamova et al. Molecular Autism 2013, 4:30 http://www.molecularautism.com/content/4/1/30 RESEARCH Open Access Evidence for differential alternative splicing in blood of young boys with autism spectrum disorders Boryana S Stamova1,2,5*, Yingfang Tian1,2,4, Christine W Nordahl1,3, Mark D Shen1,3, Sally Rogers1,3, David G Amaral1,3 and Frank R Sharp1,2 Abstract Background: Since RNA expression differences have been reported in autism spectrum disorder (ASD) for blood and brain, and differential alternative splicing (DAS) has been reported in ASD brains, we determined if there was DAS in blood mRNA of ASD subjects compared to typically developing (TD) controls, as well as in ASD subgroups related to cerebral volume. Methods: RNA from blood was processed on whole genome exon arrays for 2-4–year-old ASD and TD boys. An ANCOVA with age and batch as covariates was used to predict DAS for ALL ASD (n=30), ASD with normal total cerebral volumes (NTCV), and ASD with large total cerebral volumes (LTCV) compared to TD controls (n=20). Results: A total of 53 genes were predicted to have DAS for ALL ASD versus TD, 169 genes for ASD_NTCV versus TD, 1 gene for ASD_LTCV versus TD, and 27 genes for ASD_LTCV versus ASD_NTCV. These differences were significant at P <0.05 after false discovery rate corrections for multiple comparisons (FDR <5% false positives). A number of the genes predicted to have DAS in ASD are known to regulate DAS (SFPQ, SRPK1, SRSF11, SRSF2IP, FUS, LSM14A). In addition, a number of genes with predicted DAS are involved in pathways implicated in previous ASD studies, such as ROS monocyte/macrophage, Natural Killer Cell, mTOR, and NGF signaling.
    [Show full text]
  • 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,
    [Show full text]
  • 4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).
    [Show full text]
  • Differential Patterns of Allelic Loss in Estrogen Receptor-Positive Infiltrating Lobular and Ductal Breast Cancer
    GENES, CHROMOSOMES & CANCER 47:1049–1066 (2008) Differential Patterns of Allelic Loss in Estrogen Receptor-Positive Infiltrating Lobular and Ductal Breast Cancer L. W. M. Loo,1 C. Ton,1,2 Y.-W. Wang,2 D. I. Grove,2 H. Bouzek,1 N. Vartanian,1 M.-G. Lin,1 X. Yuan,1 T. L. Lawton,3 J. R. Daling,2 K. E. Malone,2 C. I. Li,2 L. Hsu,2 and P.L. Porter1,2,3* 1Division of Human Biology,Fred Hutchinson Cancer Research Center,Seattle,WA 2Division of Public Health Sciences,Fred Hutchinson Cancer Research Center,Seattle,WA 3Departmentof Pathology,Universityof Washington,Seattle,WA The two main histological types of infiltrating breast cancer, lobular (ILC) and the more common ductal (IDC) carcinoma are morphologically and clinically distinct. To assess the molecular alterations associated with these breast cancer subtypes, we conducted a whole-genome study of 166 archival estrogen receptor (ER)-positive tumors (89 IDC and 77 ILC) using the Affy- metrix GeneChip® Mapping 10K Array to identify sites of loss of heterozygosity (LOH) that either distinguished, or were shared by, the two phenotypes. We found single nucleotide polymorphisms (SNPs) of high-frequency LOH (>50%) common to both ILC and IDC tumors predominately in 11q, 16q, and 17p. Overall, IDC had a slightly higher frequency of LOH events across the genome than ILC (fractional allelic loss 5 0.186 and 0.156). By comparing the average frequency of LOH by chro- mosomal arm, we found IDC tumors with significantly (P < 0.05) higher frequency of LOH on 3p, 5q, 8p, 9p, 20p, and 20q than ILC tumors.
    [Show full text]
  • Α Are Regulated by Heat Shock Protein 90
    The Levels of Retinoic Acid-Inducible Gene I Are Regulated by Heat Shock Protein 90- α Tomoh Matsumiya, Tadaatsu Imaizumi, Hidemi Yoshida, Kei Satoh, Matthew K. Topham and Diana M. Stafforini This information is current as of October 2, 2021. J Immunol 2009; 182:2717-2725; ; doi: 10.4049/jimmunol.0802933 http://www.jimmunol.org/content/182/5/2717 Downloaded from References This article cites 44 articles, 19 of which you can access for free at: http://www.jimmunol.org/content/182/5/2717.full#ref-list-1 Why The JI? Submit online. http://www.jimmunol.org/ • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average by guest on October 2, 2021 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 © 2009 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology The Levels of Retinoic Acid-Inducible Gene I Are Regulated by Heat Shock Protein 90-␣1 Tomoh Matsumiya,*‡ Tadaatsu Imaizumi,‡ Hidemi Yoshida,‡ Kei Satoh,‡ Matthew K. Topham,*† and Diana M. Stafforini2*† Retinoic acid-inducible gene I (RIG-I) is an intracellular pattern recognition receptor that plays important roles during innate immune responses to viral dsRNAs.
    [Show full text]