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Impact of Natural HIV-1 Nef Alleles and Polymorphisms on SERINC3/5 Downregulation
Impact of natural HIV-1 Nef alleles and polymorphisms on SERINC3/5 downregulation by Steven W. Jin B.Sc., Simon Fraser University, 2016 Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Science in the Master of Science Program Faculty of Health Sciences © Steven W. Jin 2019 SIMON FRASER UNIVERSITY Spring 2019 Copyright in this work rests with the author. Please ensure that any reproduction or re-use is done in accordance with the relevant national copyright legislation. Approval Name: Steven W. Jin Degree: Master of Science Title: Impact of natural HIV-1 Nef alleles and polymorphisms on SERINC3/5 downregulation Examining Committee: Chair: Kanna Hayashi Assistant Professor Mark Brockman Senior Supervisor Associate Professor Masahiro Niikura Supervisor Associate Professor Ralph Pantophlet Supervisor Associate Professor Lisa Craig Examiner Professor Department of Molecular Biology and Biochemistry Date Defended/Approved: April 25, 2019 ii Ethics Statement iii Abstract HIV-1 Nef is a multifunctional accessory protein required for efficient viral pathogenesis. It was recently identified that the serine incorporators (SERINC) 3 and 5 are host restriction factors that decrease the infectivity of HIV-1 when incorporated into newly formed virions. However, Nef counteracts these effects by downregulating SERINC from the cell surface. Currently, there lacks a comprehensive study investigating the impact of primary Nef alleles on SERINC downregulation, as most studies to date utilize lab- adapted or reference HIV strains. In this thesis, I characterized and compared SERINC downregulation from >400 Nef alleles isolated from patients with distinct clinical outcomes and subtypes. I found that primary Nef alleles displayed a dynamic range of SERINC downregulation abilities, thus allowing naturally-occurring polymorphisms that modulate this activity to be identified. -
MS Ritgerð Aðalbjörg Aðalbjörnsdóttir
The Vif protein of maedi-visna virus Protein interaction and new roles Aðalbjörg Aðalbjörnsdóttir Thesis for the degree of Master of Science University of Iceland Faculty of medicine School of Health Sciences Vif prótein mæði-visnuveiru Prótein tengsl og ný hlutverk Aðalbjörg Aðalbjörnsdóttir Ritgerð til meistaragráðu í Líf og læknavísindum Umsjónarkennari: Valgerður Andrésdóttir Meistaranámsnefnd: Stefán Ragnar Jónsson og Ólafur S. Andrésson Læknadeild Heilbrigðisvísindasvið Háskóla Íslands Júní 2016 The Vif protein of maedi-visna virus Protein interaction and new roles Aðalbjörg Aðalbjörnsdóttir Thesis for the degree of Master of Science Supervisor: Valgerður Andrésdóttir Masters committee: Stefán Ragnar Jónsson and Ólafur S. Andrésson Faculty of Medicine School of Health Sciences June 2016 Ritgerð þessi er til meistaragráðu í Líf og læknavísindum og er óheimilt að afrita ritgerðina á nokkurn hátt nema með leyfi rétthafa. © Aðalbjörg Aðalbjörnsdóttir 2016 Prentun: Háskólaprent Reykjavík, Ísland 2016 Ágrip Mæði-visnuveira (MVV) er lentiveira af ættkvísl retróveira. Hún veldur hæggengri lungnabólgu (mæði) og heilabólgu (visnu) í kindum. Aðalmarkfrumur veirunnar eru mónocytar/makrófagar. Veiran er náskyld HIV og hefur verið notuð sem módel fyrir HIV sýkingar. Stöðug vopnakapphlaup milli veira og fruma hafa leitt af sér fjölda sértækra aðferða í vörnum hýsilsfrumu gegn veirusýkingum. Fruman hefur þróað með sér innrænar varnir gegn ýmsum sýkingum. Þessar varnir geta verið mjög sérhæfðar og tjáning þeirra spilar stórt hlutverk í hvaða frumur er hægt að sýkja og hverjar ekki. Dæmi um slíkan frumubundinn þátt eru APOBEC3 próteinin. APOBEC3 próteinin eru fjölskylda cytósín deaminasa sem geta hindrað retróveirur og retróstökkla. Þetta gera þau með því að afaminera cýtósín í úrasil í einþátta DNA á meðan á víxlritun stendur og valda þar með G-A stökkbreytingum í forveirunni. -
UC Merced UC Merced Undergraduate Research Journal
UC Merced UC Merced Undergraduate Research Journal Title Antiviral Drugs Targeting Host Proteins an Efficient Strategy Permalink https://escholarship.org/uc/item/66f5b4m0 Journal UC Merced Undergraduate Research Journal, 9(2) Author Karmonphet, Arrada Publication Date 2017 DOI 10.5070/M492034789 Undergraduate eScholarship.org Powered by the California Digital Library University of California Antiviral Drugs Targeting Host Proteins an Efficient Strategy Arrada Karmonphet University of California, Merced Keywords: Proteins, Viruses, Drugs 1 Abstract Viruses have the ability to spread rapidly because the proteins and enzymes from the host cell help in the development of viruses. Although there are many vaccines that can prevent some viruses from infecting the body, the antiviral drugs today have not been effective in combating viruses from the start of spreading. This is due to the fact that the processes inside a virus are still being studied. However, host proteins proved to be valuable factors responsible for viral replication and spreading. It was found that certain functions such as capsid formation of the virus utilized a biochemical pathway that involved host proteins and some proteins of the host cell were evolutionarily conserved. When the important host proteins were altered, or removed the viruses weren’t able to replicate as effectively. It was concluded that targeting the host proteins had a significant effect in viral replication. This approach can stop viral replication from the start, create less viral resistance, and help find new antiviral drugs that work for many different types of viruses. This review will analyze five research articles about protein interactions in viruses and how monitoring the proteins and biochemical pathways can lead to the discovery of druggable targets during development. -
Assessment of the Interaction Between the Human
VARIATIONS IN THE V3 CROWN OF HIV-1 ENVELOPE IMPACT AFFINITY FOR CCR5 AND AFFECT ENTRY AND REPLICATIVE FITNESS By MICHAEL ANDREW LOBRITZ Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Dissertation advisor: Eric J. Arts, Ph.D. Department of Molecular Biology and Microbiology CASE WESTERN RESERVE UNIVERSITY August 2007 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the dissertation of ______________________________________________________ candidate for the Ph.D. degree *. (signed)_______________________________________________ (chair of the committee) ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ (date) _______________________ *We also certify that written approval has been obtained for any proprietary material contained therein. Table of Contents Chapter 1: Introduction........................................................................................................................16 1.A. HIV and AIDS..............................................................................................17 1.B. Retroviruses: Structure, Organization, and Replication...............................20 1.B.1. HIV-1 Genome...............................................................................20 1.B.2. HIV-1 Particle................................................................................23 -
Autophagy and Mammalian Viruses: Roles in Immune Response, Viral Replication, and Beyond
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2016 Autophagy and mammalian viruses: roles in immune response, viral replication, and beyond Paul, P ; Münz, C Abstract: Autophagy is an important cellular catabolic process conserved from yeast to man. Double- membrane vesicles deliver their cargo to the lysosome for degradation. Hence, autophagy is one of the key mechanisms mammalian cells deploy to rid themselves of intracellular pathogens including viruses. How- ever, autophagy serves many more functions during viral infection. First, it regulates the immune response through selective degradation of immune components, thus preventing possibly harmful overactivation and inflammation. Additionally, it delivers virus-derived antigens to antigen-loading compartments for presentation to T lymphocytes. Second, it might take an active part in the viral life cycle by, eg, facili- tating its release from cells. Lastly, in the constant arms race between host and virus, autophagy is often hijacked by viruses and manipulated to their own advantage. In this review, we will highlight key steps during viral infection in which autophagy plays a role. We have selected some exemplary viruses and will describe the molecular mechanisms behind their intricate relationship with the autophagic machinery, a result of host–pathogen coevolution. DOI: https://doi.org/10.1016/bs.aivir.2016.02.002 Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-131236 Book Section Accepted Version The following work is licensed under a Creative Commons: Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) License. -
Role of Reverse Transcriptase and APOBEC3G in Survival of Human
& My gy co lo lo ro g i y V Soni et al., Virol Mycol 2013, 3:1 Virology & Mycology DOI: 10.4172/2161-0517.1000125 ISSN: 2161-0517 Review Article Open Access Role of Reverse Transcriptase and APOBEC3G in Survival of Human Immune Deficiency Virus -1 Genome Raj Kumar Soni*, Amol Kanampalliwar and Archana Tiwari School of Biotechnology, Rajiv Gandhi Proudyogiki Vishwavidyalaya (State Technological University), Madhya Pradesh, India Abstract Development of an effective vaccine against HIV-1 is a major challenge for scientists at present. Rapid mutation and replication of the virus in patients contribute to the evolution of the virus, which makes it unconquerable. Hence a deep understanding of critical elements related to HIV-1 is necessary. Errors introduced during DNA synthesis by reverse transcriptase are the primary source of genetic variation within retroviral populations. Numerous current studies have shown that apolipo protein B mRNA-editing enzyme-catalytic polypeptide-like 3G (APOBEC3G) proteins mediated sub- lethal mutagenesis of HIV-1 proviral DNA contributes in viral fitness by accelerating human immunodeficiency virus-1 evolution. This results in the loss of the immunity and development of resistance against anti-viral drugs. This review focuses on the latest biological, biochemical, and structural studies in an attempt to discuss current ideas related to mutations initiated by reverse transcriptase and APOBEC3G. It also describes their effect on immunological diversity and retroviral restriction, and their overall effect on the viral genome respectively. A new procedure for eradication of HIV-1 has also been proposed based on the previous studies and proven facts. Keywords: HIV-1; Reverse transcriptase; Recombination; defined. -
To Reduce HIV-1 Infectivity Facilitates Its Encapsidation Into the Virions GANP Interacts with APOBEC3G
GANP Interacts with APOBEC3G and Facilitates Its Encapsidation into the Virions To Reduce HIV-1 Infectivity This information is current as Kazuhiko Maeda, Sarah Ameen Almofty, Shailendra Kumar of September 23, 2021. Singh, Mohammed Mansour Abbas Eid, Mayuko Shimoda, Terumasa Ikeda, Atsushi Koito, Phuong Pham, Myron F. Goodman and Nobuo Sakaguchi J Immunol 2013; 191:6030-6039; Prepublished online 6 November 2013; Downloaded from doi: 10.4049/jimmunol.1302057 http://www.jimmunol.org/content/191/12/6030 Supplementary http://www.jimmunol.org/content/suppl/2013/11/06/jimmunol.130205 http://www.jimmunol.org/ Material 7.DC1 References This article cites 52 articles, 20 of which you can access for free at: http://www.jimmunol.org/content/191/12/6030.full#ref-list-1 Why The JI? Submit online. by guest on September 23, 2021 • 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 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 © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology GANP Interacts with APOBEC3G and Facilitates Its Encapsidation into the Virions To Reduce HIV-1 Infectivity Kazuhiko Maeda,*,1 Sarah Ameen Almofty,*,1 Shailendra Kumar Singh,* Mohammed Mansour Abbas Eid,* Mayuko Shimoda,* Terumasa Ikeda,†,2 Atsushi Koito,† Phuong Pham,‡ Myron F. -
The Battle Between Retroviruses and APOBEC3 Genes: Its Past and Present
viruses Review The Battle between Retroviruses and APOBEC3 Genes: Its Past and Present Keiya Uriu 1,2,†, Yusuke Kosugi 3,4,†, Jumpei Ito 1 and Kei Sato 1,2,* 1 Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; [email protected] (K.U.); [email protected] (J.I.) 2 Graduate School of Medicine, The University of Tokyo, Tokyo 1130033, Japan 3 Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; [email protected] 4 Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan * Correspondence: [email protected]; Tel.: +81-3-6409-2212 † These authors contributed equally to this work. Abstract: The APOBEC3 family of proteins in mammals consists of cellular cytosine deaminases and well-known restriction factors against retroviruses, including lentiviruses. APOBEC3 genes are highly amplified and diversified in mammals, suggesting that their evolution and diversification have been driven by conflicts with ancient viruses. At present, lentiviruses, including HIV, the causative agent of AIDS, are known to encode a viral protein called Vif to overcome the antiviral effects of the APOBEC3 proteins of their hosts. Recent studies have revealed that the acquisition of an anti-APOBEC3 ability by lentiviruses is a key step in achieving successful cross-species transmission. Here, we summarize the current knowledge of the interplay between mammalian APOBEC3 proteins and viral infections and introduce a scenario of the coevolution of mammalian APOBEC3 genes and viruses. Keywords: APOBEC3; lentivirus; Vif; arms race; gene diversification; coevolution Citation: Uriu, K.; Kosugi, Y.; Ito, J.; Sato, K. -
Identification of Small Endogenous Viral Elements Within Host
IDENTIFICATION OF SMALL ENDOGENOUS VIRAL ELEMENTS WITHIN HOST GENOMES by Edward C. Davis, Jr. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Computer Science Boise State University May 2016 c 2016 Edward C. Davis, Jr. ALL RIGHTS RESERVED BOISE STATE UNIVERSITY GRADUATE COLLEGE DEFENSE COMMITTEE AND FINAL READING APPROVALS of the thesis submitted by Edward C. Davis, Jr. Thesis Title: Identification of Small Endogenous Viral Elements within Host Genomes Date of Final Oral Examination: 04 March 2016 The following individuals read and discussed the thesis submitted by student Edward C. Davis, Jr., and they evaluated his presentation and response to questions during the final oral examination. They found that the student passed the final oral examination. Timothy Andersen, Ph.D. Chair, Supervisory Committee Amit Jain, Ph.D. Member, Supervisory Committee Gregory Hampikian, Ph.D. Member, Supervisory Committee The final reading approval of the thesis was granted by Timothy Andersen, Ph.D., Chair, Supervisory Committee. The thesis was approved for the Graduate College by John R. Pelton, Ph.D., Dean of the Graduate College. Dedicated to Elaina, Arianna, and Zora. iv ACKNOWLEDGMENTS The author wishes to express gratitude to the members of the supervisory com- mittee for providing guidance and patience. v ABSTRACT A parallel string matching software architecture has been developed (incorpo- rating several algorithms) to identify small genetic sequences in large genomes. En- dogenous viral elements (EVEs) are sequences originating in the genomes of viruses that have become integrated into the chromosomes of sperm or egg cells of infected hosts, and passed to subsequent generations. -
Investigation of the C-Terminal Helix of HIV-1 Matrix: a Region Essential for Multiple Functions in the Viral Life Cycle: a Dissertation
University of Massachusetts Medical School eScholarship@UMMS GSBS Dissertations and Theses Graduate School of Biomedical Sciences 2011-07-10 Investigation of the C-Terminal Helix of HIV-1 Matrix: A Region Essential for Multiple Functions in the Viral Life Cycle: A Dissertation Laura A. Brandano 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 Biological Factors Commons, Genetic Phenomena Commons, Immunology and Infectious Disease Commons, Therapeutics Commons, Virology Commons, Virus Diseases Commons, and the Viruses Commons Repository Citation Brandano LA. (2011). Investigation of the C-Terminal Helix of HIV-1 Matrix: A Region Essential for Multiple Functions in the Viral Life Cycle: A Dissertation. GSBS Dissertations and Theses. https://doi.org/ 10.13028/5zmj-9x81. Retrieved from https://escholarship.umassmed.edu/gsbs_diss/552 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 INVESTIGATION OF THE C-TERMINAL HELIX OF HIV-1 MATRIX: A REGION ESSENTIAL FOR MULTIPLE FUNCTIONS IN THE VIRAL LIFE CYCLE A Dissertation Presented by Laura A. Brandano 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 -
Studies on HIV-1 Virion Infectivity Factor
Studies on HIV-L Virion Infectivity Factor Feng Feng M.Sc. Infectious Diseases Laboratories Institute of Medical and Veterinary Science Adelaide South Australia School of Molecular & Biomedical Science University of Adelaide Adelaide South Australia ¡k ¡l.rl. {. t {. {. ¡1. ¡ß {. tk * *,1. tß * * * * {. A thesis submitted to the University of Adelaide infuffilment of the requirements far the degree of Doctor of, Philosophy October,2004 Contents VI Declaration of Originality.... .................. IX X Publications Related to this Study xll Chapter L. IntrOduCtiOn... .................. ... .... o. ........ 1 1.1 Historical Background of HMAIDS 1..2 Overview of Human Immunodeficiency Virus............ 4 1.2.1 Classification of HIV 4 1.2.2 }J.IV virion structure 5 1.2.3 Genetic organisation of HIV 5 6 1 .2.4 IF'IV replication CYcle. 1.2.4.t Viral attachment and viral fusion 7 1.2.4.2 Reverse transcription. .' . I 1.2.4.3 Viral DNA integration.. '... 9 I.2.4.4 Transcription and translation l0 1.2.4.5 Assembly of virus and viral budding. 1l 1.2.5 HIV gene expression. t2 1.2.5.1HIV proviral genome transcription - overview ... ' l2 I.2.5.2 Regulation of transcription' ' l3 1.2.6 I{IV encoded proteins and their functions. l5 I.2.6,1 The major structure proteins. 15 I.2.6.2 Regulatory proteinsiaccessary proteins. .' l8 1.2.t HIV-1 Virion infectivity factor (ViÐ'.. 24 1.2.7.1HIV-l Vif localisation and biological activity' 24 112.7 .2 Vif is required for efficient reverse transcription. .. 25 I.2.7.3 Vif interacts with viral proteins and RNA. -
At the Forefront of Virus – Host Interactions Viruses 2016 Book Viruses – Program and Abstract
At the Forefront of Virus – Host Interactions Viruses 2016 – Program and Abstract and – Program Viruses Book 2016 26 – 28 January 2016 Pharmacenter, University of Basel Basel, Switzerland Program and Abstract Book WLAN: unibas-event Login: eventbzpz Password: Virus-2016! Twitter Handle: @VirusesMDPI Twitter Hashtag: #Viruses2016 Organizing Committees and Conference Secretariat Executive Committee Chairman Members Dr. Eric O. Freed Dr. Paul Ahlquist Co-Chairman Dr. Jens H. Kuhn Dr. Thomas Klimkait Dr. Peter D. Nagy Dr. Charles M. Rice Dr. Eric M. Poeschla Dr. Ry Young Conference Secretariat Dr. Franck Vazquez Dr. Delphine Guérin Ms. Delia Mihaila Ms. Cornelia Bauer Mr. Matthias Burkhalter Dr. Shu-Kun Lin i Welcome by Dr. Eric O. Freed Dear authors and attendees, The last few years have witnessed enormous progress in virology research, with major breakthroughs taking place across a wide range of virology-related disciplines. At the same time, the global impact of viral infections on human health has never been clearer. The conference Viruses 2016 - At the Forefront of Virus–Host Interactions will bring together leading virologists from around the world to share recent developments in their research. The sessions are organized in a theme-based manner, with related topics discussed from the perspective of diverse viruses, ranging from bacteriophage, plant, and insect viruses to animal viruses. The Viruses 2016 - At the Forefront of Virus–Host Interactions will be held in Basel, Switzerland, from 26th to 28th of January 2016. It will comprise five plenary sessions to highlight the most exciting developments and the latest breakthroughs in virology. Dr. Eric O. Freed Conference Chair ii Welcome by Prof.