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Changes to Virus Taxonomy 2004
Arch Virol (2005) 150: 189–198 DOI 10.1007/s00705-004-0429-1 Changes to virus taxonomy 2004 M. A. Mayo (ICTV Secretary) Scottish Crop Research Institute, Invergowrie, Dundee, U.K. Received July 30, 2004; accepted September 25, 2004 Published online November 10, 2004 c Springer-Verlag 2004 This note presents a compilation of recent changes to virus taxonomy decided by voting by the ICTV membership following recommendations from the ICTV Executive Committee. The changes are presented in the Table as decisions promoted by the Subcommittees of the EC and are grouped according to the major hosts of the viruses involved. These new taxa will be presented in more detail in the 8th ICTV Report scheduled to be published near the end of 2004 (Fauquet et al., 2004). Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., and Ball, L.A. (eds) (2004). Virus Taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp. 1258. Recent changes to virus taxonomy Viruses of vertebrates Family Arenaviridae • Designate Cupixi virus as a species in the genus Arenavirus • Designate Bear Canyon virus as a species in the genus Arenavirus • Designate Allpahuayo virus as a species in the genus Arenavirus Family Birnaviridae • Assign Blotched snakehead virus as an unassigned species in family Birnaviridae Family Circoviridae • Create a new genus (Anellovirus) with Torque teno virus as type species Family Coronaviridae • Recognize a new species Severe acute respiratory syndrome coronavirus in the genus Coro- navirus, family Coronaviridae, order Nidovirales -
Assessment and Analysis of the Restriction of Retroviral Infection by the Murine APOBEC3 Protein
Assessment and Analysis of the Restriction of Retroviral Infection by the Murine APOBEC3 Protein Halil Aydin Thesis submitted to the Faculty of Graduate and Postdoctoral Studies of the University of Ottawa in partial fulfillment of the requirements for the degree of Masters of Science Department of Biochemistry, Microbiology and Immunology Faculty of Medicine ©Halil Aydin, Ottawa, Ontario, Canada, 2011 Learning the rules is hard work and lengthy but playing the game is exciting and fun. John Polanyi Nobel Prize Winner in Chemistry ii ABSTRACT Human APOBEC3 proteins are host-encoded intrinsic restriction factors that can prevent the replication of a broad range of human and animal retroviruses such as HIV, SIV, FIV, MLVs and XMRV. The main pathway of the restriction is believed to occur as a result of the cytidine deaminase activity of these proteins that converts cytidines into uridines in single- stranded DNA retroviral replication intermediates. Uridines in these DNA intermediates disrupt the viral replication cycle and also alter retrovirus infectivity because of the C-to-T transition mutations generated as a result of the deaminase activity on the minus strand DNA. In addition, human APOBEC3 proteins also exhibit a deamination-independent pathway to restrict retroviruses that is not currently well understood. Although the restriction of retroviruses by human APOBEC3 proteins has been intensely studied in vitro, our understanding of how the murine APOBEC3 (mA3) protein restricts retroviruses and/or prevents zoonotic infections in vivo is very limited. In contrast to humans and primates that have 7 APOBEC3 genes, mice have but a single copy. My study of the function and structure of mA3 revealed that it has an inverted functional organization for cytidine deamination in comparison to the human A3G catalytic sites. -
Tically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2021 doi:10.20944/preprints202106.0526.v1 Review Towards the forest virome: next-generation-sequencing dras- tically expands our understanding on virosphere in temperate forest ecosystems Artemis Rumbou 1,*, Eeva J. Vainio 2 and Carmen Büttner 1 1 Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Ber- lin, Germany; [email protected], [email protected] 2 Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland; [email protected] * Correspondence: [email protected] Abstract: Forest health is dependent on the variability of microorganisms interacting with the host tree/holobiont. Symbiotic mi- crobiota and pathogens engage in a permanent interplay, which influences the host. Thanks to the development of NGS technol- ogies, a vast amount of genetic information on the virosphere of temperate forests has been gained the last seven years. To estimate the qualitative/quantitative impact of NGS in forest virology, we have summarized viruses affecting major tree/shrub species and their fungal associates, including fungal plant pathogens, mutualists and saprotrophs. The contribution of NGS methods is ex- tremely significant for forest virology. Reviewed data about viral presence in holobionts, allowed us to address the role of the virome in the holobionts. Genetic variation is a crucial aspect in hologenome, significantly reinforced by horizontal gene transfer among all interacting actors. Through virus-virus interplays synergistic or antagonistic relations may evolve, which may drasti- cally affect the health of the holobiont. Novel insights of these interplays may allow practical applications for forest plant protec- tion based on endophytes and mycovirus biocontrol agents. -
Endogenous Retroviruses and the Immune System
Endogenous Retroviruses and the Immune System George Robert Young Submitted to University College London in part fulfilment of the requirements for the degree of Doctor of Philosophy 2012 Division of Infection and Immunity Division of Immunoregulation University College London National Institute for Medical Research Gower Street The Ridgeway London London WC1E 6BT NW7 1AA 2 I, George Robert Young, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. 3 Abstract ABSTRACT 4 Initial sequencing of the human and mouse genomes revealed that substantial fractions were composed of retroelements (REs) and endogenous retroviruses (ERVs), the latter being relics of ancestral retroviral infection. Further study revealed ERVs constitute up to 10% of many mammalian genomes. Despite this abundance, comparatively little is known about their interactions, beneficial or detrimental, with the host. This thesis details two distinct sets of interactions with the immune system. Firstly, the presentation of ERV-derived peptides to developing lymphocytes was shown to exert a control on the immune response to infection with Friend Virus (FV). A self peptide encoded by an ERV negatively selected a significant fraction of polyclonal FV- specific CD4+ T cells and resulted in an impaired immune response. However, CD4+ T cell-mediated antiviral activity was fully preserved and repertoire analysis revealed a deletional bias according to peptide affinity, resulting in an effective enrichment of high-affinity CD4+ T cells. Thus, ERVs exerted a significant influence on the immune response, a mechanism that may partially contribute to the heterogeneity seen in human immune responses to retroviral infections. -
Contents Part 1 DNA TUMOR VIRUSES
Contents Part 1 DNA TUMOR VIRUSES Symposium Participants V Foreword xvii Viral Oncogenes H. M. Temin Synopses Transforming Genes of DNA Tumor Viruses L. V. Crawford 9 Transforming Genes of Retroviruses P.H. Duesberg 13 DNA Tumor Viruses: Early RNAs and Early Proteins Transcription of the SV40 Genome in Virus-transformed Cells and Early Lytic Infection P. K. Ghosh, M. Piatak, V. B. Reddy, J. Swinscoe, P. Lebowitz, and S. M. Weissman 31 Regulation of SV40 Gene Expression through RNA Splicing G. Khoury, J. C. Alwine, R. Dhar, P. Gruss, C-J. Lai, S. Segal, and I. Seif 41 A Third Splice Site in SV40 Early mRNA D.F. Mark and P. Berg 55 Comparison of Polyoma Virus Transcription in Productively Infected Mouse Cells and Transformed Rodent Cell Lines R. Kamen, J. Favalom, J. Parker, R. Treisman, L. Lania, M. Fried, and A. Mellor 63 Transcription of SV40 DNA in Transformed Rat Cells M. Grigoryan, P. Chumakov, and E. Lukanidin 77 Expression of Transforming Viral Genes in Semipermissive Cells Transformed by SV40 or Adenovirus Type 2 or Type 5 S. J. Flint and G. A. Beltz 89 Catalytic Properties of the SV40 Large T Antigen R. Tfian, A. Robbins, and R. Clark 103 Enzymatic Activities Associated with the SV40 Large T Antigen J.D. Griffin, G. Spangler, and D. M. Livingston 113 DNA Binding and Sedimentation Properties of SV40 T Antigens Synthesized In Vivo and In Vitro C. Prives, Y. Beck, D. Gidoni, M. Oren, and it. Shure 123 Organization of T Antigens in the Polyoma Virus Genome T. Hunter, M. -
Presence and Expression of Friend Erythroleukemia Virus-Related Sequences in Normal and Leukemic Mouse Tissues
Proc. Natl. Acad. Sci. USA Vol. 76, No. 9, pp. 4455-4459, September 1979 Cell Biology Presence and expression of Friend erythroleukemia virus-related sequences in normal and leukemic mouse tissues (RNA tumor viruses/Friend spleen focus-forming virus/mechanism of transformation/differentiation/gene expression) ALAN BERNSTEIN, CATHERINE GAMBLE, DONNA PENROSE, AND TAK W. MAK The Ontario Cancer Institute, and Department of Medical Biophysics, University of Toronto, 500 Sherbourne Street, Toronto, Ontario, Canada M4X 1K9 Communicated by J. Tuzo Wilson, May 22, 1979 ABSTRACT The nature and distribution of sequences re- Although the origin and nature of sarcoma virus-specific lated to the murine erythroleukemia virus, Friend spleen sequences have been well characterized, no comparable studies focus-forming virus (SFFV), have been analyzed by using a ra- have been reported on the rapidly transforming mammalian dioactive cDNA probe specific for the SFFV genome (cDNAsff). From the proportion of high molecular weight viral [32PJRNA leukemia viruses. These viruses, which include the murine which hybridized to cDNAsff, it was estimated that these se- Abelson (9) and Friend (10-12) leukemia viruses, are replica- quences represent about 50% of the SFFV genome, indicating tion-defective and hence require helper virus to produce in- a genetic complexity of about 3300 nucleotides. cDNAff hy- fectious progeny. Immunological and molecular hybridization bridized extensively (80-95%) to SFFV virion RNA and to cel- analyses of cell clones nonproductively infected with the de- lular RNA from murine and rat cells productively or nonpro- fective Friend focus- ductively infected with SFFV. Only background homology was erythroleukemia-inducing virus, spleen detected between cDNAff and viral RNA from a number of forming virus (SFFV), have indicated that the SFFV genome murine [Friend murine leukemia virus (MuLV), Moloney-MuLV, contains some, but not all, of the sequences found on its helper and Kirsten sarcoma virus] and nonmurine (Rous sarcoma virus, lymphoid leukemia virus (13, 14). -
Caracterización Genómica Y Biológica De Un Nuevo Cheravirus En Babaco (Vasconcellea X Heilbornii
1 “Caracterización genómica y biológica de un nuevo Cheravirus en babaco (Vasconcellea x heilbornii. var. pentagona)” Salazar Maldonado, Liseth Carolina Departamento de Ciencias de la Vida y de la Agricultura Carrera de Ingeniería en Biotecnología Trabajo de titulación, previo a la obtención del título de Ingeniera en Biotecnología Flores Flor, Francisco Javier PhD. 9 de octubre del 2020 2 Resultado del análisis de Urkund 3 4 Departamento de Ciencias de la Vida y de la Agricultura Carrera de Ingeniería en Biotecnología Certificación 5 Departamento de Ciencias de la Vida y de la Agricultura Carrera de Ingeniería en Biotecnología Responsabilidad de autoría 6 Departamento de Ciencias de la Vida y de la Agricultura Carrera de Ingeniería en Biotecnología Autorización de publicación 7 Dedicatoria Dedico este trabajo a mi madre Silvia Maldonado, a mis abuelitos y a mi tío Fabián, quienes procuraron que no me falte nada durante el transcurso de la carrera universitaria para que así todo mi esfuerzo y concentración se centre en mis estudios. 8 Agradecimiento Agradezco a mi familia por todo el apoyo y palabras de aliento en los momentos difíciles, este logro también es de ustedes. A todos mis familiares de Yaguachi que me acogieron durante mi estancia en la costa y me hicieron sentir como en casa. A la Licenciada Carmen Plaza por recibirme en su hogar durante los meses que estuve en Guayaquil. Agradezco a mi tutor el Dr. Francisco Flores por darme todas las facilidades para culminar este proyecto y por guiarme en el transcurso de su realización. Al Dr. Diego Quito por haberme dado la apertura para la realización del proyecto y por tomarse el tiempo de compartir su conocimiento y ayudarme a despejar todas mis dudas. -
Taxonomy of Picornaviridae: Current Situation and Future Proposals
EUROPIC 2008 TaxonomyTaxonomy ofof PicornaviridaePicornaviridae:: C1 CurrentCurrent SituationSituation andand FutureFuture ProposalsProposals Nick J. Knowles1, Tapani Hovi2, Timo Hyypiä3, Andrew M.Q. King4, A. Michael Lindberg5, Philip D. Minor6, Mark A. Pallansch7, Ann C. Palmenberg8, Tim Skern9, Glyn Stanway10, Teruo Yamashita11 and Roland Zell12 (1) Institute for Animal Health, Pirbright, UK; (2) Enterovirus Laboratory, KTL, Helsinki, Finland; (3) Dept. of Virology, Univ. Turku, Finland; 4) ‘Sunfield’, Dawney Hill, Pirbright, Woking, Surrey, UK; (5) School of Pure and Applied Natural Sciences, University of Kalmar, Sweden; (6) NIBSC, South Mimms, UK; (7) CDC, Atlanta, USA; (8) Institute for Molecular Virology, Wisconsin, USA; (9) Max F. Perutz Laboratories, Medical Univ. Vienna, Austria; (10) Dept. of Biological Sci., Univ. Essex, UK; (11) Aichi Prefectural Institute of Public Health, Aichi, Japan; (12) Institut fuer Virologie und Antivirale Therapie, Jena, Germany. RECENT ICTV‐APPROVED CHANGES (ICTV LEVEL 05) “Sapelovirus” Teschovirus Porcine teschovirus "Avian sapelovirus" Four taxonomic proposals have recently been approved by the ICTV: i) to combine the "Porcine sapelovirus" "Human rhinovirus C" "Simian sapelovirus" Cardiovirus Enterovirus and Rhinovirus genera, keeping the existing name Enterovirus; ii) to combine Encephalomyocarditis virus the species Poliovirus and Human enterovirus C, retaining the latter name; iii) to assign Human rhinovirus A Theilovirus Human enterovirus C as the type species of the enterovirus genus; iv) -
Chirico Et Al. Supplementary Methods and Results
!"#$#%&'()'*+,'-.//+(0(1)*$2'3()"&45'*14'6(5.+)5' ! 7*8+('-9,'"#$%!&$'()*!+,#-)$.!.-+.+-/(+%0!$%1!2$.0(1!1#02-(./(+%' ! Taxon Total Validated Species Genome length Overlap Capsid type Capsid Species Species with (ln) proportion flexible? overlap (ln) DNA viruses Acanthamoeba-polyphaga-mimivirus 1 0 Adenoviridae 44 12 12 10.47 -3.71 icosahedral no Anellovirus 5 1 1 8.26 -1.78 icosahedral no Ascoviridae 3 0 Asfarviridae 1 0 Bacillus-phage-GIL-sixteen-c 1 1 1 9.61 -3.05 no description ? Bacillus-virus-one 1 0 Baculoviridae 43 1 1 11.78 -4.79 rod shaped yesa Bicaudaviridae 2 0 Circoviridae 16 3 3 7.65 -1.78 icosahedral no Clostridium-phage-phiC-two 1 0 Corticovirus 1 1 1 9.22 -4.76 icosahedral no Fuselloviridae 5 3 3 9.69 -3.22 lemon-shaped yesb Geminiviridae 199 82 80 8.23 -1.54 icosahedral no Geobacillus-phage-GBSVone 1 1 1 10.45 -4.69 no description ? Globuloviridae 2 0 Gryllus-bimaculatus-nudivirus 1 0 Heliothis-zea-virus-one 1 0 Herpesviridae 47 26 26 11.97 -4.44 icosahedral no His-one-virus 1 0 His-two-virus 1 0 Inoviridae 25 18 17 8.88 -4.64 filamentous yes Iridoviridae 8 1 1 11.54 -5.31 icosahedral no Lipothrixviridae 8 2 2 10.62 -4.34 rod shaped yes Microviridae 55 13 12 8.56 -2.23 icosahedral no Myoviridae 71 35 35 11.37 -4.89 icosahedral no Nanoviridae 6 1 0 Nimaviridae 1 0 Papillomaviridae 66 13 13 8.97 -3.11 icosahedral no Parvoviridae 44 8 6 8.56 -2.14 icosahedral no Phycodnaviridae 8 1 1 12.72 -5.95 icosahedral no Plasmaviridae 1 1 1 9.39 -8.00 quasi-spherical yes Podoviridae 62 32 32 10.59 -3.58 icosahedral no Polydnaviridae -
Envelope Gene of the Friend Spleen Focus-Forming Virus
Proc. NatL Acad. Sci. USA Vol. 80, pp. 4718-4722, August 1983 Biochemistry Envelope gene of the Friend spleen focus-forming virus: Deletion and insertions in 3' gp70/pl5E-encoding region have resulted in unique features in the primary structure of its protein product (retrovirus/nueleotide sequence/acute erythroleukemia/polycythemia/membrane glycoprotein) LINDA WOLFF*, EDWARD SCOLNICKt, AND SANDRA RUSCETTI* *Laboratory of Genetics, National Cancer Institute, Bethesda, Maryland 20205; and tMerck Sharp & Dohme Research Laboratories, West Point, Pennsylvania 19486 Communicated by Peter K. Vogt, May 19, 1983 ABSTRACT A nucleotide sequence was determined for the with endogenous sequences like those of xenotropic and MCF envelope (env) gene of the polycythemia-inducing strain of the acute viruses (11, 12). Our more recent experiments using mono- leukemia-inducing Friend spleen focus-forming virus (SFFV) and clonal antibody and peptide mapping indicate that the domain from this the amino acid sequence of its gene product, gp52, was of gp52 encoded by the endogenously acquired genetic region deduced. All major elements of the gene were found to be related begins at the amino terminus of the protein (13). to genes of other retroviruses that code for functional glycopro- We have determined the nucleotide sequence of the env gene teins. Although the carboxyl terminus of gp52 is encoded by se- of the molecularly cloned (14) polycythemia-inducing form of quences highly related to sequences in its putative parent, eco- SFFV (designated SFFVp) in order to obtain a better under- tropic Friend murine leukemia virus, the majority of the protein the genetic basis for some of the unusual properties (69%), including the amino terminus, is encoded by dualtropic vi- standing of rus-like sequences. -
Evidence to Support Safe Return to Clinical Practice by Oral Health Professionals in Canada During the COVID-19 Pandemic: a Repo
Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID-19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. November 2020 update This evidence synthesis was prepared for the Office of the Chief Dental Officer, based on a comprehensive review under contract by the following: Paul Allison, Faculty of Dentistry, McGill University Raphael Freitas de Souza, Faculty of Dentistry, McGill University Lilian Aboud, Faculty of Dentistry, McGill University Martin Morris, Library, McGill University November 30th, 2020 1 Contents Page Introduction 3 Project goal and specific objectives 3 Methods used to identify and include relevant literature 4 Report structure 5 Summary of update report 5 Report results a) Which patients are at greater risk of the consequences of COVID-19 and so 7 consideration should be given to delaying elective in-person oral health care? b) What are the signs and symptoms of COVID-19 that oral health professionals 9 should screen for prior to providing in-person health care? c) What evidence exists to support patient scheduling, waiting and other non- treatment management measures for in-person oral health care? 10 d) What evidence exists to support the use of various forms of personal protective equipment (PPE) while providing in-person oral health care? 13 e) What evidence exists to support the decontamination and re-use of PPE? 15 f) What evidence exists concerning the provision of aerosol-generating 16 procedures (AGP) as part of in-person -
The Coming of Age of Tumor Virology: Presidential Address1
[CANCER RESEARCH 37, 1255-1263, May 19771 The Coming of Age of Tumor Virology: Presidential Address1 Charlotte Friend The Center for Experimental Cell Biology, The Mollie B. Roth Laboratory, Mount Sinai School of Medicine, New York, New York mary carcinoma that bears his name. Nevertheless, investi gations along these lines were not completely abandoned. In 1908, the Danish scientists Ellerman and Bang (32) re ported that leukemia in chickens was caused by a filterable agent, but their findings received little attention since leu kemia was not then considered to be a neoplastic disease. Three years later, Rous described a malignant chicken sar coma caused by a virus (96). This paper, which was to become a classic, met with such “downrightdisbelief―(97) that 55 years were to pass before the author, then well over 90, was to be awarded the Nobel Prize for his work. After spending several discouraging years in a fruitless search for similar viruses in transplantable mouse tumors, Rous gave up his study of cancer for almost 20 years. He returned to this first love in 1934, when Richard Shope (105), who had discovered a virus that induced papillomas in rabbits, of fered it to him. He could not resist the study of a virus that caused neoplastic changes in the epithelial cells of a mam malian host. From then to the end of his long and produc tive life, he continued to explore the mechanisms involved in carcinogenesis, but he never again worked on the chicken sarcoma virus that he discovered (RSV).2 Although the climate did not improve much even after Bittner (13) found the virus that causes mammary tumors in mice, a small number of men and women persisted in inves tigating the role that viruses might play in causing a cancer cell to march to a different bugle.