Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns.

The ability of DNA polymerases (pols) to catalyze the template-directed synthesis of duplex oligonucleotides containing a nonstandard Watson-Crick base pair between a nucleotide bearing a 5-(2,4-diaminopyrimidine) heterocycle (d kappa) and a nucleotide bearing either deoxyxanthosine (dX) or N1-methyloxoformycin B (pi) has been investigated. The kappa-X and kappa-pi base pairs are jointed by a hydrogen bonding pattern different from and exclusive of those joining the AT and GC base pairs. Reverse transcriptase from human immunodeficiency virus type 1 (HIV-1) incorporates dXTP into an oligonucleotide opposite d kappa in a template with good fidelity. With lower efficiency and fidelity, HIV-1 reverse transcriptase also incorporates d kappa TP opposite dX in the template. With d pi in the template, no incorporation of d kappa TP was observed with HIV reverse transcriptase. The Klenow fragment of DNA pol I from Escherichia coli does not incorporate d kappa TP opposite dX in a template but does incorporate dXTP opposite d kappa. Bovine DNA pols alpha, beta, and epsilon accept neither dXTP opposite d kappa nor d kappa TP opposite d pi. DNA pols alpha and epsilon (but not beta) incorporate d kappa TP opposite dX in a template but discontinue elongation after incorporating a single additional base. These results are discussed in light of the crystal structure for pol beta and general considerations of how polymerases must interact with an incoming base pair to faithfully copy genetic information.

Decreased human immunodeficiency virus type 1 plasma viremia during antiretroviral therapy reflects downregulation of viral replication in lymphoid tissue.

Although several immunologic and virologic markers measured in peripheral blood are useful for predicting accelerated progression of human immunodeficiency virus (HIV) disease, their validity for evaluating the response to antiretroviral therapy and their ability to accurately reflect changes in lymphoid organs remain unclear. In the present study, changes in certain virologic markers have been analyzed in peripheral blood and lymphoid tissue during antiretroviral therapy. Sixteen HIV-infected individuals who were receiving antiretroviral therapy with zidovudine for > or = 6 months were randomly assigned either to continue on zidovudine alone or to add didanosine for 8 weeks. Lymph node biopsies were performed at baseline and after 8 weeks. Viral burden (i.e., HIV DNA copies per 10(6) mononuclear cells) and virus replication in mononuclear cells isolated from peripheral blood and lymph node and plasma viremia were determined by semiquantitative polymerase chain reaction assays. Virologic and immunologic markers remained unchanged in peripheral blood and lymph node of patients who continued on zidovudine alone. In contrast, a decrease in virus replication in lymph nodes was observed in four of six patients who added didanosine to their regimen, and this was associated with a decrease in plasma viremia. These results indicate that decreases in plasma viremia detected during antiretroviral therapy reflect downregulation of virus replication in lymphoid tissue.

DNA-mediated immunization to the hepatitis B surface antigen in mice: aspects of the humoral response mimic hepatitis B viral infection in humans.

Intramuscular injection of plasmid DNA expression vectors encoding the three envelope proteins of the hepatitis B virus (HBV) induced humoral responses in C57BL/6 mice specific to several antigenic determinants of the viral envelope. The first antibodies appeared within 1-2 weeks after injection of DNA and included antibodies of the IgM isotype. Over the next few weeks, an IgM to IgG class switch occurred, indicating helper T-lymphocyte activity. Peak IgG titers were reached by 4-8 weeks after a single DNA injection and were maintained for at least 6 months without further DNA injections. The antibodies to the envelope proteins reacted with group- and subtype-specific antigenic determinants of the HBV surface antigen (HBsAg). Expression vectors encoding the major (S) and middle (preS2 plus S) envelope proteins induced antibodies specific to the S protein and preS2 domain, and preS2 antibodies were prominent at early time points. In general, the expression vectors induced humoral responses in mice that mimic those observed in humans during the course of natural HBV infection.

Local nitric oxide production in viral and autoimmune diseases of the central nervous system.

Because of the short half-life of NO, previous studies implicating NO in central nervous system pathology during infection had to rely on the demonstration of elevated levels of NO synthase mRNA or enzyme expression or NO metabolites such as nitrate and nitrite in the infected brain. To more definitively investigate the potential causative role of NO in lesions of the central nervous system in animals infected with neurotropic viruses or suffering from experimental allergic encephalitis, we have determined directly the levels of NO present in the central nervous system of such animals. Using spin trapping of NO and electron paramagnetic resonance spectroscopy, we confirm here that copious amounts of NO (up to 30-fold more than control) are elaborated in the brains of rats infected with rabies virus or borna disease virus, as well as in the spinal cords of rats that had received myelin basic protein-specific T cells.

Two Drosophila nervous system antigens, Nervana 1 and 2, are homologous to the beta subunit of Na+,K(+)-ATPase.

A nervous system-specific glycoprotein antigen from adult Drosophila heads, designated Nervana (Nrv), has been purified on the basis of reactivity of its carbohydrate epitope(s) with anti-horseradish peroxidase (HRP) antibodies that are specific markers for Drosophila neurons. Anti-Nrv monoclonal antibodies (mAbs), specific for the protein moiety of Nrv, were used to screen a Drosophila embryo cDNA expression library. Three cDNA clones (designated Nrv1, Nrv2.1, and Nrv2.2) were isolated that code for proteins recognized by anti-Nrv mAbs on Western blots. DNA sequencing and Southern blot analyses established that the cDNA clones are derived from two different genes. In situ hybridization to Drosophila polytene chromosomes showed that the cDNA clones map to the third chromosome near 92C-D. Nrv1 and Nrv2.1/2.2 have open reading frames of 309 and 322/323 amino acids, respectively, and they are 43.4% identical at the amino acid level. The proteins deduced from these clones exhibit significant homology in both primary sequence and predicted topology to the beta subunit of Na+,K(+)-ATPase. Immunoaffinity-purified Nrv is associated with a protein (M(r) 100,000) recognized on Western blots by anti-ATPase alpha-subunit mAb. Our results suggest that the Drosophila nervous system-specific antigens Nrv1 and -2 are neuronal forms of the beta subunit of Na+,K(+)-ATPase.

Rep protein of tomato yellow leaf curl geminivirus has an ATPase activity required for viral DNA replication.

The Rep protein of geminiviruses is the sole viral protein required for their DNA replication. The amino acid sequence of Rep protein contains an NTP binding consensus motif (P-loop). Here we show that purified Rep protein of tomato yellow leaf curl virus expressed in Escherichia coli exhibits an ATPase activity in vitro. Amino acid exchanges in the P-loop sequence of Rep causes a substantial decrease or loss of the ATPase activity. In vivo, mutant viruses carrying these Rep mutations do not replicate in plant cells. These results show that ATP binding by the Rep protein of geminiviruses is required for its function in viral DNA replication.

Formation of brome mosaic virus RNA-dependent RNA polymerase in yeast requires coexpression of viral proteins and viral RNA.

In this report we show that yeast expressing brome mosaic virus (BMV) replication proteins 1a and 2a and replicating a BMV RNA3 derivative can be extracted to yield a template-dependent BMV RNA-dependent RNA polymerase (RdRp) able to synthesize (-)-strand RNA from BMV (+)-strand RNA templates added in vitro. This virus-specific yeast-derived RdRp mirrored the template selectivity and other characteristics of RdRp from BMV-infected plants. Equivalent extracts from yeast expressing 1a and 2a but lacking RNA3 contained normal amounts of 1a and 2a but had no RdRp activity on BMV RNAs added in vitro. To determine which RNA3 sequences were required in vivo to yield RdRp activity, we tested deletions throughout RNA3, including the 5',3', and intercistronic noncoding regions, which contain the cis-acting elements required for RNA3 replication in vivo. RdRp activity was obtained only from cells expressing 1a, 2a, and RNA3 derivatives retaining both 3' and intercistronic noncoding sequences. Strong correlation between extracted RdRp activity and BMV (-)-strand RNA accumulation in vivo was found for all RNA3 derivatives tested. Thus, extractable in vitro RdRp activity paralleled formation of a complex capable of viral RNA synthesis in vivo. The results suggest that assembly of active RdRp requires not only viral proteins but also viral RNA, either to directly contribute some nontemplate function or to recruit essential host factors into the RdRp complex and that sequences at both the 3'-terminal initiation site and distant internal sites of RNA3 templates may participate in RdRp assembly and initiation of (-)-strand synthesis.

Viral particles are required for infection in neurodegenerative Creutzfeldt-Jakob disease.

Several models have been proposed for the infectious agents that cause human Creutzfeldt-Jakob disease (CJD) and sheep scrapie. Purified proteins and extracted nucleic acids are not infectious. To further identify the critical molecular components of the CJD agent, 120S infectious material with reduced prion protein (PrP) was treated with guanidine hydrochloride or SDS. Particulate and soluble components were then separated by centrifugation and molecularly characterized. Conditions that optimally solubilized residual PrP and/or nucleic acid-protein complexes were used to produce subfractions that were assayed for infectivity. All controls retained > 90% of the 120S titer (approximately 15% of that in total brain) but lost > 99.5% of their infectivity after heat-SDS treatment (unlike scrapie fractions enriched for PrP). Exposure to 1% SDS at 22 degrees C produced particulate nucleic acid-protein complexes that were almost devoid of host PrP. These sedimenting complexes were as infectious as the controls. In contrast, when such complexes were solubilized with 2.5 M guanidine hydrochloride, the infectious titer was reduced by > 99.5%. Sedimenting PrP aggregates with little nucleic acid and no detectable nucleic acid-binding proteins had negligible infectivity, as did soluble but multimeric forms of PrP. These data strongly implicate a classical viral structure, possibly with no intrinsic PrP, as the CJD infectious agent. CJD-specific protective nucleic acid-binding protein(s) have already been identified in 120S preparations, and preliminary subtraction studies have revealed several CJD-specific nucleic acids. Such viral candidates deserve more attention, as they may be of use in preventing iatrogenic CJD and in solving a fundamental mystery.

Invariance and restriction toward a limited set of self-antigens characterize neonatal IgM antibody repertoires and prevail in autoreactive repertoires of healthy adults.

Analysis of the reactivity of IgM with self-antigens in tissues by a quantitative immunoblotting technique showed striking invariance among newborns in the human and in the mouse. The self-reactive repertoire of IgM of adults was also markedly conserved; it comprised most anti-self reactivities that prevailed among neonates. Multivariate analysis confirmed the homogeneity of IgM repertoires of neonates toward self- and non-self-antigens. Multivariate analysis discriminated between newborn and adult repertoires for reactivity with two of five sources of self-proteins and with non-self-antigens. Our observations support the concept that naturally activated B lymphocytes are selected early in development and throughout life for reactivity with a restricted set of self-antigens.

In vitro cleavage and joining at the viral origin of replication by the replication initiator protein of tomato yellow leaf curl virus.

Replication of the single-stranded DNA genome of geminiviruses occurs via a double-stranded intermediate that is subsequently used as a template for rolling-circle replication of the viral strand. Only one of the proteins encoded by the virus, here referred to as replication initiator protein (Rep protein), is indispensable for replication. We show that the Rep protein of tomato yellow leaf curl virus initiates viral-strand DNA synthesis by introducing a nick in the plus strand within the nonanucleotide 1TAATATT decreases 8AC, identical among all geminiviruses. After cleavage, the Rep protein remains bound to the 5' end of the cleaved strand. In addition, we show that the Rep protein has a joining activity, suggesting that it acts as a terminase, thus resolving the nascent viral single strand into genome-sized units.

Infection of cells by varicella zoster virus: inhibition of viral entry by mannose 6-phosphate and heparin.

Envelope glycoproteins of varicella zoster virus (VZV) contain mannose 6-phosphate (Man6P) residues. We now report that Man6P competitively and selectively inhibits infection of cells in vitro by cell-free VZV; furthermore, dephosphorylation of VZV by exposure to alkaline phosphatase rapidly destroys infectivity. Cells are also protected from VZV in a concentration-dependent manner by heparin (ED50 = 0.23 micrograms/ml; 95% confidence limits = 0.16-0.26 microgram/ml) but not by chondroitin sulfate. Both heparin and Man6P are protective only when present about the time of inoculation. Heparin but not Man6P interferes with the attachment of VZV to cell surfaces; moreover, VZV binds to heparin-affinity columns. These data are compatible with a working hypothesis, whereby VZV attaches to cell surfaces by binding to a heparin sulfate proteoglycan. This binding stabilizes VZV, making possible a low-affinity interaction with another Man6P-dependent receptor, which is necessary for viral entry.

Detecção e caracterização moleculares dos paramixovírus aviários tipo 1 em materiais provenientes de aves silvestres utilizando testes para a detecção dos vírus da família viral Paramyxoviridae

As aves silvestres são importantes reservatórios de vírus que podem acometer as aves domésticas. O monitoramento da circulação viral em aves silvestres é de extrema importância para garantir a sanidade dos plantéis avícolas. O presente estudo teve como objetivo 1) comparar dois testes moleculares de RT-PCR para a detecção dos vírus da família Paramyxoviridae em aves silvestres e sinantrópicas; 2) caracterizar os vírus detectados nestas amostras. Dois testes de RT-PCR e testes específicos de RT-PCR em tempo real (RRT-PCR) para o vírus da doença de Newcastle (NDV) e o metapneumovírus aviário (aMPV) foram utilizados para comparar o limite de detecção entre as amostras. As amostras de aves silvestres foram testadas por dois testes de RT-PCR. Um pequeno fragmento da região do sítio de clivagem do gene F das amostras positivas foi sequenciado. Os testes de RT-PCR foram validados com sucesso, mas apresentaram diferenças entre os limites de detecção quando comparados aos testes específicos de RRT-PCR utilizando diferentes vírus. No total, 100 amostras de aves (suabes) foram testados pelo teste RT-PCR que apresentou um limite de detecção similar entre os diferentes agentes virais. O teste selecionado foi capaz de detectar duas amostras de aves silvestres que foram também detectadas pelo testes específico para NDV e relacionadas às amostras de NDV vacinais do genótipo II da classe II referentes aos vírus de NDV lentogênico (113RQGR ↓ L117). Nosso estudo demonstra a deficiência na biosseguridade adotada pelos sistemas avícolas por permitir a saída dos vírus vacinais para as aves silvestres

Patrones de dispersión de una nueva enfermedad viral en el cultivo de maíz, en Argentina

El maíz es uno de los principales cereales, ubicándose tercero en el ranking de producción mundial. Las enfermedades virales en el cultivo de maíz son factores importantes de pérdidas en la producción, en el mundo. Se ha citado mundialmente la presencia de varios rhabdovirus en maíz, aunque ninguno en Argentina. Maize mosaic virus (MMV) es el más importante debido a las pérdidas que ocasiona. Durante 2006/07 se detectó en trigo Argentina, un Cytorhabdovirus denominado Cereal Rhabdovirus caracterizado serológicamente como Barley yellow striate mosaic virus (BYSMV). Desde 2000/01 hasta la actualidad, se observan plantas de maíz con achaparramiento, esterilidad y estriado amarillo en hojas, en localidades de Córdoba y Santa Fe. Se observaron al microscopio electrónico partículas de rhabdovirus en el citoplasma de las células. Pruebas serológicas para MMV resultaron negativas. Esta virosis fue transmitida a plantas de maíz sanas por el delfácido Peregrinus maidis. Se amplificó un segmento del gen de la polimerasa L de rhabdovirus, mediante RT-PCR con iniciadores degenerados y se obtuvieron las relaciones filogenéticas con otros rhabdovirus, confirmando que se trata de un miembro del género Cytorhabdovirus. Se trataría de un virus nuevo, de la familia Rhabdoviridae presente en diversas localidades del área maicera argentina. El objetivo de este proyecto es estudiar la epidemiología de este virus, mediante la reconstrucción de su historia demográfica y patrones espacio-temporales, utilizando análisis de coalescencia y filogeografía. Se busca: Determinar la secuencia genómica completa del virus en estudio; Obtener iniciadores específicos para el gen de la nucleocápside; Obtener las secuencias nucleotídicas del gen de la nucleocápside viral de aislamientos de diferentes localidades del área maicera argentina; Analizar los patrones filogeográficos de dichos aislamientos. Materiales y métodos. Recolección de material enfermo. Se colectarán plantas de maíz con sintomatología de estriado amarillo, en distintas localidades de Córdoba y Santa Fe. Secuenciación del genoma completo viral. Se purificará el virus en estudio a partir de tejido enfermo (Creamer, 1992). Se extraerá ARN total y se lo enviará al servicio de pirosecuenciación (INDEAR, Argentina). Las secuencias obtenidas serán analizadas utilizando software específico (Lasergene 10, DNASTAR, entre otros). Diseño de iniciadores específicos para el gen de la proteína N viral. Serán diseñados a partir de la secuencia del genoma completo del virus. Determinación de patrones filogeográficos. Se extraerá ARN total de plantas sintomáticas de distintas localidades argentinas. Se amplificará el gen N de cada uno de los aislamientos, se clonarán y secuenciarán estos fragmentos y se alinearán las secuencias obtenidas. Se reconstruirá la filogenia mediante metodología Bayesiana y se realizará un análisis de coalescencia. Finalmente se analizará el patrón filogeográfico del rhabdovirus en estudio. Con el presente trabajo se espera avanzar en el conocimiento de este nuevo virus que afecta cultivos de maíz en Argentina. Se pretende obtener la secuencia genómica completa viral, lo que significará un avance en la caracterización e identificación del mismo. Se busca conocer sus patrones de dispersión espacio-temporales, para comprender los orígenes y posible evolución hacia otras regiones del país. El análisis de secuencias genómicas, brinda una herramienta rápida y de menor esfuerzo de muestreo en el estudio epidemiológico de las poblaciones. El conocimiento de la distribución actual e histórica de este nuevo virus sería crucial para futuros planes de manejo de la enfermedad. El tema de investigación se lleva a cabo en el marco de una tesis doctoral con el apoyo de una beca de formación de CONICET. La transferencia es constante a traves del contacto con productores y asesores agrícolas y mediante la realización de jornadas, charlas, cursos y publicaciones periódicas en medios de difusión.