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  1 / 27514 MEDLINE  
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[PMID]:29179736
[Au] Autor:Erives AJ
[Ad] Endereço:Department of Biology, University of Iowa, Iowa City, IA, 52242-1324, USA. albert-erives@uiowa.edu.
[Ti] Título:Phylogenetic analysis of the core histone doublet and DNA topo II genes of Marseilleviridae: evidence of proto-eukaryotic provenance.
[So] Source:Epigenetics Chromatin;10(1):55, 2017 11 28.
[Is] ISSN:1756-8935
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: While the genomes of eukaryotes and Archaea both encode the histone-fold domain, only eukaryotes encode the core histone paralogs H2A, H2B, H3, and H4. With DNA, these core histones assemble into the nucleosomal octamer underlying eukaryotic chromatin. Importantly, core histones for H2A and H3 are maintained as neofunctionalized paralogs adapted for general bulk chromatin (canonical H2 and H3) or specialized chromatin (H2A.Z enriched at gene promoters and cenH3s enriched at centromeres). In this context, the identification of core histone-like "doublets" in the cytoplasmic replication factories of the Marseilleviridae (MV) is a novel finding with possible relevance to understanding the origin of eukaryotic chromatin. Here, we analyze and compare the core histone doublet genes from all known MV genomes as well as other MV genes relevant to the origin of the eukaryotic replisome. RESULTS: Using different phylogenetic approaches, we show that MV histone domains encode obligate H2B-H2A and H4-H3 dimers of possible proto-eukaryotic origin. MV core histone moieties form sister clades to each of the four eukaryotic clades of canonical and variant core histones. This suggests that MV core histone moieties diverged prior to eukaryotic neofunctionalizations associated with paired linear chromosomes and variant histone octamer assembly. We also show that MV genomes encode a proto-eukaryotic DNA topoisomerase II enzyme that forms a sister clade to eukaryotes. This is a relevant finding given that DNA topo II influences histone deposition and chromatin compaction and is the second most abundant nuclear protein after histones. CONCLUSIONS: The combined domain architecture and phylogenomic analyses presented here suggest that a primitive origin for MV histone genes is a more parsimonious explanation than horizontal gene transfers + gene fusions + sufficient divergence to eliminate relatedness to eukaryotic neofunctionalizations within the H2A and H3 clades without loss of relatedness to each of the four core histone clades. We thus suggest MV histone doublet genes and their DNA topo II gene possibly were acquired from an organism with a chromatinized replisome that diverged prior to the origin of eukaryotic core histone variants for H2/H2A.Z and H3/cenH3. These results also imply that core histones were utilized ancestrally in viral DNA compaction and/or protection from host endonucleases.
[Mh] Termos MeSH primário: DNA Topoisomerases Tipo II/genética
Vírus de DNA/genética
Histonas/genética
Filogenia
[Mh] Termos MeSH secundário: Vírus de DNA/classificação
Genes Virais
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Histones); EC 5.99.1.3 (DNA Topoisomerases, Type II)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180310
[Lr] Data última revisão:
180310
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171129
[St] Status:MEDLINE
[do] DOI:10.1186/s13072-017-0162-0


  2 / 27514 MEDLINE  
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[PMID]:29360861
[Au] Autor:Ogunsemowo O; Olaleye DO; Odaibo GN
[Ad] Endereço:Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria.
[Ti] Título:Genetic diversity of human respiratory syncytial virus circulating among children in Ibadan, Nigeria.
[So] Source:PLoS One;13(1):e0191494, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Human respiratory syncytial virus (HRSV) is the most common viral cause of acute lower respiratory tract infections (LRTIs) in infants and young children however, without an effective vaccine licensed for human use till date. Information on the circulating genotypes of HRSV from regions with high-burden of infection is vital in the global efforts towards the development of protective vaccine. We report here the genotypes of HRSV circulating among children in Ibadan, the first of such from Nigeria.Nasopharyngeal and oropharyngeal swabs collected from 231 children presenting with respiratory infections in some health facilities for care as well as those attending immunization centers for routine vaccination in Ibadan, Nigeria were used for the study. The 2nd hypervariable (HVR2) region of the glycoprotein (G) gene of HRSV was amplified and sequenced using HRSV group specific primers. HRSV was detected in 41 out of the 231 samples. Thirty-three of the isolates were successfully subtyped(22 subtype A and 11 subtype B). Fourteen of the subtype A and all the subtype B were successfully sequenced and genotyped. Phylogenetic analysis showed that genotype ON1 with 72 nucleotide (nt) duplication was the major subgroup A virus (11 of 14) detected together with genotype NA2. All the HRSV subtype B detected belong to the BA genotype with characteristic 60nt duplication. The ON1 genotypes vary considerably from the prototype strain due to amino acid substitutions including T292I which has not been reported elsewhere. The NA2 genotypes have mutations on four antigenic sites within the HVR2relative to the prototype A2. In conclusion, three genotypes of HRSV were found circulating in Ibadan, Nigeria. Additional study that will include isolates from other parts of the country will be done to determine the extent of genotype diversity of HRSV circulating in Nigeria.
[Mh] Termos MeSH primário: Variação Genética
Vírus Sincicial Respiratório Humano/genética
[Mh] Termos MeSH secundário: Criança
Pré-Escolar
Genes Virais
Genótipo
Seres Humanos
Nigéria
Filogenia
Reação em Cadeia da Polimerase
Vírus Sincicial Respiratório Humano/classificação
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180226
[Lr] Data última revisão:
180226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180124
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191494


  3 / 27514 MEDLINE  
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[PMID]:29385169
[Au] Autor:Bissa M; Forlani G; Zanotto C; Tosi G; De Giuli Morghen C; Accolla RS; Radaelli A
[Ad] Endereço:Department of Pharmacological and Biomolecular Sciences, University of Milan, via Balzaretti 9, Milan, Italy.
[Ti] Título:Fowlpoxvirus recombinants coding for the CIITA gene increase the expression of endogenous MHC-II and Fowlpox Gag/Pro and Env SIV transgenes.
[So] Source:PLoS One;13(1):e0190869, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:A complete eradication of an HIV infection has never been achieved by vaccination and the search for new immunogens that can induce long-lasting protective responses is ongoing. Avipoxvirus recombinants are host-restricted for replication to avian species and they do not have the undesired side effects induced by vaccinia recombinants. In particular, Fowlpox (FP) recombinants can express transgenes over long periods and can induce protective immunity in mammals, mainly due to CD4-dependent CD8+ T cells. In this context, the class II transactivator (CIITA) has a pivotal role in triggering the adaptive immune response through induction of the expression of class-II major histocompatibility complex molecule (MHC-II), that can present antigens to CD4+ T helper cells. Here, we report on construction of novel FPgp and FPenv recombinants that express the highly immunogenic SIV Gag-pro and Env structural antigens. Several FP-based recombinants, with single or dual genes, were also developed that express CIITA, driven from H6 or SP promoters. These recombinants were used to infect CEF and Vero cells in vitro and determine transgene expression, which was evaluated by real-time PCR and Western blotting. Subcellular localisation of the different proteins was evaluated by confocal microscopy, whereas HLA-DR or MHC-II expression was measured by flow cytometry. Fowlpox recombinants were also used to infect syngeneic T/SA tumour cells, then injected into Balb/c mice to elicit MHC-II immune response and define the presentation of the SIV transgene products in the presence or absence of FPCIITA. Antibodies to Env were measured by ELISA. Our data show that the H6 promoter was more efficient than SP to drive CIITA expression and that CIITA can enhance the levels of the gag/pro and env gene products only when infection is performed by FP single recombinants. Also, CIITA expression is higher when carried by FP single recombinants than when combined with FPgp or FPenv constructs and can induce HLA-DR cell surface expression. However, in-vivo experiments did not show any significant increase in the humoral response. As CIITA already proved to elicit immunogenicity by improving antigen presentation, further in-vivo experiments should be performed to increase the immune responses. The use of prime/boost immunisation protocols and the oral administration route of the recombinants may enhance the immunogenicity of Env peptides presented by MHC-II and provide CD4+ T-cell stimulation.
[Mh] Termos MeSH primário: Genes Virais
Complexo Principal de Histocompatibilidade/genética
Proteínas Nucleares/genética
Poxviridae/genética
Recombinação Genética
Vírus da Imunodeficiência Símia/genética
Transativadores/genética
Transgenes
[Mh] Termos MeSH secundário: Vacinas contra a AIDS/genética
Vacinas contra a AIDS/imunologia
Animais
Western Blotting
Linfócitos T CD4-Positivos/imunologia
Linfócitos T CD8-Positivos/imunologia
Linhagem Celular
Embrião de Galinha
Ensaio de Imunoadsorção Enzimática
Infecções por HIV/imunologia
Infecções por HIV/prevenção & controle
Seres Humanos
Camundongos
Camundongos Endogâmicos BALB C
Microscopia Confocal
Regiões Promotoras Genéticas
Reação em Cadeia da Polimerase em Tempo Real
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (AIDS Vaccines); 0 (MHC class II transactivator protein); 0 (Nuclear Proteins); 0 (Trans-Activators)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180221
[Lr] Data última revisão:
180221
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180201
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190869


  4 / 27514 MEDLINE  
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[PMID]:29385148
[Au] Autor:Ndjoyi-Mbiguino A; Kombe Kombe AJ; Bivigou-Mboumba B; Zoa-Assoumou S; Akombi FL; Nzengui Nzengui F; M'boyis Kamdem H; François-Souquière S
[Ad] Endereço:Laboratoire National de Référence IST/Sida, Département de Bactériologie-Virologie, Faculté de Médecine et des Sciences de la Santé, Université des Sciences de la Santé, Owendo, Gabon.
[Ti] Título:Low prevalence of HCV infection with predominance of genotype 4 among HIV patients living in Libreville, Gabon.
[So] Source:PLoS One;13(1):e0190529, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Gabon is an endemic area for human immunodeficiency virus (HIV) and hepatitis C virus (HCV) and the risk of co-infection is high. METHOD: Between November 2015 and April 2016, we conducted retrospective study on HCV infection among people living with HIV/AIDS (PLHA). A total of 491 PLHA were included in this study and tested for the presence of HCV infection. HIV viral loads were obtained using the Generic HIV viral Load® assay and the CD4+ T cells count was performed using BD FACSCount™ CD4 reagents. HCV screening was performed using the MP Diagnostics HCV ELISA 4.0 kit. HCV genotypes were determined by sequence analysis of NS5B and Core regions. The Mann-Whitney test was used to compare the groups. Chi-2 test and Fisher's Exact Test were used to compare prevalence. RESULTS: HCV seroprevalence was 2.9% (14/491), (95% confidence interval (CI):1.4-4.3%). The percentage of HCV viremic patients, defined by the detection of HCV RNA in plasma, was 57% (8/14), representing 1.6% of the total population. HCV seroprevalence and replicative infection were not statistically differ with gender. The percentage of co-infection increased with age. No correlation with CD4+ T cells count and HIV viral load level was registered in this study. Identified HCV strains were predominantly of genotype 4 (87.5%) including 4k, 4e, 4g, 4p, 4f and 4c subtypes. Only one strain belonged to genotype 2 (subtype 2q). Analysis of the NS5B region did not reveal the presence of resistance-associated substitutions for sofosbuvir. CONCLUSION: A systematic screening of hepatitis C is therefore strongly recommended as well as genotyping of HCV strains in order to adapt treatments for the specific case of people living with HIV/AIDS in Central Africa.
[Mh] Termos MeSH primário: Genótipo
Infecções por HIV/epidemiologia
Hepacivirus/genética
Hepatite C/epidemiologia
[Mh] Termos MeSH secundário: Adolescente
Adulto
Contagem de Linfócito CD4
Feminino
Gabão/epidemiologia
Genes Virais
Infecções por HIV/complicações
Infecções por HIV/virologia
HIV-1/genética
HIV-1/isolamento & purificação
Hepatite C/complicações
Hepatite C/virologia
Seres Humanos
Masculino
Meia-Idade
Prevalência
Estudos Retrospectivos
Carga Viral
Adulto Jovem
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180221
[Lr] Data última revisão:
180221
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180201
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190529


  5 / 27514 MEDLINE  
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[PMID]:29338045
[Au] Autor:Kim AR; Lee DH; Lee SH; Rubino I; Choi HJ; Quan FS
[Ad] Endereço:Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea.
[Ti] Título:Protection induced by virus-like particle vaccine containing tandem repeat gene of respiratory syncytial virus G protein.
[So] Source:PLoS One;13(1):e0191277, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract illness in infants, young children and the elderly. However, there is no licensed vaccine available against RSV infection. In this study, we generated virus-like particle (VLP) vaccine and investigated the vaccine efficacy in a mouse model. For VLP vaccines, tandem gene (1-780 bp) for V1 VLPs and tandem repeat gene (repeated 450-780 bp) for V5 VLPs were constructed in pFastBacTM vectors, respectively. Influenza matrix protein 1 (M1) was used as a core protein in the VLPs. Notably, upon challenge infection, significantly lower virus loads were measured in the lung of mice immunized with V1 or V5 VLPs compared to those of naïve mice and formalin-inactivated RSV immunized control mice. In particular, V5 VLPs immunization showed significantly lower virus titers than V1 VLPs immunization. Furthermore, V5 VLPs immunization elicited increased memory B cells responses in the spleen. These results indicated that V5 VLP vaccine containing tandem repeat gene protein provided better protection than V1 VLPs with significantly decreased inflammation in the lungs. Thus, V5 VLPs could be a potential vaccine candidate against RSV.
[Mh] Termos MeSH primário: Infecções por Vírus Respiratório Sincicial/prevenção & controle
Vacinas contra Vírus Sincicial Respiratório/farmacologia
Vírus Sincicial Respiratório Humano/genética
Vírus Sincicial Respiratório Humano/imunologia
Vacinas de Partículas Semelhantes a Vírus/farmacologia
Proteínas do Envelope Viral/genética
Proteínas do Envelope Viral/imunologia
[Mh] Termos MeSH secundário: Animais
Anticorpos Antivirais/sangue
Modelos Animais de Doenças
Feminino
Genes Virais
Seres Humanos
Pulmão/imunologia
Pulmão/patologia
Pulmão/virologia
Camundongos
Camundongos Endogâmicos BALB C
Infecções por Vírus Respiratório Sincicial/imunologia
Infecções por Vírus Respiratório Sincicial/virologia
Vacinas contra Vírus Sincicial Respiratório/genética
Sequências de Repetição em Tandem
Vacinas de Partículas Semelhantes a Vírus/genética
Carga Viral
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Antibodies, Viral); 0 (Respiratory Syncytial Virus Vaccines); 0 (Vaccines, Virus-Like Particle); 0 (Viral Envelope Proteins); 0 (attachment protein G)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180220
[Lr] Data última revisão:
180220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180117
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191277


  6 / 27514 MEDLINE  
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[PMID]:29209811
[Au] Autor:Panno S; Caruso AG; Davino S
[Ad] Endereço:Department of Agricultural, Food and Forest science, University of Palermo, Viale delle Scienze, bld 5, 90128, Palermo, Italy.
[Ti] Título:The nucleotide sequence of a recombinant tomato yellow leaf curl virus strain frequently detected in Sicily isolated from tomato plants carrying the Ty-1 resistance gene.
[So] Source:Arch Virol;163(3):795-797, 2018 Mar.
[Is] ISSN:1432-8798
[Cp] País de publicação:Austria
[La] Idioma:eng
[Ab] Resumo:In July 2016, an aggressive syndrome of tomato yellow leaf curl disease was reported in Sicily in tomato plants carrying the Ty-1 resistance gene. A total of 34 samples were collected and analyzed. Twenty-seven out of the 34 samples analyzed appeared to contain only recombinant molecules. One full sequence was obtained after cloning. Alignments and plot similarity analysis showed that the genome of the recombinant, named TYLCV-IL[IT:Sic23:16], was mostly derived from tomato yellow leaf curl virus (TYLCV), with a small region of 132 nucleotides in the non-coding region between the stem-loop and the start of the V2 ORF replaced by 124 nucleotides derived from a virus of a different species, tomato yellow leaf curl Sardinia virus. All plants in which the new recombinant was detected belonged to resistant tomato cultivars.
[Mh] Termos MeSH primário: Begomovirus/genética
Genes Virais/genética
Lycopersicon esculentum/virologia
Folhas de Planta/virologia
Recombinação Genética
[Mh] Termos MeSH secundário: Sequência de Bases
Begomovirus/classificação
Begomovirus/isolamento & purificação
Resistência à Doença/genética
Suscetibilidade a Doenças
Sequenciamento de Nucleotídeos em Larga Escala
Lycopersicon esculentum/genética
Lycopersicon esculentum/imunologia
Doenças das Plantas/genética
Doenças das Plantas/imunologia
Doenças das Plantas/virologia
Imunidade Vegetal/genética
Folhas de Planta/genética
Folhas de Planta/imunologia
Plantas Geneticamente Modificadas
Análise de Sequência de DNA
Sicília
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180220
[Lr] Data última revisão:
180220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171207
[St] Status:MEDLINE
[do] DOI:10.1007/s00705-017-3674-9


  7 / 27514 MEDLINE  
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[PMID]:29300751
[Au] Autor:Ohshima K; Mitoma S; Gibbs AJ
[Ad] Endereço:Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, Saga, Japan.
[Ti] Título:The genetic diversity of narcissus viruses related to turnip mosaic virus blur arbitrary boundaries used to discriminate potyvirus species.
[So] Source:PLoS One;13(1):e0190511, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Narcissus plants (Narcissus tazetta var. chinensis) showing mosaic or striping leaves were collected from around Japan, and tested for virus infections using potyvirus-specific primers. Many were found to be infected with a macluravirus and mixtures of different potyviruses, one third of them narcissus yellow stripe virus (NYSV)-like viruses. Genomes of nine of the NYSV-like viruses were sequenced and, together with four already published, provided data for phylogenetic and pairwise identity analyses of their place in the turnip mosaic virus (TuMV) phylogenetic group. Using existing ICTV criteria for defining potyvirus species, the narcissus viruses in TuMV group were found to be from five species; the previously described NLSYV, and four new species we call narcissus virus 1 (NV-1) and narcissus yellow stripe-1 to -3 (NYSV-1, NYSV-2 and NYSV-3). However, as all are from a single host species, and natural recombinants with NV-1 and NYSV-3 'parents have been found in China and India, we also conclude that they could be considered to be members of a single mega-species, narcissus virus; the criteria for defining such a potyvirus species would then be that their polyprotein sequences have greater than 69% identical nucleotides and greater than 75% identical amino acids.
[Mh] Termos MeSH primário: Variação Genética
Narcissus/virologia
Potyvirus/genética
[Mh] Termos MeSH secundário: Proteínas do Capsídeo/genética
Genes Virais
Filogenia
Potyvirus/classificação
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Capsid Proteins)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180215
[Lr] Data última revisão:
180215
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180105
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190511


  8 / 27514 MEDLINE  
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[PMID]:29293524
[Au] Autor:Liu WJ; Aaskov JG
[Ad] Endereço:Australian Army Malaria Institute, Weary Dunlop Drive, Enoggera, Brisbane, Australia.
[Ti] Título:Fitness peaks of dengue virus populations.
[So] Source:PLoS One;13(1):e0189554, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The role of intra-host genetic diversity in dengue viral populations remains a topic of debate, particularly the impact on transmission of changes in this diversity. Several approaches have been taken to increasing and decreasing the genetic diversity of populations of RNA viruses and have drawn what appear to be contradictory conclusions. A 2-6 fold increase in genetic diversity of a wild type population of dengue virus serotype 1(DENV1) and of an infectious clone population derived from the wild type population, produced by treatment with nucleotide analogue 5 fluorouracil (5FU), drove the populations to extinction. Removal of 5FU immediately prior to extinction, resulted in a return to pre-treatment levels of fitness and genetic diversity, albeit with novel single nucleotide polymorphisms. These observations support the concept that DENV populations exist on fitness peaks determined by their transmission requirements and either an increase or a decrease in genetic diversity may result in a loss of fitness.
[Mh] Termos MeSH primário: Vírus da Dengue/fisiologia
[Mh] Termos MeSH secundário: Vírus da Dengue/efeitos dos fármacos
Vírus da Dengue/genética
Fluoruracila/farmacologia
Genes Virais
Variação Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
U3P01618RT (Fluorouracil)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180215
[Lr] Data última revisão:
180215
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180103
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0189554


  9 / 27514 MEDLINE  
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[PMID]:29360822
[Au] Autor:Chalkias S; Gorham JM; Mazaika E; Parfenov M; Dang X; DePalma S; McKean D; Seidman CE; Seidman JG; Koralnik IJ
[Ad] Endereço:Division of NeuroImmunology, Center for Virology and Vaccine Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America.
[Ti] Título:ViroFind: A novel target-enrichment deep-sequencing platform reveals a complex JC virus population in the brain of PML patients.
[So] Source:PLoS One;13(1):e0186945, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Deep nucleotide sequencing enables the unbiased, broad-spectrum detection of viruses in clinical samples without requiring an a priori hypothesis for the source of infection. However, its use in clinical research applications is limited by low cost-effectiveness given that most of the sequencing information from clinical samples is related to the human genome, which renders the analysis of viral genomes challenging. To overcome this limitation we developed ViroFind, an in-solution target-enrichment platform for virus detection and discovery in clinical samples. ViroFind comprises 165,433 viral probes that cover the genomes of 535 selected DNA and RNA viruses that infect humans or could cause zoonosis. The ViroFind probes are used in a hybridization reaction to enrich viral sequences and therefore enhance the detection of viral genomes via deep sequencing. We used ViroFind to detect and analyze all viral populations in the brain of 5 patients with progressive multifocal leukoencephalopathy (PML) and of 18 control subjects with no known neurological disease. Compared to direct deep sequencing, by using ViroFind we enriched viral sequences present in the clinical samples up to 127-fold. We discovered highly complex polyoma virus JC populations in the PML brain samples with a remarkable degree of genetic divergence among the JC virus variants of each PML brain sample. Specifically for the viral capsid protein VP1 gene, we identified 24 single nucleotide substitutions, 12 of which were associated with amino acid changes. The most frequent (4 of 5 samples, 80%) amino acid change was D66H, which is associated with enhanced tissue tropism, and hence likely a viral fitness advantage, compared to other variants. Lastly, we also detected sparse JC virus sequences in 10 of 18 (55.5%) of control samples and sparse human herpes virus 6B (HHV6B) sequences in the brain of 11 of 18 (61.1%) control subjects. In sum, ViroFind enabled the in-depth analysis of all viral genomes in PML and control brain samples and allowed us to demonstrate a high degree of JC virus genetic divergence in vivo that has been previously underappreciated. ViroFind can be used to investigate the structure of the virome with unprecedented depth in health and disease state.
[Mh] Termos MeSH primário: Encéfalo/virologia
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Vírus JC/isolamento & purificação
Leucoencefalopatia Multifocal Progressiva/virologia
[Mh] Termos MeSH secundário: Genes Virais
Seres Humanos
Vírus JC/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180206
[Lr] Data última revisão:
180206
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180124
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0186945


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[PMID]:29284004
[Au] Autor:Fu JG; Shi C; Xu C; Lin Q; Zhang J; Yi QH; Zhang J; Bao CJ; Huo X; Zhu YF; Ai J; Xing Z
[Ad] Endereço:Medical School and Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, China.
[Ti] Título:Outbreaks of acute gastroenteritis associated with a re-emerging GII.P16-GII.2 norovirus in the spring of 2017 in Jiangsu, China.
[So] Source:PLoS One;12(12):e0186090, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:A total of 64 acute gastroenteritis outbreaks with 2,953 patients starting in December of 2016 and occurring mostly in the late spring of 2017 were reported in Jiangsu, China. A recombinant GII.P16-GII.2 norovirus variant was associated with 47 outbreaks (73.4%) for the gastroenteritis epidemic, predominantly occurring in February and March of 2017. Sequence analysis of the RNA-dependent RNA polymerase (RdRp) and capsid protein of the viral isolates from these outbreaks confirmed that this GII.P16-GII.2 strain was the GII.P16-GII.2 variant with the intergenotypic recombination, identified in Taiwan, Hong Kong, and other cities in China in 2016. This GII.P16-GII.2 recombinant variant appeared to a re-emerging strain, firstly identified in 2011-2012 from Japan and USA but might be independently originated from other GII.P16-GII.2 variants for sporadic and outbreaks of gastroenteritis in Japan and China before 2016. Further identification of unique amino acid mutations in both VP1 and RdRp of NoV strain as shown in this report may provide insight in explaining its structural and antigenic changes, potentially critical for the variant recombinant to gain its predominance in causing regional and worldwide epidemics.
[Mh] Termos MeSH primário: Infecções por Caliciviridae/epidemiologia
Surtos de Doenças
Gastroenterite/epidemiologia
Norovirus/isolamento & purificação
[Mh] Termos MeSH secundário: Doença Aguda
China/epidemiologia
Genes Virais
Seres Humanos
Norovirus/classificação
Norovirus/genética
Norovirus/patogenicidade
Filogenia
Proteínas Virais/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Viral Proteins)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180129
[Lr] Data última revisão:
180129
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171229
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0186090



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