The Experts below are selected from a list of 156 Experts worldwide ranked by ideXlab platform
Ming Shu Wang - One of the best experts on this subject based on the ideXlab platform.
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Bioinformatics Analysis of UL39 Gene from Duck Plague Virus
Advanced Materials Research, 2013Co-Authors: Guo Fu Lu, An Chun Cheng, Ming Shu WangAbstract:The structures and characteristics of the large subunit of ribonucleotide reductase (R1), encoded by UL39 gene from duck plague virus (DPV) were analyzed and predicted by using a series of free bioinformatics software packages and bioinformatics tools. The DPV UL39 gene has a base composition of 681 adenine (27.99%), 503 cytosine (20.67%), 593 guanine (24.37%) and 656 thymine (26.96%). The online analysis of the physico-chemical properties demonstrates that the protein has 40 potential phosphorylation sites and 4 N-glycosylation sites when the threshold of prediction score is above 0.5; without the signal peptide and the transmembrance region. The phylogenetic tree proved that DPV R1 protein had a close evolutionary relationship with the Mardivirus genus of the Alphaherpesviruses. In conclusion, all those results will provide some valuable information for the further research of UL39 gene.
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Bioinformatics Analysis of the Complete Nucleotide Sequence of UL17 Gene from Duck Enteritis Virus
Advanced Materials Research, 2013Co-Authors: An Chun Cheng, Ming Shu WangAbstract:Duck enteritis virus (DEV) is a herpesvirus that causes an acute, contagious, and fatal disease. Our laboratory had identified and sequenced the DEV-UL17 gene, one of the conservative genes of this viral genome. It is a 2055bp segment, GenBank accession NO. 643567. Here in this article we used kinds of bioinformatics softwares and online web servers to analyze the nucleotide sequence of this gene for further research. The phylogenetic tree of the DEV-UL17 protein and its homologs of other 19 reference herpesviruses revealed that DEV had close evolutionary relationship with Meleagrid herpesvirus1, Gallid herpesvirus 2 and Gallid herpesvirus 3, the members of genus Mardivirus. In addition, multiple epitopes and potential motifs were found in DEV-UL17 protein and they may play an important role in in the function of immune system, it may greatly influence the antibodies and genetic vaccine, or in the clinical diagnosis of DEV.
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BMEI - Analysis of synonymous codon usage on the small subunit of ribonucleotide reductase gene from duck plague virus
2012 5th International Conference on BioMedical Engineering and Informatics, 2012Co-Authors: An Chun Cheng, Ming Shu Wang, Jie Huang, Xiaoyue ChenAbstract:Duck plague virus (DPV) is a widespread virus in all members of the family Anatidae of the order Anseriformes, and it has been classified into the family Herpesviridae. In this study, the relative synonymous codon usage (RSCU) values, effective number of codons (ENC) values, and the frequencies of nucleotide G + C at the third position (GC3s) contents were investigated, meanwhile, a comparative analysis of codon usage patterns and a phylogenetic analysis for the small subunit of ribonucleotide reductase (R2) gene of DPV and the other 25 herpesviruses were performed. The optimal codons for each amino acid were A-ended or T-ended in the 59 sense codons from the RSCU values of DPV R2 gene. The comparative analysis of the ENC values, and GC3s contents showed the codon usage patterns were not phylogenetically conserved among these 26 herpesvirus R2 genes, but similarity in different genera, and that DPV was close to the Mardivirus and the iltovirus. In addition, the plot of ENC vs. GC3s of the 26 herpesvirus R2 genes indicated that the genetic characteristics of R2 gene possibly resulted from mutation pressure. Furthermore, the phylogenetic analysis revealed that DPV may be a part of the alphaherpesvirus, and exhibit a close relationship with the Mardivirus and the simplexvirus.
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BMEI - Molecular analysis of the duck plague virus US10 gene and its encoding protein
2012 5th International Conference on BioMedical Engineering and Informatics, 2012Co-Authors: An Chun Cheng, Ming Shu WangAbstract:In the past years, a number of conventional and advanced bioinformatics methods have been employed for predicting gene structure and function. Here, we used many bioinformatics softwares to analyse the duck plague virus US10 gene (GenBank accession number: EU195084). The results indicated that this gene encoded an estimated 322 putative protein, contained the conserved domain of the Gene66 (IR5) protein. The protein found many functional sites, but without any transmembrane region and signal peptide. Secondary structure prediction showed that random coil (52.48%) and alpha helix (44.10%) had a high proportion. Analysis of the antigenicity indicated that in the position of 28-44, 100-120 and 302-322 amino acids distributed the most likely epitopes. Phylogenetic tree of the amino acids sequences showed this gene had a closer evolutionary relationship with Mardivirus. These results provided rational data to elucidate biological function and physiological features of the gene and its encoding protein.
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BMEI - Characterization of codon usage bias in the US10 gene of duck enteritis virus
2012 5th International Conference on BioMedical Engineering and Informatics, 2012Co-Authors: An Chun Cheng, Ming Shu WangAbstract:In order to have some bioinformatics information about synonymous codon usage pattern of the duck enteritis virus (DEV) US10 gene (GenBank accession number: EU195084), we analyzed the DEV US10 gene and 19 other reference herpesviruses by using bioinformatics softwares, such as CAI, CHIPS and CUSP program of EMBOSS. The results revealed that codon usage bias in the US10 gene was mainly influenced by nucleotide composition, specifically manifested in adenine (A) and thymine (T) at the third codon position. The phylogenetic analysis suggested that DEV had a closer evolutionary relationship with the Mardivirus, which was clustered into Alphaherpesvirinae. There were 32 codons showing uniform usage between DEV and Escherichia coli, 41 between DEV and yeast, 38 between DEV and Homo sapiens. Therefore, the yeast expression system may be more appropriate for the expression of DEV US10 gene. The information from this research may not only have theoretical value in understanding molecular evolution, but also have potential value for the further studying of this gene.
An Chun Cheng - One of the best experts on this subject based on the ideXlab platform.
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Bioinformatics Analysis of UL39 Gene from Duck Plague Virus
Advanced Materials Research, 2013Co-Authors: Guo Fu Lu, An Chun Cheng, Ming Shu WangAbstract:The structures and characteristics of the large subunit of ribonucleotide reductase (R1), encoded by UL39 gene from duck plague virus (DPV) were analyzed and predicted by using a series of free bioinformatics software packages and bioinformatics tools. The DPV UL39 gene has a base composition of 681 adenine (27.99%), 503 cytosine (20.67%), 593 guanine (24.37%) and 656 thymine (26.96%). The online analysis of the physico-chemical properties demonstrates that the protein has 40 potential phosphorylation sites and 4 N-glycosylation sites when the threshold of prediction score is above 0.5; without the signal peptide and the transmembrance region. The phylogenetic tree proved that DPV R1 protein had a close evolutionary relationship with the Mardivirus genus of the Alphaherpesviruses. In conclusion, all those results will provide some valuable information for the further research of UL39 gene.
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Bioinformatics Analysis of the Complete Nucleotide Sequence of UL17 Gene from Duck Enteritis Virus
Advanced Materials Research, 2013Co-Authors: An Chun Cheng, Ming Shu WangAbstract:Duck enteritis virus (DEV) is a herpesvirus that causes an acute, contagious, and fatal disease. Our laboratory had identified and sequenced the DEV-UL17 gene, one of the conservative genes of this viral genome. It is a 2055bp segment, GenBank accession NO. 643567. Here in this article we used kinds of bioinformatics softwares and online web servers to analyze the nucleotide sequence of this gene for further research. The phylogenetic tree of the DEV-UL17 protein and its homologs of other 19 reference herpesviruses revealed that DEV had close evolutionary relationship with Meleagrid herpesvirus1, Gallid herpesvirus 2 and Gallid herpesvirus 3, the members of genus Mardivirus. In addition, multiple epitopes and potential motifs were found in DEV-UL17 protein and they may play an important role in in the function of immune system, it may greatly influence the antibodies and genetic vaccine, or in the clinical diagnosis of DEV.
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BMEI - Analysis of synonymous codon usage on the small subunit of ribonucleotide reductase gene from duck plague virus
2012 5th International Conference on BioMedical Engineering and Informatics, 2012Co-Authors: An Chun Cheng, Ming Shu Wang, Jie Huang, Xiaoyue ChenAbstract:Duck plague virus (DPV) is a widespread virus in all members of the family Anatidae of the order Anseriformes, and it has been classified into the family Herpesviridae. In this study, the relative synonymous codon usage (RSCU) values, effective number of codons (ENC) values, and the frequencies of nucleotide G + C at the third position (GC3s) contents were investigated, meanwhile, a comparative analysis of codon usage patterns and a phylogenetic analysis for the small subunit of ribonucleotide reductase (R2) gene of DPV and the other 25 herpesviruses were performed. The optimal codons for each amino acid were A-ended or T-ended in the 59 sense codons from the RSCU values of DPV R2 gene. The comparative analysis of the ENC values, and GC3s contents showed the codon usage patterns were not phylogenetically conserved among these 26 herpesvirus R2 genes, but similarity in different genera, and that DPV was close to the Mardivirus and the iltovirus. In addition, the plot of ENC vs. GC3s of the 26 herpesvirus R2 genes indicated that the genetic characteristics of R2 gene possibly resulted from mutation pressure. Furthermore, the phylogenetic analysis revealed that DPV may be a part of the alphaherpesvirus, and exhibit a close relationship with the Mardivirus and the simplexvirus.
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BMEI - Molecular analysis of the duck plague virus US10 gene and its encoding protein
2012 5th International Conference on BioMedical Engineering and Informatics, 2012Co-Authors: An Chun Cheng, Ming Shu WangAbstract:In the past years, a number of conventional and advanced bioinformatics methods have been employed for predicting gene structure and function. Here, we used many bioinformatics softwares to analyse the duck plague virus US10 gene (GenBank accession number: EU195084). The results indicated that this gene encoded an estimated 322 putative protein, contained the conserved domain of the Gene66 (IR5) protein. The protein found many functional sites, but without any transmembrane region and signal peptide. Secondary structure prediction showed that random coil (52.48%) and alpha helix (44.10%) had a high proportion. Analysis of the antigenicity indicated that in the position of 28-44, 100-120 and 302-322 amino acids distributed the most likely epitopes. Phylogenetic tree of the amino acids sequences showed this gene had a closer evolutionary relationship with Mardivirus. These results provided rational data to elucidate biological function and physiological features of the gene and its encoding protein.
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BMEI - Characterization of codon usage bias in the US10 gene of duck enteritis virus
2012 5th International Conference on BioMedical Engineering and Informatics, 2012Co-Authors: An Chun Cheng, Ming Shu WangAbstract:In order to have some bioinformatics information about synonymous codon usage pattern of the duck enteritis virus (DEV) US10 gene (GenBank accession number: EU195084), we analyzed the DEV US10 gene and 19 other reference herpesviruses by using bioinformatics softwares, such as CAI, CHIPS and CUSP program of EMBOSS. The results revealed that codon usage bias in the US10 gene was mainly influenced by nucleotide composition, specifically manifested in adenine (A) and thymine (T) at the third codon position. The phylogenetic analysis suggested that DEV had a closer evolutionary relationship with the Mardivirus, which was clustered into Alphaherpesvirinae. There were 32 codons showing uniform usage between DEV and Escherichia coli, 41 between DEV and yeast, 38 between DEV and Homo sapiens. Therefore, the yeast expression system may be more appropriate for the expression of DEV US10 gene. The information from this research may not only have theoretical value in understanding molecular evolution, but also have potential value for the further studying of this gene.
Ying Wu - One of the best experts on this subject based on the ideXlab platform.
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Molecular Cloning and Phylogenetic Analysis of the Duck Enteritis Virus UL55 Gene
Advanced Materials Research, 2011Co-Authors: Ying Wu, An Chun Cheng, Ming Shu Wang, De Kang Zhu, X. Y. ChenAbstract:A 561-bp complete open reading frame of the duck enteritis virus(DEV) UL55 gene (GenBank accession No EU071034) was isolated in our laboratory and amplified by common PCR using a pair of specific primers .PCR product containing this ORF was cloned into the vector of PMD18-T. Four evolutionary analysis approaches were used to construct phylogenetic trees of DEV in relation to herpesviruses based on the nucleotide sequences. Bootstrap was used as statistic method to testify the reliablity of the constructed phylogenetic tree. Phylogenetic trees indicated that DEV and other herpesviruses generated from one ancestor and DEV were grouped into the subfamily Alphaherpesvirinae. In our result, DEV showed a close relationship with the genus Mardivirus, but formed a single branch. Partial genomic organization and phylogenetic analysis in the present study provides evidence that DEV was a member of the subfamily Alphaherpesvirinae and should be assigned as an individual genus or group.
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Molecular Characterization Analysis of Newly Identified Duck Enteritis Virus UL55 Gene
2010 4th International Conference on Bioinformatics and Biomedical Engineering, 2010Co-Authors: Ying Wu, An Chun Cheng, Ming Shu Wang, Zhiwen Xu, Yi Wang, Zhengli ChenAbstract:The focus of this paper is on the newly identified UL55 gene of DEV in our laboratory.Available bioinformatic tools were used to describe its molecular characteristics. A identified nucleotide sequence about 561bp of DEV UL55 ,consisting a complete ORF, was deduced to encode a protein with 186 amino acids.The 20.7981 kDa protein whose singnal peptide and transmembrane region are both absent. Codon usage analysis shows the gene could be well expressed in Escherichia BL21.The putative protein is hydrophilic on the whole,its antigen epitope centralizes at the Extended strand (Ee) and Random coil (Cc) regions as well as the corresponding hydrophilic regions.It was predicted to be a nucleoprotein, which is probably invovled in viron entry,assembly,egress,maturation and release as its homologous.However, UL55 protein just plays an accessory role. Phylogenetic tree based on amino acids and its reference herpesvirus reaveals that there is a close relationship between DEV and Mardivirus genus.However, DEV is clustered within a monophyletic clade among others , suggests it is an intermediate taxonomic entity and should be placed in a single genus within the herpetoviridae subfamily.Despite its preliminary characterization, this study can clearly direct our research to elucidate its biological function and physiological features of this newly identified UL55 gene.
Zhengli Chen - One of the best experts on this subject based on the ideXlab platform.
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Molecular Characterization Analysis of Newly Identified Duck Enteritis Virus UL55 Gene
2010 4th International Conference on Bioinformatics and Biomedical Engineering, 2010Co-Authors: Ying Wu, An Chun Cheng, Ming Shu Wang, Zhiwen Xu, Yi Wang, Zhengli ChenAbstract:The focus of this paper is on the newly identified UL55 gene of DEV in our laboratory.Available bioinformatic tools were used to describe its molecular characteristics. A identified nucleotide sequence about 561bp of DEV UL55 ,consisting a complete ORF, was deduced to encode a protein with 186 amino acids.The 20.7981 kDa protein whose singnal peptide and transmembrane region are both absent. Codon usage analysis shows the gene could be well expressed in Escherichia BL21.The putative protein is hydrophilic on the whole,its antigen epitope centralizes at the Extended strand (Ee) and Random coil (Cc) regions as well as the corresponding hydrophilic regions.It was predicted to be a nucleoprotein, which is probably invovled in viron entry,assembly,egress,maturation and release as its homologous.However, UL55 protein just plays an accessory role. Phylogenetic tree based on amino acids and its reference herpesvirus reaveals that there is a close relationship between DEV and Mardivirus genus.However, DEV is clustered within a monophyletic clade among others , suggests it is an intermediate taxonomic entity and should be placed in a single genus within the herpetoviridae subfamily.Despite its preliminary characterization, this study can clearly direct our research to elucidate its biological function and physiological features of this newly identified UL55 gene.
Venugopal Nair - One of the best experts on this subject based on the ideXlab platform.
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Molecular characterization of Marek's disease virus in a poultry layer farm from Colombia
Poultry Science, 2017Co-Authors: Sara López-osorio, Venugopal Nair, Diego Piedrahita, Maria A. Espinal-restrepo, Gloria Ramirez-nieto, Susan M. Williams, Susan J. Baigent, César Ventura-polite, Diego A. Aranzazu-taborda, Jenny J. Chaparro-gutiérrezAbstract:Abstract Marek's disease (MD) is a lymphoproliferative disease caused by an Alphaherpesvirus, genus Mardivirus, serotype 1 (Gallid Herpesvirus 2, GaHV-2) that includes all known pathogenic strains. In addition to Marek's disease virus (MDV) serotype 1, the genus includes 2 distinct nonpathogenic serotypes: serotype 2 (GaHV-3) and serotype 3 (Meleagridis Herpesvirus 1, MeHV-1) which are used in commercially available vaccines against MD. As a result of vaccination, clinical signs are not commonly observed, and new cases are usually associated with emerging variant strains against which the vaccines are less effective. In this study, a commercial layer farm showing clinical signs compatible with MDV infection was evaluated. Histological lesions and positive immunohistochemistry in the sciatic nerve and thymus were compatible with cytolytic phase of MD. GaHV-2, GaHV-3 and MeHV-1 were identified by PCR and qPCR in blood samples from 17 birds with suspected MD. Analysis of the Meq gene of the Colombian GaHV-2 isolate revealed a 99% sequence identity with Asian strains, and in the phylogenetic analysis clustered with vv+ MDV. The analysis of amino acid alignments demonstrated an interruption of the proline rich region in P176A, P217A and P233L positions, which are generally associated with vv+ strains. Some of these changes, such as P233L and L258S positions have not been reported previously. In addition, primary cell cultures inoculated with lymphocytes isolated from the spleen showed typical cytopathic effect of GaHV-2 at 5 d post infection. Based on the molecular analysis, the results from this study indicate the presence of vv+ MDV infection in commercial birds for the first time in Colombia. It is recommended to perform further assays in order to demonstrate the pathotype characteristics in vivo.
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Novel microRNAs encoded by duck enteritis virus
Journal of General Virology, 2012Co-Authors: Lorraine P. Smith, Lawrence Petherbridge, Mick Watson, Venugopal NairAbstract:Duck enteritis virus (DEV) is an important herpesvirus pathogen associated with acute, highly contagious lethal disease in waterfowls. Using a deep sequencing approach on RNA from infected chicken embryo fibroblast cultures, we identified several novel DEV-encoded micro (mi)RNAs. Unlike most Mardivirus-encoded miRNAs, DEV-encoded miRNAs mapped mostly to the unique long region of the genome. The precursors of DEV miR-D18 and miR-D19 overlapped with each other, suggesting similarities to miRNA-offset RNAs, although only the DEV-miR-D18-3p was functional in reporter assays. Identification of these novel miRNAs will add to the growing list of virus-encoded miRNAs enabling the exploration of their roles in pathogenesis.
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Cloning of Gallid herpesvirus 3 (Marek's disease virus serotype-2) genome as infectious bacterial artificial chromosomes for analysis of viral gene functions.
Journal of virological methods, 2009Co-Authors: Lawrence Petherbridge, Lorraine P. Smith, Hongtao Xu, Yuguang Zhao, Jennifer Simpson, Susan Baigent, Venugopal NairAbstract:Marek's disease virus serotype 2 (Gallid herpesvirus 3) is a non-pathogenic alphaherpesvirus belonging to the Mardivirus genus, used widely in live vaccines against Marek's disease. Although the complete genome sequence of the MDV-2 strain HPRS-24 has been published, very little is known about the gene functions. As a first step for carrying out functional genomic analysis of MDV-2, the full-length genome of the MDV-2 vaccine strain SB-1 was cloned as an infectious bacterial artificial chromosome (BAC) clone pSB-1. Virus reconstituted from the pSB-1 clone showed morphological and growth characteristics in cell culture very similar to the parent virus. Generation of SB-1 constructs deleted in glycoprotein E and viruses expressing Citrine-UL35 fusion protein by the application of different BAC mutagenesis techniques demonstrated the amenability of the pSB-1 clone for reverse genetics approaches to identify molecular determinants associated with different biological features of this virus. The generation of replication-competent infectious clones of SB-1, together with those of CVI988 and herpesvirus of turkey strains described previously, completes the portfolio of generating infectious BAC clones of the MD vaccine strains belonging to all the three serotypes, paving the way for the application of reverse genetics for functional analysis of immunogenic determinants of these vaccines as well as for developing novel recombinant vectors.
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Marek's Disease Virus Type 2 (MDV-2)-Encoded MicroRNAs Show No Sequence Conservation with Those Encoded by MDV-1
Journal of Virology, 2007Co-Authors: Yuguang Zhao, Lorraine P. Smith, Hongtao Xu, Charles H. Lawrie, Alain Sewer, Mihaela Zavolan, Venugopal NairAbstract:MicroRNAs (miRNAs) are increasingly being recognized as major regulators of gene expression in many organisms, including viruses. Among viruses, members of the family Herpesviridae account for the majority of the currently known virus-encoded miRNAs. The highly oncogenic Marek's disease virus type 1 (MDV-1), an avian herpesvirus, has recently been shown to encode eight miRNAs clustered in the MEQ and LAT regions of the viral genome. The genus Mardivirus, to which MDV-1 belongs, also includes the nononcogenic but antigenically related MDV-2. As MDV-1 and MDV-2 are evolutionarily very close, we sought to determine if MDV-2 also encodes miRNAs. For this, we cloned, sequenced, and analyzed a library of small RNAs from the lymphoblastoid cell line MSB-1, previously shown to be coinfected with both MDV-1 and MDV-2. Among the 5,099 small RNA sequences determined from the library, we identified 17 novel MDV-2-specific miRNAs. Out of these, 16 were clustered in a 4.2-kb long repeat region that encodes R-LORF2 to R-LORF5. The single miRNA outside the cluster was located in the short repeat region, within the C-terminal region of the ICP4 homolog. The expression of these miRNAs in MSB-1 cells and infected chicken embryo fibroblasts was further confirmed by Northern blotting analysis. The identification of miRNA clusters within the repeat regions of MDV-2 demonstrates conservation of the relative genomic positions of miRNA clusters in MDV-1 and MDV-2, despite the lack of sequence homology among the miRNAs of the two viruses. The identification of these novel miRNAs adds to the growing list of virus-encoded miRNAs.