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1.  Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses 
PLoS ONE  2014;9(3):e90905.
Chikungunya virus (CHIKV) is an arthropod-borne virus of the family Togaviridae that is transmitted to humans by Aedes spp. mosquitoes. Its genome comprises a 12 kb single-strand positive-sense RNA. In the present study, we report the patterns of synonymous codon usage in 141 CHIKV genomes by calculating several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis showed that the preferred synonymous codons were G/C and A-ended. A comparative analysis of RSCU between CHIKV and its hosts showed that codon usage patterns of CHIKV are a mixture of coincidence and antagonism. Similarity index analysis showed that the overall codon usage patterns of CHIKV have been strongly influenced by Pan troglodytes and Aedes albopictus during evolution. The overall codon usage bias was low in CHIKV genomes, as inferred from the analysis of effective number of codons (ENC) and codon adaptation index (CAI). Our data suggested that although mutation pressure dominates codon usage in CHIKV, patterns of codon usage in CHIKV are also under the influence of natural selection from its hosts and geography. To the best of our knowledge, this is first report describing codon usage analysis in CHIKV genomes. The findings from this study are expected to increase our understanding of factors involved in viral evolution, and fitness towards hosts and the environment.
doi:10.1371/journal.pone.0090905
PMCID: PMC3942501  PMID: 24595095
2.  Construction of a Chimeric Secretory IgA and Its Neutralization Activity against Avian Influenza Virus H5N1 
Journal of Immunology Research  2014;2014:394127.
Secretory immunoglobulin A (SIgA) acts as the first line of defense against respiratory pathogens. In this assay, the variable regions of heavy chain (VH) and Light chain (VL) genes from a mouse monoclonal antibody against H5N1 were cloned and fused with human IgA constant regions. The full-length chimeric light and heavy chains were inserted into a eukaryotic expressing vector and then transfected into CHO/dhfr-cells. The chimeric monomeric IgA antibody expression was confirmed by using ELISA, SDS-PAGE, and Western blot. In order to obtain a dimeric secretory IgA, another two expressing plasmids, namely, pcDNA4/His A-IgJ and pcDNA4/His A-SC, were cotransfected into the CHO/dhfr-cells. The expression of dimeric SIgA was confirmed by using ELISA assay and native gel electrophoresis. In microneutralization assay on 96-well immunoplate, the chimeric SIgA showed neutralization activity against H5N1 virus on MDCK cells and the titer was determined to be 1 : 64. On preadministrating intranasally, the chimeric SIgA could prevent mice from lethal attack by using A/Vietnam/1194/04 H5N1 with a survival rate of 80%. So we concluded that the constructed recombinant chimeric SIgA has a neutralization capability targeting avian influenza virus H5N1 infection in vitro and in vivo.
doi:10.1155/2014/394127
PMCID: PMC3987799  PMID: 24741594
3.  Correction: Comparative Genomics Analysis of Mycobacterium ulcerans for the Identification of Putative Essential Genes and Therapeutic Candidates 
PLoS ONE  2013;8(9):10.1371/annotation/8ce51727-91b0-463f-9b4c-768aab0a230a.
doi:10.1371/annotation/8ce51727-91b0-463f-9b4c-768aab0a230a
PMCID: PMC3776887
4.  Comparative Genomics Analysis of Mycobacterium ulcerans for the Identification of Putative Essential Genes and Therapeutic Candidates 
PLoS ONE  2012;7(8):e43080.
Mycobacterium ulcerans, the causative agent of Buruli ulcer, is the third most common mycobacterial disease after tuberculosis and leprosy. The present treatment options are limited and emergence of treatment resistant isolates represents a serious concern and a need for better therapeutics. Conventional drug discovery methods are time consuming and labor-intensive. Unfortunately, the slow growing nature of M. ulcerans in experimental conditions is also a barrier for drug discovery and development. In contrast, recent advancements in complete genome sequencing, in combination with cheminformatics and computational biology, represent an attractive alternative approach for the identification of therapeutic candidates worthy of experimental research. A computational, comparative genomics workflow was defined for the identification of novel therapeutic candidates against M. ulcerans, with the aim that a selected target should be essential to the pathogen, and have no homology in the human host. Initially, a total of 424 genes were predicted as essential from the M. ulcerans genome, via homology searching of essential genome content from 20 different bacteria. Metabolic pathway analysis showed that the most essential genes are associated with carbohydrate and amino acid metabolism. Among these, 236 proteins were identified as non-host and essential, and could serve as potential drug and vaccine candidates. Several drug target prioritization parameters including druggability were also calculated. Enzymes from several pathways are discussed as potential drug targets, including those from cell wall synthesis, thiamine biosynthesis, protein biosynthesis, and histidine biosynthesis. It is expected that our data will facilitate selection of M. ulcerans proteins for successful entry into drug design pipelines.
doi:10.1371/journal.pone.0043080
PMCID: PMC3418265  PMID: 22912793
5.  Computational Identification and Modeling of Crosstalk between Phosphorylation, O-β-glycosylation and Methylation of FoxO3 and Implications for Cancer Therapeutics 
FoxO3 is a member of the forkhead class of transcription factors and plays a major role in the regulation of diverse cellular processes, including cell cycle arrest, DNA repair, and protection from stress stimuli by detoxification of reactive oxygen species. In addition, FoxO3 is a tumor suppressor and has been considered as a novel target for cancer therapeutics. Phosphorylation of FoxO3 via the AKT, IKK, and ERK pathways leads to deregulation, cytoplasmic retention, degradation of FoxO3 and favors tumor progression. Identification of the amino acid residues that are the target of different posttranslational modifications (PTMs) provides a foundation for understanding the molecular mechanisms of FoxO3 modifications and associated outcomes. In addition to phosphorylation, serine and threonine residues of several proteins are regulated by a unique type of PTM known as O-β-glycosylation, which serves as a functional switch. We sought to investigate the crosstalk of different PTMs on the FoxO3 which leads to the onset/progression of various cancers and that could also potentially be targeted as a therapeutic point of intervention. A computational workflow and set of selection parameters have been defined for the identification of target sites and crosstalk between different PTMs. We identified phosphorylation, O-β-GlcNAc modification, and Yin Yang sites on Ser/Thr residues, and propose a potential novel mechanism of crosstalk between these PTMs. Furthermore, methylation potential of human FoxO3 at arginine and lysine residues and crosstalk between methylation and phosphorylation have also been described. Our findings may facilitate the study of therapeutic strategies targeting posttranslational events.
doi:10.3390/ijms13032918
PMCID: PMC3317383  PMID: 22489133
FoxO3; FoxO; in silico; posttranslational modifications; phosphorylation; O-β-glycosylation; methylation; cancer; Yin Yang sites
6.  Homology modeling, comparative genomics and functional annotation of Mycoplasma genitalium hypothetical protein MG_237 
Bioinformation  2011;7(6):299-303.
Mycoplasma genitalium is a human pathogen associated with several sexually transmitted diseases. The complete genome of M. genitalium G37 has been sequenced and provides an opportunity to understand the pathogenesis and identification of therapeutic targets. However, complete understanding of bacterial function requires proper annotation of its proteins. The genome of M. genitalium consists of 475 proteins. Among these, 94 are without any known function and are described as ‘hypothetical proteins’. We selected MG_237 for sequence and structural analysis using a bioinformatics approach. Primary and secondary structure analysis suggested that MG_237 is a hydrophilic protein containing a significant proportion of alpha helices, and subcellular localization predictions suggested it is a cytoplasmic protein. Homology modeling was used to define the three-dimensional (3D) structure of MG-237. A search for templates revealed that MG_237 shares 63% homology to a hypothetical protein of Mycoplasma pneumoniae, indicating this protein is evolutionary conserved. The refined 3D model was generated using (PS)2­v2 sever that incorporates MODELLER. Several quality assessment and validation parameters were computed and indicated that the homology model is reliable. Furthermore, comparative genomics analysis suggested MG_237 as non-homologous protein and involved in four different metabolic pathways. Experimental validation will provide more insight into the actual function of this protein in microbial pathways.
PMCID: PMC3280499  PMID: 22355225
Mycoplasma genitalium; homology modelling; hypothetical proteins; comparative genomics; metabolic pathways

Results 1-6 (6)