Background Hepatitis E virus (HEV) is the major pathogen responsible for chronic hepatitis infect... more Background Hepatitis E virus (HEV) is the major pathogen responsible for chronic hepatitis infection (CHE) in solid organ transplant recipients. As CHE seems to be dependent on patient’s immunological status, in this context, a comprehensive assessment of gene-, pathway-, and network-level interaction was accomplished to identify key regulators in CHE. To our knowledge, this study conducted novel analysis on the NCBI-GEO obtained mRNA expression profile comprising all three HEV infection stages, i.e., mild, moderate and severe. Methods The patients with CHE were separated into 3 groups according to the time of HEV clearance (early, late, or no HEV clearance at the time of analysis). Gene expression analysis was applied on microarray profile dataset, consisting of control samples (kidney transplant recipients without HEV) and infected samples (kidney transplant recipients with HEV), to unveil the differentially expressed genes (DEGs). Interrelationship among DEGs was studied to ident...
DOAJ (DOAJ: Directory of Open Access Journals), Jun 1, 2022
http://www.iaees.org/publications/journals/nb/articles/2022-12(2)/1-Shafat-Abstract.asp Hepatitis... more http://www.iaees.org/publications/journals/nb/articles/2022-12(2)/1-Shafat-Abstract.asp Hepatitis E virus (HEV) is the chief cause of hepatitis E (inflammation of liver) across the globe. The Norway rat HEV genome consists of six open reading frames (ORFs), i.e., ORF1, ORF2, ORF3, ORF4, ORF5 and ORF5. The additional reading frame encoded protein ORF5 protein's structure and function remain to be explored. Therefore, the presented study was conceptualized to analyze the ORF5 protein for its physiochemical properties, primary structure, secondary structure, tertiary structure and functional characteristics using bioinformatics tools. The initial analysis revealed ORF5 protein as unstable, thermostable, hydrophilic and highly basic in nature. The primary structural analysis revealed higher percentages of amino acids Arg, Leu, Pro, Ser and Gly, which suggested that the ORF5 protein is richly endowed with some regulatory amino acids (Leu, Pro and Gly). The secondary structure of ORF5 protein showed all three major components (alpha-helix, beta-strand and random coil). The tertiary structure generated through homology modelling revealed mixed α/β structural fold with subsequently higher percentage of strands and abundance of coils. Moreover, the surface analysis revealed the several clefts and tunnels along with few pores, clearly suggested the ability of ORF5 protein towards interaction with other molecules. The ORF5 protein was also identified with several post-translationally modified sites including glycosylation, phosphorylation and myriystoylation. The presence of these modified sites indicated the role of ORF5 protein in regulation. Thus, our analyses taken together interpret the ORF5 protein's essentiality in HEV. This data will help in exploring the prospective role of this additional genomic component of rat HEV through the sequence, structure and functional annotation of ORF5 protein.
Background Hepatitis E virus (HEV) is the cause of a liver disease hepatitis E. The translation p... more Background Hepatitis E virus (HEV) is the cause of a liver disease hepatitis E. The translation product of HEV ORF2 has recently been demonstrated as a protein involved in multiple functions besides performing its major role of a viral capsid. As intrinsically disordered regions (IDRs) are linked to various essential roles in the virus’s life cycle, we analyzed the disorder pattern distribution of the retrieved ORF2 protein sequences by employing different online predictors. Our findings might provide some clues on the disorder-based functions of ORF2 protein that possibly help us in understanding its behavior other than as a HEV capsid protein. Results The modeled three dimensional (3D) structures of ORF2 showed the predominance of random coils or unstructured regions in addition to major secondary structure components (alpha helix and beta strand). After initial scrutinization, the predictors VLXT and VSL2 predicted ORF2 as a highly disordered protein while the predictors VL3 and ...
Chronic kidney disease (CKD) is defined as a persistent abnormality in the structure and function... more Chronic kidney disease (CKD) is defined as a persistent abnormality in the structure and function of kidneys and leads to high morbidity and mortality in individuals across the world. Globally, approximately 8%–16% of the population is affected by CKD. Proper screening, staging, diagnosis, and the appropriate management of CKD by primary care clinicians are essential in preventing the adverse outcomes associated with CKD worldwide. In light of this, the identification of biomarkers for the appropriate management of CKD is urgently required. Growing evidence has suggested the role of mRNAs and microRNAs in CKD, however, the gene expression profile of CKD is presently uncertain. The present study aimed to identify diagnostic biomarkers and therapeutic targets for patients with CKD. The human microarray profile datasets, consisting of normal samples and treated samples were analyzed thoroughly to unveil the differentially expressed genes (DEGs). After selection, the interrelationship a...
Background Hepatitis E virus (HEV) is the major pathogen responsible for chronic hepatitis infect... more Background Hepatitis E virus (HEV) is the major pathogen responsible for chronic hepatitis infection (CHE) in solid organ transplant recipients. As CHE seems to be dependent on patient’s immunological status, in this context, a comprehensive assessment of gene-, pathway-, and network-level interaction was accomplished to identify key regulators in CHE. To our knowledge, this study conducted novel analysis on the NCBI-GEO obtained mRNA expression profile comprising all three HEV infection stages, i.e., mild, moderate and severe. Methods The patients with CHE were separated into 3 groups according to the time of HEV clearance (early, late, or no HEV clearance at the time of analysis). Gene expression analysis was applied on microarray profile dataset, consisting of control samples (kidney transplant recipients without HEV) and infected samples (kidney transplant recipients with HEV), to unveil the differentially expressed genes (DEGs). Interrelationship among DEGs was studied to ident...
DOAJ (DOAJ: Directory of Open Access Journals), Jun 1, 2022
http://www.iaees.org/publications/journals/nb/articles/2022-12(2)/1-Shafat-Abstract.asp Hepatitis... more http://www.iaees.org/publications/journals/nb/articles/2022-12(2)/1-Shafat-Abstract.asp Hepatitis E virus (HEV) is the chief cause of hepatitis E (inflammation of liver) across the globe. The Norway rat HEV genome consists of six open reading frames (ORFs), i.e., ORF1, ORF2, ORF3, ORF4, ORF5 and ORF5. The additional reading frame encoded protein ORF5 protein's structure and function remain to be explored. Therefore, the presented study was conceptualized to analyze the ORF5 protein for its physiochemical properties, primary structure, secondary structure, tertiary structure and functional characteristics using bioinformatics tools. The initial analysis revealed ORF5 protein as unstable, thermostable, hydrophilic and highly basic in nature. The primary structural analysis revealed higher percentages of amino acids Arg, Leu, Pro, Ser and Gly, which suggested that the ORF5 protein is richly endowed with some regulatory amino acids (Leu, Pro and Gly). The secondary structure of ORF5 protein showed all three major components (alpha-helix, beta-strand and random coil). The tertiary structure generated through homology modelling revealed mixed α/β structural fold with subsequently higher percentage of strands and abundance of coils. Moreover, the surface analysis revealed the several clefts and tunnels along with few pores, clearly suggested the ability of ORF5 protein towards interaction with other molecules. The ORF5 protein was also identified with several post-translationally modified sites including glycosylation, phosphorylation and myriystoylation. The presence of these modified sites indicated the role of ORF5 protein in regulation. Thus, our analyses taken together interpret the ORF5 protein's essentiality in HEV. This data will help in exploring the prospective role of this additional genomic component of rat HEV through the sequence, structure and functional annotation of ORF5 protein.
Background Hepatitis E virus (HEV) is the cause of a liver disease hepatitis E. The translation p... more Background Hepatitis E virus (HEV) is the cause of a liver disease hepatitis E. The translation product of HEV ORF2 has recently been demonstrated as a protein involved in multiple functions besides performing its major role of a viral capsid. As intrinsically disordered regions (IDRs) are linked to various essential roles in the virus’s life cycle, we analyzed the disorder pattern distribution of the retrieved ORF2 protein sequences by employing different online predictors. Our findings might provide some clues on the disorder-based functions of ORF2 protein that possibly help us in understanding its behavior other than as a HEV capsid protein. Results The modeled three dimensional (3D) structures of ORF2 showed the predominance of random coils or unstructured regions in addition to major secondary structure components (alpha helix and beta strand). After initial scrutinization, the predictors VLXT and VSL2 predicted ORF2 as a highly disordered protein while the predictors VL3 and ...
Chronic kidney disease (CKD) is defined as a persistent abnormality in the structure and function... more Chronic kidney disease (CKD) is defined as a persistent abnormality in the structure and function of kidneys and leads to high morbidity and mortality in individuals across the world. Globally, approximately 8%–16% of the population is affected by CKD. Proper screening, staging, diagnosis, and the appropriate management of CKD by primary care clinicians are essential in preventing the adverse outcomes associated with CKD worldwide. In light of this, the identification of biomarkers for the appropriate management of CKD is urgently required. Growing evidence has suggested the role of mRNAs and microRNAs in CKD, however, the gene expression profile of CKD is presently uncertain. The present study aimed to identify diagnostic biomarkers and therapeutic targets for patients with CKD. The human microarray profile datasets, consisting of normal samples and treated samples were analyzed thoroughly to unveil the differentially expressed genes (DEGs). After selection, the interrelationship a...
Uploads