Biology subjects

Mani, I.

Publications and source records attributed to Mani, I..

4 recordsLinked to original sources

bioRxiv2026

In silico codon optimization and phylogenetic analysis of various strains of Sapovirus

Introduction: Sapovirus (SaV) is an emerging enteric pathogen of rising public health importance, responsible for acute gastroenteritis in people of all ages and most often in children under five. Its genome is approximately 7.1-7.7 kb long, positive-sense, single-stranded RNA, comprising two principal open reading frames; processing of the ORF1 product yields seven non-structural proteins and the major capsid protein VP1, while ORF2 encodes the minor structural protein VP2. Given the absence of therapies or an approved vaccine and the low yields of recombinant capsid protein, improving expression remains a priority. Methods: VP1 and VP2 sequences from twelve selected human SaV strains were aligned, phylogenetic trees were reconstructed by maximum likelihood method under the Tamura-Nei model with 1,000 bootstrap replicates, and both genes were optimized in silico for Escherichia coli using the OPTIMIZER. Results: The trees resolved three genogroups, GI, GII and GV, each strain placed alike by both genes. Every optimized sequence reached the ceiling value of 1.000 for the codon adaptation index (CAI). Mean CAI and GC% increased by 3.07 (207.0%) and 1.11 (11.1%) fold for VP1, and 3.11 (210.9%) and 1.14 (14.1%) fold for VP2, while AT% decreased. All changes were statistically significant (p < 0.001) and the encoded amino acid sequences were unaltered. Conclusion: Our findings indicate that Optmization raised host-matched codon usage in both capsid genes with no truncated proteins produced. The redesigned VP1 and VP2 sequences warrant further investigation as potential candidates for biotherapeutic and vaccine development. KEYWORDS: Sapovirus,CAI, codon optimization, VP1 capsid protein, GC content, DNA, phylogenetic analysis, vaccines

bioinformatics↗

bioRxiv2023

In silico codon optimization of the variant antigen-encoding genes of diverse strains of Zika Virus

AbstractWith the recent emergence of the coronavirus pandemic, the scare for other viral pandemics is on the rise. Already having caused an epidemic in 2015-16, Zika virus (ZIKV) poses a threat for potential havoc. Thus, there is an urgent need to produce drugs and vaccines for the same as no approved vaccinations exist for the virus as of now. With the optimization of codon usage, the process of vaccine development can be accelerated and efficacy can be ensured. ZIKV genome has 3 structural genes (envelope, capsid and membrane which is obtained from pre membrane) and 7 nonstructural genes (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5). We have used these 10 genes in 5 different strains of ZIKV for in silico DNA optimization in Escherichia coli. The mean CAI, GC% and AT% of wild-type DNA and optimized DNA of each were compared. It was observed that the CAI and GC% had increased in optimized DNA as compared to wild- type while the opposite was seen for AT%. The results show that codon optimization helps in efficient expression of proteins in the host. These could be used in the development of biotherapeutics. The ideal genes to be overexpressed in development of biotherapeutics are the membrane precursor (prM) and envelope (E) genes as the results have shown.

bioinformatics↗

bioRxiv2023

In silico optimization of DNA codons in genes encoded by various strains of Ebola Virus

Ebola hemorrhagic fever (HF) is a severe and often lethal disease that occurs in primates, including humans. It was first identified in 1976 during two outbreaks of fatal haemorrhagic fever in Central Africa. Due to its high fatality rate and lack of a widespread cure, Ebola HF poses a considerable challenge in treatment, making Ebola virus disease (EVD) one of the deadliest zoonotic diseases. The viral genome is [~]19kb long, linear, non-segmented, and negative single-stranded (-SS) RNA. The genome of the Ebola virus (EBOV) comprises seven genes, namely NP, GP, L, and VP (VP30, VP24, VP40, VP35), which encode nucleoprotein, glycoprotein, RNA polymerase, and viral proteins. By optimizing the DNA sequence through codon adaptation, we observed significant enhancements in the codon adaptation index (CAI) and the GC content compared to the wild-type strain. These findings demonstrate that optimized genes hold the potential for improved expression in the host organism without the production of truncated proteins. Further, these optimized genes can facilitate proper protein folding and function. In conclusion, these results have implications for vaccine production, as higher codon optimization enhances the expression of the genes, making them appropriate amounts for vaccine development.

bioinformatics↗

bioRxiv2021

In silico DNA codon optimization of the variant antigen-encoding genes of diverse strains of Nipah virus

Due to an increase in human and wildlife interaction, more and more zoonotic diseases are emerging. A prime example of this is the emergence of the Nipah virus (NiV). Due to high rate of mortality specifically in India and Bangladesh, there is an urgent need for accelerated research for NiV involving the development of vaccines or drugs. The genome of NiV consists of six genes (N, P, M, F, G and L) encoding yielding nucleoprotein, phosphoprotein, matrix, fusion, glycoprotein and large RNA polymerase. We have used these six genes for in silico assessment of DNA codon optimization in Escherichia coli. It was observed that the codon adaptation index (CAI) and GC content of the genes in optimized DNA were enhanced significantly as compared to wild-type strain. On an average, CAI and GC content of N gene in optimized DNA was enhanced by 2.3 (135.1%) and 1.2(9.9 %) fold respectively, while in P/V/C it was increased by 2.0 (98.3 %) and 1.1(7.8%) fold respectively. Further, the CAI and GC content in optimized DNA of M gene and F gene was enhanced by 2.0(99.0%) and 1.1(7.2%) fold respectively for gene M and 2.4(142.5 %), 1.2(15.4%) fold respectively for gene F. Gene G showed an increase of 2.1(114.8 %) fold for CAI, 1.1(11.2%) fold for GC content and gene L showed an increase of 2.4(143.7%) fold for CAI, 1.2(17.2%) fold for GC content. Our result demonstrates that the optimized genes could be useful for better expression in host without any truncated proteins and also useful for protein folding and function.

bioinformatics↗