Biology subjects

Majumdar, T.

Publications and source records attributed to Majumdar, T..

6 recordsLinked to original sources

bioRxiv2025

Chemical Environment of the Confinement Governs Thermal Stability of the Folded Telomere G-Quadruplex

In this study, the effect of the chemical nature of the confinement on the folding and thermal stability of the telomere G-quadruplex (G4) has been investigated by studying the folding pattern of different telomere DNA sequences with varying numbers and arrangements of thymine loop nucleobases in the presence of anionic and cationic nanosized water pools. The findings suggest that both anionic and cationic water pools fold the telomere sequences into G4 of the same topology. However, the thermal stability of the folded G4 in the cationic water pool is significantly lower than that of the anionic case. The overall data indicate that the topology of the folded G4 is insensitive to the nature of the confinement, however, the thermal stability of the folded telomeric G4 depends significantly on the chemical nature of the confinement. It is plausible that the interfacial water inside the cationic water pools has a different orientation and hydrogen bonding than the case of anionic water pools, which may cause the different thermal stability of the G4 on these two water pools. These findings may be important in understanding the folding and stability of telomere G4 inside the confined cellular system.

biochemistry↗

bioRxiv2024

Construction of an Immunoinformatics-Based Multi-Epitope Vaccine Candidate targeting Kyasanur Forest Disease Virus

Kyasanur Forest Disease (KFD) is one of the neglected tick-borne viral zoonoses. KFD virus was initially considered endemic to the Western Ghats region of Karnataka. Still, over the years, there have been reports of its spread to newer areas within and outside Karnataka. The absence of an effective treatment for KFD expedites the need for further research and development of novel vaccines. The present study was designed to develop a multi-epitope vaccine candidate against KFDV using immunoinformatic tools. After analyzing 74 complete KFDV genome sequences for genetic recombination and phylogeny, different prioritized B and T cell epitopes were combined using various linkers to construct the vaccine candidate. Docking analysis of the designed vaccine construct revealed a stable interaction with the TLR2-TLR6 receptor complex. After confirming the stability of the vaccine receptor complex, codon optimization was done to ensure the efficient translation of the designed multi-epitope vaccine in the prokaryotic host system, and the subsequent in-silico cloning into the pET30b(+) expression vector was carried out. Immunoinformatics analysis of the multi-epitope vaccine in the current study is satisfactory as it can significantly accelerate the initial stages of vaccine development by narrowing down potential vaccine candidates and providing insights into their design. Experimental validation of the potential multi-epitope vaccine candidate remains crucial to confirm effectiveness and safety in real-world conditions.

bioinformatics↗

bioRxiv2022

Genome characterization of monkeypox cases detected in India: Identification of three sub clusters among A.2 lineage

Since May 2022, Monkeypox, a zoonotic Orthopox DNA virus was reported in more than 102 countries indicating expansion of its geographic range. We analyzed the complete genomes sequences of Monkeypox cases from Kerala (n=5 travelled from UAE) and Delhi (n=5 no travel history), India confirmed during July to August 2022. All the retrieved MPXV sequences from India covering 90 to 99% genome belong to A.2 lineage of clade IIb. The A.2 MPXV lineage divided in three sub clusters; first cluster Kerala n=5, Delhi n=2 aligned with the USA-2022 ON674051.1; while second of Delhi n=3 aligned with USA-2022 ON675438.1 and third consists of the UK, USA and Thailand. Recent update in MPXV lineage designated all the five sequences from Kerala as A.2.1. In addition to known 16 single nucleotide polymorphisms (SNPs) along with 13 APOBEC3 cytosine deaminase activity determined specific lineage defining mutations in A.2 lineage, 25 additional APOBEC3 mutations were found in 10 reported sequences. The study emphasizes need of enhancing genomic surveillance to understand the mutation and its linkage.

microbiology↗

bioRxiv2022

An in vitro and in vivo approach for the isolation of Omicron variant from human clinical specimens

Due to failure of virus isolation of Omicron variant in Vero CCL-81 from the clinical specimens of COVID-19 cases, we infected Syrian hamsters and then passage into Vero CCL-81 cells. The Omicron sequences were studied to assess if hamster could incorporate any mutation to changes its susceptibility. L212C mutation, Tyrosine 69 deletion, and C25000T nucleotide change in spike gene and absence of V17I mutation in E gene was observed in sequences of hamster passage unlike human clinical specimen and Vero CCL-81 passages. No change was observed in the furin cleavage site in any of the specimen sequence which suggests usefulness of these isolates in future studies.

microbiology↗

bioRxiv2021

Possible role of accessory proteins in the viral replication for the 20I/501Y.V1 (B.1.1.7) SARS-CoV-2 variant

The study investigates the replication cycle and transcriptional pattern of the B.1.1.7 variant. It was observed that the B.1.1.7 variant required a longer maturation time. The transcriptional response demonstrated higher expression of ORF6 and ORF8 compared to nucleocapsid transcript till the eclipse period which might influence higher viral replication. The number of infectious viruses titer is higher in the B.1.1.7, despite a lesser copy number than B.1, indicating higher infectivity.

microbiology↗

bioRxiv2021

Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2

Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness as well as DFT properties. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, the proposed kinase inhibitors and a few of the predicted nucleotidyl transferase inhibitors significantly inhibited the aforementioned enzymatic activity. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.

bioinformatics↗