Prativa Majee

Bio: Prativa Majee is an academic researcher from Indian Institute of Technology Indore. The author has contributed to research in topics: Genome & Virus. The author has an hindex of 6, co-authored 11 publications receiving 76 citations.

Identification and characterization of two conserved G-quadruplex forming motifs in the Nipah virus genome and their interaction with G-quadruplex specific ligands.

Abstract: The G-quadruplex (GQ) motifs are considered as potential drug-target sites for several human pathogenic viruses such as Zika, Hepatitis, Ebola, and Human Herpesviruses. The recent outbreaks of Nipah virus (NiV) in India, the highly fatal emerging zoonotic virus is a potential threat to global health security as no anti-viral drug or vaccine in currently available. Therefore, here in the present study, we sought to assess the ability of the putative G-quadruplex forming sequences in the NiV genome to form G-quadruplex structures and act as targets for anti-viral compounds. Bioinformatics analysis underpinned by various biophysical and biochemical techniques (such as NMR, CD, EMSA, DMS footprinting assay) confirmed the presence of two highly conserved G-quadruplex forming sequences (HGQs) in the G and L genes of NiV. These genes encode the cell attachment glycoprotein and RNA-dependent RNA polymerase, respectively and are essential for the virus entry and replication within the host cell. It remains possible that stabilization of these HGQs by the known G-quadruplex binding ligands like TMPyP4 and Braco-19 represents a promising strategy to inhibit the expression of the HGQ harboring genes and thereby stop the viral entry and replication inside the host cell. Accordingly, we report for the first time, that HGQs in Nipah virus genome are targets for G-quadruplex specific ligands; therefore, could serve as potential targets for anti-viral therapy.

Inhibition of Zika virus replication by G-quadruplex-binding ligands

Abstract: Zika virus (ZIKV), a mosquito-transmitted Flavivirus, emerged in the last decade causing serious diseases and affecting human health globally. Currently, no licensed vaccines or antivirals are available to combat ZIKV, although several vaccine candidates are in the pipeline. In recent years, the presence of non-canonical G-quadruplex (GQ) secondary structures in viral genomes has ignited significant attention as potential targets for antiviral strategy. In this study, we identified several novel conserved potential GQ structures by analyzing published ZIKV genome sequences using an in-house algorithm. Biophysical and biochemical analysis of the RNA sequences containing these potential GQ sequences suggested the existence of such structures in the ZIKV genomes. Studies with known GQ structure-binding and -stabilizing ligands such as Braco-19 and TMPyP4 provided support for this contention. The presence of these ligands in cell culture media led to significant inhibition of infectious ZIKV yield, as well as reduced viral genome replication and viral protein production. Overall, our results, for the first time, show that ZIKV replication can be inhibited by GQ structure-binding and -stabilizing compounds and suggest a new strategy against ZIKV infection mitigation and control.

Designing of a multi-epitope vaccine candidate against Nipah virus by in silico approach: a putative prophylactic solution for the deadly virus

Abstract: Nipah virus (NPV) is one of the most notorious viruses with a very high fatality rate. Because of the recurrent advent of this virus and its severe neurological implications, often leading to high ...

Carbon Dots as Nanodispersants for Multiwalled Carbon Nanotubes: Reduced Cytotoxicity and Metal Nanoparticle Functionalization

Abstract: The colloidal stabilization of multiwalled carbon nanotubes (MWCNTs) in an aqueous medium through noncovalent interactions has potential benefits toward the practical use of this one-dimensional carbonaceous material for biomedical applications. Here, we report that fluorescent carbon nanodots can efficiently function as dispersing agents in the preparation of stable aqueous suspensions of CNTs at significant concentrations (0.5 mg/mL). The amphiphilic nature of carbon dots with a hydrophobic graphitic core could effectively interact with the CNT surface, whereas hydrophilic oxygenated functionalization on the C-dot surface provided excellent water dispersibility. The resultant CNT-C-dot composite showed significantly reduced cytotoxicity compared to that of unmodified or protein-coated CNTs, as demonstrated by cell viability and proliferation assays. Furthermore, the reducing capability of C-dots could be envisaged toward the formation of a catalytically active metal nanoparticle-CNT-C-dot composite with...

Improved Slime Mould Algorithm based on Firefly Algorithm for feature selection: A case study on QSAR model

Abstract: Feature selection (FS) methods are necessary to develop intelligent analysis tools that require data preprocessing and enhancing the performance of the machine learning algorithms. FS aims to maximize the classification accuracy by minimizing the number of selected features. This paper presents a new FS method using a modified Slime mould algorithm (SMA) based on the firefly algorithm (FA). In the developed SMAFA, FA is adopted to improve the exploration of SMA, since it has high ability to discover the feasible regions which have optima solution. This will lead to enhance the convergence by increasing the quality of the final output. SMAFA is evaluated using twenty UCI datasets and also with comprehensive comparisons to a number of the existing MH algorithms. To further assess the applicability of SMAFA, two high-dimensional datasets related to the QSAR modeling are used. Experimental results verified the promising performance of SMAFA using different performance measures.

RNA G-quadruplexes (rG4s): genomics and biological functions.

Abstract: G-quadruplexes (G4s) are non-classical DNA or RNA secondary structures that have been first observed decades ago. Over the years, these four-stranded structural motifs have been demonstrated to have significant regulatory roles in diverse biological processes, but challenges remain in detecting them globally and reliably. Compared to DNA G4s (dG4s), the study of RNA G4s (rG4s) has received less attention until recently. In this review, we will summarize the innovative high-throughput methods recently developed to detect rG4s on a transcriptome-wide scale, highlight the many novel and important functions of rG4 being discovered in vivo across the tree of life, and discuss the key biological questions to be addressed in the near future.