Shiv Nadar University

About: Shiv Nadar University is a education organization based out in Dadri, Uttar Pradesh, India. It is known for research contribution in the topics: Population & Graphene. The organization has 1015 authors who have published 1924 publications receiving 18420 citations.

Development of BacMam Induced Hepatitis E Virus Replication Model in Hepatoma Cells to Study the Polyprotein Processing

Abstract: The processing of polyprotein(s) to form structural and non-structural components remains an enigma due to the non-existence of an efficient and robust Hepatitis E Virus (HEV) culture system. We used the BacMam approach to construct an HEV replication model in which the HEV genome was cloned in the BacMam vector under the CMV promoter. The recombinant BacMam was used to infect Huh7 cells to transfer the HEV genome. HEV replication was authenticated by the presence of RNAs of both the polarity (+) and (-) and formation of hybrid RNA, a replication intermediate. The presence of genes for Papain-like Cysteine Protease (PCP), methyltransferase (MeT), RNA dependent RNA polymerase (RdRp), and ORF2 was confirmed by PCR amplification. Further, the infectious nature of the culture system was established as evidenced by the cross-infection of uninfected cells using the cell lysate from the infected cells. The HEV replication model was validated by detection of the ORF1 (Open Reading Frame1) encoded proteins, identified by Western blotting and Immunofluorescence by using epitope-specific antibodies against each protein. Consequently, discrete bands of 18, 35, 37, and 56 kDa corresponding to PCP, MeT, RdRp, and ORF2, respectively, were seen. Besides demonstrating the presence of non-structural enzymes of HEV along with ORF2, activity of a key enzyme, HEV-methyltransferase has also been observed. A 20% decrease in the replicative forms of RNA could be seen in presence of 100 μM Ribavirin after 48 h of treatment. The inhibition gradually increased from 0 to 24 to 48 h post-treatment. Summarily, infectious HEV culture system has been established, which could demonstrate the presence of HEV replicative RNA forms, the structural and non-structural proteins and the methyltransferase in its active form. The system may also be used to study the mechanism of action of Ribavirin in inhibiting HEV replication and develop a therapy.

Draft genome and transcriptome analyses of halophyte rice Oryza coarctata provide resources for salinity and submergence stress response factors.

Abstract: Oryza coarctata is a wild relative of rice that has adapted to diverse ecological environments, including high salinity and submergence. Thus, it can provide an important resource for discovering candidate genes/factors involved in tolerance to these stresses. Here, we report a draft genome assembly of 573 Mb comprised of 8,877 scaffolds with N50 length of 205 kb. We predicted a total of 50,562 protein-coding genes, of which a significant fraction was found to be involved in secondary metabolite biosynthesis and hormone signal transduction pathways. Several salinity and submergence stress-responsive protein-coding and long non-coding RNAs involved in diverse biological processes were identified using RNA-sequencing data. Based on small RNA sequencing, we identified 168 unique miRNAs and 3219 target transcripts (coding and non-coding) involved in several biological processes, including abiotic stress responses. Further, whole genome bisulphite sequencing data analysis revealed at least 19-48% methylcytosines in different sequence contexts and the influence of methylation status on gene expression. The genome assembly along with other datasets have been made publicly available at http://ccbb.jnu.ac.in/ory-coar. Altogether, we provide a comprehensive genomic resource for understanding the regulation of salinity and submergence stress responses and identification of candidate genes/factors involved for functional genomics studies. This article is protected by copyright. All rights reserved.

Particle-in-cell simulation study of PCE-gun for different hollow cathode aperture sizes

Abstract: Pseudospark (PS) discharge is promising source for high brightness and high intensity electron beam pulses. In the present paper, an effort has been made to analyse the temporal behaviour of discharge current, applied voltage, plasma density in the PS discharge based PCE-Gun at different hollow cathode aperture sizes using 3-D particle-in-cell (PIC) simulation code “VORPAL”. The peak discharge current in the PS discharge is a function of hollow cathode dimensions. The plasma generation process by self ionization discharge is examined at different operating conditions. Argon is taken as the background neutral gas. It has been observed that the decrease in the aperture size from 8 mm to 3 mm increases the discharge current, the electron confinement time and the plasma density.