Biology subjects

GUPTA, V.

Publications and source records attributed to GUPTA, V..

3 recordsLinked to original sources

bioRxiv2022

Comparative genomics and integrated system biology approach unveiled undirected phylogeny patterns, mutational hot spots, functional patterns and molecule repurposing for monkey pox virus

Monkeypox is a viral zoonosis with symptoms that are reminiscent to those experienced in previous smallpox cases. GSAID databases (Global Initiative on Sharing Avian Influenza Data) was used to assess 630 genomes of MPXV. Six primary clades were inferred from the phylogenetic study, coupled with a lesser percentage in radiating clades. Individual clades that make up various nationalities may have formed as a result of a particular SNP hotspot type, which may have mutated in a particular population type. The most significant mutation, based on a mutational hotspot analysis, was found at G3729A and G5143A. The gene ORF138, which encodes the Ankyrin repeat (ANK) protein, was found to have the most mutations. This protein is known to mediate molecular recognition via protein-protein interactions. It was shown that 243 host proteins interacted with 10 monkeypox proteins identified as the hub proteins E3, SPI2, C5, K7, E8, G6, N2, B14, CRMB, and A41 through 262 direct connections. The interaction with chemokine system-related proteins provides further evidence that the human protein is being suppressed by the monkey pox virus in order to facilitate its survival against innate immunity. A few FDA-approved molecules were likely used as possible inhibitors after being researched for blocking F13, a significant envelope protein on the membrane of extracellular versions of virus. A total of 2500 putative ligands were docked individually with the F13 protein. The F13 protein and these molecules interaction may help prevent the monkey pox virus from spreading. As a result, after being confirmed by experiments, these putative inhibitors might have an impact on the activity of these proteins and be utilised in monkeypox treatments.

genomics↗

bioRxiv2022

Genetic mapping of some key plant architecture traits in Brassica juncea using a cross between two distinct lines - vegetable type Tumida and oleiferous Varuna

Brassica juncea (AABB, 2n=36), commonly called mustard is an allopolyploid crop of recent origin but has considerable morphological and underlying genetic variation. An F1-derived doubled haploid (F1DH) population developed from a cross between a Indian oleiferous line, Varuna, and a Chinese stem type vegetable mustard, Tumida showed significant variability for some key plant architectural traits, including four stem strength-related traits, stem diameter, plant height, branch initiation height, number of primary branches (Pbr), and days to flowering (Df). Multi-environment QTL analysis identified twenty environmentally stable QTL for the nine plant architectural traits. Both Tumida and Varuna contain some positive QTL that can be used to breed superior ideotypes in mustard. A QTL cluster on LG A10 contained environmentally stable QTL for seven architectural traits. This region also contained overlapping environmentally stable major QTL (phenotypic variance [≥] 10%) for Df and Pbr, with Tumida contributing the trait enhancing alleles for both the traits. Since early flowering is critical for the cultivation of mustard in the Indian subcontinent, this QTL cannot be used for the improvement of Pbr in the Indian gene pool lines. Conditional QTL analysis for Pbr identified the QTL for improvement of Pbr without negative effects on Df. The environmentally stable QTL were projected on the genome assemblies of Tumida and Varuna for the identification of candidate genes. These findings provide insights into the genetics of plant architectural traits in two diverse gene pools of B. juncea and provide opportunities for improvement of the plant architecture through marker-assisted introgressions. Key MessageGenetic mapping of some key plant architectural traits in a vegetable type and an oleiferous B. juncea cross revealed environmentally stable QTL and candidate genes for breeding more productive ideotypes.

genetics↗

bioRxiv2018

Identification of microRNA-27a as a key regulator of cholesterol homeostasis

Hypercholesterolemia is a strong predictor of cardiovascular diseases. 3-Hydroxy-3-methylglutaryl-coenzyme A reductase gene (Hmgcr) coding for the rate-limiting enzyme in the cholesterol biosynthesis pathway is a crucial regulator of plasma cholesterol levels. However, the post-transcriptional regulation of Hmgcr remains poorly understood. The main objective of this study was to explore the role of miRNAs in the regulation of Hmgcr expression. Systematic in silico predictions and experimental analyses reveal that miR-27a specifically interacts with the Hmgcr 3-untranslated region in murine and human hepatocytes. Moreover, our data shows that Hmgcr expression is inversely correlated with miR-27a levels in various cultured cell lines, human and rodent tissues. Actinomycin D chase assays and relevant experiments demonstrate that miR-27a regulates Hmgcr by translational attenuation followed by mRNA degradation. Early Growth Response 1 (Egr1) regulates miR-27a expression under basal and cholesterol-modulated conditions. miR-27a augmentation via tail-vein injection of miR-27a mimic in high cholesterol diet-fed Apoe-/- mice shows down-regulation of hepatic Hmgcr and plasma cholesterol levels. Pathway and gene expression analyses show that miR-27a also targets several other genes (apart from Hmgcr) in cholesterol biosynthesis pathway. Taken together, miR-27a emerges as a key regulator of cholesterol biosynthesis and has therapeutic potential for clinical management of hypercholesterolemia.

molecular biology↗