Biology subjects

Tabassum, A.

Publications and source records attributed to Tabassum, A..

3 recordsLinked to original sources

bioRxiv2024

Genome-wide identification of MAPK gene family and comparative transcriptional profiling among different organ and stress response in two jute species

Mitogen activated protein kinase (MAPK) cascade is evolutionary conserved universal signal transduction module that plays central role in the growth and development of plants as well as in biotic and abiotic stress response. Although, MAPKs have been investigated in several model plants, no systematic analysis has been conducted in jute species (Corchorus olitorius and C. capsularis) even though, their genome sequencing has been completed. In the present study we identified 11 and 12 putative MAPKs in C. olitorius and C. capsularis using their genomic database, respectively. Here we provide a comprehensive bioinformatics analysis of the MAPK family from both Corchorus species including identification and nomenclature, chromosomal localization, sequence alignment, domain and Motif, gene structure, phylogenetic, functional analysis and investigation of expression analysis in response to abiotic stress and fiber cell development. The phylogenetic analysis of predicted MAPKs were clustered into four different clades and assigned with specific name based on their orthology based evolutionary relationship with Arabidopsis. Structural analysis of the MAPK genes revealed that there was a large variation among the exon number in both Corchorus species ranged from 2 to 11 but genes with the same clade had similar exon-intron structure. The sequence alignment analysis concede the presence of several conserved domain and motif including crucial signature phosphorylation motif TDY or TEY where first one is harbor in group D sequence and rest of the sequence contain TEY motif in their activation loop. Transcriptome analysis against salinity, drought along with fiber cell formation showed that MAPK4-1 genes in both jute genome highly expressed and may play a potential role in jute on adverse condition as well as jute fiber formation. These findings yielded new insights into the transcriptional control of MAPK gene expression, provide an improved understanding of abiotic stress responses and signaling transduction in jute, that lead to potential applications in the genetic improvement of jute cultivars.

molecular biology↗

bioRxiv2024

GENOME-WIDE IDENTIFICATION, CHARACTERIZATION AND EXPRESSION ANALYSIS OF NA+/H+ EXCHANGER GENE FAMILY IN TWO CORCHORUS SPECIES

Na+/H+ exchangers (NHXs) are secondary ion transporter to exchange H+ and transfer Na+ or K+ across membrane plays crucial role in cellular pH and Na+ and K+ homeostasis in plant. In the present study, we have performed genomewide identification, characterization and comparative analysis of NHXs genes in two cultivated jute species and found seven Co and Cc NHXs in each genome. Subsequently phylogenetic analysis demonstrated that Co and Cc NHXs have three sub-group that correlate with other plant species containing 10-12 transmembrane helices (TMH) and a hydrophilic C-terminal domain in the cytoplasmic region, the TMH compose a hollow cylinder to provide the channel for Na+ and H+ transport. Promoter profiling of both species NHXs genes revealed in enrichment of cis element involved in stress responsiveness reflecting their potential involvement against abiotic stress. Transcriptome data and real time PCR of Co and Cc NHXs gene expression analysis under saline and drought condition showed significant differences, which suggest their potential role in abiotic stress conditions. This is the first comprehensive analysis providing baseline information of Co and Cc NHXs genes in abiotic stress condition which can be used for the development of abiotic stress tolerant jute variety.

bioinformatics↗

bioRxiv2020

In silico prediction of ARB resistance: A first step in creating personalized ARB therapy

Angiotensin II type 1 receptor (AT1R) blockers (ARBs) are among the most prescribed drugs. However, ARB effectiveness varies widely, and some patients do not respond to ARB therapy. One reason for the variability between patients is non-synonymous single nucleotide polymorphisms (nsSNPs) within agtr1, the AT1R gene. There are over 100 nsSNPs in the AT1R; therefore, this study embarked on determining which nsSNPs may abrogate the binding of selective ARBs. The crystal structure of olmesartan-bound human AT1R (PDB:4ZUD) served as a template to create an inactive empty AT1R via molecular dynamics simulation (n = 3). All simulations resulted in a smaller ligand-binding pocket than 4ZUD due to the absence of olmesartan in the simulation yet remained inactive with little movement in the receptor core. A single frame representing the average stable AT1R was used as a template to thrice (n = 3) dock each ARB via AutoDock to obtain a predicted affinity from the weighted average of 100 docking simulations. The results were far from known values; thus, an optimization protocol was initiated, resulting in the predicted binding affinities within experimentally determined ranges (n = 6). The empty model AT1R was altered and minimized in Molecular Operating Environment software to represent 103 of the known human AT1R polymorphisms. Each of the eight ARBs was then docked, using the optimized parameters, to each polymorphic AT1R (n = 6). Although each nsSNP has little effect on global AT1R structure, most nsSNPs drastically alter a sub-set of ARBs affinity to the AT1R. Comparisons to previous binding studies suggest that the results have a 60% chance of predicting ARB resistance. Although more biochemical studies and refinement of the model are required to increase the accuracy of the prediction of ARB resistance, personalized ARB therapy based on agtr1 sequence could increase overall ARB effectiveness. Author SummaryThe term "personalized medicine" was coined at the turn of the century, but most medicines are currently prescribed based on disease categories and occasionally racial demographics, but not personalized attributes. In cardiovascular medicine, the personalization of medication is minimal; however, it is accepted that not all patients respond equally to common cardiovascular medications. Here we chose one prominent cardiovascular drug target, the angiotensin receptor, and, using computer modeling, created preliminary models of over 100 known alterations to the angiotensin receptor to determine if the alterations changed the ability of clinically used drugs to interact with the angiotensin receptor. The strength of interaction was compared to the unaltered angiotensin receptor, generating a map predicting which alteration affected each drug. It is expected that in the future, a patients receptors can be sequenced, and maps, such as the one presented here, can be used to select the optimum medication based on the patients genetics. Such a process would allow for the personalization of current medication therapy.

pharmacology and toxicology↗