Biology subjects

Ullah, M.

Publications and source records attributed to Ullah, M..

3 recordsLinked to original sources

bioRxiv2025

RetiGene, a comprehensive gene atlas for inherited retinal diseases (IRDs)

Inherited retinal diseases (IRDs) are rare disorders, typically presenting as Mendelian traits, that result in stationary or progressive visual impairment. They are characterized by extensive genetic heterogeneity, possibly the highest among all human genetic diseases, as well as diverse inheritance patterns. Despite advances in gene discovery, limited understanding of gene function and challenges in accurately interpreting variants continue to hinder both molecular diagnosis and genetic research in IRDs. One key problem is the absence of a comprehensive and widely accepted catalogue of disease genes, which would ensure consistent genetic testing and reliable molecular diagnoses. With the rapid pace of IRD gene discovery, gene catalogues require frequent validation and updates to remain clinically and scientifically useful. To address these gaps, we developed RetiGene, an expert-curated gene atlas that integrates variant data, bulk and single-cell RNA sequencing, and functional annotations. Through the integration of diverse data sources, RetiGene supports candidate gene prioritization, functional studies, and therapeutic development in IRDs.

genetics↗

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↗

bioRxiv2018

Computational Analysis of Dynamical Fluctuations of Oncoprotein E7 (HPV) for the Hot Spot Residue Identification Using Elastic Network Model

Virus proteins after invading human body alter host protein-protein interaction networks, resulting in the creation of new interactions, along with destroying or modifying other interactions or proteins. Topological features of new or modified networks compromise the host system causing increased production of viral particles. The molecular basis for this alteration of proteins interactivity is short linear peptide motifs similar in both virus and humans. These motifs are identified by modular domains, which are the subunits of a protein, in the human body, resulting in stabilization or moderation of these protein interactions Protein molecules can be modeled by elastic network models showing the fluctuations of residues when they are biologically active. We focused our computational study on the binding and competing interactions of the E7 protein of HPV with Rb protein. Our study was based on analysis of dynamic fluctuations of E7 in host cell and correlation analysis of specific residue found in motif of LxCxE, that is the key region in stabilizing interaction between E7 and Rb. Hot spot residue of E7 were also identified which could provide platform for drug prediction in future. Nevertheless, our study validates the role of linear binding motifs LxCxE of E7 of HPV in interacting with Rb as an important event in propagation of HPV in human cells and transformation of infection into cervical cancer.

bioinformatics↗