Biology subjects

Asif, M. H.

Publications and source records attributed to Asif, M. H..

4 recordsLinked to original sources

bioRxiv2026

Sugarcane bZIP16 regulates internode elongation by targeting gibberellic acid biosynthesis pathway

Modern sugarcane cultivars are vegetatively propagated interspecific hybrids developed by extensive breeding and selection method to enhance sugar content, culm dimensions, desired plant architecture and disease resistance. Internode length greatly varies among existing sugarcane cultivars which determines culm length, biomass and sugar storage. Molecular factors responsible for this trait remains largely unknown in sugarcane. In this study, we characterized short and long internode sugarcane varieties and elucidated gene regulatory module interplaying with hormonal-network underneath the internodal growth. The genome size, pigment content and juice characteristics of short and long internode varieties differed with each other and correlated with gene expressions pattern. We established tissue and spatial transcriptome dataset, and comparative analyses demonstrated number of genes involved in cell cycle, cell expansion, transcription factors and hormone pathway including bZIP16 are differentially expressed between short and long internode varieties. Biochemical, DNA-protein interactions and molecular evidences revealed that ScbZIP16 inversely related to GA content by repressing transcripts of ent-isokaurene C2/C3-hydroxylase and GA20 Oxidase in sugarcane. The further genetic evidences confirmed role of ScbZIP16 in reducing GA biosynthesis pathway, flowering time and growth in Arabidopsis. This report of ScbZIP16 regulatory module offers a potential candidate for sugarcane improvement programs.

plant biology↗

bioRxiv2023

Histone mark age of human tissues and cells

BackgroundAging involves intricate epigenetic changes, with histone modifications playing a pivotal role in dynamically regulating gene expression. Our research comprehensively analyzes seven key histone modifications across various tissues to understand their behavior during human aging and formulate age prediction models. ResultsThese histone-centric prediction models exhibit remarkable accuracy and resilience against experimental and artificial noise. They showcase comparable efficacy when compared with DNA methylation age predictors through simulation experiments. Intriguingly, our gene set enrichment analysis pinpoints vital developmental pathways crucial for age prediction. Unlike in DNA methylation age predictors, genes previously recognized in animal studies as integral to aging are amongst the most important features of our models. We also introduce a pan-histone-mark, pan-tissue age predictor that operates across multiple tissues and histone marks, reinforcing that age-related epigenetic markers are not restricted to particular histone modifications. ConclusionOur findings underscore the potential of histone marks in crafting robust age predictors and shed light on the intricate tapestry of epigenetic alterations in aging.

systems biology↗

bioRxiv2022

miRNA408 and its encoded peptide, miPEP408, regulate arsenic stress response in Arabidopsis

MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in regulating various developmental and biological processes. The expression of miRNAs is differentially modulated in response to various stresses. Based on the recent findings, it has been shown that some of the pri-miRNAs encode small regulatory peptides, microRNA-encoded peptides (miPEP). miPEPs are reported to regulate the growth and development of plants by modulating corresponding miRNA expression; however, the role of these peptides in different stresses has not been explored yet. Here, we reported that pri-miR408 encodes a small peptide, miPEP408, that regulates the expression of miR408, its targets, and associated phenotype in Arabidopsis. Plants overexpressing miR408 showed severe sensitivity under low sulphur (LS), Arsenite As(III) and LS+As(III) stress, while miR408 mutant developed through the CRISPR/Cas9 approach showed tolerance. Transgenic lines showed phenotypic alteration and modulation in the expression of genes involved in the sulphur reduction pathway and affect sulphate and glutathione accumulation. Similar to miR408 overexpressing lines, the exogenous application of synthetic miPEP408 or miPEP408 overexpression led to sensitivity in plants under LS, As(III) and combined LS+As(III) stress compared to control. This study suggests the involvement of miR408 and miPEP408 in heavy metal and nutrient deficiency responses. One-sentence summarymiR408 and peptide encoded by miR408, miPEP408, regulate arsenic stress and low sulphur responses in Arabidopsis.

plant biology↗

bioRxiv2020

Unique mutational changes in SARS-CoV2 genome of different state of India

COVID-19 is a global pandemic causing more than 8 million deaths till mid-August, 2020. In India, more than 3 million confirmed cases have been reported although with relatively low death rate of 1.8%. In this study, we sequenced 47 genomes of SARS-CoV-2 from the patients of 13 districts of Uttar Pradesh (UP), the largest state of India using third-generation sequencing technique. The phylogenetic clustering revealed that no UP sample was aligned with the previously defined USA clade, where the mortality was high. We identified 56 distinct SNP variations in the genomes of UP resulting in a unique mutation rate of 1.19% per sequence, which is greater than the value 0.88% obtained for the rest of India. The relatively less death rate in UP indicates that the mutation in the virus is deleterious. Further investigation is required with larger sample size to determine the degree of virulence vis-a-vis SNP variation.

bioinformatics↗