Biology subjects

Dash, M.

Publications and source records attributed to Dash, M..

8 recordsLinked to original sources

bioRxiv2026

Prime editing of an evolutionarily informed PEPC residue enhances photosynthesis and grain nutrition in C₃ rice

C4 photosynthesis evolved through adaptive changes in key metabolic enzymes that enhance carbon fixation efficiency, yet transferring such traits into C3 crops has met limited success. Using precision prime editing, we introduced an evolutionarily conserved single amino acid substitution (Arg[->]Gly) into phosphoenolpyruvate carboxylase (PEPC) in rice. Edited plants exhibited enhanced PEPC activity in the presence of the feedback inhibitor malate, increased chlorophyll content, elevated photosynthetic rates under ambient CO2, and increased seed size and weight. Remarkably, seeds from the edited lines showed simultaneous enrichment of zinc (Zn), iron (Fe), and protein, hereafter referred to as ZiP rice. This work demonstrates that a single, evolutionarily guided residue change can reprogram core carbon metabolism in a C3 crop, enabling concurrent improvements in photosynthesis and grain nutritional quality.

plant biology↗

bioRxiv2025

Tissue specific de novo transcriptome sequencing and expression analysis of candidate genes for terpenoid biosynthesis in Piper longum.

Piper longum L. an economically important plant lacks adequate molecular resources towards unmasking molecular mechanisms for terpenoid biosynthesis. The transcriptome profiling generated 36.91 and 36.24 million raw reads in leaf and fruit tissue respectively. The de novo transcriptome assembly was performed with 36,688,460 and 36,011,305 clean reads, which subsequently produced 40,033 and 44,025 coding sequences (CDS) in leaf and fruit samples, respectively. The CDS were annotated using different databases such as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). These annotations resulted mining of various trait specific genes including important terpenoid biosynthesis genes. Presence of 53 and 58 terpenoid compounds in essential oils of leaf and fruit of long pepper have also been identified using GC-MS. Additionally, relative gene expression of eight terpenoid biosynthesis genes each for both leaf and fruit were conducted using real-time polymerase chain reaction (RT-PCR). For further genetic diversity study, 4085 and 4564 number of SSRs were identified in leaf and fruit, respectively. This study significantly contributes to the understanding of long pepper at the molecular level by expanding the available genetic resources. This paves the way to improve long pepper varieties and develop new genotype with desirable quality traits.

plant biology↗

bioRxiv2025

Caveolin-1 dependent regulation of cell-matrix interphase in 3D collagen gels.

Cell and extracellular matrix (ECM) interactions are essential for maintaining tissue function and homeostasis. Changes in the biochemical or mechanical properties of the ECM can lead to diseases such as fibrosis or cancer. In a 3D microenvironment, cell-matrix interaction is vital to how cells sense and respond to biochemical and biophysical cues. This study examines the reciprocal interactions between fibroblasts and collagen in 3D hydrogels. We quantitatively measured changes in collagen branch number and junctions in 3D hydrogels using confocal reflectance microscopy and existing analysis protocols. This reveals the impact small changes in collagen concertation (1.0 vs 1.5 mg/ml) over time (15 minutes to 4 hours) have on 3D gels. Embedded in 3D hydrogels, wild-type mouse fibroblasts differentially affect collagen organisation in their immediate proximity with changing concentration and time. This regulation is interestingly lost in Caveolin-1 null fibroblasts with altered stiffness, mechanosensing and cytoskeletal regulation. Inhibition of the Rho-ROCK pathway (known to be changed in Caveolin-1 null fibroblasts) drives cellular protrusions and concentration-dependent 3D collagen organisation in wildtype fibroblasts, but surprisingly not in Caveolin-1 null fibroblasts. This depends on dynamin-dependent endocytosis, which, when inhibited, disrupts ROCK-dependent protrusions and alters collagen organisation in 3D collagen. Together, these observations quantitatively demonstrate how cells respond at the cell-matrix interphase to subtle changes in collagen concentration and organisation in 3D hydrogels, regulated by the presence of Caveolin-1. Statement of SignificanceThis study highlights the critical role of Caveolin-1 in cell-mediated regulation of the extracellular matrix (ECM) in a 3D microenvironment. Using confocal reflectance microscopy, we demonstrate that subtle changes in collagen concentration significantly influence collagen organisation over time. While wild-type fibroblasts exhibit dynamic, concentration-dependent regulation of the cell-matrix interphase, Caveolin-1 null fibroblasts lose this regulation. Furthermore, Rho-ROCK pathway inhibition promotes protrusions and collagen reorganisation in wild-type cells but not Caveolin-1 null fibroblasts. Dynamin-dependent endocytosis also emerges as a key modulator of this process. These findings provide quantitative insights into how mechanosensing and cytoskeletal regulation, dependent on endocytosis can control the cell-matrix interphase, with possible implications for understanding disease-associated matrix changes.

cell biology↗

bioRxiv2025

Clostridium novyi type B causes fatal hemorrhagic disease in wild Asian elephants

The population of Asian elephants, an endangered species, is decreasing significantly due to anthropogenic interference in India. Research on Asian elephant disease is largely confined to observations reported from captive populations. The present study explored 11 disease investigation cases whose clinicopathological changes were similar to those of fatal hemorrhagic disease caused by Bacillus anthracis. We used molecular diagnostic approaches such as PCR (polymerase chain reaction), quantitative PCR, 16S metagenomics analysis and whole-metagenome sequencing for identification of the etiological agent responsible for these wild elephant mortalities. 16S metagenomics analysis revealed the presence of Clostridium hemolyticum as the dominant bacteria in all the mortality events. In contrast, flagellin gene-specific identification of all the samples and whole metagenomics analysis of blood samples collected from the ear pinna of a freshly deceased elephant revealed Clostridium novyi type B as the sole pathogenic agent responsible for the death of elephants. This study provides the first evidence of the involvement of Clostridium novyi type B in the death of wild elephants with similar clinical manifestations to anthrax. The current study also provides ample evidence of the need to explore investigations of emerging diseases of wild elephants to conserve these large mammals.

microbiology↗

bioRxiv2023

Evolution of tandem repeats in putative CSP to enhance its function: A recent and exclusive event in Plasmodium vivax in India

The molecular hitchhiking model proposes that linked non-coding regions also undergo fixation, while fixing a beneficial allele in a population. This concept can be applied to identify loci with functional and evolutionary significance. Putative circumsporozoite protein (CSP) in Plasmodium vivax (PvpuCSP) identified following the molecular hitchhiking model, holds evolutionary significance. We investigated the extent of genetic polymorphism in PvpuCSP and the role of natural selection which shapes the genetic composition and maintains the diversity in P. vivax isolates from India. Sequencing the putative CSP of P. vivax (PvpuCSP) in 71 isolates revealed a well-conserved N- and C-terminal, constituting around 80% of the gene. PCR amplification and sequencing validated extensive diversity in the repeat region, ranging from 1.8 to 2.2 kb towards the C-terminal, identifying 37 different alleles from 71 samples. The recent and exclusive accumulation of repeats in puCSP within P. vivax highlights its highly variable length polymorphism, making it a potential marker for estimating diversity and infection complexity. Episodic diversifying selection in the PvpuCSP repeat region, evidenced by statistically significant p-values and likelihood ratios, enhances amino acid diversity at various phylogenetic levels, facilitating adaptation for accommodating different substrates for degradation.

evolutionary biology↗

bioRxiv2022

Synonymous polymorphism difference relating to codon degeneracy between co-transcribed genes in the genome of Escherichia coli

The previous findings suggest that replication and transcription are two major reasons behind the different substitution patterns of mutations in genomic DNA. In the current work, we have compared the adjacent co-transcribed gene pairs regarding synonymous polymorphism in five different operons in Escherichia coli. It is interesting that the co-transcribed genes were different from each other regarding the polymorphism spectra. The transition to transversion ratio between gene pairs were different due to their compositional differences regarding two-fold degenerate codon and four-fold degenerate codons. Further, the polymorphism spectra difference between the gene pairs was more prominent in four-fold and six-fold degenerate codons than in the two-fold degenerate codons. In case of rpoB and rpoC, the major difference was found at UCC, GUA, CCG, GCU, GGC and CGC codons. Similarly, in case of the other four pairs of co-transcribed genes, the difference was more prominent in the higher degenerate codons than the two-fold degenerate codons. It may be that the restriction of two-fold degenerate codons to transition substitutions only regarding synonymous polymorphism is making these codons different from the higher degeneracy codons in this study.

evolutionary biology↗

bioRxiv2022

Modified dN/dS for accounting transition and transversion frequency difference and non-sense substitution in genomes

The dN/dS value is estimated in homologous protein coding gene sequences between two closely related organisms for studying selection on the genes. In the usual method of calculation of synonymous (S) and non-synonymous (NS) sites in codons, the transition and transversion rates are considered same as well as no difference of pretermination codons from the other codons regarding NS substitutions is considered. In this study we are proposing a modification in the method by estimating the S and the NS sites in codons by considering difference between the transition and transversion rates and the NS substitutions leading to non-sense codons in pretermination codons. So, the dN/dS value calculated by our approach was higher than that calculated by the earlier method. The modified method was applied in estimating dN/dS in 29 homologous gene sequences of Escherichia coli and Salmonella enterica. Impact of codon degeneracy and pretermination codons on the dN/dS values estimated by our method were observed clearly. Our method of estimation that considers the above features is a realistic representation of dN/dS values in coding sequences.

evolutionary biology↗

bioRxiv2020

Exosomes isolated from two different cell lines using three different isolation techniques show variation in physical and molecular characteristics

Exosomes are the nanoscopic lipid bi-layered extracellular vesicles with the potential to be utilized as targeted therapeutics. In our investigation, we compared three major exosome isolation techniques that were Total Exosome Isolation reagent (TEI), Protein organic solvent precipitation (PROSPR) and differential ultracentrifugation (UC) based on the biophysical and physicochemical characteristics of exosomes isolated from COLO 205 and MCF-7 cancer cells conditioned media with an aim to select a suitable method for translational studies. 3D image analysis and particle size distribution of exosomes from their HRTEM images depicted the morphological differences. Molecular and analytical characterization of exosomes using western blotting, Raman and ATR-FTIR spectroscopy and the multivariate analysis on the spectral data obtained, assessed for better molecular specifications and purity of particle. TEI method isolated exosomes with higher exosomal yield, purity, and recovery directly translatable into drug delivery and targeted therapeutics whereas ultracentrifuge had good recovery of particle morphology but showed particle aggregation and yielded exosomes with smaller mean size. PROSPR technique isolated a mixture of EVs, showed lower protein recovery in PAGE and western blotting but higher spectroscopic protein to lipid ratio and distinguishable EV population in multivariate analysis compared to exosomes isolated by TEI and UC. This comparative study should help in choosing a specific exosome isolation technique required for the objective of downstream applications.

cell biology↗