Biology subjects

Zahra, S.

Publications and source records attributed to Zahra, S..

6 recordsLinked to original sources

bioRxiv2025

Abiotic Stress-Mediated Modulation of the tncRNome: Unraveling tRNA-Derived RNA Networks in Plant Adaptive Responses

Transfer RNA-derived non-coding RNAs (tncRNAs) are potential regulators of gene expression in plants, and its crucial to understand their diversity and functional roles in modulating plant stress responses. Here, we have investigated abiotic stress-responsive tncRNAs in two important crops, rice and chickpea, under drought and salt stress conditions. Small RNA sequencing revealed that 70.2% of tncRNAs in rice and 45% in chickpea were commonly expressed across multiple stress conditions. qRT-PCR validation showed that most tRF-5s were upregulated in both rice and chickpea under drought and salt stress. In rice, 3'tRHs were specifically induced by drought, whereas 5'tRHs responded predominantly to salt stress. In chickpea, tRF-3s were upregulated during drought but downregulated under salt stress. Furthermore, we confirmed the mRNA targets of these stress-associated tRNA fragments using RLM-RACE, thereby verifying the cleavage of specific target mRNAs in both species. Expression profiling of target genes revealed a negative association with their corresponding tRFs in both species. Subcellular localization demonstrated that OsGEM and OsPPR were primarily localized in the nucleus, while CaMIZ1 and CaSKP1 were detected at the plasma membrane. Overall, we identified abiotic stress-responsive tncRNAs from rice and chickpea that suggest their potential contribution to plant resilience under changing environmental conditions.

bioinformatics↗

bioRxiv2025

BLADE-R: streamlined RNA extraction for molecular diagnostics and high-throughput applications

Efficient nucleic acid extraction and purification are crucial for cellular and molecular biology research, yet they pose challenges for large-scale clinical RNA sequencing and PCR assays. Here, we present BLADE-R, a magnetic bead-based protocol that simplifies the process by combining cellular lysis and nucleic acid binding into a single step, followed by a unique on-bead rinse for nuclease-free separation of genomic DNA and RNA. The Agilent TapeStation and RT-qPCR analyses show that RNA extracted from HEK293T cell line using BLADE-R outperforms the TRIzol protocol in terms of time and cost. RNA sequencing reveals no differences in sequence quality or gene count variance between samples processed with BLADE-R and those processed with TRIzol followed by RNA kit clean-up. Additionally, BLADE-R outperformed TRIzol in RNA extraction from frozen tissue and whole blood samples, as confirmed by RT-qPCR. Our protocol can be adapted to a 96-well plate format, enabling RNA purification of up to 96 human blood samples in less time than a single-sample traditional extraction. Using BLADE-R in this format, we confirmed minimal well-to-well contamination in RNA purification, cDNA synthesis, and PCR. Therefore, our novel BLADE-R protocol, suitable for both low and high-throughput formats, is effective even in limited-resource settings for preparing clinical samples for PCR and sequencing assays. Thus, our new BLADE-R technique works well even in low-resource environments to prepare clinical samples for PCR and sequencing experiments. It can be adapted for both low- and high-throughput formats.

molecular biology↗

bioRxiv2025

Mesenchymal Stem Cell-Derived Extracellular Vesicles Mitigate Immune Cell Activation in an In Vitro Model of Post-Resuscitation Inflammation

BackgroundSystemic inflammation is a well-established component of post-cardiac arrest syndrome (PCAS), a condition responsible for significant morbidity and mortality in patients who are initially resuscitated from sudden cardiac arrest. Mesenchymal stem cell-derived extracellular vesicles (MSC-EVs) have emerged as promising immunomodulatory agents in various inflammatory conditions, including after ischemia-reperfusion injury (IRI). Here, we investigated the therapeutic potential of MSC-EVs in porcine peripheral blood mononuclear cells (PBMCs) stimulated with lipopolysaccharide (LPS) or mitochondrial DNA (mtDNA) to mimic immune cell activation in PCAS. MethodsPBMCs were isolated from healthy pigs (Sus scrofa), cultured in vitro, stimulated with LPS or mtDNA, and treated with a range of MSC-EV concentrations. Flow cytometry, quantitative PCR, ELISA, and ROS/RNS measurements were performed to assess PBMC activation. ResultsMSC-EV treatment reduced LPS-induced inflammatory granulocyte activation and selectively modulated cytokine transcripts, including IFN, IL-1{beta}, and TNF-, in a concentration-dependent manner. Similar immunosuppressive effects were observed in mtDNA-stimulated PBMCs, where MSC-EVs attenuated dendritic cell activation and inflammatory cytokine release. Furthermore, higher concentrations of MSC-EVs significantly decreased ROS/RNS production in both LPS- and mtDNA-challenged PBMCs. ConclusionsMSC-EVs exhibit potent immunomodulatory properties against LPS- and mtDNA-induced activation of porcine PBMCs, highlighting their broad capacity to modulate immune responses and mitigate oxidative stress induced by pro-inflammatory stimuli that are relevant to PCAS. These findings provide further support for the administration of MSCs, or MSC-EVs themselves, as a potential therapeutic intervention to target immune activation in PCAS and other disorders characterized by an acute systemic inflammatory state.

immunology↗

bioRxiv2022

PtRNAdb: A web resource of Plant tRNA genes from a wide range of plant species

tRNA, as well as their derived products such as short interspersed nuclear elements (SINEs), pseudogenes and transfer-RNA, derived fragments (tRFs) has now been shown to be vital for cellular life, functioning and adaptation during different stress conditions in all diverse life forms. In this study, we have developed PtRNAdb (www.nipgr.ac.in/PtRNAdb), a plant exclusive tRNA database containing 113849 tRNA gene sequences from phylogenetically diverse plant species. We have analysed a total of 106 nuclear, 89 plastidial and 38 mitochondrial genomes of plants by tRNAscan-SE software package, and after careful curation of the output data, we developed this database and integrated the data. The information about the tRNA gene sequences obtained, were further enriched with consensus sequence based study of tRNA genes based on their isoacceptors and isodecoders. We have also built covariance models based on the isoacceptors and isodecoders of all the tRNA sequences using infernal tool. The user can also perform BLAST not only against PtRNAdb entries but also against all the tRNA sequences stored in PlantRNA databases; and annotated tRNA genes across the plant kingdom available at NCBI. For the users ease, we have also incorporated the tRNAscan-SE tool for tRNA gene prediction, and ViennaRNA package for structural analysis on the home page of PtRNAdb. This resource is believed to be of high utility for plant researchers as well as molecular biologists to carry out further exploration of plant tRNAome on a wider spectrum, as well as for performing comparative and evolutionary studies related to tRNAs and their derivatives across all domains of life. Database URLhttp://www.nipgr.ac.in/PtRNAdb/

bioinformatics↗

bioRxiv2021

Transfer RNA-derived non-coding RNAs (tncRNAs): Uncovering hidden regulators of transcriptional regulatory circuits in plants

The lateral emergence of distinct classes of non-coding RNAs has led to better insights into the eukaryotic regulatory networks. Among them, the existence of transfer RNA (tRNA)-derived non-coding RNAs (tncRNAs) demands their exploration in the plant kingdom. Here, we have designed a methodology to uncover the bigger picture of tncRNAome in plants. Using this, we have identified diverse tncRNAs of length 14-50 nt in ~2500 small RNA sequencing (sRNA-seq) samples of six major angiosperms, and further studied their various features including length, codon-usage, cleavage pattern, and modified tRNA nucleosides. Codon-dependent generation of tncRNAs indicates that the process is highly specific rather than being mere random tRNA degradation. Analysis for nucleotide composition of tncRNA cleavage positions indicates that they are generated through precise endoribonucleolytic machinery. Certain tRNA nucleoside modifications on tncRNAs were found to be conserved across the plants, and hence may influence tRNA cleavage, as well as tncRNA functions. Pathway enrichment analysis revealed that common tncRNA targets were majorly involved in the metabolic and developmental processes of plants. Also, many tRFs were found to be associated with transposable elements. Distinct tissue-specific tncRNA clusters indicate their role in plant development under normal physiological conditions. Furthermore, the identification of a significant number of differentially expressed tncRNAs under several abiotic and biotic stresses highlights their probable role as gene expression modulators during various stress conditions. Thus, this study will be beneficial to investigate the emerging role of tncRNAs as prospective biomarkers in plant development and stress. HighlightsO_LIComputational pipeline for accurate identification of genuine transfer RNA-derived non-coding RNAs (tncRNAs) using small RNA sequencing (sRNA-seq) datasets. C_LIO_LISix major tncRNA classes of length ranging from 14 to 50 nt were identified in ~2,500 sRNA-seq datasets in six different angiosperms. C_LIO_LItRNA nucleoside modifications may affect tncRNA cleavage in plants. C_LIO_LIConserved tncRNAs target transcripts are involved in plant growth, development, and metabolism. C_LIO_LItncRNAs are expressed in a tissue-dependent, and stress-specific manner in plants. C_LI

bioinformatics↗

bioRxiv2021

EMS-based mutants are useful for enhancing drought tolerance in spring wheat

Sustainable wheat production in drought prone areas can be achieved by developing resilient wheat varieties. In the present study, chemical mutagenesis was used to induce mutations in a cultivated wheat variety NN-Gandum-1. In total, 44 mutants were selected based on their high yield potential for exposing to well-watered (W1) and rainfed (W2) conditions for one season. Then 24 mutants were selected, and were exposed to W1 and W2 regimes. On the basis of least relative reduction in physiological parameters under W2 regime, five mutants were selected for conducting exome capturing assays. In total, 184 SNPs were identified in nine genes (ABC transporter type 1, Aspartic peptidase, Cytochrome P450, transmembrane domain, Heavy metal-associated domain, HMA, NAC domain, NAD (P)-binding domain, S-type anion channel, Ubiquitin-conjugating enzyme E2 and UDP-glucuronosyl/UDP-glucosyltransferase). Maximum number of mutations were observed in chr.2D, which contained mutations in three genes i.e. ABC transporter type 1, NAD (P)-binding domain and UDP-glucuronosyl/UDP-glucosyltransferase which may have a role in conferring drought tolerance. The selected mutants were further tested for studying their biochemical responses under both the regimes for two years. The extent of membrane damage was estimated through malondialdehydeand hydrogen per oxidase and tolerance to drought stress was assessed via antioxidant enzymes in leaves. The selected mutants under drought stress increased the accumulation of proline content, total soluble sugars, total free amino acids, while decreased total chlorophyll content, carotenoids and total soluble protein. Finally, the procedure of narrowing down the number of developed mutants from a large mutation population (>4000) is found useful for exploring the complex trait like drought without compromising yield potential. These mutants can further be explored to understand the genetic circuits of drought tolerance in wheat which will pave the way towards improving livelihood of resource poor farming community mostly relying on cereal food.

plant biology↗