Biology subjects

Raghuvanshi, S.

Publications and source records attributed to Raghuvanshi, S..

4 recordsLinked to original sources

bioRxiv2023

Monocot-specific miR528 act as the post-transcriptional regulator of strigolactone signaling via Dwarf 3 in rice

miRNAs are a critical component of regulatory mechanisms involved in plant growth, development, and stress response including phytohormone action. The role of miRNAs in regulating the strigolactone (SL) signaling in plants is still unexplored. Here we report that miR528 impacts the SL signaling via the post-transcriptional regulation of Dwarf 3 (OsD3). Comparative miRNome analysis under drought conditions in flag leaf, inflorescence, and roots uncovered the tissue-biased unique stress response of miR528 in drought-tolerant N22 (down in inflorescence and roots; up in flag leaf). Consequently, its target, OsD3 which encodes for the F-BOX/LRR-REPEAT MAX2 HOMOLOG and is a critical component of the rice SL signaling pathway exhibit opposite expression to miR528 in all three tissues. Interestingly, OsD3 is a rice-specific target of miR528. miR528 overexpression plants exhibited early heading, increment in the number of tillers, flag leaf length, and width, number of panicle branches, grain per panicle, effective grains per panicle, seed length, and photosynthesis rate. miR528 overexpression plants exhibited similar traits to Osd3 mutants including high tiller number, root architecture under low nitrogen conditions, and moderate insensitivity to GR24 and TIS1 levels in addition to shared transcriptional regulation. Furthermore, SL (GR24) negatively impacts the miR528 transcription. The impact of the miR528:D3 module is also reflected in the D53-mediated downstream signaling involving IPA1 regulon.

plant biology↗

bioRxiv2023

PlotS: web-based application for data visualization and analysis

BackgroundData visualisation technique has greatly improved as technology has advanced. While representing the data through graph, it has made the underlying data structure become more transparent and interpretable. However, the informational scope of freely available generic visualisation tools is still limited since they only support descriptive statistics as well as no metainformation can be incorporated. Additionally, there is a need to promote the use of accepted scientific standards when performing and reporting statistical analysis. ResultPlotS is a visualization centric web-based application that allows the integration of statistical analysis into a single workflow. The current version has eight types of graphs (bar, box, density, frequency polygon, histogram, line, scatter and violin plot) and four statistical methods (T-test, ANOVA, Wilcoxon test and Krushkal-Wallis test). It is an interactive application that provide many useful customization options for data analysis-focused visualization. It support incorporation of metainformation in the graph and multivariate data analysis by adding layer with or without secondary y-axis, side graphs, inset graph or through faceting. It can handle variety of data formats with or without replicates and inferential statistical analysis can be incorporated in the graph. Necessary statistical results are explicitly displayed for inferences and reporting. ConclusionPlotS is freely available at https://plots-application.shinyapps.io/plots/. We hope it will be a useful tool for data visualisation and analysis that will also encourage the widespread use of proper statistical methods in research and teaching.

bioinformatics↗

bioRxiv2023

Continuous muscle, glial, epithelial, neuronal, and hemocyte cell lines for Drosophila research

Expression of activated Ras, RasV12, provides Drosophila cultured cells with a proliferation and survival advantage that simplifies the generation of continuous cell lines. Here we used lineage restricted RasV12 expression to generate continuous cell lines of muscle, glial, and epithelial cell type. Additionally, cell lines with neuronal and hemocyte characteristics were isolated by cloning from cell cultures established with broad RasV12 expression. Differentiation with the hormone ecdysone caused maturation of cells from mesoderm lines into active muscle tissue and enhanced dendritic features in neuronal-like lines. Transcriptome analysis showed expression of key cell-type specific genes and the expected alignment with single cell sequencing data in several cases. Overall, the technique has produced in vitro cell models with characteristics of glia, epithelium, muscle, nerve, and hemocyte. The cells and associated data are available from the Drosophila Genomic Resource Center.

cell biology↗

bioRxiv2021

Investigations on regulation of miRNAs in rice reveal cyt signal transduction regulated miRNAs

MicroRNAs are critical components of the multi-dimensional regulatory networks in eukaryotic systems. They regulate a spectrum of developmental and metabolic processes in both plants and animals. Thus, it is quite apparent that the transcription, processing as well as activity of the miRNAs themselves is very dynamically regulated. One of the most important and universally implicated signalling molecule is [Ca2+]cyt. It is known to regulate a plethora of developmental and metabolic processes in both plants and animals, however their impact on the regulation of miRNA expression is relatively less explored. The current study employed a combination of internal and external calcium channel inhibitors, to establish that [Ca2+]cyt signatures actively regulate miRNA expression in rice. Involvement of [Ca2+]cyt in regulation of miRNA expression was further confirmed by treatment with calcimycin, the calcium ionophore. Modulation of the cytosolic calcium levels was also found to regulate the drought responsive expression as well as ABA mediated response of miRNA genes in rice seedlings. The study further establishes the role of calmodulins and Calmodulin-binding Transcription Activators (CAMTAs) as important components of the signal transduction schema that regulates miRNA expression. Yeast-one-hybrid assay established that OsCAMTA4 & 6 are involved in the transcriptional regulation of miR156a and miR167h. Thus, the study was able to clearly establish that [Ca2+]cyt is actively involved in regulating expression of miRNA genes both under control and stress conditions.

plant biology↗