Biology subjects

Roy, J. K.

Publications and source records attributed to Roy, J. K..

9 recordsLinked to original sources

bioRxiv2024

Phenotypically wild barley shows evidence of introgression from cultivated barley

Plant conservation hinges on preserving biodiversity, which is crucial for long-term adaptation. Multiple studies have reported genetic evidence of crop-to-wild introgression in phenotypically wild accessions of wild barley (Hordeum vulgare ssp. spontaneum). We examined 318 Wild Barley Diversity Collection (WBDC) accessions for evidence of introgression from cultivated barley. Using SNP genotype and exome capture data, we performed local ancestry inference between the 318 WBDC accessions and cultivated barley to identify genomic regions with evidence of introgression. Using the genomic intervals for well-characterized genes involved in domestication and improvement, we examined the evidence for introgression at genomic regions potentially important for maintaining a wild phenotype. Our analysis revealed that nearly 16% (48 of 318) of WBDC accessions showed evidence of introgression from cultivated barley, and up to 16.6% of the genome has been introgressed. All accessions identified as introgressed based on domestication-related phenotypes show clear genetic evidence of introgression. The size of runs of identity by state and local ancestry inference suggests that most introgression did not occur recently. This study suggests a long history of genetic exchange between wild and cultivated barley, highlighting the potential for introgression to influence the genetic makeup and future adaptation of wild populations, with implications for plant conservation strategies.

evolutionary biology↗

bioRxiv2023

From gonadogenesis to testicular cancer: Unravelling the novel regulators and identification of drug candidates against FGF9 and PTGDS

Sex determination is the preliminary step toward gonadogenesis in mammals. Antagonistic interactions of key regulators have been only fragmentarily mentioned so far. Therefore, exploring regulators underlying the phenomena is required to solve questions, especially regarding female gonad development and gonadal disorders in congenital or adults. Inhibiting discrepancies in PPI pathways and combating related disorders are of urgent necessity, for which novel drugs are constantly required. Here, we performed in silico analysis using robust bioinformatics methods, which is unprecedented work in sex determination studies, providing large-scale analysis without exorbitant wet lab procedures. Analyzed regulators were overlapped with our RNA-seq data for authentication, to obtain differentially expressed elements. Additionally, CADD approach was used to discover inhibitors for FGF9 and PTGDS to search for potential drugs combating gonadal disorders in adults. Along with druggable properties, only FGF9 and PTGDS had full-length protein structures available, among 25 key genes under investigation. Our large-scale analysis of PPIN, produced highly interacting hub-bottleneck nodes as novel genes. Further, functional enrichment analysis revealed importance of these regulators in gonadogenesis. We identified sex-specific novel genes, miRNAs-target pairs, and lncRNAs-target pairs, which appear to play an important role in regulation of ovary development. CADD with molecular docking, MD simulations, and molecular mechanics confirmed stability of two novel compounds, DB12884 and DB12412 that could potentially inhibit FGF9 and PTGDS respectively. Taken together our study provides valuable information regarding involvement of crucial regulators in antagonistic mechanism of gonadogenesis and their related disorders, which will further assist in refining wet lab experiments.

bioinformatics↗

bioRxiv2022

Transcriptome and biochemical analysis pinpoint multi-layered molecular processes associated with iron deficiency tolerance in hexaploid wheat

Iron (Fe) is an essential nutrient for plants that is indispensable for many physiological activities. Although few genotypes were identified with contrasting tolerance to Fe deficiency, the molecular insight into the distinct biochemical and transcriptional responses determining the trait is poorly known. This study aimed to identify the molecular and biochemical basis for the contrasting Fe deficiency tolerance in wheat genotype showing tolerance to Fe deficiency (cv. Kanchan-KAN) compared to susceptible (cv. PBW343-PBW) cultivar. Under Fe deficiency, the KAN show delayed chlorosis, high SPAD values and low malondialdehyde activity compared to PBW. The shoot transcriptomics studies show that a large set of genes for photosynthetic pathways were highly induced in PBW, suggesting its sensitivity to Fe deficiency. Although, under Fe deficiency, both the cultivars show distinct molecular re-arrangements, including high expression of genes involved in Fe uptake (including membrane transporters) and mobilization, the gene expression level was higher in KAN. Furthermore, the KAN cultivar also shows high ubiquitination activity in the shoot tissue suggesting a high turnover of proteins in the tolerant cultivar. These observations were also co-related with the high root phytosiderophores biosynthesis and its release that contributes to the enhanced Fe translocation index in KAN. Overall, our work provides the key link to understanding the mechanistic insight for the Fe deficiency tolerance in hexaploid wheat. This will enable wheat breeders to select genotypes for better Fe use efficiency for agriculture.

plant biology↗

bioRxiv2021

Rab11 negatively regulates Wingless preventing JNK mediated apoptosis in Drosophila epithelium during embryonic dorsal closure

Cell signaling pathways involved in epithelial wound healing, show a lot of complexities when it comes to their regulation. Remarkably, a large proportion of these signaling pathways are triggered at the time of morphogenetic events which usually involve epithelial sheet fusions during embryonic development, such as the event of dorsal cloure in Drosophila embryos. One such conserved pathway in the wound healing process is the JNK-Dpp signaling pathway. Recent observations suggest that one such upstream regulator of JNK mediated apoptosis could be Rab11, a small Ras like GTPase, which is functionally associated with the membrane and cortical cytoskeletal organization of epithelial cells. Using Drosophila embryonic dorsal closure as a model of wound healing, we observed that a targeted expression of a Rab11 loss of function mutant in the dorso-lateral epidermis of fly embryos (tissue which extends contra-laterally in order to fill the intervening gap) undergoing dorsal closure leads to an ectopic expression of Caspase-3 and a concomitant up-regulation of the JNK-Dpp signaling. This resulted in the death of the dorso-lateral epithelial cells with a consequent embryonic lethality due to dorsal closure defects. Interestingly, a simultaneous knockdown of wingless (another developmentally conserved gene) in Rab11 mutants resulted in a rescue of the lethal phenotype and also a significant level of successful completion of the dorsal closure process. In our experiments we suggest Rab11 could promote cross talk between the JNK-Dpp pathway and the canonical wingless pathway in the regulation of apoptosis in the dorsolateral epithelium of fly embryos undergoing dorsal closure. One Sentence SummaryRab11 functions through a conserved Wingless mediated JNK-Dpp pathway during embryonic dorsal closure.

developmental biology↗

bioRxiv2021

The Drosophila DCP2 is evolutionarily conserved in sequence and structure : insights from in silico studies of DmDCP2 orthologs and paralogs

The mRNA decapping proteins (DCPs) function to hydrolyze the 7-methylguanosine cap at the 5 end of mRNAs thereby, exposing the transcript for degradation by the exonuclease(s) and hence, play a pioneering role in the mRNA decay pathway. In Drosophila melanogaster, the mRNA decapping protein 2 (DCP2) is the only catalytically active mRNA decapping enzyme present. Despite its presence being reported across diverse species in the phylogenetic tree, a quantitative approach to the index of its conservation in terms of its sequence has not been reported so far. With structural and mechanistic insights being explored in the yeasts, the insect DCP2 has never been explored in the perspectives of structure and the indices of the conservation of its sequence and/or structure vis-a-vis topological facets. Being an evolutionarily conserved protein, the present endeavor aimed at deciphering the evolutionary relationship(s) and the pattern of conservation of the sequence of DCP2 across the phylogenetic tree as well as in sibling species of D. melanogaster through a semi-quantitative approach relying on multiple sequence alignment and analyses of percentage identity matrices. Since NUDIX proteins are functionally diverse, an attempt to identify the other NUDIX proteins (or, DCP2 paralogs) in D. melanogaster and compare and align their structural features with that of DCP2 through in silico approaches was endeavored in parallel. Our observations provide quantitative and structural bases for the observed evolutionary conservation of DCP2 across the diverse phyla and also, identify and reinforce the structural conservation of the NUDIX family in D. melanogaster.

bioinformatics↗

bioRxiv2020

A forward genetic approach to mapping a P-element second site mutation identifies DCP2 as a novel tumor suppressor in Drosophila melanogaster

The use of transposons to create mutants has been the cornerstone of Drosophila genetics in the past few decades. Transpositions often create second-site mutations, devoid of transposon insertion and thereby affect subsequent phenotype analyses. In a P-element mutagenesis screen, a second site mutant was discovered on chromosome 3 wherein the homozygous mutant individuals show the classic hallmarks of mutations in tumor suppressor genes including brain tumour and lethality, hence the mutant line was initially named as lethal (3) tumorous brain [l(3)tb]. Classical genetic approaches relying on meiotic recombination and subsequent complementation with chromosomal deletions and gene mutations mapped the mutation to CG6169, the mRNA decapping protein 2 (DCP2), on the left arm of the third chromosome (3L), and thus the mutation was renamed as DCP2l(3)tb. Fine mapping of the mutation further identified the presence of a Gypsy-LTR like sequence in the 5UTR coding region of DCP2, alongwith expansion of the adjacent upstream intergenic AT-rich sequence. The mutant phenotypes are rescued by Introduction of a functional copy of DCP2 in the mutant background, thereby establishing the causal role of the mutation and providing a genetic validation of the allelism. With the increasing repertoire of genes being associated with tumor biology this is the first instance that the mRNA decapping protein is being implicated in Drosophila tumourigenesis. Our findings therefore imply a plausible role for mRNA degradation pathway in tumorigenesis and identify DCP2 as a potential candidate for future explorations of cell cycle regulatory mechanisms.

genetics↗

bioRxiv2019

DCP2 plays multiple roles during Drosophila development - possible case of moonlighting?

mRNA decapping proteins (DCPs) are components of the P-bodies in the cell which are hubs of mRNAs targeted for decay and they provide the cell with a reversible pool of mRNAs in response to cellular demands. The Drosophila genome codes for two decapping proteins, DCP1 and DCP2 out of which DCP2 is the cognate decapping enzyme. The present endeavour explores the endogenous promoter firing, transcript and protein expression of DCP2 in Drosophila wherein, besides a ubiquitous expression across development, we identify active expression paradigm during dorsal closure and a plausible moonlighting expression in the Corazonin neurons of the larval brain. We also demonstrate that the ablation of DCP2 leads to embryonic lethality and defects in vital morphogenetic processes whereas a knockdown of DCP2 in the Corazonin neurons reduces the sensitivity to ethanol in adults, thereby ascribing novel regulatory roles to DCP2. Our findings unravel novel putative roles for DCP2 and identify it as a candidate for studies on the regulated interplay of essential molecules during early development in Drosophila, nay the living world.

cell biology↗

bioRxiv2019

Rab11 is essential for lgl mediated JNK-Dpp signaling in dorsal closure and epithelial morphogenesis in Drosophila

Dorsal closure in Drosophila provides a robust genetic platform providing deep insights into the basic cellular mechanisms that govern epithelial wound healing and morphogenesis. As dorsal closure proceeds, the adjacent epithelia advance contra-laterally involving coordinated cell shape changes in order to successfully accomplish the process. The JNK-Dpp signaling in these cells plays an instrumental role in guiding their fate as gastrulation completes. A huge number of genes have been reported to be involved in the regulation of this core signaling pathway, yet the mechanisms by which they do so is hitherto unclear, which forms the objective of our present study. Here we show that lgl, which is a potent tumour suppressor gene, conserved across the phyla till humans, regulates the JNK-Dpp pathway in the dorsal closure and epithelial morphogenesis process where in ectopic knockdown of this gene results in the failure of dorsal closure. Interestingly, we also find Rab11 to be interacting with lgl as they together regulate the core JNK-Dpp signaling pathway during dorsal closure and also during pupal thorax closure process. Using the robust Gal4-UAS system of targeted gene expression, we show here that Rab11 and lgl synergize to successfully execute the dorsal closure and the similar thorax closure process, ensuring proper spatio-temporal JNK-Dpp signaling.

developmental biology↗

bioRxiv2019

Characterisation of l(3)tb as a novel tumour suppressor allele of DCP2 in Drosophila melanogaster

Mutants provide an excellent platform for the discovery and characterization of gene functions. The present communication is a pioneering treatise on a hitherto undescribed function of the gene coding for the mRNA decapping protein 2 (DCP2) in Drosophila melanogaster. DCP2, the gene coding for the mRNA decapping enzyme, has been studied in various model organisms in the light of maintenance of transcript abundance and stability but has never been implicated in tumourigenesis. Herein, we describe the mapping and characterization of a novel tumour suppressor allele of DCP2 (CG6169), which we named as lethal(3)tumorous brain [l(3)tb]. The homozygous mutant individuals show prolonged larval life, develop larval brain tumors and are lethal in the larval/pupal stages. The tumour is characterized by the presence of increased number of superficial neuroblasts, abnormal chromosomal condensation and causes overgrowth in the wing and the eye-antennal discs of the homozygous mutant larvae, all of which are rescued by the introduction of a functional copy of DCP2 in the mutant background, thereby establishing the causal role of the mutation and providing a genetic validation of the allelism. Our findings therefore ascribe a novel role of tumor suppression to DCP2 besides its cognate function of mRNA decapping and thereby identify it as a potential candidate for future research on tumorigenesis.

genetics↗