Biology subjects

Jaiswal, P.

Publications and source records attributed to Jaiswal, P..

14 recordsLinked to original sources

bioRxiv2026

Growth and molecular responses of potato to lunar regolith simulants

BackgroundOn-site food production will be required to achieve NASAs goal of a sustainable Lunar habitat. Toward this end, the use of fine, soil-like material on the Lunar surface, known as regolith, has been proposed as a plant growth substrate. However, how this substrate may affect plant growth is not well understood. Lunar regolith is devoid of the organic materials that make soils on earth fertile for plant growth, and has been weathered by solar winds, cosmic rays, and micrometeorite impacts. Additionally, regolith at certain lunar sites may contain heavy metals. These metal ions may leech, thus posing challenges with accumulation in plant material. To address and verify the efficacy of regolith-based crop production, we used lunar regolith simulants (LRS). We investigated the effects of LRS on potato (Solanum tuberosum cv Modoc) plant and tuber development, gene expression, and nutrition profiles. ResultsGrowth in LRS negatively impacted the potato plant size and tuber yield. While the degree of impact differed between simulants, all plants grown in LRS were statistically significantly shorter in height than plants grown in control soil. Further experiments with the lunar mare simulant 1E (LMS-1E) show that these effects can be ameliorated through the addition of vermicompost, an organic component, with a 70:30 v/v ratio of LMS-1E to compost being virtually indistinguishable from controls. Changes in gene expression profiles also differed between simulants, with genes related to photosynthesis, biotic and abiotic stress responses, signaling, and terpenes and flavonoids metabolism being commonly altered. Despite these observed differences in transcription, broad changes in metabolite profiles were not observed. ConclusionsLRS are clearly stressful on plants. However, amendment of the substrate with composted materials appears to be a viable strategy to alleviate stress. Given these observations, regolith-based agriculture may not be viable for very early food production when organic matter content is low. However, this would improve over time with continual incorporation of organic matter to regolith. As such, we believe regolith-based agriculture is a viable long-term strategy.

plant biology↗

bioRxiv2025

Gadd45 regulates fate decisions of myeloid-type blood progenitor cells in Drosophila

Gadd45 is a highly conserved stress response protein that interacts with multiple cellular proteins, playing a crucial role in regulating the cell cycle and responding to various forms of stress. Altered expression of Gadd45 is linked to several solid tumors and hematopoietic malignancies. It is also identified as a gene crucial for cytokine-induced myeloid differentiation, although the precise molecular mechanisms underlying this process remain unclear. We utilized the Drosophila hematopoietic system to investigate the role of Gadd45 in the development of myeloid-type blood cells, employing in vivo genetics and cell biological methods. We show that the absence of Gadd45 reduces the number of crystal cells but does not significantly impact macrophage-like cell plasmatocyte differentiation. However, Gadd45 overexpression caused intermediate progenitors to differentiate into lamellocytes and plasmatocytes to transdifferentiate into lamellocytes, a response typically observed during larval stages in response to immune challenges and injury. Interestingly, Gadd45 overexpression initiated the lamellocyte differentiation program by activating a combination of Toll, JNK, and JAK/STAT signaling pathways. This closely resembles the process by which specialized macrophages are derived in mammals. Moreover, Gadd45 overexpression does not induce cell death but alters the cell cycle status of hematopoietic progenitor cells. This study enhances our understanding of how Gadd45 functions during myeloid cell development. Significance StatementO_LILoss of Gadd45 causes a reduction in crystal cells but does not significantly impact macrophage-like plasmatocyte differentiation. C_LIO_LIGadd45 overexpression causes myeloid-type progenitor cells to differentiate into lamellocyte, as well as plasmatocyte transdifferentiate to lamellocyte. Gadd45 triggers differentiation by activating a combination of Toll, JNK, and JAK/STAT signaling pathways. C_LIO_LIOverexpressing Gadd45 does not induce apoptosis but alters the cell cycle behavior of hematopoietic progenitor cells. C_LI

developmental biology↗

bioRxiv2025

Decoding Rice Seed Storage Proteins: From Gene Identification to Structural Prediction

Rice seed storage proteins (SSPs) serve as the primary source of dietary protein, energy, and nutrition; however, our understanding of these proteins remains limited, hindering efforts aimed at enhancing grain nutritional quality. To address this, we conducted a comprehensive genome-wide analysis of rice SSPs, encompassing phylogenetic relationships, domain and motif characterization, promoter cis-element mapping, expression profiling, and 3D structural modeling. Through homology- and domain-based searches, we identified 65 SSP-encoding genes, including 19 previously uncharacterized members. Phylogenetic analysis and domain comparisons revealed evolutionary proximity between albumins and prolamins; and between globulins and glutelins. Albumins, glutelins and prolamins clustered tandemly implying that duplication has driven SSP expansion. Transcriptomic evidence indicated that albumins, globulins, and glutelins were transcriptionally active from S2 seed development stage, whereas prolamins initiated expression from S3 stage. Promoter analysis revealed several seed-specific cis-regulatory elements, with CAATBOX1, EBOXBNNAPA, and DOFCOREZM being the most prevalent. Structural modeling showed that albumins and prolamins predominantly adopted -helical conformations, whereas globulins and glutelins were enriched in {beta}-strands and coils. This integrated analysis offers valuable insights into the classification, evolution, regulation, and structure of rice SSPs, providing a foundational resource for advancing grain nutritional improvement strategies.

plant biology↗

bioRxiv2025

A pan-gene catalogue of Asian cultivated rice

The rice genome underpins fundamental research and breeding, but the Nipponbare (japonica) reference does not fully encompass the genetic diversity of Asian rice. To address this gap, the Rice Population Reference Panel (RPRP) was developed, comprising high-quality assemblies of 16 rice cultivars to represent japonica, indica, aus, and aromatic varietal groups. The RPRP has been consistently annotated, supported by extensive experimental data and here we report the computational assignment, characterization and dissemination of stably identified pan-genes. We identified 25,178 core pan-genes shared across all cultivars, alongside cultivar-specific and family-enriched genes. Core genes exhibit higher gene expression and proteomic evidence, higher confidence protein domains and AlphaFold structures, while cultivar-specific genes were enriched for domains under selective breeding pressure, such as for disease resistance. This resource, integrated into public databases, enables researchers to explore genetic and functional diversity via a population-aware "reference guide" across rice genomes, advancing both basic and applied research.

genomics↗

bioRxiv2024

A novel repressor-activator-competitor module comprising C2H2 zinc finger and NAC transcription factors regulates rice grain development

Grain size and quality are crucial agronomic traits. We have characterized a seed-preferential C2H2 zinc finger transcriptional repressor, ZOS1-15. Its overexpression, knock-down and knock-out plants indicated a negative control over grain size due to altered cell expansion. ZOS1-15 homodimerized and directly interacted with co-repressor TOPLESS and histone deacetylases to form a repression complex. ZOS1-15 also interacted with Mediator subunit MED14_1 and a seed-preferential transcriptional activator, ONAC024, with three alternatively spliced isoforms. The ectopic expression of ONAC024 negatively affected plant growth and development. Seed-preferential overexpression and knock-down plants showed ONAC024 as a positive regulator of grain length due to increased cell proliferation and expansion. CRES-T generated transgenic rice plants indicated a functional divergence amongst ONAC024 isoforms. Tandem interactions were observed between ONAC024-ONAC023-ONAC026-ONAC020. ZOS1-15 and ONAC024 functioned antagonistically to regulate grain amylose and SSP accumulation while ONAC023 affected only amylose. ZOS1-15 and ONAC024 directly regulated the expression of two SSP encoding genes. Binding of ONAC024 was competed by ONAC025-MADS29 complex. The seed-preferential overexpression of SS1/ ONAC025 resulted in decreased grain size and amylose content, but higher yield. This study proposes a repressor-activator-competitor module, wherein ZOS1-15, ONAC024, ONAC023, ONAC025 along with their interactors synergistically and antagonistically regulate multiple aspects of rice grain development.

plant biology↗

bioRxiv2024

A zinc finger transcriptional repressor ZOS5-09 regulates rice grain size, starch and protein biosynthesis

HighlightA rice seed-preferential transcriptional repressor, ZOS5-09 controls grain size by affecting cell proliferation and expansion; and regulates starch and protein biosynthesis. It acts as a repressor by deacetylation. Grain size is the one of the key determinants of grain yield. Transcription factors form an important class of regulatory proteins that play crucial roles in regulating developmental responses. Our study focuses on a novel seed-preferential C2H2 zinc finger transcription factor, ZOS5-09 (LOC_Os05g38600) that plays an important role in regulating grain related traits in rice. Rice plants with ZOS5-09 promoter::GUS construct showed its high expression in rice endosperm. In planta reporter effector assays and localization studies showed that ZOS5-09 is a nuclear localized transcriptional repressor. It has a C-terminal NoRS (nucleolar retention signal). Ectopic and seed-preferential overexpression of ZOS5-09 resulted in lethality. Seed-preferential overexpression without NoRS was detrimental to grain filling. Rice plants with knock-down or CRISPR based knock-out of ZOS5-09 displayed reduced grain length and weight but increased grain width. Plant height, second leaf width, and panicle number were reduced and second leaf length were increased. The change in grain size was due to lower cell proliferation and increased cell size in the transverse direction due to down regulation of cell cycle related genes and increased expression of expansins. Decreased expression of ZOS5-09 also resulted in reduced total starch and protein content and higher endosperm chalkiness, thus, negatively affecting grain quality. ZOS5-09 directly regulated a seed storage protein encoding gene, GLU6 by binding to the zinc finger binding site in its promoter. It acted as a repressor by promoting deacetylation upon interaction with a histone deacetylase. In summary, our results indicate that optimum expression of ZOS5-09 is essential for proper rice grain development. Our study highlights the role of a transcriptional repressor in regulating rice grain traits and improves our understanding of the transcriptional regulatory networks affecting grain size.

plant biology↗

bioRxiv2023

Post-GWAS Prioritization of Genome-Phenome Associations in Sorghum

Genome-Wide Association Studies (GWAS) are widely used to infer the genetic basis of traits in organisms, yet selecting appropriate thresholds for analysis remains a significant challenge. In this study, we developed the Sequential SNP Prioritization Algorithm (SSPA) to elucidate the genetic underpinnings of two key phenotypes in Sorghum bicolor: maximum canopy height and maximum growth rate. Utilizing a subset of the Sorghum Bioenergy Association Panel cultivated at the Maricopa Agricultural Center in Arizona, our objective was to employ GWAS with specific permissive-filtered thresholds to identify the genetic markers associated with these traits, allowing for a broader collection of explanatory candidate genes. Following this, our proposed method incorporates a feature engineering approach based on statistical correlation coefficient to reveal patterns between phenotypic similarity and genetic proximity across 274 accessions. This approach helps prioritize Single Nucleotide Polymorphisms (SNPs) likely to be associated with the studied phenotype. Additionally, we evaluated the impact of SSPA by considering all variants (SNPs) as inputs, without any GWAS filtering, as a complementary analysis. Empirical evidence including ontology- based gene function, spatial and temporal expression, and similarity to known homologs, demonstrated that SSPA effectively prioritizes SNPs and genes influencing the phenotype of interest, providing valuable insights for functional genetics research.

genomics↗

bioRxiv2023

Transcriptional modulation during photomorphogenesis in rice seedlings

Light is one of the most important factors regulating plant gene expression patterns, metabolism, physiology, growth, and development. To explore how light may induce or alter transcript splicing, we conducted RNA-Seq-based transcriptome analyses by comparing the samples harvested as etiolated seedlings grown under continuous dark conditions vs. the light-treated green seedlings. We identified 14,766 differentially expressed genes, of which 4369 genes showed alternative splicing. We observed that genes mapped to the plastid-localized methyl-erythritol-phosphate (MEP) pathway were light-upregulated compared to the cytosolic mevalonate (MVA) pathway genes. Many of these genes also undergo splicing. These pathways provide crucial metabolite precursors for the biosynthesis of secondary metabolic compounds needed for chloroplast biogenesis, the establishment of successful photosynthetic apparatus, and photomorphogenesis. In the chromosome-wide survey of the light-induced transcriptome, we observed intron retention as the most predominant splicing event. In addition, we identified 1709 novel lncRNA transcripts in our transcriptome data.

plant biology↗

bioRxiv2023

Comparative Analysis of Salinity Response Transcriptomes in Salt-Tolerant Pokkali and Susceptible IR29 Rice

Rice is a major cereal crop responsible for feeding the worlds population. To improve grain yield and quality, meet growing demand, and face the challenges posed by abiotic and biotic stress, it is imperative to explore genetic diversity in rice for candidate genes and loci that may contribute to stress tolerance. High salinity abiotic stress in the rice growth environment affects growth, yield, and quality. Therefore, we conducted a salt stress-responsive RNA-Seq-based transcriptome study of two rice (Oryza sativa) varieties, the salt-tolerant Pokkali and the salt-sensitive breeding line IR29. To identify early and late salinity response genes, we collected samples from the treated and untreated plants in this study at 1, 2, 5, 10, and 24 hours after treatment with 300 mM NaCl solution. We identified 7,209 and 6,595 salt-induced differentially expressed transcripts from Pokkali and IR29, respectively, over all time points. We identified [~]190,000 single nucleotide polymorphism (SNP) sites and [~]40,000 simple sequence repeat (SSR) sites, allowing analysis of their consequences on genetic diversity, transcript structure, gene function, and differential expression. We identified and validated the polymorphic SSRs in the differentially expressed salt-responsive genes Respiratory Burst Oxidase Homolog B (RBOHB) and Rice Salt Sensitive 1 (RSS1) that underly nearby salt tolerance QTLs. This study provides insight into transcriptional programming during salt stress, evidence for improving Oryza genome annotations, and reveals SNP and SSR sites associated with differential gene expression and potential gene function.

plant biology↗

bioRxiv2021

Hypoxia induces early neurogenesis in human fetal neural stem cells by activating the WNT pathway.

Fetal neural stem cells (FNSCs) are present in the brain of human fetuses that differentiate into cells of neuronal and glial lineages. Difference in oxygen concentration between maternal and fetal circulation indicates that the developing fetus may be exposed to lower oxygen concentrations compared to adults. This physiological hypoxia may influence the growth and differentiation of the FNSCs. This study aimed to evaluate the effect of hypoxia on the differentiation potential of human FNSCs isolated from the sub-ventricular zone of aborted fetal brains (n=5). FNSCs were isolated, expanded, and characterized by Nestin and Sox2 expression, using immunocytochemistry and flowcytometry respectively. These FNSCs were exposed to 20% oxygen (normoxia) and 0.2% oxygen (hypoxia) concentrations for 48 hours, and hypoxia exposure (n=5) was evaluated by a panel of markers (CA9, PGK1 and VEGF). Whole human genome transcriptomic analyses (Genespring GX13) of FNSCs exposed to hypoxia (Agilent 4x44K human array slides), highlighted that genes associated with neurogenesis were getting enriched. The pathway analysis of these enriched genes (using Metacore) showed that WNT signaling played a role in determining the cell fate of FNSCs exposed to hypoxic environment. Microarray analyses was validated using neuronal and glial lineage commitment markers such as Ngn1, Ngn2, ASCL1, DCX, GFAP, Olig2 and Nkx2.2 using qPCR (n=9). This demonstrated upregulation of the neuronal commitment markers on hypoxia exposure, while no change was observed in astrocytic and oligodendrocyte lineage commitment markers. Increased expression of downstream targets of the WNT signaling pathway, TCF4 and ID2, by qPCR (n=9), indicated its involvement in mediating neuronal differentiation on exposure to hypoxia.

neuroscience↗

bioRxiv2021

Human fetal neural stem cell-derived astrocytes maintain glutamate transport after hypoxic injury in vitro

Astrocytes are the most abundant glial cells that play many critical roles in the central nervous system physiology including the uptake of excess glutamate from the synapse by Excitatory Amino Acid Transporters (EAATs). Among the EAATs, EAAT2 are predominantly functional, astrocyte-specific glutamate transporters in the forebrain. Hypoxic brain injury is a pathological phenomenon seen in various clinical conditions including stroke and neonatal hypoxic ischemic encephalopathy. Glutamate excitotoxicity is an important cause of neuronal cell death in disorders involving hypoxic brain injury. As findings from rodent models cannot always be reliably extrapolated to humans, we aimed to develop a homogenous population of primary human astrocytes to study the effect of hypoxic injury on astrocyte function, especially glutamate uptake. We successfully isolated, established and characterized cultures of human fetal neural stem cells (FNSCs) from aborted fetal brains. FNSCs were differentiated into astrocytes, and characterized by increased expression of the astrocyte markers, glial fibrillary acidic protein (GFAP), EAAT1 and EAAT2. A concomitant decrease in neural stem cell marker, Nestin, was observed. Differentiated astrocytes were exposed to various oxygen concentrations mimicking normoxia (20% and 6%), moderate and severe hypoxia (2% and 0.2% respectively). Interestingly, no change was observed in the expression of glutamate transporter, EAAT2 and glutamate uptake by astrocytes, even after exposure to hypoxia. Our novel model of human FNSC derived astrocytes exposed to hypoxic injury, establishes that astrocytes are able to maintain glutamate uptake even after exposure to severe hypoxia for 48 hours, and thus provides evidence for the neuroprotective role of astrocytes in hypoxic injury.

neuroscience↗

bioRxiv2020

Chia (Salvia hispanica) gene expression atlas elucidates dynamic spatio-temporal changes associated with plant growth and development

Chia (Salvia hispanica L.), now a popular superfood, is one of the richest sources of dietary nutrients such as protein, fiber, and polyunsaturated fatty acids. At present, the genomic and genetic information available in the public domain for this crop is scanty, which hinders understanding its growth and developmental processes and impedes genetic improvement through genomics-assisted methods. We report RNA-seq based comprehensive transcriptome atlas of Chia across 13 different tissue types covering vegetative and reproductive growth stages. We generated [~]394 million raw reads from transcriptome sequencing, of which [~]355 million high-quality reads were used to generate de novo reference transcriptome assembly and the tissue-specific transcript assemblies. After quality assessment of merged assemblies and using redundancy reduction methods, 82,663 reference transcripts were identified. Of these, 53,200 transcripts show differential expression in at least one sample and provide information on spatio-temporal modulation of gene expression in Chia. We identified genes involved in the biosynthesis of omega-3 and omega-6 polyunsaturated fatty acids, and various terpenoid compounds. The study also led to the identification of 633 differentially expressed transcription factors from 53 gene families. The coexpression analysis suggested that members of the B3, bZIP, ERF, WOX, AP2, MYB, C3H, EIL, LBD, DBB, Nin-like, and HSF transcription factor gene families play key roles in the regulation of target gene expression across various developmental stages. This study also identified 2,411 simple sequence repeat (SSRs) as potential genetic markers residing in the transcribed regions. The transcriptome atlas provides essential genomic resources for basic research, applications in plant breeding, and annotation of the Chia genome.

genomics↗

bioRxiv2019

Loss of premature stop codon in the Wall-Associated Kinase 91 (OsWAK91) gene confers sheath blight disease resistance in rice

The genetic arms race between pathogen and host plant is a tug of war that has been ongoing for millennia. The \"battles\" are those of disruption, restoration of signaling and information transmission on a subcellular level. One such battle occurs between rice an important crop that feeds 50% of the world population and the sheath blight disease (SB) caused by the fungus Rhizoctonia solani. It results in 10{square}30% global yield loss annually and can reach 50% under severe outbreak. Many Receptor{square}like kinases (RLKs) are recruited as soldiers in these battles. Wall Associated Receptor Kinases (WAKs) a subfamily of receptor-like kinases have been shown to play a role in fungal defense. Here we show that rice gene OsWAK91, present in the major SB resistance QTL region on Chromosome{square}9 is a key component in defense against rice sheath blight. An SNP mutation C/T separates susceptible variety, Cocodrie (CCDR) from the resistant line MCR010277 (MCR). The resistant allele C results in the stop codon loss that results in 68 amino acids longer C{square}terminus carrying longer protein kinase domain and phosphorylation sites. Our genotype and phenotype analysis of the top 20 individuals of the double haploid SB population shows a strong correlation with the SNP. The susceptible allele appears as a recent introduction found in the japonica subspecies reference genome and a majority of the tropical and temperate japonica lines sequenced by the 3000 rice genome project. Multiple US commercial varieties with japonica background carry the susceptible allele and are known for SB susceptibility. This discovery opens the possibility of introducing resistance alleles into high yielding commercial varieties to reduce yield losses incurred by the disease.

plant biology↗

bioRxiv2018

Intronic miRNA Mediated Gene Expression Regulation Controls Protein Crowding Inside the Cell

SUMMARYGene regulatory effects of microRNAs at a posttranscriptional level has been established over the last decade. In this study, we analyze the interaction networks of mRNA translation regulation through intronic miRNA, under various tissue-specific cellular contexts, taking into account the thermodynamic affinity, kinetics, and the presence of competitive interactors. This database, and analysis has been made available through an open-access web-server, miRiam, to promote further exploration.\n\nHere we report that expression of genes involved in Apoptosis Processes, Immune System Processes, Translation Regulator Activities, and Molecular Transport Activities within the cell are predominately regulated by miRNA mediation. Our findings further indicate that this regulatory effect has a profound effect in controlling protein crowding inside the cell. A miRNA mediated gene expression regulation serves as a temporal regulator, allowing the cellular machinery to temporarily pause the translation of mRNA, indicating that the miRNA-mRNA interactions may be important for governing the optimal usage of cell volume.

bioinformatics↗