Microarray based differential transcriptomics study to understand arsenic-thiourea interaction in rice.
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE71492 | GEO | 2015/09/15
SECONDARY ACCESSION(S): PRJNA291391
REPOSITORIES: GEO
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Project description:In our earlier study, thiourea has been shown to improve the growth of rice and reduce the arsenic load from aerial parts of the seedlings. We have also shown the applicability of thiourea to delineate the redox regulatory mechansisms under arsenic stress in rice. To move further, present microarray was performed to reveal the involvement of overall gene and regulatory netwrok under arsenic with/without thiourea treatment in rice. Agilent custom one-color experiment,Organism:Oryza sativa, Whole Genome Rice 8x60k (AMADID: 064722) designed by Genotypic Technology Private Limited.
2015-09-15 | E-GEOD-71492 | biostudies-arrayexpress
Project description:Arsenic (As) is highly toxic element to all forms of life and is a major environmental contaminant. Understanding acquisition, detoxification, and adaptation mechanisms in bacteria that are associated with host in arsenic-rich conditions can provide novel insights into dynamics of host-microbe-microenvironment interactions. In the present study, we have investigated an arsenic resistance mechanism acquired during the evolution of a particular lineage in the population of Xanthomonas oryzae pv. oryzae (Xoo), which is a serious plant pathogen infecting rice. Our study revealed the horizontal acquisition of a novel chromosomal 12kb ars cassette in Xoo IXO1088 that confers high resistance to arsenate/arsenite. The ars cassette comprises several genes that constitute an operon induced in the presence of arsenate/arsenite. This cassette has spread in lineage with highly virulent strains owing to a particular lineage’s evolutionary success. Further, we performed the transcriptomic analysis of Xoo strain IXO1088 under arsenate/arsenite exposure using RNA sequencing. The transcriptomic analysis revealed that arsenic detoxification and efflux, oxidative stress response, iron acquisition/storage, and damage repair are the main cellular responses to arsenic exposure. The study provides useful insights into the acquisition, detoxification, and adaptation mechanisms among Xoo populations to adapt under arsenic-rich environmental conditions.
2021-05-17 | GSE163417 | GEO
Project description:RNA from stem containing first node and internodes during dough stage was considered for the above purpose. Satabdi, (popularly known as Minikit) most popular cultivar of West Bengal and Palman, another high yielding variety were considered for microarray analysis for comparison to each other. Two rice genotypes were grown in identical conditions (same field with contaminated ground water) to obtain the most meaningful conclusion. Dough stage was considered as variation in arsenic accumulation among the genotypes starts during dough stage to maturity. Plant tissues were collected from stem for transcriptomic analysis as expression profiling of such tissue in response to arsenic would be most useful as arsenic transport/loading in grain was assumed to be controlled by arsenic translocation behavior at inter vascular level or from xylem to phloem. Satabdi accumulates more than twice of arsenic in brown rice (0.346 mg/kg) than that of Palman (0.156 mg/kg) whereas accumulation in straw (2.07 mg/kg) was approximately less than half of the Palman (4.491 mg/kg)
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Project description:The Atlantic killifish (Fundulus heteroclitus), native to estuarine areas of the Atlantic coast of the United States, has become a valuable ecotoxicological model due to its ability to acclimate to rapid environmental changes and adapt to polluted habitats. Killifish respond to rapid increases in salinity with an immediate change in gene expression, as well as long-term remodeling of the gills. Arsenic, a major environmental toxicant, was previously shown to inhibit the ability of killifish gill to respond to a rapid increase in salinity. We characterized miRNA expression in killifish gill under salinity acclimation with and without arsenic and identified a small group of highly expressed, well-conserved miRNAs as well as 16 novel miRNAs not yet identified in other organisms.
2018-12-26 | GSE118062 | GEO
Project description:Arsenic is environmental risk factor and has been linked to urothelial carcinoma incidence. Arsenic exposure-induced malignant transformed cells was established from normal urothelial cells by chronic arsenic exposure for 10 months. The purpose of the present study is to elucidate the relevant molecular alterationon on arsenic-induced malignant transformation.
2016-11-19 | GSE90023 | GEO
Project description:Arsenic (As) bioavailability in the rice rhizosphere is influenced by many microbial interactions, particularly by metal-transforming functional groups at the root-soil interface. This study was conducted to examine As-transforming microbes and As-speciation in the rice rhizosphere compartments, in response to two different water management practices (continuous and intermittently flooded), established on fields with high to low soil-As concentration. Microbial functional gene composition in the rhizosphere and root-plaque compartments were characterized using the GeoChip 4.0 microarray. Arsenic speciation and concentrations were analyzed in the rhizosphere soil, root-plaque, porewater and grain samples. Results indicated that intermittent flooding significantly altered As-speciation in the rhizosphere, and reduced methyl-As and AsIII concentrations in the pore water, root-plaque and rice grain. Ordination and taxonomic analysis of detected gene-probes indicated that root-plaque and rhizosphere assembled significantly different metal-transforming functional groups. Taxonomic non-redundancy was evident, suggesting that As-reduction, -oxidation and -methylation processes were performed by different microbial groups. As-transformation was coupled to different biogeochemical cycling processes establishing functional non-redundancy of rice-rhizosphere microbiome in response to both rhizosphere compartmentalization and experimental treatments. This study confirmed diverse As-biotransformation at root-soil interface and provided novel insights on their responses to water management, which can be applied for mitigating As-bioavailability and accumulation in rice grains.
2021-07-12 | GSE179671 | GEO
Project description:Arsenic is a carcinogen that is known to induce cell transformation and tumor formation. Although studies have been performed to examine the modulation of signaling molecules caused by arsenic exposure, the molecular mechanisms by which arsenic causes cancer are still unclear. We hypothesized that arsenic alters gene expression leading to carcinogenesis in the lung. In this study, we examined global gene expression in response to 0.75 µM arsenic treatment for 1-7 days in a rat lung epithelial cell line (L2) using an in-house 10k rat DNA microarray. One hundred thirty one genes were identified using the one-class statistical analysis of microarray (SAM) test. Of them, 33 genes had a fold change of ≥ 2 at least between two time points. These genes were then clustered into 5 groups using K-means cluster analysis based on their expression patterns. Seven selected genes, all associated with cancer, were confirmed by real-time PCR. These genes have functions directly or indirectly related to metabolism, glycolysis, cell proliferation and differentiation, and regulation of transcription, all of which may be involved in neoplastic transformation of cells. Our findings provide important insight for the future studies of arsenic-mediated lung cancer. Keywords: Lung, aresenic, L2, micorarray
2011-12-23 | GSE9790 | GEO
Project description:Arsenic (As) is a carcinogenic metalloid that is a contaminant widely polluting rice paddy soils around the world. In order to gain better insight into molecular mechanism of rice exposed to As(III) stress, we used next-generation sequencing technology to acquire global transcriptome alteration and miRNA regulation in rice upon As(III) treatments. Our results suggest time course and As(III)-dosing treatments were devised. Cluster analyses show that root and shoot samples were differentially grouped. For roots, sub-clusters were more distinct in the dosage course whereas for shoots they were most recognizable for the time course treatments. Other than the significantly regulated gene expression in the heavy metal-responsive sulfur and glutathione metabolism pathways, the expression of genes related to heavy metal transportation, jasmonate biosynthesis and signaling pathways, lipid metabolism and gene transcription were sharply regulated, indicating that rice allocates energy and resources from growth to stress response under As(III) stress. In addition to the detection of previously identified stress-related miRNAs, we further discovered 36 new As(III)-responsive miRNAs. These results expand our understanding of As(III) stress mechanism to the As(III)-responsive mRNA and miRNA transcriptomes, which provide a foundation for subsequent functional research. 10 mRNA samples examined 10 miRNA samples examined
2013-01-09 | E-GEOD-36696 | biostudies-arrayexpress
Project description:Talemi2014 - Arsenic toxicity and
detoxification mechanisms in yeast
The model implements arsenite (AsIII)
transport regulation, its distribution within main cellular AsIII
pools and detoxification. The intracellular As pools considered are
free AsIII (AsIIIin), protein-bound AsIII (AsIIIprot), glutathione
conjugated AsIII (AsGS3) and vacuolar sequestered AsIII (vAsGS3).
This model is described in the article:
Mathematical modelling of
arsenic transport, distribution and detoxification processes in
yeast.
Talemi SR, Jacobson T, Garla V,
Navarrete C, Wagner A, Tamás MJ, Schaber J.
Mol. Microbiol. 2014 Jun; 92(6):
1343-1356
Abstract:
Arsenic has a dual role as causative and curative agent of
human disease. Therefore, there is considerable interest in
elucidating arsenic toxicity and detoxification mechanisms. By
an ensemble modelling approach, we identified a best
parsimonious mathematical model which recapitulates and
predicts intracellular arsenic dynamics for different
conditions and mutants, thereby providing novel insights into
arsenic toxicity and detoxification mechanisms in yeast, which
could partly be confirmed experimentally by dedicated
experiments. Specifically, our analyses suggest that: (i)
arsenic is mainly protein-bound during short-term (acute)
exposure, whereas glutathione-conjugated arsenic dominates
during long-term (chronic) exposure, (ii) arsenic is not stably
retained, but can leave the vacuole via an export mechanism,
and (iii) Fps1 is controlled by Hog1-dependent and
Hog1-independent mechanisms during arsenite stress. Our results
challenge glutathione depletion as a key mechanism for arsenic
toxicity and instead suggest that (iv) increased glutathione
biosynthesis protects the proteome against the damaging effects
of arsenic and that (v) widespread protein inactivation
contributes to the toxicity of this metalloid. Our work in
yeast may prove useful to elucidate similar mechanisms in
higher eukaryotes and have implications for the use of arsenic
in medical therapy.
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BIOMD0000000547.
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2014-09-04 | BIOMD0000000547 | BioModels
Project description:Genetic analysis of women from the Andes Mountains that are exposed to arsenic in drinking water.
| EGAS00001001168 | EGA