Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA360249 | ENA |
REPOSITORIES: ENA
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Project description:au14-09_silice - clustop transcriptomics. - Understand and categorize plant mechanisms implicated in the interaction with nanoparticles, both in the phenomena responsible for toxicity as in accommodation, see detoxication. - Phytotoxicity of Cs2[Mo6Br14]@SiO2 nanoparticles and their components, i.e. Cs2[Mo6Br14] clusters and SiO2 nanoparticles, has been studied usign Arabidopsis thaliana cell suspension culture. Cs2[Mo6Br14]@SiO2 nanoparticles used here are composed of 7,5% clusters and 92,5% SiO2. Thus, to compare to the impact of a 100 mg/L Cs2[Mo6Br14]@SiO2 nanoparticle treatment (CS), we also treated Arabidopsis cells with clusters at 7,5 mg/L (C), SiO2 at 92,5 mg/L (S), and combined 7,5 mgCMB/L plus 92,5 mgSiO2/L (C+S).
2017-02-01 | GSE93182 | GEO
Project description:Metal oxide engineered nanoparticles, which are widely used in diverse applications, are known to impact terrestrial plants. These nanoparticles have a potential to induce changes in plant tissue transcriptomes, and thereby the productivity. Here we looked at how the two commonly used nanoparticles, nano-titania (TiO2) and nano-ceria (CeO2) can impact the underlying mechanisms associated plant growth at genome level. We used microarrays to detail the global programme of gene expression underlying various physiological processes associated with growth and development, and identified distinct classes of up-regulated genes during this process. 29 day old Arabidopsis plants were selected for RNA extraction from roots and rosette leaves, followed by hybridization on Affymetrix microarrays. Arabidopsis plants were exposed twice during the germination stage (Days 0 and 4), and once during the primary rosette stage (Day 17), to 500mg/L concentration of nano-titania and nano-ceria, followed by extraction of RNA from 29-day old plant tissues (roots and rosette leaves) for Microarray analysis. 0.1mM KCl was used as control for nano-titania, whereas sterilized millipore water was used as control for nano-ceria.
2016-05-31 | E-GEOD-80461 | biostudies-arrayexpress
Project description:Gold is widely considered to be a biologically inert element; however, it can elicit a profound biological response in plants. Plants can be exposed to significant levels of this precious metal in the environment from naturally occurring sources, as the result of mining activities or more recently resulting from the escalating use of nanoparticles in industry. In this microarray study we have investigated the gene expression response of Arabidopsis thaliana (Arabidopsis) to gold. Although the uptake of metal cations by plant transporters is well characterised, little is known about the uptake of gold, which exists in soil predominantly in a zero-valent state (Au0). We used this study to monitor the expression of candidate genes involved in metal uptake and transport. These show the down-regulation of a discreet number of genes known to be involved in the transport of copper, cadmium, nickel and iron. The experiment comprised three replicate jars of hydropnically-grown Arabidopsis, each treated with 0.125 mM KAuCl4, and three replicate jars of hydropnically-grown Arabidopsis which were treated with water only.
2013-08-01 | E-GEOD-46958 | biostudies-arrayexpress
Project description:Gold is widely considered to be a biologically inert element; however, it can elicit a profound biological response in plants. Plants can be exposed to significant levels of this precious metal in the environment from naturally occurring sources, as the result of mining activities or more recently resulting from the escalating use of nanoparticles in industry. In this microarray study we have investigated the gene expression response of Arabidopsis thaliana (Arabidopsis) to gold. Although the uptake of metal cations by plant transporters is well characterised, little is known about the uptake of gold, which exists in soil predominantly in a zero-valent state (Au0). We used this study to monitor the expression of candidate genes involved in metal uptake and transport. These show the down-regulation of a discreet number of genes known to be involved in the transport of copper, cadmium, nickel and iron.
2013-08-01 | GSE46958 | GEO
Project description:Amorphous silica nanoparticles induce malignant transformation and tumorigenesis of human lung epithelial cells. We used microarrays to detail the global programme of gene expression underlying the cellular malignant transformation induced by amorphous silica nanoparticles and identified distinct classes of up-regulated and down-regulated genes during this process. The human lung epithelial cells, Beas-2B were continuously exposed to 5 μg/mL amorphous silica nanoparticles for 40 passages, and named as BeasSiNPs-P40 (shortly as P40-5 during the further microarray detection). Meanwhile, the passage-matched control Beas-2B cells, named as Beas-P40 (shortly as NC during the further microarray detection).
2016-06-01 | E-GEOD-82062 | biostudies-arrayexpress
Project description:Amorphous silica nanoparticles induce malignant transformation and tumorigenesis of human lung epithelial cells. We used microarrays to detail the global programme of gene expression underlying the cellular malignant transformation induced by amorphous silica nanoparticles and identified distinct classes of up-regulated and down-regulated genes during this process.
2016-06-01 | GSE82062 | GEO
Project description:Metal oxide engineered nanoparticles, which are widely used in diverse applications, are known to impact terrestrial plants. These nanoparticles have a potential to induce changes in plant tissue transcriptomes, and thereby the productivity. Here we looked at how the two commonly used nanoparticles, nano-titania (TiO2) and nano-ceria (CeO2) can impact the underlying mechanisms associated plant growth at genome level. We used microarrays to detail the global programme of gene expression underlying various physiological processes associated with growth and development, and identified distinct classes of up-regulated genes during this process.
2016-05-31 | GSE80461 | GEO
Project description:Gene copy number variation (CNV) is a form of genetic polymorphism that contributes significantly to genome size and function but remains poorly characterized due to technological limitations. Inter-specific comparisons of CNVs in recently diverged plant species are crucial to uncover selection patterns underlying adaptation of a species to stressful environments. Especially given that gene amplifications have long been implicated in emergence of species-specific traits, we conducted a genome-wide survey to identify species-specific gene copy number expansions and deletions in the model extremophile species - Arabidopsis halleri that has diverged in evolutionarily recent time from Arabidopsis thaliana. Cross-species cDNA array based comparative genomic hybridization was employed to compare and identify gene copy number variation in the two sister-species - the metallophyte Arabidopsis halleri and non-metallophyte Arabidopsis lyrata, both relative to Arabidopsis thaliana. We uncovered an unprecedented level of gene copy number polymorphism in Arabidopsis halleri, with a species-specific enrichment of metal homeostasis function in the genes found to be copy number expanded, thus indicating CNV as a mechanism that underlies the key physiological trait of metal hyperaccumulation and hypetolerance in A. halleri.
2016-09-30 | GSE52003 | GEO
Project description:Expansion of nanotechnology will bring many potential benefits as adversely effects on human health. Protection of the human respiratory system from exposure of volatile nanoparticles has become an emerging health concern. The understanding of the biological processes involved in the development and maintenance of a variety of pathologies is improved by genome-wide approaches. Technical feasibility of this type of experiment has perfected in recent years, but data analysis remains challenging. In this context, gene set analysis has emerged as a fundamental tool for the interpretation of the results. We demonstrate how the use of a combination of gene-by-gene and gene set analyses can enhance the interpretation of results. Gene set analyses are able to distinguish responses due to nanoparticle size also discriminating between long and short time recovery after exposure. Transcription regulation and cell proliferation modulation appear to be an early response while oxidative stress and mitochondrial perturbation are late response. Moreover, smaller the particle higher the effect on inflammatory response and DNA damage activation. By integrating the two approaches, we evidenced the importance of MMP1, MMP9, MMP7 and MMP14 genes in response to Ludox® silica nanoparticles and the involvement apoptosis process in cell viability. This study is based on the treatment of A549 cells with two different silica nanoparticles (SM30, 9 nm of diameter, and AS30, 18 nm of diameter). Treatment with nanoparticles were performed independently. We performed three biological replicates for each condition.
2014-09-08 | E-GEOD-53700 | biostudies-arrayexpress