Translatome-cd-Analysis of the translatome of Arabidopsis in response to Cadmium stress
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE8061 | GEO | 2007/06/20
SECONDARY ACCESSION(S): PRJNA100893
REPOSITORIES: GEO
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Project description:rs05-08_no - no - Cadmium treatment induces slow but long lasting nitric oxide production in plant tissues. This NO production can be suppressed using the commonly used Nitric Oxide Synthase inhibitor L-NAME. This inhibitor tends to partially alleviate Cd toxicity. This effect is correlated with a strong diminution of Cd content in roots of plants treated both with Cd and L-NAME compared to roots from plants treated with Cd only. The main goal of this study is the identification of transcriptionnal changes caused by Cd-induced nitric oxide, and that could potentially result in enhanced Cd root accumulation. - Germination of surface sterilized seeds was performed on solid MS/2 medium. After 2 weeks, the young plantlets were placed on sand for an additional 3 week period in a controlled environment (8 h photoperiod of 300 umol m-2 s-1, 22degreeC, 70% relative humidity) . Plants of similar rosette diameters were then transfered to an hydroponic culture using the nutritive solution described in [Gravot et al. 2004 FEBS Letters 561:22-28] for an acclimation of 3 days. L-NAME and cadmium treatments were respectively started 1 and 2 hours after the start of illumination and root tissues were collected 24 h later and immediatly frozen in liquid nitrogen before RNA extraction. Treatments were : 1 : control 2 : L-NAME 5 mM 3 : Cd 30 uM 4 : L-NAME 5mM + Cd 30 uM 5 : Cd 15 uM For each condition, 3 independent biological repetitions were conducted. RNA were extracted separatly and checked for quality before pooling together. Keywords: treated vs untreated comparison
2007-05-31 | GSE7945 | GEO
Project description:Purpose: In this study, we have used a translatomic approach by coupling polysome profiling and deep RNA-sequencing to estimate changes in the translatome of antimony-resistant Leishmania parasites Methods: Leishmania tropica promastigotes were stepwise selected for resistance to trivalent antimony. Two different strains were studied, the L. tropica SbIII-sensitive or wildtype strain (WT) and the derived highly resistant strain (HR). After polysome profiling four types of samples were evaluated by deep RNAseq: total mRNA used as input, monosomes (MS), light polysomes (LP), and heavy polysomes (HP). The DESeq2 algorithm was used for differential expression analysis to identify translational changes at the basal level (HR Vs. WT), translational changes to combat the drug (HR+SbIII Vs. HR), and to compare translatomic Vs. transcriptomic changes (HP Vs. Total input) [see overall design section below]. Results: Differential translational analysis (cutoff of fold change ≥ 1.5 and p-value corrected by Benjamini-Hochberg FDR ≤ 0.05) showed that transcripts composition per polysome fraction was different in the resistant strain. It included several upregulated (Up) and downregulated (Down) transcripts. At the basal level, 2431 different transcripts were differentially translated: monosome (Down: 4, Up: 0), light polysomes (Down: 906, Up: 951), and heavy polysomes (Down: 1096, Up: 1064). Under the antimony challenge, 189 different transcripts were differentially translated: monosome (Down: 0, Up: 2), light polysomes (Down: 9, Up: 57), and heavy polysomes (Down: 30, Up: 134). Overall, most of the changes were identified in polysome fraction when compared with monosomes or total transcriptome. Conclusions: Our study shows evidence that translational control has a main role in coordinating the resistance to antimony in Leishmania parasites. We propose a novel model that establishes translational control as a major driver of antimony-resistant phenotypes in Leishmania parasites.
2023-04-04 | GSE173848 | GEO
Project description:rs06-03_cd-mirna - cadmium-mirna - trancriptional and post-transcriptional response to cadmium. - After 5 days of grown in a fresh medium (5% PCV at day0), CdCl2 was added to tested cells (Cad) to a final concentration of 200uM. Nothing was added to control cells (Tem). After 12 and 24 hours of growth +/- cadmium, cells were harvested and frozen in liquid nitrogen. 4 dye-swap - treated vs untreated comparison
2012-03-25 | E-GEOD-36627 | biostudies-arrayexpress
Project description:Metal tolerance is often a result of metal storage or distribution. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, natural variation of metal tolerance in Arabidopsis thaliana was investigated. Substantial variation exists in tolerance of excess copper (Cu), zinc (Zn) and cadmium (Cd). Two accessions, Col-0 and Bur-0, and a recombinant inbred line (RIL) population derived from these parents were chosen for further analysis of Cd and Zn tolerance variation, which is evident at different plant ages in various experimental systems and appears to be genetically linked. Three QTLs, explaining in total nearly 50 % of the variation in Cd tolerance, were mapped. The one obvious candidate gene in the mapped intervals, HMA3, is unlikely to contribute to the variation. In order to identify additional candidate genes the Cd responses of Col-0 and Bur-0 were compared at the transcriptome level. The sustained common Cd response of the two accessions was dominated by processes implicated in plant pathogen defense. Accession-specific differences suggested a more efficient activation of acclimative responses as underlying the higher Cd tolerance of Bur-0. The second hypothesis derived from the physiological characterization of the accessions is a reduced Cd accumulation in Bur-0. The microarray analysis was used to identify candidate genes for Cd-tolerance and -accumulation differences between the accessions Bur-0 and Col-0 as well as to analyse the expressional response of A.thaliana to Cd-stress.
2017-07-24 | GSE94314 | GEO
Project description:OsNRAMP5 is involved in iron, manganese and cadmium transport. Goal was to determine the effects of knocking down OsNRAMP5 on global rice gene expression. Two experiments: Control condition experiment: root or shoot of WT vs. OsNRAMP5 RNAi plants. WT Cd treatment experiment: 4 weeks old WT plants grown under 0 or 10uM Cd for two weeks
2012-02-03 | E-GEOD-35502 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE17823: Mouse cardiac tissue, polysomes and monosomes: Vehicle treated control vs. 15mg/kg doxorubicin GSE17826: Mouse cardiac tissue: Vehicle treated control vs. 15mg/kg doxorubicin GSE17830: Mouse cardiac tissue, polysomes and monosomes: Vehicle treated control vs. 25mg/kg DMNQ GSE17915: Mouse cardiac tissue: Vehicle treated control vs. 25mg/kg DMNQ Refer to individual Series
2010-08-05 | E-GEOD-18459 | biostudies-arrayexpress
Project description:Heavy metal cadmium (Cd) affects seriously crop growth, quality and yield, and has potential threats to human safety. We found the difference of two ryegrasses (Lolium multiflorum Lam.), a high-Cd tolerance (LmHC) and a low-Cd tolerance (LmLC) cultivars , in response to cadmium stress. The germination rate, plant growth, and fresh weight of LmHC were much better than that of LmLC. So we use RNA sequencing to investigate the differentially expressed genes(DEGs) about cadmium response between LmHC and LmLC. Real-time quantitative PCR analysis showed that the same DEGs of LmLC and LmHC had obviously difference expression level under Cd treatment. It was suggestion that differential expression of DEGs might be involved in regulating Cd tolerance, accumulation and translocation.These results will be helpful for understanding the underlying molecular mechanism in Cd toxicity and provide references for improving the ecological environment through genetic improvement.
2020-01-30 | GSE144460 | GEO
Project description:Cadmium (Cd) administered to female C57BL/6 mice on gestation day 8 induces a high incidence of anterior neural tube defects (exencephaly). This adverse effect can be attenuated by maternal pretreatment with zinc (Zn). In this study we used replicated microarray analysis to investigate gene expression changes induced in the embryo 5 h after maternal Cd exposure in the absence or presence of Zn pretreatment.
2006-04-11 | E-MEXP-529 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) play crucial roles in regulating the expression of various stress responses genes in plant. To investigate soybean (Glycine max) miRNAs involved in the response to cadmium (Cd), microarrays containing 953 unique miRNA probes were employed to identify differences in the expression patterns of the miRNA between different genotypes, Huaxia3 (HX3, Cd-tolerant) and Zhonghuang24 (ZH24, Cd-sensitive). A total of 26 Cd-responsive miRNAs were identified, of which nine were detected in both cultivars, while five were expressed only in HX3 and 12 were only in ZH24. In the study presented here, four root samples from two contrast soybean cultivars, HX3 (Cd-tolerant) and ZH24 (Cd-sensitive), with or without (Cd) cadmium, harvested at 6, 12, 24, 48, 96 and 144 h after the initiation of Cd treatment, was used to acquire expression profiles of a total of 953 unique genes, leading to the successful construction of supervised.
2013-08-31 | E-GEOD-50388 | biostudies-arrayexpress
Project description:The contamination of agricultural soil by heavy metal cadmium (Cd) poses a significant environmental challenge, affecting crop growth, development and, human health. Previous studies have established the pivotal role of the ZmHMA3 gene, a P-type ATPase heavy metal transporter, in determining variable Cd accumulation in maize grains among 513 inbred lines. To decipher the molecular mechanism underlying mutation-induced phenotypic differences mediated by ZmHMA3, we conducted a quantitative Tandem Mass Tag (TMT)-based proteomic analysis of immature maize kernels. This analysis aimed to identify differentially expressed proteins (DEPs) in wild-type B73 and zmhma3 null mutant under Cd stress. The findings demonstrated that zhma3 accumulated higher levels of Cd compared to B73 when exposed to varying Cd concentrations in the soil. In comparison to low Cd concentration soil, B73 and zmhma3 exhibited 75 and 142 DEPs, respectively, with 24 common DEPs shared between them. Zmhma3 showed a higher induction of upregulated genes related to Cd stres than B73. Amino sugar and nucleotide sugar metabolism were specifically enriched in B73, while phenylpropanoid biosynthesis, nitrogen metabolism, and glyoxylate and dicarboxylate metabolism appeared to play a more significant role in zmhma3. This study provides proteomics insights into unraveling the molecular mechanism underlying the differences in Cd accumulation in maize kernel.
2024-01-26 | PXD047578 | Pride