Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1008684 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25744652_1.fastq.gz | Fastqsanger.gz | |||
| SRR25744652_2.fastq.gz | Fastqsanger.gz | |||
| SRR25744653_1.fastq.gz | Fastqsanger.gz | |||
| SRR25744653_2.fastq.gz | Fastqsanger.gz | |||
| SRR25744654_1.fastq.gz | Fastqsanger.gz |
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Project description:Cupriavidus metallidurans CH34 is a metal resistant beta-proteobacterium. The genome of this bacterium contain many genes involved in heavy metal resistance. Gene expression of C. metallidurans was studied after the addition of of Zn(II), Cd(II), Cu(II), Ni(II), Pb(II), Hg(II) or Co(II). Keywords: Heavy metal stress response Cultures of C. metallidurans CH34 were grown at 30°C until OD reached 0.6 (mid- exponential phase cultures). Heavy metals (0.8 mM of Zn(II), 0.5 mM of Cd(II), 0.1 mM of Cu(II), 0.6 mM of Ni(II), 0.4 mM of Pb(II), 5 uM of Hg(II) and 0.5 mM of Co(II)) were added to the culture for 30 minutes induction time. Total RNA was extracted, reverse-transcribed and labeled with Cy3-dCTP for the control (without metal) and with Cy5-dCTP for each conditions (challenged with one metal). Labeled cDNA were (control and one condition) added to a spotted slide for overnight hybridization at 42°C. Slides were scanned with a laser at 532 and 635 nm.
2010-06-11 | E-GEOD-7272 | biostudies-arrayexpress
Project description:We hypothesize that microarray-based analysis of Lycopersicon esculentum is a sensitive tool for the early detection of potential toxicity of heavy metals, as well as an effective tool for identifying the heavy metal-specific genes. To test the hypothesis, the Agilent whole-genome cDNA microarrays were used to assess the effects of heavy metal on L. esculentum at relatively low concentrations (1/10 LC50 of heavy metals). Results showed that the characteristic gene expression profiles induced by Cd, Cr, Hg and Pb were not only distinct from the control but also distinct from one another, demonstrating the feasibility of discriminating between the effects of these four heavy metals present at relatively low concentrations. Moreover, heavy metal-specific genes were identified by microarray analysis. These findings support the above hypothesis.
2014-11-06 | GSE63024 | GEO
Project description:Heavy metals residue in the natural ecosystem had become one global environmental problem that was eager to solve. Due to the non-biodegradability, organism could deposit excessive heavy metals elements into tissues. Existing literature proposed that prolonged heavy metals enrichment had comprehensive toxicity to multi-organs of vertebrates. However, little research focus on the molecular mechanism for the hepatotoxicity of heavy metal enrichment to Chiroptera. In the present study, ten Hipposideros armiger individuals from Yingde City (YD, relatively pollution-free) and Chunwan City (CW, excessive heavy metals emission) were dissected while environment samples were also obtained. To corroborate the toxicity mechanism of heavy metals to bats liver, multi-omics, pathology and molecular biology methods were performed. Our results showed that more Cd and Pb elements were significantly enriched in bats liver and food sources in the CW group. In addition, prolonged heavy metals accumulation disturbed the hepatic transcription profiling associated with solute carriers family, ribosome pathway, ATP usage and heat shock proteins. Excessive heavy metals enrichment also altered the relative abundance of typical gut microbe taxa to inhibit the tight-junction protein expression. We also found that the levels of superoxide dismutase, glutathione peroxidase and glutathione were decreased while ROS density and malondialdehyde content were elevated after excessive heavy metals enrichment. Besides, hepatic fat accumulation and inflammation injury were also observed under the excessive heavy metals enrichment while the metabolism biomarkers contents were decreased. Therefore, prolonged heavy metals enrichment would induce a series of hepatotoxicity by disturbing the microbes-gut-liver axis and hepatic transcription modes, which could decrease the overall metabolism level in bats. Our study provided protection strategy for biodiversity conservation and raised public attention to environment pollution.
2024-01-28 | GSE254017 | GEO
Project description:We hypothesize that microarray-based analysis of Lycopersicon esculentum is a sensitive tool for the early detection of potential toxicity of heavy metals, as well as an effective tool for identifying the heavy metal-specific genes. To test the hypothesis, the Agilent whole-genome cDNA microarrays were used to assess the effects of heavy metal on L. esculentum at relatively low concentrations (1/10 LC50 of heavy metals). Results showed that the characteristic gene expression profiles induced by Cd, Cr, Hg and Pb were not only distinct from the control but also distinct from one another, demonstrating the feasibility of discriminating between the effects of these four heavy metals present at relatively low concentrations. Moreover, heavy metal-specific genes were identified by microarray analysis. These findings support the above hypothesis. A total of fifteen microarrays (4*44K tomato gene expression microarray; G2519F-022270) were used to hybridize with RNA extracted from Cd-, Cr-, Hg-, Pb-treated and the untreated roots (control) of Lycopersicon esculentum. Each treatment was carried out for three replicates. A total of thirty seedlings were used for each treatment. Root samples from ten seedlings randomly selected from each Petri dish were pooled together to obtain three biological replicates.
2014-11-06 | E-GEOD-63024 | biostudies-arrayexpress
Project description:Environmental contamination from heavy metals poses a global concern for the marine environment, as heavy metals are passed up the food chain and persist in the environment long after the pollution source is contained. Cnidarians, dating back to 700 million years ago, play an important role in shaping marine ecosystems, but environmental pollution profoundly affects their vitality. Among the cnidarians, the sea anemone Nematostella vectensis is an advantageous model for addressing questions in molecular ecology and toxicology as it tolerates extreme environments and its genome has been published. Here we employed a transcriptome-wide RNA-Seq approach to analyze N.vectensis molecular defense mechanisms against four heavy metals: Hg, Cu, Cd and Zn. Altogether, more than 5000 transcripts showed significant changes in gene expression, with Hg having the greatest impact on up-regulating transcripts, followed by Cu, Cd and Zn. We identified, for the first time, co-up-regulation of immediate-early transcription factors such as Egr1, AP1 and NF-κB. Time-course analysis of these genes revealed their early expression as rapidly as one hour after exposure to heavy metals, suggesting that they may complement or substitute for the roles of the metal mediating Mtf1 transcripton factor. We further characterized regulation of a large array of stress-response gene families including Hsp, ABC, CYP members and phytochelatin synthase that may regulate synthesis of the metal-binding phytochelatins instead of the methallothioneins that are absent from Cnidaria genome. This study provides mechanistic insight into heavy-metal toxicity in N.vectensis and sheds light on ancestral stress adaptations. 4 metals were tested in triplicates in comparison to control (4 replicates)
2015-12-22 | E-GEOD-58769 | biostudies-arrayexpress
Project description:Cupriavidus metallidurans CH34 is a metal resistant beta-proteobacterium. The genome of this bacterium contain many genes involved in heavy metal resistance. Gene expression of C. metallidurans was studied after the addition of of Zn(II), Cd(II), Cu(II), Ni(II), Pb(II), Hg(II) or Co(II). Keywords: Heavy metal stress response
2007-03-16 | GSE7272 | GEO
Project description:Environmental contamination from heavy metals poses a global concern for the marine environment, as heavy metals are passed up the food chain and persist in the environment long after the pollution source is contained. Cnidarians, dating back to 700 million years ago, play an important role in shaping marine ecosystems, but environmental pollution profoundly affects their vitality. Among the cnidarians, the sea anemone Nematostella vectensis is an advantageous model for addressing questions in molecular ecology and toxicology as it tolerates extreme environments and its genome has been published. Here we employed a transcriptome-wide RNA-Seq approach to analyze N.vectensis molecular defense mechanisms against four heavy metals: Hg, Cu, Cd and Zn. Altogether, more than 5000 transcripts showed significant changes in gene expression, with Hg having the greatest impact on up-regulating transcripts, followed by Cu, Cd and Zn. We identified, for the first time, co-up-regulation of immediate-early transcription factors such as Egr1, AP1 and NF-κB. Time-course analysis of these genes revealed their early expression as rapidly as one hour after exposure to heavy metals, suggesting that they may complement or substitute for the roles of the metal mediating Mtf1 transcripton factor. We further characterized regulation of a large array of stress-response gene families including Hsp, ABC, CYP members and phytochelatin synthase that may regulate synthesis of the metal-binding phytochelatins instead of the methallothioneins that are absent from Cnidaria genome. This study provides mechanistic insight into heavy-metal toxicity in N.vectensis and sheds light on ancestral stress adaptations.
2015-12-22 | GSE58769 | GEO
Project description:Our main objective was to study the changes in cDNA microarray gene expression profiles of E. coli cells exposed to different doses of a polymetallic solution containing Ag (I), Pb (II), Cd (II), Cu (II), Ni (II) and Zn (II)) over three exposure times (5, 10 and 15 minutes). Control cells grown in the absence of metals were also included in the experiment.
2013-10-31 | E-MTAB-2023 | biostudies-arrayexpress