Mixed culture metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB11984 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR308997_1.fastq.gz | Fastqsanger.gz | |||
| DRR308997_2.fastq.gz | Fastqsanger.gz | |||
| DRR308998_1.fastq.gz | Fastqsanger.gz | |||
| DRR308998_2.fastq.gz | Fastqsanger.gz |
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Project description:Chromium (Cr) is an important environmental contaminant and also a genotoxic metal ion at high concentration, but its molecular mechanisms and signalling pathways of action in plants is still poorly unraveled. To help characterize the mechanism of molecular and signalling of rice, we present the large-scale, transcriptomic analysis of rice root responses to Cr(VI). We examined the possible involvement of reactive of reactive oxygen species (ROS) and calcium in Cr(VI) signaling transduction pathways, as well as the effect of Cr (VI) on CDPK and MAPK activity. Specially, we used the microarray assay to assess different stage Cr (VI) induced alteration in rice gene expression. This gene discovery effort will help expand our understanding of cellular responses to Cr (VI) treatment, and will identify candidate genes for enhancement of Cr resistance in crop.
2014-12-21 | GSE41733 | GEO
Project description:Chromium (Cr) is a non-essential metal for normal plants and is toxic to plants at high concentration. In spite of many previous studies having been conducted on the effects of Cr stress, the precise molecular mechanisms and signaling pathways of action of Cr remain poorly understood. In this study, the transcriptome at the early of Cr (VI) stress were assayed in rice roots. To gain more insight into these cellular responses, we analyzed whole-genome transcriptome of rice expose to Cr (VI) for 1 and 3 h. Analysis revealed 1,261 and 267 up and down-regulated genes by Cr (VI). Cr (VI) stress triggered changes in transcript levels of genes related to secondary metabolism process, biosynthetic process, specially jasmonic acid biosynthetic process, response to abiotic stress, specially response to toxin, transcription regulator activity, specially transcription factors activity. The most predominant transcription factor families were WRKY, AP2/ERF, NAC, C2H2, MYB. In addition, many protein kinase, including eight MAPKKK, two CDPK, and one MAPK, showed significant increase in transcriptional level under Cr (VI) stress. Molecular mechanisms for the excess Cr(VI) in rice roots Comparison of mock control and rice seedlings treated with 200 M-NM-<M Cr(VI); Biological replicates: 3 control replicates, 3 Cr(VI)-treated replicates.
2013-10-31 | E-GEOD-33376 | biostudies-arrayexpress
Project description:Hexavalent chromium (Cr(VI)) is a highly toxic contaminant, some bacteria are able to transform it to less toxic and less soluble trivalent chromium (Cr(III)). Klebsiella sp. strain AqSCr, isolated from Cr(VI)-polluted groundwater, reduces Cr(VI) both aerobically and anaerobically, and resists up 35 mM of Cr(VI); Subculturing of AqSCr in the presence of Cr(VI) conduces to adaptation. In this study, we performed RNA-Seq of Cr(VI) adapted stage, finding 255 genes upregulated and 240 downregulated with respect to controls without Cr(VI). Genes differentially expressed are mostly associated with oxidative stress response, DNA repair and replication, sulfur starvation response, envelope-osmotic stress response, fatty acid metabolism, ribosomal subunits and energy metabolism. Among them, genes not previously associated with chromium resistance as cybB, encoding a putative superoxide oxidase, gltA2, encoding an alternative citrate synthase, and des, encoding a fatty acid desaturase were upregulated. The alternative sigma factors fecl, rpoE and rpoS were upredgulated in Cr(VI) adapted cells, then they participate in orchestate the Cr(VI)-resistance mechanisms in AqSCr strain
2021-05-20 | GSE160968 | GEO
Project description:Chromium (Cr) is an important environmental contaminant and also a genotoxic metal ion at high concentration, but its molecular mechanisms and signalling pathways of action in plants is still poorly unraveled. To help characterize the mechanism of molecular and signalling of rice, we present the large-scale, transcriptomic analysis of rice root responses to Cr(VI). We examined the possible involvement of reactive of reactive oxygen species (ROS) and calcium in Cr(VI) signaling transduction pathways, as well as the effect of Cr (VI) on CDPK and MAPK activity. Specially, we used the microarray assay to assess different stage Cr (VI) induced alteration in rice gene expression. This gene discovery effort will help expand our understanding of cellular responses to Cr (VI) treatment, and will identify candidate genes for enhancement of Cr resistance in crop. Two-condition experiment, short exposures and long exposures. Comparison of mock control and rice seedlings treated with 50 μM Cr(VI) during short (pooled from 1- and 3-h treatments), as compared to long (24 h) exposures.; Biological replicates: 3 control replicates (short and long exposures), 3 Cr(VI)-treated replicates (short and long exposures).
2014-12-21 | E-GEOD-41733 | biostudies-arrayexpress
Project description:Chromium (Cr) is a non-essential metal for normal plants and is toxic to plants at high concentration. In spite of many previous studies having been conducted on the effects of Cr stress, the precise molecular mechanisms and signaling pathways of action of Cr remain poorly understood. In this study, the transcriptome at the early of Cr (VI) stress were assayed in rice roots. To gain more insight into these cellular responses, we analyzed whole-genome transcriptome of rice expose to Cr (VI) for 1 and 3 h. Analysis revealed 1,261 and 267 up and down-regulated genes by Cr (VI). Cr (VI) stress triggered changes in transcript levels of genes related to secondary metabolism process, biosynthetic process, specially jasmonic acid biosynthetic process, response to abiotic stress, specially response to toxin, transcription regulator activity, specially transcription factors activity. The most predominant transcription factor families were WRKY, AP2/ERF, NAC, C2H2, MYB. In addition, many protein kinase, including eight MAPKKK, two CDPK, and one MAPK, showed significant increase in transcriptional level under Cr (VI) stress. Molecular mechanisms for the excess Cr(VI) in rice roots
2013-10-31 | GSE33376 | GEO
Project description:Hexavalent chromium [Cr(VI)] is an environmental toxicant extensively used in a variety of industrial processes including chrome plating, leather tanning, textile manufacturing, aircraft production, and stainless-steel production. Our previous study showed that exposure to Cr(VI) impaired C2C12 myogenic differentiation in a dose-dependent manner, yet the transcriptional mechanisms underlying Cr(VI)-induced disruption of myogenesis remains poorly understood. Here, we performed bulk RNA-sequencing on C2C12 myoblasts undergoing differentiation in the presence of 0, 2, or 5 µM of Cr(VI). Differential gene expression analysis demonstrated a dose- and time-dependent increase in transcriptional dysregulation. Fuzzy c-means clustering identified 12 distinct gene expression patterns, with Clusters 3, 10, and 12 showing significant overlap with Cr(VI)-regulated genes. Functional enrichment analyses revealed Cr(VI) disrupts genes involved in early-stage cell cycle regulation and DNA repair as well as terminal differentiation processes like sarcomere organization and muscle contraction. Specifically, Cr(VI) impaired expression of key structural and contractile genes and disrupted DNA repair and cell cycle regulatory pathways, including downregulation of p21 and upregulation of proliferative marker PCNA. Furthermore, we identified suppression of Hippo signaling through downregulation of Tead4 and its muscle-specific downstream targets, providing a mechanism for impaired differentiation. These findings highlight widespread alterations in transcriptional programs governing muscle development and maturation, offering insight into how Cr(VI) exposure affects skeletal muscle health.
2025-09-03 | GSE294800 | GEO
Project description:In order to evaluate the mechanisms underlying hexavalent chromium (Cr(VI)) responses, mice and rats were treated with varying concentrations of Cr(VI) in drinking water, as sodium dichromate dihydrate (SDD). Potential transcriptomic responses were evaluated through microarray analysis.
2016-09-24 | GSE87261 | GEO
Project description:In order to evaluate the mechanisms underlying hexavalent chromium (Cr(VI)) responses, mice and rats were treated with varying concentrations of Cr(VI) in drinking water, as sodium dichromate dihydrate (SDD). Potential transcriptomic responses were evaluated through microarray analysis.
2016-09-24 | GSE87259 | GEO
Project description:Chromium (Cr) is a common heavy-metal pollutant that poses a significant threat to both the environment and human health. Herein, a novel strain Lysinibacillus capsici FPHNCRA4-48, with a high Cr tolerance and removal performance, was isolated from Cr-contaminated plant water in Changde, Hunan Province. Structural characterization and proteomic analyses were performed to investigate the Cr removal performance and molecular mechanism of L. capsici FPHNCRA4-48. FPHNCRA4-48 can effectively re-move more than 99% of the Cr(VI) at an initial concentration of 1000 μmol/L. The FTIR, 3D-EEM, and XPS results revealed that -OH, -NH2, and -CO-NH2 derived from extra-cellular polymeric substances (EPSs) were mainly involved in Cr(VI) removal. Interest-ingly, the protein content in the EPS increased significantly (1.32-fold) after exposure to Cr(VI). Moreover, proteomic analysis revealed that genes (rpmA, rpmI, rpmC, rplI, rpmD, deoB, deoC) related to translation and carbohydrate metabolism, and genes (pyk, icd, rpiB, eno) related to amino acid biosynthesis were all significantly up-regulated, suggesting that these pathways related to protein synthesis in L. capsici FPHNCRA4-48 were activated under Cr(VI) stress. Finally, KEGG ribosome pathway enrichment oc-curred. These data highlight the importance of microbial EPSs in bioremediation in Cr-polluted environments. This study identified highly efficient Cr(VI)-removing bac-terial strains and conducted an in-depth analysis of the removal mechanism of their extracellular polymeric substances (EPSs), thereby providing theoretical foundations and technical support for the biological remediation of Cr(VI)-contaminated water bodies.
2026-03-04 | PXD075244 |