Microbiome assembly corresponding to different substrates influences the trichloroethylene dechlorination performance
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PROVIDER: PRJEB42902 | ENA |
REPOSITORIES: ENA
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Project description:A functional microarray targeting 24 genes involved in chlorinated solvent biodegradation pathways has been developed and used to monitor the gene diversity present in four trichloroethylene (TCE) contaminated sites under ERD (enhanced reductive dechlorination) treatment. The microarray format provided by NimbleGen and used in this study is 12x135K. 2 µg of labelled gDNA from 30 groundwater samples were hybridized on the microarrays.
2012-04-03 | GSE28606 | GEO
Project description:A functional microarray targeting 24 genes involved in chlorinated solvent biodegradation pathways has been developed and used to monitor the gene diversity present in four trichloroethylene (TCE) contaminated sites under ERD (enhanced reductive dechlorination) treatment. The microarray format provided by NimbleGen and used in this study is 12x135K. 2 M-BM-5g of labelled gDNA from 30 groundwater samples were hybridized on the microarrays. A 30-chip study was performed, each chip corresponding to hybridization with 2 M-BM-5g of labelled gDNA retrieved from a monitoring well from one of the four contaminated sites. Each probe (760nt) on the microarray was synthesized in eight replicates, and a total of 5,707 random probes was used to determine the background noise. Groundwater samples were collected from four contaminated sites (B, F, G and H), four monitoring wells per site (P1, P2, P3 and P4). P1: well located upstream to the contamination source. P2: well in the contamination source. P3 and P4: wells located downstream to the contamination source. For site B, the monitoring of ERD demonstration was performed through a total of 5 sampling campaigns: C1 (T=0), C2 (T=104 days), C3 (T=231 days), C4 (T=291 days) and C5 (T=378 days). For the three other sites (F, G and H), only one sampling campaign was performed after the treatment.
2012-04-02 | E-GEOD-28606 | biostudies-arrayexpress
Project description:Fruquintinib DDI Study with P-gp and BCRP Substrates
| 2729773 | ecrin-mdr-crc
Project description:Microbial reductive dechlorination of trichloroethene (TCE) in groundwater often results in the accumulation of dichloroethenes (DCEs). Dehalococcoides mccartyi (Dhc) are the only known bacteria capable of dechlorination beyond DCE to non-toxic ethene. In this study, two newly isolated Dhc strains (11a and 11a5) with dissimilar functional abilities are described. Strain 11a reductively dechlorinates TCE, 1,1-DCE, cis-DCE, trans-DCE, and vinyl chloride (VC) to ethene, while strain 11a5 dechlorinates TCE and all three DCE isomers only to VC. Each of these dechlorination reactions are coupled to growth by these strains. The VC dechlorination rate of strain 11a occurs at a rate of 258 nmol per min per mg of protein, about two times faster than previously reported stains. Strain 11a possesses the vcrA gene while strain 11a5 contains the tceA gene. Strains 11a and 11a5 share 100% 16S rRNA gene sequence identity with previously sequenced Dhc strains BAV1 and CBDB1, placing it within the Pinellas subgroup, and 85.4% and 89.5% of all genes present in the CBDB1 and BAV1 genomes were detected in strains 11a and 11a5, respectively, using a custom-designed microarray targeting four sequenced Dhc strains. Genes that were not detected in strains 11a and 11a5 are mostly within the high plasticity regions or integrated elements of the sequenced strains. This study reports the functional description and comparative genomics of two additional Dhc isolates and provides evidence that the observed functional incongruence between the activity and core genome phylogenies of Dhc strains is likely driven by the horizontal transfer of key reductive dehalogenase-encoding genes.
2013-03-01 | GSE27611 | GEO
Project description:The role of iron anode on electrochemical dechlorination of aqueous trichloroethylene (TCE) is evaluated using batch mixed-electrolyte experiments. A significantly higher dechlorination rate, up to 99%, is reported when iron anode and copper foam cathodes are used. In contrast to the oxygen-releasing inert anode, the cast iron anode generates ferrous species, which regulate the electrolyte to a reducing condition (low ORP value) and favor the reduction of TCE. The main products of TCE electrochemical reduction on copper foam cathode include ethene and ethane. The ratio of these two hydrocarbons gases varied with the electrolyte ORP condition and current density as more ethane gas generates at more reducing electrolyte condition and at higher current condition. A pseudofirst-order model is used to describe the degradation of TCE; the first-order rate constant (k) increases with the current applied but exhibits a negative relation with initial concentration. Depending on the current, electrolysis by iron anode causes a reduction in the ORP and an increase in the pH of the mixed electrolyte. Enhanced reaction rates in this investigation indicate that the electrochemical reduction using copper foam and iron anode may be a promising process for remediation of groundwater contaminated with chlorinated organic compounds.
| S-EPMC3150566 | biostudies-literature
Project description:To examine changes, if any, in the expression of mRNAs in the liver tissue of mice, we have employed whole genome microarray expression profiling as a discovery platform to identify genes responsive to Trichloroethylene (TCE) treatment. In our results, the expression levels of 431 mRNAs were changed after TCE exposure, of which 291 were up-regulated and 140 were down-regulated. Using qPCR, we validated six of the mRNA expression changed genes, viz., Jun, Cdkn1a, Rad51b, Uhrf1, Svil and Ihh.
2014-11-14 | GSE58819 | GEO
Project description:To know if Trichloroethylene (TCE) can induce miRNA expression changes in mouse liver, we use microarray to screen for differentially expressed miRNAs in the liver of mice exposed to TCE at a dose of 1000 mg/kg b.w. for 5days . In our results, nine miRNAs were selected by volcano plot filtering (fold change ≥ 2 and P-value ≤ 0.05), out of which eight were up-regulated and one was down-regulated. The differential expression of miR-182-5p, miR-34a-5p and miR-451a were validated by qPCR.
2016-11-22 | GSE85904 | GEO
Project description:Trichloroethylene (TCE) and more in general chlorinated aliphatic hydrocarbons (CAHs) can be removed from a contaminated matrix thanks to microorganisms able to perform the reductive dechlorination reaction (RD). Due to the lack of electron donors in the contaminated matrix, CAHs' reductive dechlorination can be stimulated by fermentable organic substrates, which slowly release molecular hydrogen through their fermentation. In this paper, three different electron donors constituted by lactate, hydrogen, and a biocathode of a bioelectrochemical cell have been studied in TCE dechlorination batch experiments. The batch reactors evaluated in terms of reductive dechlorination rate and utilization efficiency of the electron donor reported that the bio-electrochemical system (BES) showed a lower RD rate with respect of lactate reactor (51 ± 9 µeq/d compared to 98 ± 4 µeq/d), while the direct utilization of molecular hydrogen gave a significantly lower RD rate (19 ± 8 µeq/d), due to hydrogen low solubility in liquid media. The study also gives a comparative evaluation of the different electron donors showing the capability of the bioelectrochemical system to reach comparable efficiencies with a fermentable substrate without the use of other chemicals, 10.7 ± 3.3% for BES with respect of 3.5 ± 0.2% for the lactate-fed batch reactor. This study shows the BES capability of being an alternative at classic remediation approaches.
| S-EPMC8777833 | biostudies-literature
Project description:Trichloroethylene (TCE) is a widely used industrial chemical, and a common environmental contaminant. It is a well-known carcinogen in rodents and a probable carcinogen in humans. Studies utilizing panels of mouse inbred strains afford a unique opportunity to understand both metabolic and genetic basis for differences in responses to TCE. We tested the hypothesis that individual and liver-specific toxic effects of TCE are genetically controlled and that the mechanisms of toxicity and susceptibility can be uncovered by exploring responses to TCE using a diverse panel of inbred mouse strains. TCE (2100 mg/kg) or corn oil vehicle were administered by gavage to 6-8 wk old male mice of 15 mouse strains. Serum and liver were collected at 2, 8, and 24 hr post dosing and were analyzed for TCE metabolites, hepatocellular injury and gene expression of liver. TCE metabolism, as evident from the levels of individual oxidative and conjugative metabolites, varied considerably between strains. TCE treatment-specific effect on the liver transcriptome was strongly dependent on the individual’s genetic background. PPAR-mediated molecular networks, consisting of the metabolism genes known to be induced by TCE, represent some of the most pronounced molecular effects of TCE treatment in mouse liver that are dependent on the individual’s genetic background. Conversely, cell death, liver necrosis, and immune mediated response pathways which are affected by TCE treatment in liver are largely genetic background-independent. These studies provide better understanding of the mechanisms of TCE-induced toxicity anchored on metabolism and genotype-phenotype correlations that may define susceptibility or resistance. 16 mouse strains were studied, vehicle control and mice treated by gavage with 2100 mg/kg Trichloroethylene and sacrificed 24 hrs after dosing
2011-02-01 | E-GEOD-24278 | biostudies-arrayexpress
Project description:To examine changes, if any, in the expression of mRNAs in the liver tissue of mice, we have employed whole genome microarray expression profiling as a discovery platform to identify genes responsive to Trichloroethylene (TCE) treatment. In our results, the expression levels of 431 mRNAs were changed after TCE exposure, of which 291 were up-regulated and 140 were down-regulated. Using qPCR, we validated six of the mRNA expression changed genes, viz., Jun, Cdkn1a, Rad51b, Uhrf1, Svil and Ihh. Six B6C3F1 male mice were oral administrated with either corn oil or TCE (dissolved in corn oil, 1000mg/kg b.w per day) for 5 days. The expression changes of mRNAs in TCE exposured mouse liver were screened by whole genome microarray expression profiling and were validated by qPCR.
2014-11-14 | E-GEOD-58819 | biostudies-arrayexpress