RNAseq of zebrafish (Danio rerio) developmentally exposed to the polychlorinated biphenyl 3,3'-dichlorobiphenyl (PCB-11)
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE118955 | GEO | 2019/08/22
REPOSITORIES: GEO
Similar Datasets
Project description:RNAseq of zebrafish (Danio rerio) developmentally exposed to the polychlorinated biphenyl 3,3'-dichlorobiphenyl (PCB-11)
| PRJNA487523 | ENA
Project description:We analyzed the transcriptional response of the actinomycete Rhodococcus aetherivorans I24 to biphenyl and polychlorinated biphenyls (PCBs). This species has not been extensively exposed to PCBs, as it was first isolated from a toluene contaminated aquifer, rather than a site contaminated with polychlorinated hydrocarbons. Using a microarray targeting 3524 genes, we assessed gene expression in minimal medium supplemented with various substrates (e.g. PCBs) and in both PCB-contaminated and non-contaminated sediment slurries. Relative to the reference condition (minimal medium supplemented with glucose), 408 genes were up-regulated in the various treatments. In medium and in sediment, PCBs elicited the up-regulation of a common set of 100 genes, including chaperones (groEL), a superoxide dismutase (sodA), alkyl hydroperoxide reductase protein C (ahpC), and a catalase/peroxidase (katG). Analysis of the R. aetherivorans I24 genome sequence identified orthologs of many of the genes in the canonical biphenyl pathway, but very few of these genes were up-regulated in response to PCBs or biphenyl. This study is one of the first which utilizes microarrays to assess the transcriptional response of a soil bacterium to a pollutant under conditions which more closely resemble the natural environment. Our results indicate that the transcriptional response of R. aetherivorans I24 to PCBs, in both medium and sediment, is primarily directed towards reducing oxidative stress, rather than catabolism. In addition, the identification of numerous genes expressed in contaminated soil specifically may have implications for the development of biosensors. Finally, comparative genomic and transcriptomic analyses suggest that the mere presence of orthologs of the required enzymes may not be sufficient to confer a vigorous biphenyl/PCB metabolism. RNA was isolated from cells incubated in the following: sediment from a PCB-contaminated industrial site, uncontaminated sediment from a comparable site, and defined media supplemented with glucose (3 g/L), glucose and biphenyl (3 g/L, 4.5 μM), or glucose and PCBs (3 g/L, 5 mg/L Aroclor 1254). In all cases, there were 3 biological replicates and 2 technical replicates (repeat hybridizations). A total of 3524 genes are represented on the arrays; of these, 41 and 176 are found on the plasmids pRA2 and pRA3, respectively. On average, there are 3 distinct 24nt probes per gene.
2010-03-20 | E-GEOD-17033 | biostudies-arrayexpress
Project description:We analyzed the transcriptional response of the actinomycete Rhodococcus aetherivorans I24 to biphenyl and polychlorinated biphenyls (PCBs). This species has not been extensively exposed to PCBs, as it was first isolated from a toluene contaminated aquifer, rather than a site contaminated with polychlorinated hydrocarbons. Using a microarray targeting 3524 genes, we assessed gene expression in minimal medium supplemented with various substrates (e.g. PCBs) and in both PCB-contaminated and non-contaminated sediment slurries. Relative to the reference condition (minimal medium supplemented with glucose), 408 genes were up-regulated in the various treatments. In medium and in sediment, PCBs elicited the up-regulation of a common set of 100 genes, including chaperones (groEL), a superoxide dismutase (sodA), alkyl hydroperoxide reductase protein C (ahpC), and a catalase/peroxidase (katG). Analysis of the R. aetherivorans I24 genome sequence identified orthologs of many of the genes in the canonical biphenyl pathway, but very few of these genes were up-regulated in response to PCBs or biphenyl. This study is one of the first which utilizes microarrays to assess the transcriptional response of a soil bacterium to a pollutant under conditions which more closely resemble the natural environment. Our results indicate that the transcriptional response of R. aetherivorans I24 to PCBs, in both medium and sediment, is primarily directed towards reducing oxidative stress, rather than catabolism. In addition, the identification of numerous genes expressed in contaminated soil specifically may have implications for the development of biosensors. Finally, comparative genomic and transcriptomic analyses suggest that the mere presence of orthologs of the required enzymes may not be sufficient to confer a vigorous biphenyl/PCB metabolism.
2010-03-20 | GSE17033 | GEO
Project description:Rare variants enriched for functions in chromatin regulation and neuronal synapses have been linked to autism. How chromatin and DNA methylation interact with environmental exposures at synaptic genes in autism etiologies is currently unclear. Using whole-genome bisulfite sequencing in brain tissue and a neuronal cell culture model carrying a 15q11.2-q13.3 maternal duplication, we find that significant global DNA hypomethylation is enriched over autism candidate genes and affects gene expression. The cumulative effect of multiple chromosomal duplications and exposure to the pervasive persistent organic pollutant PCB 95 altered methylation of more than 1,000 genes. Hypomethylated genes were enriched for H2A.Z, increased maternal UBE3A in Dup15q corresponded to reduced levels of RING1B, and bivalently modified H2A.Z was altered by PCB 95 and duplication. These results demonstrate the compounding effects of genetic and environmental insults on the neuronal methylome that converge upon dysregulation of chromatin and synaptic genes.
2016-12-13 | GSE81541 | GEO
Project description:Recent analysis of air samples from Chicago and Lake Michigan areas observed a ubiquitous airborne polychlorinated biphenyl (PCB) congener, 3,3'-dichlorobiphenyl (PCB11). Our analysis of serum samples also revealed the existence of hydroxylated metabolites of PCB11 in human blood. Because PCBs and PCB metabolites have been suggested to induce oxidative stress, this study sought to determine whether environmental exposure to PCB11 and its 4-hydroxyl metabolite could induce alterations in steady-state levels of reactive oxygen species (ROS) and cytotoxicity in immortalized human prostate epithelial cells (RWPE-1). This study also examines if antioxidants could protect the cells from PCB11-induced cytotoxicity. Exponentially growing RWPE-1 cells were exposed to PCB11 and its metabolite, 3,3'-dichlorobiphenyl-4-ol (4-OH-PCB11), as well as an airborne PCB mixture resembling the Chicago ambient air congener profile, every day for 5 days. Results showed that 4-OH-PCB11 could significantly induce cell growth suppression and decrease the viability and plating efficiency of RWPE-1 cells. 4-OH-PCB11 also significantly increased steady-state levels of intracellular superoxide, O?•?), as well as hydroperoxides. Finally, treatment with the combination of polyethylene glycol-conjugated CuZn superoxide dismutase and catalase added 1h after 4-OH-PCB11 exposures, significantly protected RWPE-1 cells from PCB toxicity. The results strongly support the hypothesis that exposure to a hydroxylated metabolite of PCB11 can inhibit cell proliferation and cause cytotoxicity by increasing steady-state levels of ROS. Furthermore, antioxidant treatments following PCBs exposure could significantly mitigate the PCB-induced cytotoxicity in exponentially growing human prostate epithelial cells.
| S-EPMC3829572 | biostudies-literature
Project description:In this study, we explore the implications of oral exposure to the MARBLES mixture on the brain in adult female mice through two omics approaches, metabolomics and transcriptomics. The individual PCB congeners (PCB 11, 28, 52, 84, 95, 101, 118, 135, 138, 149, 153, and 180) used to make the MARBLES PCB mix. Female C57Bl/6J mice (> 6-week-old) were randomized into exposure groups (N = 4-6) and orally exposed to 0, 0.1, 1, or 6 mg/kg bw/day of the MARBLES mix in organic peanut butter/organic peanut oil for 7 weeks.The striatum and prefrontal cortex were isolated and, together with the liver, prepared for RNA sequencing.
2024-11-08 | GSE252621 | GEO
Project description:The title compound, C(12)H(14)N(4), has a crystallographically imposed centre of symmetry. Inter-molecular N-H?N hydrogen bonds between amino groups link adjacent mol-ecules into a three-dimensional network where ten-membered hydrogen-bonded rings are observed.
| S-EPMC2979072 | biostudies-literature
Project description:The asymmetric unit of the title compound, C(14)H(10)O(4), contains one half mol-ecule, the complete mol-ecule being generated by a twofold axis. The two benzene rings form a dihedral angle of 43.11?(5)°. Inter-molecular O-H?O hydrogen bonds link the mol-ecules into one-dimensional zigzag chains. These chains are further connected into two-dimensional supra-molecular layers by weak ?-? stacking inter-actions between neighbouring benzene rings, with centroid-centroid distances of 3.7648?(8)?Å.
| S-EPMC3089151 | biostudies-literature
Project description:Membranes have been widely used in water remediation (e.g. desalination and heavy metal removal) because of the ability to control membrane pore size and surface charge. The incorporation of nanomaterials into the membranes provides added benefits through increased reactivity with different functionality. In this study, we report the dechlorination of 2-chlorobiphenyl in the aqueous phase by a reactive membrane system. Fe/Pd bimetallic nanoparticles (NPs) were synthesized (in-situ) within polyacrylic acid (PAA) functionalized polyvinylidene fluoride (PVDF) membranes for degradation of polychlorinated biphenyls (PCBs). Biphenyl formed in the reduction was further oxidized into hydroxylated biphenyls and benzoic acid by an iron-catalyzed hydroxyl radical (OH•) reaction. The formation of magnetite on Fe surface was observed. This combined pathway (reductive/oxidative) could reduce the toxicity of PCBs effectively while eliminating the formation of chlorinated degradation byproducts. The successful manufacturing of full-scale functionalized membranes demonstrates the possibility of applying reactive membranes in practical water treatment.
| S-EPMC4061716 | biostudies-literature
Project description:Expression profiling of isoflavone and 3,3’-diindolylmethane treated C4-2B prostate cancer cells was conducted using Affymetrix Human Genome U133 Plus 2.0. Array
2012-01-25 | GSE35324 | GEO