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Transcriptome Sequencing of Solid Fermentation under Different Induced Carbon Sources II

ABSTRACT: Transcriptomic profiling and real-time quantitative reverse transcription-PCR analyses revealed that TP05746 dynamically regulated the expression of genes encoding major PBDEs. Furthermore, in vitro binding experiments confirmed that TP05746 directly bound to the promoter regions of these major enzyme genes. Transcription factors mediated the regulation of plant-biomass-degrading enzyme (PBDE) gene expression in Talaromyces pinophilus.

ORGANISM(S): Talaromyces pinophilus

PROVIDER: GSE131872 | GEO | 2020/01/13

REPOSITORIES: GEO

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A Mixture Reflecting Polybrominated Diphenyl Ether (PBDE) Profiles Detected in Human Follicular Fluid Significantly Affects Steroidogenesis and Induces Oxidative Stress in a Human Granulosa Cell Line

Project description:Brominated flame retardants (BFRs) are incorporated into consumer products to prevent flame propagation. These compounds leach into the domestic environment, resulting in chronic exposure and contamination. Pregnancy failure is associated with high levels of BFRs in human follicular fluid, raising serious questions regarding their impact on female fertility. Our goal was to elucidate effects of a mixture reflecting human follicular fluid levels of polybrominated flame retardants (PBDEs), the major class of BFRs, on an immortalized human granulosa cell line, the KGN cell line. We showed that cell viability was altered and oxidative stress was induced, as reflected by increased reactive oxygen species formation, at 20 µM of the PBDE mixture. Transcriptomic analysis revealed that several genes showing an altered expression after the PBDE treatment were involved in oxidative stress signaling pathways. Significant dose-dependent reduction of progesterone and estradiol levels was measured after PBDE treatment; expression of genes involved in steroid hormone metabolism, namely CYP1A1, was significantly affected by PBDEs. Treatment with the PBDE mixture also modified genes encoding for members of the transforming growth factor β superfamily like inhibins and cytokines, including the pro-inflammatory factor, interleukin-6 (IL6). Concentration of IL-6 in KGN cell culture media was consistently increased after treatment with the PBDE mixture. Our results clearly demonstrate that the PBDEs detected in human follicular fluid alter human granulosa cell functions by inducing oxidative stress, disrupting steroidogenesis and triggering an inflammatory response. This strengthens the fact that PBDEs are detrimental to ovarian functions and thus, to women’s reproductive health.

2016-05-25 | GSE77963 | GEO

OH-PBDE-induced gene expression profiling in H295R adrenocortical carcinoma cells

Project description:Polybrominated diphenyl ethers (PBDEs) are commonly used as flame retardants in a variety of commercial and household products. They have been detected in the environment and accumulate in mammalian tissues and fluids. PBDE toxicity is thought to be associated with endocrine disruption, developmental neurotoxicity and changes in fetal development. Although humans are exposed to PBDEs, our knowledge of the effects of PBDE metabolites on human cells with respect to health risk is insufficient. Two hydroxylated PBDEs (OH-PBDEs), 2-OH-BDE47 and 2-OH-BDE85, were investigated for their effects on cell viability/proliferation, DNA damage, cell cycle distribution and gene expression profiling in H295R adrenocortical carcinoma cells. We show that the two agents are cytotoxic in a dose-dependent manner only at micromolar concentrations, with 2-OH-BDE85 being more toxic than 2-OH-BDE47. However, no DNA damage was observed for either chemical, suggesting that the biological effects of OH-PBDEs occur primarily via non-genotoxic routes. Furthermore, no evidence of aryl hydrocarbon receptor (AHR)-mediated, dioxin-like toxicity was observed. Instead, we report that a micromolar concentration of OH-PBDEs induces transcriptional changes associated with endoplasmic reticulum stress and the unfolded protein response. We discuss whether OH-PBDE bioaccumulation could result in impairment of the adrenocortical secretory function.

2008-12-25 | GSE8588 | GEO

reductive debromination of polybrominated diphenyl ethers by Dehalococcoides

Project description:Extensive use of polybrominated diphenyl ethers (PBDEs) has resulted in widespread environmental distribution and concerns remain about risks to human health and ecosystems from legacy PBDE contamination. Though bioremediation has been proven to be a cost-effective and efficient technology for treating halogenated pollutants in situ, application of bioremediation technologies at PBDE-contaminated sites is restricted by a lack of knowledge about functional PBDE-dehalogenating microbes. In the current study, we observed distinct PBDE-dehalogenation activity by three previously isolated Dehalococcoides mccartyi strains (CG1, CG4, and 11a5). PBDE debromination proceeded via distinct pathways in each D. mccartyi strain and involved previously characterized (TceA11a5, PcbA1, and PcbA4) and uncharacterized (11a5_e001) reductive dehalogenases (RDase), suggesting that this phenotype may be more widespread among the Dehalococcoides than is currently recognized.

2022-05-26 | PXD026932 | Pride

Bifunctional dehalogenases in Dehalococcoides mediate complete debromination of penta- and tetra-brominated diphenyl ethers

Project description:Polybrominated diphenyl ethers (PBDEs) are persistent, highly toxic, and widely distributed environmental pollutants. The microbial populations and functional reductive dehalogenases (RDases) responsible for PBDEs debromination in anoxic systems remain poorly understood, which confounds bioremediation of PBDE-contaminated sites. Here we report a PBDE-debrominating enrichment culture dominated by a previously undescribed Dehalococcoides mccartyi population. A D. mccartyi strain, designated TZ50, whose genome contains 25 putative RDase encoding genes was isolated from the debrominating enrichment culture. Strain TZ50 dehalogenated a mixture of penta- and tetra-BDE congeners (total BDEs 1.48 uM) to diphenyl ether within two weeks (0.58 uM Br- /d) via ortho- and meta- bromine elimination; strain TZ50 also dechlorinated tetrachloroethene (PCE) to vinyl chloride and ethene (260.2 M Cl- /d). Native-PAGE, proteomic profiling, and in vitro enzymatic activity assays implicated the involvement of three RDases in PBDEs and PCE dehalogenation. Two RDases, TZ50_0172 (PteATZ50) and TZ50_1083 (TceATZ50), were responsible for debromination of penta- and tetra-BDEs to di-BDE. TZ50_0172 and TZ50_1083 were also implicated in dechlorination of PCE to TCE and of TCE to vinyl chloride/ethene, respectively. The other expressed dehalogenase, TZ50_0090, was associated with debromination of di-BDE to diphenyl ether, but its role in PCE dechlorination was unclear. Comparatively few RDases are known to be involved in PBDE debromination and the identification of PteATZ50, TceATZ50, and TZ50_0090 provides additional information for evaluating debromination potential at contaminated sites. Moreover, the bifunctionality of the PteATZ50 and TceATZ50 in both PBDEs and PCE dehalogenation makes strain TZ50 a suitable candidate for remediation of co-contaminated sites.

2021-06-16 | PXD024983 | Pride

RNA-seq of mutant delta POX01387after transfer from glucose medium to Avicel medium for 24 hours

Project description:To explore the effect of transcription factor POX01387 on transcription levels of plant-biomass-degrading enzyme-encoding genes in Penicillium oxalicum

2023-06-15 | GSE166519 | GEO

Expression data from PBDE treated rats at PND22 and Week 13

Project description:Liver gene transcripts patterns were used to characterize toxicity from exposure to polybrominated diphenyl ethers (PBDEs), flame retardant components. In this study, Wistar Han dams were exposed by gavage to the PBDE mixture (DE71) starting at gestation day 6 (GD 6) and continuing to weaning on postnatal day 21 (PND 21). Offspring from the dams began PBDE direct dosing on PND 12 and were dosed daily through PND 21. After weaning, they were dosed 5 days per week for another 13 weeks. Liver samples were collected at PND 22 and week 13 for liver gene expression analysis and interrogated with the Affymetrix Rat Genome 230 2.0 Array. PBDE treatment induced 1,066 liver gene transcript changes in females and 1,200 transcriptional changes in males at PND 22 (false discovery rate (FDR) < 0.01), but only 263 liver transcriptional changes at 13 weeks in male rats (FDR <0.05). No significant differences in dose response were found between male and female pups. There were a total of 6 groups and 5x replication for each group, for 30 total samples that were analyzed. The groups were (1) pup-male-CTL, (2) pup-female-CTL, (3) pup-male-PBDE, (4) pup-female-PBDE, (5) rat-male-CTL, (6) rat-male-PBDE. We generated the following pairwise comparisons using R/maanova: malePups(PBDE vs CTL), femalePups(PBDE vs CTL), maleRats(PBDE vs CTL), CTLpups(male vs female), PBDEpups(male vs female). We also performed ANOVA test for SEX-by-DOSE (pups) and AGE-by-DOSE (males). For pups, genes with an FDR≤1% were selected; for rats, genes with FDR < 5% were selected.

2011-10-04 | E-GEOD-32156 | biostudies-arrayexpress

Characterization of estrogen and the endocrine-disrupting chemical-induced mouse mammary gland reorganization via bulk RNA-sequencing

Project description:Similar to the scRNA-Seq data (GSE125272), a surgical menopausal (ovariectomized) mouse model was used to assess how mammary gland tissue was affected by both 17β-estradiol (E2) and polybrominated diphenyl ethers (PBDEs). The PBDE treatments include three analyzed flame retardants: BDE-47, BDE-100 and BDE-153. Bulk RNA-Seq data was created with treatment conditions lasting 1 week. Gene expression changes for PBDE treatment are relatively small compared to E2 treatment. However, along with other studies and experiments, this data is meant to contribute to greater understanding of the interaction of PBDE exposure and estrogen signaling.

2023-03-24 | GSE227872 | GEO

RNA-seq of mutant delta POX03070 and delta PoxCxrA after transfer from glucose medium to Avicel medium for 24 hours

Project description:To explore the effect of POX03070 on transcription levels of plant-biomass-degrading enzyme-encoding genes in Penicillium oxalicum,and the interaction between POX03070 and PoxCxrA in transcriptional level.

2023-04-28 | GSE206840 | GEO

Transcription profiling of human H295R adrenocortical carcinoma cells to investigate OH-PBDE-induced gene expression

Project description:Affymetrix high-density oligonucleotide microarray analysis was performed to analyse hydroxylated polybrominated diphenyl ethers (OH-PBDE)-induced gene expression changes in H295R adrenocortical carcinoma cells. Cells were treated with growth medium in the presence or absence of 10 µM 2-OH-BDE47 or 2-OH-BDE85 for 24 hours before the gene expression changes were investigated. Experiment Overall Design: Gene expression changes in response to hydroxylated polybrominated diphenyl ethers (OH-PBDEs) were analysed by Microarray technology in H295R adrenocortical carcinoma cells. Cells were treated with 10 µM of 2-OH-BDE47 or 2-OH-BDE85 (or growth medium alone) for 24 hours before the OH-PBDE-induced gene expression changes were investigated. Control, 2-OH-BDE47- and 2-OH-BDE85-treated samples were collected from three independent experiments each.

2009-01-02 | E-GEOD-8588 | biostudies-arrayexpress

Transcriptome Sequencing of Solid Fermentation under Different Induced Carbon Sources

Project description:Here comparative transcriptomic analyses of Penicillium oxalicum grown on wheat bran (WB), WB plus rice straw (WR) and WB plus Avicel (WA) as the sole carbon source under solid-state fermentation (SSF) revealed that most of differentially expressed genes (DEGs) were involved in metabolism specifically carbohydrate metabolism.

2019-10-15 | GSE131173 | GEO

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