Ontology highlight
ABSTRACT:
PROVIDER: PRJNA976896 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24751366_1.fastq.gz | Fastqsanger.gz | |||
| SRR24751366_2.fastq.gz | Fastqsanger.gz |
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Project description:Azo-dye-degrading bacteria from Brazilian tropical forests
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Project description:Here, we established a successive Fe0-enhanced microbe system to remove azo dye (a typical organic pollutant) by Shewanella decolorationis S12 (S. decolorationis S12, an effective azo dye degradation bacterium) and examined the gene expression time course (10, 30, 60, and 120 min) in whole genome transcriptional level. Comparing with the treatment without ZVI, approximately 8% genes affiliated with 10 different gene expression profiles in S. decolorationis S12 were significantly changed in 120 min during the ZVI-enhanced microbial azo reduction. Intriguingly, MarR transcriptional factor might play a vital role in regulating ZVI-enhanced azo reduction in the aspect of energy production, iron homeostasis, and detoxification. Further investigation showed that induced [Ni-Fe] H2ase genes (hyaABCDEF) and azoreductase genes (mtrABC-omcA) contributed to ZVI-enhanced energy production, while reduced iron uptake (hmuVCB and feoAB), induced sulfate assimilation (cysPTWA) and cysteine biosynthesis (cysM) related genes were essential to iron homeostasis and detoxification. This study disentangles underlying mechanisms of ZVI-enhanced azo reduction in S. decolorationis S12 and lays a foundation for further optimization of integrated ZVI-microbial system for efficient organic pollution treatment.
2021-10-01 | GSE160493 | GEO
Project description:Congo Red (CR) dye is historically used for histochemical staining of amyloid deposition in tissue. Its characteristic aryl azo moiety renders it chemically stable as a non-covalent pan-amyloid binder. Here, we discover in serendipity that the CR dye can covalently modify amyloid proteins by activation of the inert azo bond using neutral borate buffer at ambient temperature. We first show that boronic acid is responsible for azo bond-mediated protein bioconjugation. Furthermore, we also observe that ultraviolet light-induced azo trans-to-cis isomerization significantly enhances the labeling efficiency. Leveraging the discovered covalent chemistry, we apply CR-alkyne derivative with a click enrichment handle to label, capture and enrich amyloid deposits in Alzheimer’s disease (AD) mouse brain tissue. Finally, we identify the composition of amyloid deposits by proteomics profiling, revealing typical neurodegenerative diseases biomarkers, including MAPT and 14-3-3 family proteins. Overall, this work presents a new type of azo based bioconjugation chemistry previously known to be inert but herein activated by neutral borate buffer.
2025-03-27 | PXD062299 | Pride
Project description:<p>Wide contamination of MPs including polyvinyl chloride (PVC) has been reported in remote regions such as Qinghai-Tibet Plateau (QTP). Microbial degradation of plastics is frequently coupled with lignocellulose-degrading enzymatic machinery. Given its status as a widespread biological sampler in QTP, the Tibetan herbivore plateau pika (Ochotona curzoniae), which harbors lignocellulose-degrading enzymes, represent a promising reservoir for novel PVC-degrading enzymes. In this study, a polyvinyl chloride (PVC)-feeding trial of Tibetan plateau pikas (Ochotona curzoniae) revealed gut microbiota recruitment of plastic degraders. Subsequent enrichment experiment yielded a PVC-degrading consortium that depolymerized PVC into long-chain alkanes, with Rhodococcus and Leifsonia identified as PVC-response specialist and generalist, respectively. Multi-omics analysis supported a putative degradation pathway initiated by haloalkane dehalogenase (HLD) and involving oxidases. Furthermore, novel haloalkane dehalogenase RhHLD (from Rhodococcus MAG) released 11.5 mg/L chloride ions from PVC films, whereas dye-decolorizing peroxidase LeDyP from Leifsonia MAG generated PVC degrading intermediates. Further analysis of 39 metagenomic datasets confirmed that haloalkane dehalogenase and dye-decolorizing peroxidase are prevalent in wild pikas gut. This study elucidates the PVC-degrading potential of herbivore gut microbiota and expands the catalytic toolkit for plastic bioremediation, opens new avenues for enzyme discovery in natural ecosystems.</p>
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Project description:Biodegradation of azo dye by L. lactis
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Project description:Dyes used in fabric and leather industry are being released and accumulated into Canadian ecosystems. Recent studies have demonstrated that dyes made of azo compounds significantly increase toxicity in biota, which is explained by their toxic metabolites (e.g., aromatic amines). The metabolites of azo compounds interact with hydrophobic surfaces of cell membranes causing expansion of the membrane which impede normal cellular functions. It has been suggested that this process leads to cell death due to improper ion balance. Currently, it is estimated that between 10 and 15% of azo dyes are released in the environment as effluent. The aim of this study was to evaluate toxicity and gene networks altered by azo compounds in amphibians using ecotoxicogenomic approaches. Larvae of the frog Silurana tropicalis (Western clawed frog) were exposed to sediment contaminated to 887 ppm Disperse Yellow 7 (DY7). Larvae were exposed from Nieuwkoop-Faber developmental stage 12 to 46. Data suggest that the azo dye DY7 induced cellular stress and interfered with androgen biosynthesis in early tadpole development. At exposure completion, RNA was isolated from whole larvae and quality was ascertained using bioanalyzer analysis. A custom Agilent 4 X 44 K microarray for S. tropicalis was used to characterize gene regulatory networks underlying toxicity. This study presents the transcriptional regulatory pathways affected by DY7 in S. tropicalis early development. Embryos were exposed to the DY7 dye during development. There were 4 control groups exposed and 4 treatment groups exposed.
2012-11-30 | E-GEOD-40149 | biostudies-arrayexpress