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Meta-transcriptomic analysis of the response of river biofilms to pharmaceutical products using anonymous DNA microarray

ABSTRACT: Low concentrations of pharmaceutical compounds were shown to induce transcriptional responses in isolated microorganisms, which could have consequences on ecosystem dynamics. In order to test if these transcriptional responses could also be observed in complex river microbial communities, biofilm reactors were inoculated with water from two distinct rivers and supplemented with environmentally relevant doses of four pharmaceutical products (erythromycin-ER, gemfibrozil-GM, sulfamethazine-SN and sulfamethoxazole-SL). To follow the expression of functional genes, we constructed a 9,600 features anonymous DNA microarray platform onto which cDNA from the various biofilms was hybridized.

ORGANISM(S): environmental samples environmental samples

PROVIDER: GSE20501 | GEO | 2010/07/06

SECONDARY ACCESSION(S): PRJNA125083

REPOSITORIES: GEO

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Meta-transcriptomic analysis of the response of river biofilms to pharmaceutical products using anonymous DNA microarray

Project description:Low concentrations of pharmaceutical compounds were shown to induce transcriptional responses in isolated microorganisms, which could have consequences on ecosystem dynamics. In order to test if these transcriptional responses could also be observed in complex river microbial communities, biofilm reactors were inoculated with water from two distinct rivers and supplemented with environmentally relevant doses of four pharmaceutical products (erythromycin-ER, gemfibrozil-GM, sulfamethazine-SN and sulfamethoxazole-SL). To follow the expression of functional genes, we constructed a 9,600 features anonymous DNA microarray platform onto which cDNA from the various biofilms was hybridized. The reactor design for biofilm development has been previously described (Lawrence et al., 2004; Lawrence et al., 2000). Two duplicate experiments were carried out, with reactors being inoculated with either water from the WC (nutrient rich) or the SSR (nutrient poor). Treatments consisted in the addition of various pharmaceutical compounds: 1 µg l-1 erythromycin (ER), 1 µg l-1 gemfibrozil (GM), 0.5 µg l-1 sulfamethazine (SN), 0.5 µg l-1 sulfamethoxazole (SL). Nothing was added to control reactors (CO). All treatments were replicated independently three times. A reference sample (composite sample from Wascana Creek reactors used to construct the microarray) was hybridized (Cy5) on each slide.

2010-07-06 | E-GEOD-20501 | biostudies-arrayexpress

Hepatic transcriptional responses of zebrafish to chronic, low dose pharmaceutical exposures

Project description:Our study makes use of zebrafish and has determined hepatic transcriptional changes after exposure to four single pharmaceuticals, a pharmaceutical mixture (MIX), and wastewater effluent (WWE) exposures. The pharmaceuticals chosen include acetaminophen, carbamazepine, gemfibrozil, and venlafaxine. We have performed chronic (6 week), low concentration (0.5 and 10 μgL-1 or 5 and 25% effluent) exposure of male and female fish and previously determined a range of effects (reproductive, histological, hormonal) after exposure to single compounds, a mixture of these compounds or wastewater effluent. Herein we determine by microarray the hepatic transcriptional responses of male and female zebrafish from the same exposures.

2019-12-23 | GSE43491 | GEO

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Meta-transcriptomic analysis of the response of river biofilms to pharmaceutical products using anonymous DNA microarray

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Reverse engineering of industrial pharmaceutical-producing actinomycete strains

Project description:Abstract: Transcript levels in production cultures of wildtype and classically improved strains of the actinomycete bacteria Saccharopolyspora erythraea and Streptomyces fradiae were monitored using microarrays of the sequenced actinomycete S. coelicolor. Sac. erythraea and S. fradiae synthesize the polyketide antibiotics erythromycin and tylosin, respectively, and the classically improved strains contain unknown overproduction mutations. The Sac. erythraea overproducer was found to express the entire 56-kb erythromycin gene cluster several days longer than the wildtype strain. In contrast, the S. fradiae wildtype and overproducer strains expressed the 85-kb tylosin biosynthetic gene cluster similarly, while they expressed several tens of other S. fradiae genes and S. coelicolor homologs differently, including the acyl-CoA dehydrogenase gene aco and the S. coelicolor isobutyryl-CoA mutase homolog icmA. These observations indicated that overproduction mechanisms in classically improved strains can affect both the timing and rate of antibiotic synthesis, and alter the regulation of antibiotic biosynthetic enzymes and enzymes involved in precursor metabolism. This SuperSeries is composed of the SubSeries listed below.

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Activated sludge from Pharmaceutical industry

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Reverse engineering of industrial pharmaceutical-producing actinomycete strains

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Proteomic analysis of Acinetobacter baylyi ADP1 under exposure of non-antibiotic pharmaceuticals

Project description:The goals of this study are to use SWATH-MS to detect bacterial proteomic profiles of wild-type Acinetobacter baylyi ADP1, and its protein response under the exposure of non-antibiotic pharmaceuticals, including ibuprofen, naproxen, gemfibrozil, diclofenac, propanolol, and iopromide. The concentrations were 0.5 mg/L for ibuprofen, naproxen, gemfibrozil, diclofenac, propanolol, and 1.0 mg/L for iopromide. The group without dosing pharmaceutical was the control group. Each concentration was conducted in triplicate. By comparing the proteomic profiles of experimental groups and control group, the effects of non-antibiotic pharmaceuticals on translational levels can be revealed.

2020-05-22 | PXD016798 | Pride

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