Ontology highlight
ABSTRACT:
PROVIDER: PRJNA445362 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6882053_1.fastq.gz | Fastqsanger.gz | |||
| SRR6882054_1.fastq.gz | Fastqsanger.gz | |||
| SRR6882055_1.fastq.gz | Fastqsanger.gz | |||
| SRR6882056_1.fastq.gz | Fastqsanger.gz | |||
| SRR6882057_1.fastq.gz | Fastqsanger.gz |
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Project description:The goals of this study are to use SWATH-MS to detect bacterial proteomic profiles of wild-type E. coli K-12 LE392, P. putida KT2440, and their quantitative protein response under the exposure of antiepileptic drug carbamazepine. Three concentrations of carbamazepine were applied, which were 0.05 mg/L, 10.0 mg/L and 50.0 mg/L. The group without dosing carbamazepine was the control group. Each concentration was conducted in triplicate. By comparing the proteomic profiles of experimental groups and control group, the effects of carbamazepine on bacterial translational levels can be revealed.
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Project description:Transcriptomic profiling of Daphnia magna samples exposed to carbamazepine (CBZ), diazepan (DZP), propranolol (PR) and to an equitoxic mixture of them (M). Assessing the risks of emerging contaminants such as neuro-active pharmaceuticals in the environment requires an understanding of their joint effects at low concentrations across species. Here, we assessed reproductive and transcriptional effect of propranolol, diazepam and carbamazepine on the crustacean Daphnia magna at environmentally relevant concentrations. The three compounds enhanced reproductive parameters in adults, and induced specific transcriptome changes in pre-adolescent individuals. Comparing results from single exposures and of ternary equi-effective mixtures showed additive action for both effects. Transcriptomic analyses identified 3248 genes affected by at least one of the treatment, which were grouped into four clusters. Two clusters included 1897 gene transcripts in total, that behaved similarly (appearing either over- or underrepresented relative to control) in single and mixture treatments. The third and fourth clusters grouped genes differently transcribed upon exposure to diazepam and propranolol, respectively. Functional transcriptomics indicated that the four clusters shared major de-regulated signalling pathways implicated on energy, growth, reproduction, and neurologically- related processes, which may be responsible for the observed reproductive effects. Our study, thus, showed additive effects at the transcriptional and physiological level and is providing a novel approach to the analysis of environmental relevant mixtures of neuro-active compounds
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Project description:we assessed characteristic molecular and proteomic signatures in rat liver treated with drugs (pyrazinamide, ranitidine, enalapril, carbamazepine, and chlorpromazine) that are known to cause DILI in humans.
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Project description:Characterisation of peptides presented by the Human Leukocyte Antigen (HLA) class I molecule HLA-B*15:02 in the presence and absence of carbamazepine (CBZ), and related molecules carbamazepine-10,11-epoxide (ECBZ) and oxcarbazepine (OXC).
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Project description:Horizontal transfer of plasmids is one of the main drivers of bacterial adaptation, resulting e.g. in the spread of antibiotic resistance. We investigated the marine Roseobacter group and studied how conjugation affects the gene expression and biology of the new host. We showed that the two syntenic 126 kb and 191 kb plasmids of Dinoroseobacter shibae can be conjugated into representatives of all major lineages of Rhodobacteraceae. In the model organism Phaeobacter inhibens their acquisition resulted in differential expression of genes related to motility, transport and the synthesis of vitamins. Moreover, the decrease of the potent antibiotic tropodithietic acid reduced the energetic burden of Phaeobacter and resulted in an enhanced growth. While the T4SS systems of both plasmids were silenced in the new host, the ability to kill the dinoflagellate was exclusively transferred via the 191 kb plasmid from D. shibae to P. inhibens. Our findings showed drastic consequences of plasmid conjugation; genetic reprogramming of the novel host resulted in considerable fitness changes leading to the prediction that horizontal gene transfer triggers bacterial speciation.
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Project description:The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of wild-type E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid, and their mRNA response under the exposure of antiepileptic drug carbamazepine. Three concentrations of carbamazepine were applied, which were 0.05 mg/L, 10.0 mg/L and 50.0 mg/L (refer to low, medium and high, respectively). The group without dosing carbamazepine was the control group. Each concentration was conducted in triplicate. By comparing the mRNA profiles of experimental groups and control group, the effects of carbamazepine on transcriptional levels can be revealed. Illumina HiSeq 2500 was applied. The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913), P.putida reference genome (NC_002947), and IncPα plasmid reference genome (NC_00) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.
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