Ontology highlight
ABSTRACT:
PROVIDER: PRJNA982597 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24957342_1.fastq.gz | Fastqsanger.gz | |||
| SRR24957342_2.fastq.gz | Fastqsanger.gz | |||
| SRR24957343_1.fastq.gz | Fastqsanger.gz | |||
| SRR24957343_2.fastq.gz | Fastqsanger.gz | |||
| SRR24957344_1.fastq.gz | Fastqsanger.gz |
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Project description:Multiple infection sources for enterohemorrhagic Escherichia coli O157:H7 are known, including food of animal origin and produce. The ecology of this pathogen outside its human host is largely unknown. One third of its annotated genes still are hypothetical. To identify genetic determinants expressed under environmental factors, we applied strand-specific RNA-sequencing of strain E. coli EDL933 under 11 different biotic and abiotic conditions: LB medium at pH4, pH7, pH9, or at 15°C; LB with nitrite or trimethoprim-sulfamethoxazole; LB-agar surface, M9 minimal medium, spinach leaf juice, surface of living radish sprouts, and cattle feces. Of 5379 annotated genes, only 144 are transcriptionally completely inactive under all conditions. Of 1,771 hypothetical genes, 1,672 exhibit significant transcriptional signals under at least one condition. The pathogenicity island LEE showed highest transcriptional activity in LB medium, minimal medium, and after treatment with antibiotics. Unique sets of genes, including many hypothetical genes, are highly up regulated on radish sprouts, cattle feces, or in the presence of antibiotics. For instance, azoR is biotechnologically important, but its environmental function has been elusive. This gene is highly active on radish sprouts. Further, we observed induction of the shiga-toxin carrying phages by antibiotics and confirmed active biofilm related genes on radish sprouts, in cattle feces, and on agar plates. Thus, environmental transcriptomics uncovers hitherto unknown gene functions and regulatory patterns of Escherichia coli O157:H7. Eleven different conditions were sequenced on the SOLiD system. Of two of the condtions, spinach medium and LB-nitrite, technical replicates were sequenced. Of LB medium and radish sprouts, biological replicates were sequenced on an Illumina MiSeq.
2014-07-20 | E-GEOD-48199 | biostudies-arrayexpress
Project description:Multiple infection sources for enterohemorrhagic Escherichia coli O157:H7 are known, including food of animal origin and produce. The ecology of this pathogen outside its human host is largely unknown. One third of its annotated genes still are hypothetical. To identify genetic determinants expressed under environmental factors, we applied strand-specific RNA-sequencing of strain E. coli EDL933 under 11 different biotic and abiotic conditions: LB medium at pH4, pH7, pH9, or at 15°C; LB with nitrite or trimethoprim-sulfamethoxazole; LB-agar surface, M9 minimal medium, spinach leaf juice, surface of living radish sprouts, and cattle feces. Of 5379 annotated genes, only 144 are transcriptionally completely inactive under all conditions. Of 1,771 hypothetical genes, 1,672 exhibit significant transcriptional signals under at least one condition. The pathogenicity island LEE showed highest transcriptional activity in LB medium, minimal medium, and after treatment with antibiotics. Unique sets of genes, including many hypothetical genes, are highly up regulated on radish sprouts, cattle feces, or in the presence of antibiotics. For instance, azoR is biotechnologically important, but its environmental function has been elusive. This gene is highly active on radish sprouts. Further, we observed induction of the shiga-toxin carrying phages by antibiotics and confirmed active biofilm related genes on radish sprouts, in cattle feces, and on agar plates. Thus, environmental transcriptomics uncovers hitherto unknown gene functions and regulatory patterns of Escherichia coli O157:H7.
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Project description:Plants will meet various abiotic stresses during their growth and development. One of the important strategies for plants to deal with the stress is involved in metabolic regulation, causing the dramatic changes of metabolite profiles. Metabolomic studies have been intensively conducted to reveal the responses of plants to abiotic stress, but most of them were limited to one or at most two abiotic stresses in a single experiment. In this study, we compared the metabolite profiles of barley seedlings exposed to seven abiotic stresses simultaneously, including drought, salt stress, aluminum (Al), cadmium (Cd), deficiency of nitrogen (N), phosphorus (P) and potassium (K). The results showed that metabolite profiles of barley under these stresses could be classified into three types: osmotic stresses (drought and salt); metal stresses (Al and Cd) and nutrient deficiencies (N, P and K deficiencies). Compared with the control, some metabolites (including polyamines, raffinose and piperonic acid) in plants exposed to all abiotic stresses changed significantly, while some other metabolites showed the specific change only under a certain abiotic stress, such as proline being largely increased by osmotic stress (drought and salinity), the P-containing metabolites being largely decreased under P deficiency, some amino acids (lysine, tyrosine, threonine, ornithine， glutamine and so on) showing the dramatic reduction in the plants exposed to N deficiencies, respectively. The current meta-analysis obtained a comprehensive view on the metabolic responses to various abiotic stress, and improved the understanding of the mechanisms for tolerance of barley to abiotic stress.
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