Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of LD13 mutant E. coli planktonic cultures and flow-cell biofilm after 24, 48, 72, 96 and 144 hours

ABSTRACT: LD13 mutant was considered for this analysis since it generated mushroom-type mature biofilm. This strain looses 17.6% of parental chromosome and lacks of several bacterial surface structures/genes but still has some novel autoaggregation genes. The global gene-expression profiles of LD13 flow-cell biofilm were compared after 24, 48, 72, 96, and 144 hr, respectively, as well as with those of LD13 planktonic cultures.

ORGANISM(S): Escherichia coli

SUBMITTER: Thithiwat May

PROVIDER: E-MEXP-1408 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The physiological and transcriptional response of Nitrosomonas europaea biofilms to phenol and toluene was examined and compared to suspended cells. Biofilms were grown in Drip Flow Biofilm Reactors under continuous flow conditions of growth medium containing ammonia as growth substrate. The responses of N. europaea biofilms to the aromatic hydrocarbons phenol and toluene were determined during short-term (3 h) additions of each compound to the biofilms. Ammonia oxidation in the biofilms was inhibited 50% by 60 uM phenol and 100 uM toluene. These concentrations were chosen for microarray analysis of phenol- and toluene-exposed N. europaea biofilms. Liquid batch cultures of exponentially growing N. europaea cells were harvested alongside the biofilms to determine differential gene expression between attached and suspended growth of N. europaea. Four sample groups of N. europaea cells were used in this study, with biological triplicates of each group. Groups were: Control (untreated) biofilms, phenol-exposed biofilms, toluene-exposed biofilms, and exponentially growing suspended cells. Biofilms were grown in Drip Flow Biofilm Reactors containing 4 independent growth channels and subject to 2 hour inhibition tests. During each experiment, 2 biofilm channels served as control with no inhibitor present and the other 2 biofilm channels were exposed to either 60 uM phenol or 100 uM toluene. Nitrite production was monitored throughout the experiment, and the given concentrations of phenol and toluene resulted in 50% inhibition of ammonia oxidation by the biofilms. Suspended cells were grown in batch reactors. Three 4-plex NimbleGen microarray chips were used, and each chip contained one sample from each experimental group. QC of samples was determined by spectrophotometric methods and using Agilent bioanalyzer traces to determine purity and integrity of RNA and cDNA. A sample tracking report was used to verify the correct hybridization of each sample to the intended array.

Dataset Information

Transcription profiling of LD13 mutant E. coli planktonic cultures and flow-cell biofilm after 24, 48, 72, 96 and 144 hours

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