Transcription profiling of P. putida KT2440 cultivated at 7 bar and at 7 bar with elevated dissolved oxygen tension
ABSTRACT: We investigated the changes of gene expression in PHA-producing Pseudomonas putida KT2440 cultivated under elevated pressure (7 bar) and under combined elevated pressure (7 bar) and elevated dissolved oxygen tension by means of DNA microarrays. RNA samples were isolated from cells cultivated in chemostat under very well defined growth conditions (growth rate, medium, temperature, pH,...)
BACKGROUND: Elevated pressure, elevated oxygen tension (DOT) and elevated carbon dioxide tension (DCT) are readily encountered at the bottom of large industrial bioreactors and during bioprocesses where pressure is applied for enhancing the oxygen transfer. Yet information about their effect on bacteria and on the gene expression thereof is scarce. To shed light on the cellular functions affected by these specific environmental conditions, the transcriptome of Pseudomonas putida KT2440, a bacter ...[more]
Project description:A genome-wide analysis of gene expression of the root-colonizing bacterium Pseudomonas putida KT2440 in the rhizosphere of corn (Zea mays var. Girona). To identify reliable rhizosphere differentially expressed genes by this bacterium, populations of P. putida KT2440 previously exposed to a rhizospheric life style for seven days in the rhizosphere of corn were compared with populations previously exposed to a rhizospheric life style for a long period of 138 days.
Project description:The response of antibiotic adapted resistant mutants of B. cenocepacia J2315 to antibiotic stress was investigated using expression profiling of three biological replicates and comparing the profiles to the J2315 parent control grown without antibiotics.<br>A reference design was used with Cy3 labeled genomic DNA of B. cenocepacia J2315 as common reference. Three test conditions with three biological replicates each were compared to three replicates of the control condition.<br>Test conditions: J2315-A grown in the presence of 250 ug per ml amikacin, J2315-M grown in the presence of 8 ug per ml meropenem and J2315-T grown in the presence of 60 ug per ml trimethoprim and 300 ug per ml sulfamethoxazole.<br>Control condition: J2315 parent strain grown without antibiotics.
Project description:Cells were transfected with 100 nM c-Jun siRNA (Santa Cruz Biotechnology, sc-44204) using elecroporation (conditions?). 48 hours after transfection, cells were irradiated with 5 Gy and incubated at 37 C for 2 hours. They were then harvested and RNA and protein were prepared and processed for microarray analysis and Western Blot verification respectively. Affymetrix Gene Array 1.0 ST arrays were hybridized as standard (www.affymetrix.co.uk)
Project description:We used a reference design with a dye swap. We used 6 experimental probes grouped by treatment and sample day. "Treatment" fish consisted of rockfish exposed to forced decompression resulting in barotrauma, followed by subsequent recompression to their original depth. Control fish did not experience forced decompression. Fish were sampled at day 3, day 15 and day 31 post-decompression.
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.
Project description:The response of P. putida KT2440 (PB2440) to preferential carbon source and varying nitrogen levels was studied in this experiment. The culture was grown in minimal medium with 2mM glucose as carbon source and different concentration of ammonium chloride as nitrogen source. For nitrogen limiting condition 2mM ammonium chloride was used whereas, for nitrogen rich condition 20mM ammonium chloride was added in the medium. Overall it was seen that the strain could grow efficiently in varying nitrogen conditions by adapting or regulating their metabolism without compromising on the growth rate. To ascertain how the cells were coping with the nitrogen stress, gene expression by microarray was performed. RNA extraction was done using Qiagen RNeasy minikit (Germany). Standard Affymetrix protocol was followed for hybridization with GeneChip P. aeruginosa Genome Array supplied by Affymetrix as GeneChip for P. putida were not supplied by any company.
Project description:We used Progenika oligonucleotide arrays to monitore the gene expression of P. putida during carbon source stimulus experiments. After ensuring steady state conditions on benzoate, the stimuli were introduced by changing the carbon source from benzoate to glucose, from glucose to fructose and from fructose to benzoate, respectively. The single stimuli were monitored over a time period from 10 to 120 minutes after changing the carbon source by three representative timepoints. Moreover, the steady state conditions were compared among each other. Supplementary file: Individual normalized signal intensity VALUES for each channel of each array are provided in the FullNormalizedMatrix.txt file.
Project description:Comparative genome hybridization was used to study genomic diversity among S. suis strains in more detail. All strains were hybridized to an oligo-array based on the genome of P1/7 with P1/7 as an internal reference in all experiments.