Project description:S. Typhimurium parent, ppGpp0 and dksA strains were grown to OD's of 2.3 (ESP) and 4.2 (LSP) and subjected to ChIP-chip analysis at 60 nt resolution. Overall design: 38 samples (parent strain, ΔrelAΔspoT, ΔdksA grown to ESP or LSP, protein-DNA crosslinked and fragments immunoprecipitated with Ab against E.coli RNAP beta subunit (Neoclone, cat # WP023), or minus Ab as control. DNA fragments purified & labelled with dCTP-Cy5 and hybridised against Cy3-dCTP labelled gDNA on OGT 4 x 44K 60 mer S. Typhimurium SL1344 array).
Project description:The purpose of this study was to define the TZD effect in Pseudomonas aeruginosa. Transcriptional profiling of Pseudomonas aeruginosa wild-type strain,reference strain PAO1, as control Vs. PAO1 strain exposed to a final 0.02mM of TZD derivative ((z)-5-octylidenethiazolidine-2,4-dione).
Project description:Sohn2010 - Genome-scale metabolic network of
Pseudomonas putida (PpuMBEL1071)
This model is described in the article:
In silico genome-scale
metabolic analysis of Pseudomonas putida KT2440 for
polyhydroxyalkanoate synthesis, degradation of aromatics and
Sohn SB, Kim TY, Park JM, Lee
Biotechnol J 2010 Jul; 5(7):
Genome-scale metabolic models have been appearing with
increasing frequency and have been employed in a wide range of
biotechnological applications as well as in biological studies.
With the metabolic model as a platform, engineering strategies
have become more systematic and focused, unlike the random
shotgun approach used in the past. Here we present the
genome-scale metabolic model of the versatile Gram-negative
bacterium Pseudomonas putida, which has gained widespread
interest for various biotechnological applications. With the
construction of the genome-scale metabolic model of P. putida
KT2440, PpuMBEL1071, we investigated various characteristics of
P. putida, such as its capacity for synthesizing
polyhydroxyalkanoates (PHA) and degrading aromatics. Although
P. putida has been characterized as a strict aerobic bacterium,
the physiological characteristics required to achieve anaerobic
survival were investigated. Through analysis of PpuMBEL1071,
extended survival of P. putida under anaerobic stress was
achieved by introducing the ackA gene from Pseudomonas
aeruginosa and Escherichia coli.
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