Expression data from Arabidopsis seedlings expressing a synthetic oxygen sensor device
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ABSTRACT:
PROVIDER: PRJNA485328 | ENA |
REPOSITORIES: ENA
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Project description:Saeidi2012 - Quorum sensing device that produces GFP
Saeidi et al.
(2012) has modelled a quorum sensing device that produces green fluorescent protein (GFP) as reporter in the presence of Acyl Homoserine Lactone (AHL).
This model is described in the article:
Characterization of a quorum sensing device for synthetic biology design: Experimental and modeling validation
Nazanin Saeidi, Mohamed Arshath, Matthew Wook Chang, Chueh Loo Poh
Chemical Engineering Science. December 2012.
Abstract:
Modeling of biological parts is of crucial importance as it enables the in silico study of synthetic biological systems prior to the actual construction of genetic circuits, which can be time consuming and costly. Because standard biological parts are utilized to build the synthetic systems, it is important that each of these standard parts is well characterized and has a corresponding mathematical model that could simulate the characteristics of the part. These models could be used in computer aided design (CAD) tools during the design stage to facilitate the building of the model of biological systems. This paper describes the development of a mathematical model that is able to simulate both the dynamic and static performance of a biological device created using standard parts. We modeled an example quorum sensing device that produces green fluorescent protein (GFP) as reporter in the presence of Acyl Homoserine Lactone (AHL). The parameters of the model were estimated using experimental results. The simulation results show that the model was able to simulate behavior similar to experimental results. Since it is important that these models and the content in the models can be searchable and readable by machines, standard SBML (system biology markup language) format was used to store the models. All parts and reactions are fully annotated to enable easy searching, and the models follow the Minimum Information Requested In the Annotation of Models (MIRIAM) compliance as well as the Minimum Information About a Simulation Experiment (MIASE).
Figure 4a of the reference publication has been reproduced as curation figure. The plot shows the performance of the model at different concentrations of the inducer (3OC12HSL=5E-10, 5E-07, 5E-07).
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