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Project properties |
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| Title | Using genome-scale metabolic models to evaluate energy conservation strategies in E. coli |
| Group | Systems and Synthetic Biology |
| Project type | thesis |
| Credits | 36 |
| Supervisor(s) | Claudia de Buck, Prof. Maria Suarez Diez |
| Examiner(s) | Prof. Maria Suarez Diez, Rob Smith |
| Contact info | Robert1.smith@wur.nl |
| Begin date | 2025/11/14 |
| End date | |
| Description | At SSB, our projects are either offered as computational or experimental projects. Nearly all projects can be altered for either BSc or MSc students (as required). For more information, please contact Rob Smith (robert1.smith@wur.nl). Note that we will evaluate applications based on discussing the match between a student’s current competencies and the competencies needed for the project – sending a CV is not required.
This thesis project will be a computational project. The project will be supervised by Claudia de Buck and Prof. Maria Suarez Diez. Microbial cell factories run the most efficiently when the process does not require oxygen, because fermentation processes (without oxygen) can be designed to obtain yields close to the maximum theoretical yield. However, some products like L-lysine or citrate require an ATP investment in the metabolic production pathway, which cannot be supported by conditions without oxygen (as the ATP conservation during fermentation is significantly lower compared to respiration). As a result, these bioprocesses have to be run with oxygen, which increases the costs of production due to more stirring, cooling and a loss of yield. Within the ICEMAN project we’ve developed a metabolic engineering strategy to increase the conservation of energy in Escherichia coli in conditions without oxygen. The initial design was based on a proof-of-concept strain that produces ethanol from glucose. We would like to explore the full potential of this strategy in a broader context: starting from different carbon-sources, producing different products, under varying levels of oxygen. We will use a genome scale metabolic model of E coli to answer this question and to explore this scenario. The student working in this project will: - Write python scripts to perform constraint based modelling. - Adapt existing model of E. coli to different C sources and products. - Evaluate the feasibility of metabolic engineering strategies. References related to project: Monk, J. M., Lloyd, C. J., Brunk, E., Mih, N., Sastry, A., King, Z., Takeuchi, R., Nomura, W., Zhang, Z., Mori, H., Feist, A. M., & Palsson, B. O. (2017). iML1515, a knowledgebase that computes Escherichia coli traits. Nature Biotechnology, 35(10), 904. https://doi.org/10.1038/NBT.3956 Zhang, C., & Hua, Q. (2015). Applications of Genome-Scale Metabolic Models in Biotechnology and Systems Medicine. Frontiers in Physiology, 6(JAN), 413. https://doi.org/10.3389/FPHYS.2015.00413 |
| Used skills | |
| Requirements | programming (python) and modelling of microbial metabolism (such as BPE34306, metabolic engineering of industrial microorganisms. |