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Project properties |
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| Title | Modelling the impact of pH in the performance of microbial cell factories. |
| Group | Systems and Synthetic Biology |
| Project type | thesis |
| Credits | 36 |
| Supervisor(s) | Maria Suarez Diez |
| Examiner(s) | Prof. Maria Suarez Diez (SSB) Dr Rob Smith |
| Contact info | robert1.smith@wur.nl |
| Begin date | 2025/02/03 |
| End date | |
| Description | pH levels are critical for performance of microbial cell factories. pH affects production profiles, a typical example are solventogens, such as Clostridium acetobutylicum or Clostridium kluivery that at high pH produce acids and a low pH produce solvents. Accurate predictions of pH effects would benefit the design and operation of microbial cell factories.
We have developed a framework to model the impact of pH based on [1] and [2]. In brief, ODE describe changes in concentrations of extracellular metabolites, biomass and pH; uptake rates of metabolites are linked to their concentrations using Michaelis-Menten kinetics; pH affects proton flux in the model; finally, uptake rates are used in the constraint-based model to compute growth and production rates. Preliminary results show the correct characterization of the impact of pH the production profiles of C. acetobutylicum. The goal of the project is to expand the framework and adapt it to species such as C. kluivery, Pseuodomonas putida or Escherichia coli. References [1]Sánchez-Clemente et al 2018, https://doi.org/10.3390/proceedings2201297 [2] Gottstein et al. 2016 , https://doi.org/ 10.1098/rsif.2016.0627. |
| Used skills | Dynamic Flux Balance Analysis and methods for data and model integration. |
| Requirements | Knowledge of ordinary differential equations (ODEs) and /or constraint based modelling and Flux Balance Analysis (FBA). Basic Python knowledge. |