Team:Wageningen UR/Notebook
Notebook
Curious to know more about our lab life and how we built our models and software tools? On this page you can find a short description of our projects and links to our notebooks. Enjoy reading!
Wetlab
Synthetic nitrification in Pseudomonas putida
Nitrification genes originating from autotrophic nitrifier Nitrosomonas europaea were expressed in Pseudomonas putida. This would allow P. putida to convert ammonia to hydroxylamine and subsequently nitrite, the first steps in the conversion of ammonia to dinitrogen in our biofilter.
Synthetic denitrification in Pseudomonas putida (1)
Denitrification genes originating from several native denitrifiers were expressed in Pseudomonas putida. This would allow P. putida to convert nitrate or nitrite to dinitrogen gas via the intermediates nitric oxide and nitrous oxide. These are the final steps in the conversion of ammonia to dinitrogen in our biofilter.
Synthetic denitrification in Pseudomonas putida (2)
Denitrification genes originating from several native denitrifiers were expressed in Pseudomonas putida. This would allow P. putida to convert nitrate or nitrite to dinitrogen gas via the intermediates nitric oxide and nitrous oxide. These are the final steps in the conversion of ammonia to dinitrogen in our biofilter.
Limiting nitrous oxide production in Pseudomonas putida
Steady nitrogen conversions were ensured by redirecting the electron flux towards the denitrification machinery in Pseudomonas putida. This was realized by creating denitrification machinery and downregulating native P. putida's ability to respire with oxygen, in parallel.
Synthetic methane oxidation in Escherichia coli (1)
The heterologous expression of soluble and particulate methane monooxygenase, and the expression of methanoldehydrogenase, completing the C1 conversion pathway from methane to biomass and carbondioxide in C1 auxotrophic Escherichia coli strains.
Synthetic methane oxidation in Escherichia coli (2)
The heterologous expression of soluble and particulate methane monooxygenase, and the expression of methanoldehydrogenase, completing the C1 conversion pathway from methane to biomass and carbondioxide in C1 auxotrophic Escherichia coli strains.
Methane-dependent kill switch in Escherichia coli
This kill switch couples methane concentration to a toxin-antitoxin system in Escherichia coli. Should the bacterium escape the biofilter, where the methane concentration is lower, toxin production is activated, thereby killing the cells.
Proximity-dependent kill switch in a microbial coculture
This kill switch will kill Pseudomonas putida and Escherichia coli if they escape from the biofilter. Outside the biofilter they lose the close proximity of each other, activating the kill switch.
Bacterial
co-dependency
A co-dependency was established between Escherichia coli and Pseudomonas putida by creating a cross-feeding community. The cross-feeding is based on amino acid exchange/auxotrophy and a carbon-source dependency.
Modeling
Modeling Coupled Nitrification and Aerobic Denitrification
To increase our conceptual understanding of the HNAD phenomenon, we developed a dynamic model. This model is able to simulate nitrogen dynamics connected to the increase in cell population.
Modeling a formaldehyde-dependent toxin-antitoxin system
To gain understanding of the dynamics of the methane-based biosafety circuit, a model was built using ordinary differential equations. Hypothetical systems incorporating protein X and a competitor protein were created to improve formaldehyde sensitivity.
Modeling biofilter
performance
To investigate the combined reduction of methane and ammonia emissions, a biofilter model was developed that determines the reactor size and performance for the microbial culture options we have considered for Cattlelyst. The model combines metabolic and reactor modeling with three different scales based on mass balances: single cell, single particle, and reactor scale.
Software
The iGEM PIPE
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Wikibase
Creation of Semantic Database to comprehensively search The iGEM Registry of Standard Biological Parts.