The development of synthetic biology cannot be separated from the assistance of stem experiments at various levels, such as gene, cell, and protein, in which mathematical models and protein modeling play an increasingly important role. These models can better predict material expression at the gene level and behavioral interactions at the cell level. Through the simulation and prediction of models under various conditions, they can provide guidance for the conduct of wet experiments, saving labor and time. And at the application level, optimal strategies can be given to maximize the benefits.
How our model contributes to project
We divided the topic into three levels: gene, cell and application, and established mathematical models for three different scenarios: engineered bacterial gene expression, engineered bacterial interaction with SRBs, and engineered bacterial preparation delivery, respectively.
Based on differential equation modeling, we simulated three scenarios, including AHL production by SRB, QS-based suicide and induced expression system of E.coli, and predator-prey model of SRB and E.coli interaction, respectively. By simulating the growth and mutual competition process of the two bacteria, it was predicted that the populations of the two bacteria would eventually show an oscillating effect and be maintained at a low level, providing data support for the construction of the Cell Layer Model.
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We established the Flux Balance Analysis and Agent-Based Model (FBA-ABM) to explore the interaction between engineered bacteria and SRB, and the effect of engineered bacteria on the biofilm generation process. By simulating the growth process of two kinds of bacteria and biofilm, it was predicted to obtain that our engineered bacteria could inhibit the growth of biofilm by about 70% and significantly reduce the SRB biomass, which provided a theoretical basis for the feasibility of the topic.
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Based on aerodynamics and hydrodynamics, we simulated the physical process of E.coli placement into the sewer, the distribution of SRB in the sewer before and after the placement of E. coli, as well as the calculation of the maintenance cost saved after the placement of E.coli. By simulating the changes in SRB distribution and taking into account the current price of 45 RMB per 1m long sewer pipe, we concluded that for a 30m long sewer pipe, we can save 211.5 RMB in the daily maintenance cost of SRB treatment by the placement of E.coli.
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Based on the idea of semi-rational design, we constructed and screened several mutants that have the potential to improve the stability and activity of the AHL enzyme, which will be able to better degrade the population-sensing molecules of SRBs in the sewer environment.
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The safe secretion of the antimicrobial peptide and some targeting of the SRB microenvironment was achieved by designing a degradable disulfide bond-based connector to link the antimicrobial peptide with two enzymes in the form of a fusion protein. This gives our engineered bacteria the ability to target kill SRB.
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