Team:OUC-China
Overview
Nowadays, strain quality has become a major factor limiting the yield of fermentation industry. We "Dispers" plan to design a software and hardware platform that automatically regulates the production and screening of strains to extract product simply to ensure high-quality strains and improve the fermentation yield.
Application
software
We are trying to develop software to help more teams design their own fermentation schemes. The functions of the software include setting your login account, helping you use the software, and collecting personal history records. After the team obtains its login account, it can log into our system. Then we will judge whether the scheme is feasible through our algorithm according to the team's selected bacteria species, existing pathways, current yield, target yield, expected yield, suicide yield and other data. We hope to improve the function of our fermentation platform through this software and make it more in line with the fermentation schemes of different teams.
hardware
We intend to design an automated fermentation and product screening device. We can ferment strains in fermenters and use expansion bed adsorption to isolate and purify the products. We selected CroCD-TuC3 as our adsorbent. Through the design of infrared sensors and computational processor, the speed of fermentation liquid outflow can be kept constant, achieving the long-term continuous use of our designed device.
Safety Aspects
We are convinced that we are responsible for the environment and our colleagues in the experiment. For the sake of environments, all the chassis organisms in our experiment will be sterilized before being abandoned to prevent the genes from leaking.
Selection of Suicide Proteins
At the beginning of the project design, we chose YopE as the suicide protein of our engineering bacteria. The YopE cytotoxin of Yersinia pseudotuberculosis is an essential virulence determinant that is injected into the eukaryotic target cell via a plasmid-encoded type III secretion system. Injection of YopE into eukaryotic cells induces depolymerization of actin stress fibres. After communicating with other teams, we found that using YopE as the suicide protein in our design not only posed a security threat to the platform's R&D personnel, but also posed a greater security problem to the staff of the microbial factory. After communicating with the DUT-China team to test the sacB toxic protein in their project, we decided to use sacB as the final suicide protein of our platform because of its good killing effect and better biosafety.
Prevent escape
Considering that the engineering bacteria designed on the platform will be used in the fermentation tank of the factory, in order to prevent a large number of production engineering bacteria from escaping into the environment and causing pollution, we decided to design a switch to prevent escape. We design another kill riboswitch switch which can detect the concentration of an improtant element in culture medium If it spreads into environment accidentally, our kill switch can detect the low concentration of the important element and kill the engineered bacteria. This suicide switch is coupled with the copy number system. We designed to place it in the reintroduced PFK gene. When the engineering bacteria are stored in the fermentation tank, because there are enough detected substances, the PFK gene is normally expressed. When the engineering bacteria escape to the environment, the lack of detected substances causes the PFK gene expression to be closed and the engineering bacteria to die.
Challenge
The challenge of the project is how to quantitatively analyze our various parts and the production of engineering bacteria. Due to the time limit and the epidemic situation, we only quantitatively analyzed our components respectively. And sadly, we are unable to detect the production of engineering bacteria in the fermentation tank and the expression characteristics of our components. In order to see the situation in the fermentation tank used by our platform, we simulated the fluctuation of the production of engineering bacteria in the platform design of the fermentation tank using modeling cellular automata.
In the future, we may need to import all our parts into engineering bacteria to detect the combined expression of platform elements. At the same time, we will also test the productivity of the platform to further upgrade the software. For hardware, we will also contact interested companies and factories to test our ideas. In the process of HP communication, Vland was very interested in our project and glad to provide the company with engineering bacteria to test the performance of our platform software and hardware.
