Team:SCU-China/Medals
MEDALS
MEDALS
This year we got:
Best Model Nominee
Gold Medal
Bronze
#3 Attribution
We give a description of the work known from previous articles, and the work done by ourselves. The attribution of each of our team member is listed in the attribution page.
#4 Inspiration and Description
The project, CORegulaTIN, first came up by one of our team members according to his experience. We give a detailed description on the page Description.
#5 Characterization
In order to perform verification of all the promoters we use, we selected 3 alternative reporter proteins, yeGFP, amilCP and amilGFP and we chose amilGFP to characterize (BBa_K592010).
Silver
#1 Validated Part
We have designed many new parts related to our project and documented them on the Part's Registry. And we tested two of them in detail. (BBa_K3221009) and (BBa_K3221200).
#2 Collaboration
This year our team had many meaningful collaborations with teams Peking, SYSU-Medicine and Tianjing and we had helped each other in the projects. We also attended some iGEMer meetups to communicate with other teams. We have more information on pages collaborations and meetup.
#3 Human Practices
Our human practices include five parts: Meetup, Collaborations, Public and engagement, Consultation and Market. We took part in several meetups with other teams and got many pragmatic suggestions from professors. To propagate our project and synthetic biology, we held a community class and ACMA. We also made a board game and two videos. To ensure our engineered yeast has market prospect and can become an industrial product, we did some researches and a survey on the market, and we also made a business plan.
Gold
#1 Integrated Human Practices
To determine our project, we compared the main methods of producing cordycepin and consulted professor Huang. Then we decided to improve the biosynthesis route. After that, we went to a cordycepin company for a field trip and learned to focus only on increasing the yield.
To improve our project, we consulted professor Wang and decided to study HisG domain of Cns3 instead of NK. We also followed the judge’s suggestion and built a library of the linker between cns1 and cns2 protein and screened for the best one.
During the experiments, we used yeGFP provided by Peking as a signal to represent our protein and revised our experimental procedures based on the suggestions from Tianjin University. Besides, professor Liu helped us change to a better chassis to construct Met/Gal4 delay expression system and professor Cao helped us with modeling.
To make sure that our product has practical value and potential market, with professor Wang and Nan Zhang’s suggestions, we conducted a questionnaire and made a business plan. (More information about integrated HP pages).
#2 Improve a Previous Part
The yamilCP (BBa_K3221205) was improved from amilCP (BBa_K592009), which is a blue chromoprotein gene from Acropora millepora submitted by Team 2011 Uppsala-Sweden
We expected amilCP to be expressed efficiently in S. cerevisiae, so we chose amilCP for improvement. We processed codon optimization on the original amilCP sequence and added a consensus sequence (AAAAAA) for its usage in S. cerevisiae. And the new sequence was named yamilCP.
We respectively cloned the amilCP and yamilCP on the vector of pYES2-NTA. Then we transformed pYES2-amilCP and pYES2-yamilCP into S. cerevisiae and used galactose to induce blue chromoprotein expression respectively.
Finally, we observed a blue colony on the pYES2-yamilCP plate, which was earlier than the pYES2-amilCP plate. This confirmed that yamilCP express more quickly than amilCP. It shows that our improvement is successful.
#3 Model Your Project
The modeling section in 2019 SCU-China project is fully integrated, utilizing data from experiments and giving helpful guidelines to experiments. We conducted computational biological analysis including protein prediction, molecular dynamics, and molecular docking to enrich the characterization of the structural properties of the enzymes and provide linker evaluation for cns1-cns2 fusion-expression protein. We calculated the optimal synthesis level of cordycepin and pentostatin by enzyme kinetics to maximize cordycepin production, which is beneficial in industrial manufacture. We performed simulation of expression details of enzymes expressed in the delay system in silico, taking into account transcription regulation, translation, and degradation. We established a quantitative link between delayed time and initial methionine concentration, from which we could calculate corresponding initial methionine concentration according to the required delayed time. All the modeling results are instructive in subsequent researches and manufacturing. (More information about our modeling).
#4 Demonstration of Your Work
2019 SCU-China plans to ferment cordycepin and pentostatin together this year. During our fermentation, Cns3 is constitutively expressed that synthesize pentostatin (PTN) to inhibit adenosine deaminases (ADA) gradually. We want Cns1 and Cns2 to express when the yeast grows to the plat stage. And at this stage, the ADA is nearly denatured by PTN. So, it reaches a wonderful time for COR production.
As this is the first-time using S. cerevisiae for COR fermentation, the primary task is to prove that our design can work in yeast.
There are three parts in our design: Cns1 and Cns2 for COR production, Cns3 for PTN synthesis and the delay expression system.
Finally, we successfully verified functions of Cns1, Cns2, and Cns3, getting cordycepin and pentostatin. Also, we demonstrated delay expression system basically. For the future, we plan to explore a proper fermentation method and produce more data to optimize our fermenting modeling (More information about our demonstration).