Team:YiYe-China/Collaborations
With BIT Team
BITis organized by the Beijing Institute of Technology. As a college team, BIT has been participating in iGEM since 2013 and has received five golds, three silvers medals, and one special nomination. This year, BIT's project is also about the early detection of colorectalcancer. Different from ours, BIT aims to detect cancer polyps through the content of mRNA. Thereofore, we decided to host a virtual workshop on the night of July 30th. Before the event, our team met with the BIT team to go over specific details about our first public online activity on July 19th.
1. In what form should we host this activity? Should it be through zoom or other platforms?
2. Who is the target audience for this lecture? Students like us or older adults.
3. What should the content of our slides be? Should we focus more on the knowledge about CRC or the biologic concept of our project?
4. How should we publicize this activity? Online, in-person, or both? Should we prepare a poster, an invitation, or a registration form?
5. More ideas for future collaboration.
Both teams actively engaged in the discussion and willingly shared our ideas. At the end, we made the final decision. Our workshop will be both through zoom and another platform called Bilibili, where audiences can see it live. Since it may be more time-consuming and expensive to do the invitation in person (the cost of printing poster as well as little brochures), we agreed to make an e-poster and invitation and then share them through social media. Most likely, we will expect more students like us coming, along with some parents. While it may require some deeper understanding of biology and this may make our workshop dull, we tend to focus more on the knowlege about CRC so that everyone would understand and learn something at the end.
In terms of work assignment, both teams will in charge of their slides, and at the end, we will combine them together. If there are any overlaps, we could either delete some part of it or do some paraphrase. While our team will be responsible for making poster and invitations, BIT will ensure that both zomm and Bilibili work on that day. Last but not least, we planned to meet again the day before the workshop to make sure that everything went smoothly.
After the plan was devised, our team expressed sincere gratitude to BIT again. It is no doubt that we will get much help from such a wonderful and talented team. Likewise, BIT showed their awe in us. One of their team members exclaimed, "We are so amazed that you guys do so well as high school students. We are really proud of you! Keep up the good work!"
On July 30th, the online workshop was fabulous. We had over 20 peopel coming to zoom. and nearly 5000 on Bilibili. Everyone's efferts parid off, and both teams look forward to our future collaboration.
Collaboration with HZAU-China
On Aug.15th, we had a virtual meeting with HZAU-China,who aimed at the detection of IBD of pets. We've heared that HZAU has a wonderful modeling team. YiYe, as a high school track, knows little about modeling, so we decided to consult with HZAU and hoped that they would offer us some advice.
First, both teams gave a brief presentation on their project. After understanding each other's lab processes, we cut right into our main topic.
One of our team members shared some of our thoughts to them.
1. For our project, as CRC and the status of methylation are closely related, so measuring the status of methylation is our main method of cancer detection.
So for modeling, first we need to do some research on such colleration, aka the relationship between the degree of methylation and the stages of cancer. Then, we need to find a way to quantify the measurement of methylation. Our current results are all qualitative. We could tell by seeing the color changing, but to optimize and make our results more explicable, they'd better be quantitative.
2. To make our project more efficient, we have to show the status of methylation in a more straightforward way. Now based on our lab design, we try to show the results through a Red Fluorescent Protein, mCherry. Idealistically, we would be able to use the results through our naked eyes.
In the case of modeling, there should be a quantitative relationship between the status of methylation and the concentration of our fluorescent protein. The results we got through qPCR reflected that there was a distinct difference between these two, and we may take advantage of those to create our model.
3. Toehold switch helps with how the trigger expresses, but the amount of expression is directed by the contentration of the trigger. Our lab design is a single trigger opening, so we remain uncertain about the efficacy of triggering the florescent protein.
We hope that we could know more about the relationship between the trigger and toehold through modeling so that we could amplify the signal to make our results more direct.
After hearing our thoughts, HZAU gave us the following suggestions:
● For the relationship between CRC and methylation, we could go over previous IGEM teams to see if any of them did toehold or methylation model. We could learn from them and get a basic idea.
● We could think about all possibilities first. One option is to calculate the T/C. As we already have the data from qPCR, we don't have to consider T and C respectively; instead, we could directly got the ratio from qPCR.
● We have to do some research to find the the specific baseline for the degree of methlation based on the medical theory. Then we need convert the degree into the ratio of T/C to verify the accuracy of the model.
● When it comes to toehold modeling, we have to think about themal energy model. We can get some reference from nature RBS calculator in 2013, Stanford IGEM 2020, and CSMU IGEM 2020.
We felt much clearer about what we should do after talking with HZAU, . They offered that if we have future questions, we are walcomed to text them, and they would love to help more.
Collaboration Within IGEM Community
At the end of August, we participated in the 8th CCiC meeting. Unfortunately, becuase of COVID, our team joined the meeting online, but we still took advantage of the opportunity to learn from other teams. Besides that, CCiC hosted many other workshops, such as Modeling, Safety and Security, and a high-school-track one.
In the Q&A part, our biological design to detect CRC by using DNA methylation and toehold switch got recognition from judges. They asked us how we picked our target DNA and if our method could be applied to all stages of CRC. Later in a breakout room, more people from other teams came to know more about our project. They asked some questions, and we tried our best to clarify them. Still, there are some that we feel uncertain.
When the meeting was over, our team members gathered to have a discussion with our advisors.Here is the list we made based on the questions:
1. There are many stages in CRC, like stage I, II, III, etc. Which stage is our method aim at?
The target DNA used in our method have an accuracy rate of 76%--89% among all stages of CRC. Therefore, theoretically, it should be able to be applied to all stages. But since it would be better to detect it earlier, the therapeutic effects would no doubt be the best in stage I, with a survival rate up to 90%. That is why we aim for the early detection of CRC.
2. The target DNA TFPI-2 and SDC2, are they the cause of CRC or the result of it?
According to the research, most of them talk about methylationas a signal for CRC, while there is few about methylation causing CRC. So there is no direct evidence to prove whether or not methylation is the cause. We also look forward for future research.
3. How to avoid false positive/negative? What is our current accuracy rate?
To avoid such issues, we will take Professor Li's (who we interviewed) suggestions, which is using two target DNAs to improve its accuracy and sensitivity. Currently, due to the conditional restrictions, we couldn't do clinical trials. However, the project's high sensitivity and accuracy are the prioity. In the future, we will strive to enhance these two indexes. If we have similar target DNAs, our product's sentivity could reach up to 98% and have a 95% accuracy.
4. Besides being less uncomfortable, what is another advantage of our project?
Our project's main purpose is to lessen the discomfort people feel during other detection tests. In addition to that, we also take other facotrs into account. For instance, the medical condition is not so good in less developed areas. While our product only requires the basic equipments, clinics in those places could also use it for detection. If so, more people could get detected at the ealy stage. Moreover, the equipment used in our product are portable, which makes detection even more convenient.
We all agreed that those were excellent questions. To be honest, there were some that we had never thought of before; thus, it is really helpful for us to improve our project and get better prepared for future Q&A session.
Collaboration
Collaborate with other 2021 iGEM teams
- With BIT
- With HZAU-China
- iGEM community