On August 18th, 2020, our team KUAS had an academic conference with our new collaborator: team KSA. We had online conversations regarding ecofriendly materials and synthetic biological countermeasures for COVID-19 before the meeting. Team KSA had “Eco-friendly production/recycling of paper through the removal of lignin with genetically engineered bacteria” as their main interest this year. We discussed experimental methods with biological insights and proposed new methods such as agarose gel electrophoresis.
Their research was aimed at not only water/waste minimization & eco-friendly material development, but also revolutionizing the paper production industry. We offered counsel about activities for human practices such as interviewing field workers or educating elementary school children online.
Even though they were only high schoolers, our discussions consisted of vigorous partnership vision and not just a temporary exchange of ideas. We, as a more experienced team, conferred knowledge such as how modeling could be done for their project and how relevant enzymes could be found in the Parts Registry. In turn, they suggested new potential usages of our temperature measuring apparatus. In spite of their young age, it was a meaningful encounter with mutual gains.
Our team KUAS collaborated with a Korean high school team named SIS this year. We presented our topics and the progress made so far. Team SIS had great interest in securing food availability by developing fungal pathogen detection methods in food storages. SIS mainly focused applying their project on developing countries, especially Sri Lanka which suffer from malnutrition in 25 districts. Their topic was aimed to solve the situation in which people suffer from malnutrition, even though the country’s rice production is enough for their population, because so much rice is lost during storage.
After we shared our topics for this year, we exchanged opinions and advice about each other’s project. We also proposed a guideline for their dry lab activities and suggested possible activities for human practices. It was a very meaningful time sharing our views on synthetic biology and had a chance to look back on our project.
Through this collaboration, we could share our understandings and views on iGEM and have a chance to look back on our project.
When we were designing our RNA thermosensor. We were looking for sequences to start with. During the early stage of our project, we were inspired by Jilin China's project in 2018. Their project was about designing RNA parts which responds to changes in temperature
We sent an email and discussed how they achieved their results. Through the conversation, it helped us to set our destination and methods to get to it.
These are the questions we sent and the answers - some of them are summarized.
1. What advantages do you think synthetic biology-based thermometers have over digital thermometers?
1. the temperature of the fermenter may not be even and the intracellular thermometer allows the bacteria to react with much more accuracy.
2. temperature can be the switch of bacteria’s metabolism, shutting down some biochemical reactions in the bacteria without artificial control. Since the optimal temperatures at different fermenting stages are different, bacteria’s metabolic pressure as well as the resource assumption can both be cut down.
2. What were some critical questions your team received after presentation and during the poster session?
A. 1. How to make sure our thermosensor is under translational control rather than transcriptional control? (it’s a pity that we didn’t answer this question) And now, I think we may quantify mRNA by RT-qPCR and then calculate the fluorescence intensity of certain amount of mRNA (Unit defined by yourself).
2. In what field will you put your thermosensor into practice? (about its application)
3. Why is your team’s bio-thermometer suitable for yogurt production and in which form did your team expect the final product to be (e.g. packaged in a glass tube)? Also could you explain more about how your thermometer can reduce the energy expenditure during yogurt production?
The optimal temperatures of bacteria growth and bacteria fermentation are different, which means we should change to different temperatures during the process of fermentation. According to our Modelling and HP, energy can be saved when the initial temperature is turned down.
4. Did judges raise any issues about biosafety? If any, how did your team solve it?
A. No, they didn’t.
1. How were the RNA sequence candidates chosen (where stem-loop and SD sequence are contained)? Did you use the program Mfold during the process?
A. At first, we chose loops including AAUAA，AAAUAA，AAAAUAUAAA，AAAAAAUAUAAA，AAAAAUAUAUAUAAAA, etc. and use Mfold(program) to predict the secondary structure of RNA. And parameters like the chosen Tm, structures and so on matched our expectation. Then we did a screening selection with our model.
2. We are planning to put CHA sequence in our RNA thermosensor instead of SD sequence in yours. Can you advise how to find the candidates - tools or methods?
A. You can design with Anti-CHA sequence. You can additionally add mismatch, and the anti sequence length. Next, predict parameters for RNA, and select the optimums you need.
But of course, this is just my personal suggestion.
(CHA sequence is a sequence which binds to other RNA sequence of interest. You have to know no more than it is just a specific sequence we want to put in)
3. When you are using the SynRT to yogurt fermentation temperature measurement, there must be a problem of specificity. Even though the temperature didn't reach over the melting temperature, there must be some GFP because the RNA would unfold gradually making Hill function. How did you solve the problem?
A. Due to the problem of leakage which is prevalent in biology, it’s a challenge for us to find parts with reduced leakage. Because it usually takes a long time to find the one. Therefore, we utilized Normalized Fluorescence for characterization.
According to our previous experiment, protein’s expression is linearly increased as the temperature increases. [Link]
Despite this, parts like this cannot be fully satisfactory when put into industrial practice. I hope in the future, parts with little leakage can be found.
With numerous iGEM teams
We surveyed iGEM teams last year to make primary data for research about synthetic biology. STEPI - a government institute in South Korea - researched the field and made a survey. We took the papers and did the research there. 38 iGEM teams contributed to fill the survey. So finally this year, a research paper - Foresight for Policy on Science, Technology, and Innovation Ⅺ - Science and Technology Outlook: Synthetic Biology - was published where our data is.