Week 1

WL:

Wet Lab group were divided into four groups. To seek inspiration for our project, each group is tasked with researching and reporting on previous award-winning iGEM teams.

HP:

1. Project brainstorming and previous case studies.
2. Ensure scholarship deadlines and apply requirement.

Week 2

WL:

We were still studying the past winning projects and tried to derive possible themes from their projects. In this week, four proposals emerged.

HP:

1. Brainstorm Projects and previous case studies.
2. Ensure scholarship deadlines and apply requirement.

Week 3

WL:

1. We attempted to identify more promising projects.
2. Consequently, four additional new proposals came to fruition this week.

HP:

1. Brainstorm Projects and previous case studies.
2. Ensure scholarship deadlines and apply requirement.

Week 4

WL:

We provided more detailed redesigns for four out of the eight proposals discussed in the last two weeks. Following this, we had a discussion to determine their feasibility.

HP:

1. Brainstorm Projects and previous case studies.
2. Ensure scholarship deadlines and apply requirement.

Week 1

WL:

In this week, the WL team was divided into two groups instead of four. Each group had to choose one out of the four proposals discussed last week and delve into further discussions. We faced a difficult decision between 'disease detection' and 'bio-electricity'. In the end, we opted to pursue 'bio-electricity' as our subject, aiming to generate electricity through microorganisms.

DL:

Discuss the application of microbial fuel cell and to think up an innovative solution to apply.

HP:

1. Contact entrepreneurs and inquiry of our project suggestion.
2. Explan different thoughts of biodegradable materials for kit's cover.
3. Discuss online educational program.
4. Design advertisement music.
5. Apply and prepare of current scholarships.

Week 2

WL:

We came up with two ideas related to bio-electricity. Firstly, we aimed to desalinate seawater using a microbial fuel cell. Secondly, we proposed to degrade polylactate, synthesized by E. coli, into lactate using an optogenetic system. The lactate would then be utilized to generate electricity through Shewanella bacteria.

DL:

Understand the working principle of detection kit and find the appropriate professors to help. Also determine the structure of Dry Lab.

HP:

1. We discussed an online educational program.
2. We designed advertisement music.
3. Apply and prepare for current scholarships.

Week 3

WL:

After conducting extensive data querying, we discovered that the development of microbial fuel cells has reached an advanced stage. Consequently, we shifted our focus towards identifying promising proposals in the field of disease detection, which was the right issue we tried to deal with.

DL:

Separate the job by individual strength. Also discuss about using proper method to predict the structure.

HP:

1. We prepared posting scientific-related knowledge on an Instagram account for promoting synthetic biology.
2. Discussed about comic book design.

Week 4

WL:

1. We opted to utilize circular RNA present in human saliva as a biomarker for cancer detection.
2. Tried to use several DNA oligo with hairpin structure to recognized and amplify circular RNA.
3. Planned to employ a lateral flow strip to display the test results.

DL:

Try to use KinDA to simulate the hairpins, while using the 3D RNA score to compare and select the most ideal target.

HP:

1. We prepared posting scientific-related knowledge on an Instagram account for promoting synthetic biology.
2. We contact professors and inquiry of project direction and further research methods.

Week 5

WL:

1. We identified three circular RNA that highly related to breast cancer.
2. After consulting with some professors, they advised us to explore types of cancer other than breast cancer that are challenging to detect using current diagnostic methods.
3. Discovered some isothermal amplification methods. Such as rolling circle amplification(RCA), recombinase polymerase amplification(RPA), reverse transcription recombinase polymerase amplification (RT-RPA) and Loop-mediated Isothermal Amplification(LAMP).

HP:

Finish our project report power point file and prepared meeting with professor meeting.

Week 1

WL:

Comprehended the mechanism and reaction temperature of RCA, RT-RPA, RPA, and LAMP, respectively.

DL:

Choose the target circRNA and determine how to calculate the reaction rate. Further discuss the detail about 3D RNA score and RPA model.

HP:

1. Scholarship apply schedule (platform researching and email contact) arranged.
2. Educational project content preparation.
3. Preparation for interviewing doctors.
4. Preparation for interviewing professors.

Week 2

WL:

1. Discovered PCRD, a lateral flow cassette we applied to detect cancer.
2. We tried to explore the experimental protocols of RCA and RT-RPA using circular RNA as a template. In the end, we couldn't discover any literature mentioned how to amplify circular RNA through RT-RPA.

DL:

Need to change the target circRNA and solve the problems of the reaction rate and 3D RNA score. Heating equipment needs to find a battery for heating.

HP:

1. We arranged the scholarship application schedule (platform research and email contact).
2. We prepared the educational project content.
3. We prepared interviews with doctors.
4. We prepared to interview professors.

Week 3

WL:

1. Since there were no references mentioned on how to amplify circular RNA by RT-RPA, we came up with another solution to fix this problem. We planned to transform circular RNA to complementary DNA utilizing reverse transcription, then amplify the cDNA through RPA.
2. We found that ProtoScript II reverse transcriptase exhibited higher efficiency. We were curious about its potential inclusion in the RCA process.
3. Investigated the mechanism of PCRD, then determined its feasibility.

DL:

Building up the models of RPA/ RCA/ Lamp, PCRD/ Hairpin and fluid. Also establishing the software and wiki structure.

HP:

1. Team logo design.
2. Explanation about who the sponsors are.

Week 1

WL:

Investigated the MgCl2 concentration causing the aggregation of RCA products, and determine the presence of modified probes or hairpin structures on gold nanoparticles.

DL:

Check the sequence that cDNA is replacing. Also establishing the buffer diffusion model. Then use software to judge the reaction is completed.

HP:

1. Discussion and preparation of an academic conference.
2. Grant prize apply—preparation and check.
3. Voting for the final decision of team logo design.

Week 2

WL:

1. We found that after the circularization process, RNase R is needed to eliminate linear form RNA. By adding RNase R, we could ensure the purity of our circularization product.
2. Utilize selected circRNA as our target, design a corresponding RCA primer.

DL:

Need to set up a terminal time for the diffusion model to stop. The heating equipment needs to combine with software.

HP:

1. We designed our promotion video.
2. We discussed and contacted the biotechnological companies and sponsors.
3. We contacted the travel agency and inquired about the travel schedules.
4. We prepared our questionnaire.

Week 3

WL:

1. Ensure whether the sequence in circBank is complementary to circRNA or cDNA of circRNA.
2. Design a primer for RPA and RCA.
3. Design a DNA probe which is attached to a gold particle.

DL:

PCRD model needs to wait for the input value to be tested and also think up the storing method and look up the changing color trend. For hardware, designing the automatic placement of the salt.

HP:

1. Educational science camp preparation and discussion.
2. Inviting foreign and other iGEM teams for iGEM map collaboration.

Week 4

WL:

1. Ensure all the chemicals and kits are needed. Check protocols and detailed information for further experiments.
2. Find access to thiol-modified DNA, then find protocols for attaching thiol-modified DNA to gold nanoparticles.

DL:

List out the exact components for heating equipment. Think up the tool for creating the application. Apply for the sponsorship or tuition.

HP:

1. Voting for the final decision of team logo design.
2. Wiki preparation and suggestion.

Week 1

WL:

1. Clarify cloning process, consider enzyme restriction site for digesting insert and vector sequence.
2. Clarify each step for enzymatic circularization, including the verification way using gel electrophoresis method.

DL:

Use Simscale for the diffusion model. Get familiar with RCA, RPA, DnaProbe, and the PCRD model. Ask senior about the details of the heating equipment.

HP:

1. Wiki designing & concept brainstorming.
2. Wiki characters design.

Week 2

WL:

1. Comparing the pros and cons of T4 RNA ligase 1 and T4 RNA ligase 2. Determine using splint to bring the sequence close together, elevate circularization efficiency.
2. Determine to use pyrophosphate in the monophosphorylation process in circRNA synthesis.

HP:

1. Wiki designing & concept brainstorming.
2. Wiki characters design.

Week 3

WL:

1. Design a splint for circularization. According to research, we found that RNA might not spontaneously form a circular structure, thus we design a splint targeting back-splicing junction for higher specificity.
2. Use RNAfold web server to predict the splint structure.
Avoid secondary structure of splint, also design the entropy of the splint close to 1.

HP:

1. Preparation and discussion of educational science camp and life science camp promotion.
2. Shoot photos for each lab.

Week 4

WL:

1. We found that we should eliminate redundant splint DNA after circularization. So we determine to use DNase I for degradation of splint DNA.
2. Determine the type of gel we used to verify the circularization process. Candidates including polyacrylamide gel, agarose gel. Find the pros and cons of each type of gel.
3. Determine the vector we're going to use in the cloning project.

DL:

Reaching the tutorial of Simbiology. Briefly setting up the geometric factors of the diffusion model. Wiki had added the progress list and the sidebar.

HP:

1. Making our own questionnaire.
2. Preparation for NYCU academic conference communication.

Week 5

WL:

1. We tried to find previous research related to developing long-repeated ligased insert sequence in AELA-PCR.
2. Ensure the condition to ligase splint to our target sequence for circularization.

HP:

We made the final decision of the traveling agency and traveling schedule.

Week 1

WL:

1. Clarify each step in our workflow pathways.
2. Try to synthesize gold nanoparticles.

DL:

1. Understand that the radius may affect the segregation extent. Purchase the essential components and discuss the possible game type to create.
2. Discuss the game design thoughts with Human Practice. Determine the game content, background and how to combine the information in it.

HP:

1. Collaboration response of World Nature Conservation Day.
2. Wiki character design progress.
3. Colorectal Cancer alliance contact and biotech companies contact.
4. Preparation of educational science camp.
5. Preparation for flight to France.

Week 2

WL:

1. Clarify condition of protocols in our workflow pathways.
2. Confirm rotating speed of hula mixer and stir bar with advisor.

DL:

Understand the reasons of segregation and changing color, further quantify the extent. Add some word effects in wiki page.

HP:

1. Wiki character design progress.
2. Preparation for interviewing Colorectal Cancer's patient and doctor.
3. Research for funding platform.
4. Preparation for online meeting collaboration.
5. Instagram post of educational content brainstorming.
6. Scholarship and sponsors contact.
7. Wiki page and report model design.

Week 3

WL:

1. Clarify condition of protocols in our workflow pathways.
2. Doing research and making comparisons of running circRNA in E-Gel EX and Agarose gel.
3. We found that band position of linear RNA and circRNA have difference in E-Gel EX, we could use the difference to distinguish linear RNA from circRNA.

DL:

Have solved the problems of heating equipment. Try to use machine learning for setting up the model. Improving the game fluency.

HP:

1. Wiki character design progress.
2. Preparation for interviewing Colorectal Cancer's patient and doctor.
3. Research for funding platform.
4. Preparation for online meeting collaboration.
5. Instagram post of educational content brainstorming.
6. Scholarship and sponsors contact.
7. Wiki page and report model design.

Week 4

WL:

1. Clarify condition of protocols in our workflow pathways.
2. Try to synthesize gold nanoparticles, modified O.D. value by centrifuge synthesized gold nanoparticle samples.

DL:

Can use Simbiology to generate ODEs and simulate the graph. The blueshift range has determined. Renewing the games and thoughts on the wiki page.

HP:

1. Instagram reels collaboration of lab life.
2. Team roster check.
3. Mentorship contact and problem solving.
4. Wiki graphic preparation.
5. Traveling agency contacting.
6. Apply for current scholarship.

Week 1

WL:

1. We prepared the needed buffer for gold nanoparticle synthesis in advance.
2. Senior Peter took us to combine nanogold + probe on 8/5.
3. Prepare the report and poster of the Linkou exchange meeting.

DL:

Collaborate with several teams, prepare the script and rehearse beforehand. Thinking up the structure of application for machine learning.

HP:

1. Preparation and discussion for promotion video.
2. Discussion of wiki page design.
3. Preparation of NYCU educational podcast collaboration and Instagram reels collaboration.
4. Preparation of educational science camp work sheets.
5. Contact for entrepreneurship interview.

Week 2

WL:

1. Rehearsal for the Linkou exchange conference.
2. Read carefully about judging criteria, judging form from iGEM.

DL:

Rehearse for the upcoming collaboration and giving some possible problems. Revise the script to improve fluency.

HP:

1. Preparation and discussion for promotion video.
2. Discussion of wiki page design.
3. Preparation of NYCU educational podcast collaboration and Instagram reels collaboration.
4. Preparation of educational science camp work sheets.
5. Contact for entrepreneurship interview.

Week 3

WL:

1. Prepare for the education camp and decide how to convey the synthetic biology concept to children so they can understand.
2. Conducting ligation with vector experiment part in AELA-PCR, we tried to endlong the time for better ligation outcome.
3. Organize wiki structure and content.

DL:

Rehearse for the collaboration. Finding the relationship of cDNA radius to the segregation of the particles. Put the collaboration team by geographical location in wiki page.

HP:

1. Wiki background design and wiki game progress report.
2. Discussion for team cloth design.
3. Preparation for entrepreneur intervie with doctor interview.
4. Final check of NYCU academic conference communicational preparation and discussion.
5. Preparation for educational science camp.
6. Preparation and final checking of scholarship applying document.

Week 4

WL:

1. We successfully synthesized 13nm AuNPs.
2. We found out that EDS cannot detect the probe, so we seek to use XPS to assist in the detection of probes conjugated with AuNPs.
3. We conducted RT-RPA experiment, however failed due to no template control shows band.
4. Conduct Insert PCR, and colony PCR.

DL:

Discuss about the volcano plot, distribution of particles and calculate the segregate extent. Had added the reset button, music, etc. in the game.

HP:

1. Explanation of project related SDGs.
2. Questionnaire form discussion.
3. Advices and suggestions explaining for presentation methods.
4. Judging rubric explanation.
5. Wiki game progress report.
6. Reminder for Michigan Synthetic Biology team collaboration.
7. Preparation for traveling.

Week 5

WL:

1. We saw 13nm gold nanoparticle under XPS.
2. We diluted the RT-RPA sample and run gel to see the testing limit of the amplification method.

DL:

Determine the necessity of AUC/ ROC graphs. Simulate the diffusion phenomenon in several ways. Redesign the title and add maps of wiki page.

HP:

1. Animation making of experimental process of RCA, RPA, nano particles gathering, circular RNA detecting and wiki game.
2. Preparation and discussion of promotion video timeline.

Week 1

WL:

1. We discussed safety form content, and finished them.
2. We conduct circularization experiment. we analyzed and reviewed problems which may lead to circularization experiment failure.
3. We conduct AELA experiment. We successfully finished the parts including insert ligation, digestion, ligation with vector, however failed at the process of transform.
4. We prepared a waiver for the gold nanoparticle we have synthesized.
4. We conduct RT-RPA experiment. Unfortunately, we failed the experiment since there is always a band in no template control (NTC). We tried to analyze and review the problems in each step which may lead to RT-RPA experiment failure.
5. We successfully conducted RPA experiment to ensure the RPA primer we designed works.

DL:

Add some effects in the game and discuss the ranking system. The hardware simulation graph has been elaborated.

HP:

1. Completing scholarship applying document.
2. Discussion of presentation way for NYCU academic conference communication.
3. Reminder of promoting synthetic biology on science camp.

Week 2

WL:

1. Try the condition of adding how much MgCl2 will lead to gold nanoparticle solution color change.
2. Referring Wiki page from the 7th-grade NTHU iGEM team.
3. We found out that there should be a minimum concentration of IVT concentration before conducting the circularization experiment.
4. We successfully conduct the circularization experiment.

DL:

Can use R language to run the cluster heat map. The revision on hardware equipment.

HP:

1. Checking for scholarship applying document.
2. Explanation and discussion of wiki game transcription.
3. Presentation video editing.

Week 3

WL:

1. Starting the blue print of our wiki design-Experiment.
2. Starting the blueprint of our wiki design-Proof of Concept.
3. Starting the blueprint of our wiki design-Engineering Cycle.
4. Revising our reagents used for the RCA experiment, by changing ProtoScript II RT to Induro, since we couldn't get multiple copies of cDNA.

DL:

Update the wiki page. Revise the equations of the PCRD model and transform the equations into ODEs. Design a handbook of the hardware. Need some pictures for the PCRD model for machine learning.

HP:

1. Completing promotion video shooting, editing, and uploading.
2. Preparation of traveling schedule.

Week 4

WL:

1. Revising the process of the Circularization experiment to get a better yield of the target circularized RNA.
2. Referenced the iGEM Wiki of three other schools.
3. Decide how to express our Wiki design-Proof of Concept.
4. Decide how to express our Wiki design-Engineering cycle by dividing into 3 main sections.

DL:

Confirming and retrieving the data with Wet Lab, further integrate the model. Upload the code onto github and renovate the hardware.

HP:

1. Writing wiki content for human practice pages and related graphic drawing.
2. Final check for scholarship applying document.
3. Report for traveling schedule.

Week 1

WL:

1. Wiki content submission: continue modifying Wiki layout, Wiki content.
2. Uploading experiment pictures and diagrams onto Wiki.

DL:

Using the initial value from paper. Need to set up a time-depending function for diffusion. Do the animation of the whole automatic procedure. Debug the wiki page.

HP:

1. Checking and modifying the judging form.
2. Wiki content completing and discussion.

Week 2

WL:

1. We successfully conduct the RT-RPA experiment with no band showing on the no template control line.
2. We finished Wiki content based on the wet labs part.

DL:

Finish up the application, machine learning model. Do the diffusion model and compare under different concentrations.

HP:

1. Preparation and discussion of the presentation video.
2. Shooting and editing the presentation video.

Week 3

HP:

1. Preparation for France traveling.
2. Preparation for final presentation and questions.

Week 4

HP:

1. Preparation for France traveling.
2. Preparation for final presentation and questions.

Week 5

HP:

Fly to France.