Bronze Medal Criteria

Competition Deliverables

• Wiki
• Project Promotion Video
• Presentation Video
• Judging Form
• Judging Session
• Project Attributions
  • Our Attributions page provides detailed information about each member’s contributions and external support. It summarizes the roles of members in each part of the project.

Project Description

• By visiting our Project Description page, you can learn in detail about the challenges in treating inflammatory bowel disease and our solution, the “Xylego” project.

Contribution

• Our team provided many resources that future iGEM teams can learn from and utilize, such as creating new BioBrick parts, developing intestinal colonization of E. coli using xylitol, and establishing the iGEM Keio team. For more details, please refer to the Contributions page.

Silver Medal Criteria

Engineering Success

• On the Engineering page, you can see how we applied the DBTL (Design-Build-Test-Learn) cycle to various systems such as Mucosal healing system, Colonization support system, and Kill Switch system. We have improved our project by applying the lessons learned from each cycle.

Human Practices

• The Integrated Human Practices page introduces our process of engaging with various stakeholders, including doctors, PhDs from pharmaceutical companies, and inflammatory bowel disease specialists, to ensure our project meets real-world needs and satisfies safety and regulatory requirements. We incorporated the valuable feedback gained from these dialogues into our project.

Gold Medal Criteria

Integrated Human Practices

We aimed not only to utilize synthetic biology to solve social issues, but also to deeply understand the impact that such technology has on society and people, with the goal of creating maximum positive impact.

Classification of Activities

1. Problem Identification and Concept Creation

• Through interviews with experts, we clarified the current state and issues of inflammatory bowel disease and related conditions.
• We proposed the concept of reducing the frequency of medication and stopping the negative loop, and verified its feasibility through dialogue with experts.

1. Concept Verification and Reconstruction

• We identified challenges with substances to be produced as therapeutic agents, and reviewed the project direction, including determining therapeutic substances, through renewed dialogue with stakeholders.
• Based on feedback from various stakeholders, including physicians and instructors from pharmaceutical companies, we expanded the project’s focus to treatments that can be used in conjunction with current immunosuppressive therapies.

1. Solution Development

• We established a new concept called Xylego, and developed specific methods for repairing damaged intestinal epithelial cells and reducing medication frequency.
• We aimed to evaluate implementation feasibility through the construction of Kill Switch models, xylitol utilization models, and more.
• Through interviews with experts in molecular biology, protein structure, and microbiology, we planned and verified necessary experiments for actual experimental conditions and implementation.

1. Solution Deployment and Evaluation

• Through interviews with doctors and inflammatory bowel disease specialists, we examined the potential impacts and challenges of Xylego’s social implementation.

1. Results and Implementation

• We incorporated the needs and concerns obtained from dialogues with stakeholders into our project and made technical improvements.
• Throughout the project, we aimed to develop technologies that can be applied to treatments for other intestinal diseases and therapies using microorganisms.

For more details, please see the Integrated Human Practices page.

Education

Our team organized events for a wide range of audiences, from preschoolers to high school students and adults, to introduce them to synthetic biology and our project.

Overview

Events for Elementary and Middle School Students

• GENKI LABO FES: We held an event where participants created keychains by extracting DNA from broccoli, bananas, and their own oral epithelial cells.

Events for High School Students

• Exchange with Funabashi Prefectural High School
• Lecture at Tokyo University of Science: We gave a presentation about our project and iGEM.
• Interaction with the Biology Club: We conducted a small lecture on biology and provided hands-on experience with protein structure prediction using AlphaFold3.

iGEM Internship: Through project planning experiences, students had the opportunity to solve social issues using biology.

Events for University Students

• Brainstorming session for new members: We held an event for new members who joined in April to learn about iGEM through project planning while also enhancing team communication.

Events for All Ages (Preschool Children to Adults)

• School Festival (Kodaisai) iGEM Ennichi: At the school festival, we offered an experience of plasmid transformation into E. coli, DNA replication, and microbial collection using a traditional Japanese format called “ennichi.”
• Homecoming Day: Through poster sessions, we introduced iGEM to the public and held discussions with general visitors about our previous projects as well as this year’s project.

Conclusion

By hosting events for people of various age groups, we were not only able to provide opportunities to learn about synthetic biology to those who had never encountered it before, but also to inform those interested in biology about the iGEM platform and the effects that synthetic biology can have on society. Furthermore, through these activities, we were also able to receive feedback on our project.

For more details, please see the Education page.

Model

Our team constructed comprehensive mathematical models to support the development and optimization of “Xylego,” an E. coli that treats inflammatory bowel disease.

Overview

To support various aspects of the project, we developed the following models:

1. Ecological Distribution and Engraftment Modeling of Xylitol Metabolism: We investigated how many bacteria in the intestinal microbiota are capable of metabolizing xylitol.
2. Kill Switch: We conducted mathematical simulations to optimize protein expression levels for the Kill Switch, which is difficult to accomplish through experiments.
3. enzyme-constrained Flux Balance Analysis (ecFBA): We analyzed the xylitol metabolic pathway and proposed more efficient pathways.
4. Pharmacological Modeling:To quantitatively evaluate our therapeutic strategy, we developed two pharmacokinetic　pharmacodynamic models: one for the conventional therapy, and a second model for our engineered bacteria to simulate its local drug delivery and self-regulation.

Impact on the Project

Our modeling work provided the following key insights:

• The feasibility of Xylego colonizing the intestine by metabolizing xylitol
• Optimization of Kill Switch operating conditions, considering promoter leakage from the results of wet experiments, and optimization of degradation tag conditions
• Optimization of xylitol metabolic pathway
• Evaluation of therapeutic strategies at the implementation stage, such as drug delivery and self-regulation

Conclusion

The models we developed were essential for the design and optimization of our project, enabling us to predict results, optimize parameters, and make informed decisions throughout the development process.

For more details, please see the Model page.