iGEM represents a collaborative and warm-hearted community that thrives on the spirit of sharing and learning. As we embarked on our journey this year, we were greeted with the wisdom of our predecessors and the camaraderie of fellow competitors. Their guidance was invaluable, and the support was unwavering, creating an atmosphere of collective growth and innovation. In the true spirit of iGEM, we aim to contribute to this community by sharing the knowledge we've gained and the challenges we've overcome. Our hope is that by offering these insights, we can provide a foundation for the success of future teams, ensuring that the cycle of mentorship and collaboration continues to flourish. Together, we can push the boundaries of synthetic biology and inspire the next generation of scientists.
We have engineered bacteria based on CsgA by inserting Tet v2.0 to achieve the prodrug Click-to-release application. In our project, we explored the application of non-natural amino acids in Tet v2.0 with CsgA, and based on previous literature and data simulation predictions, we identified two sites: S89TAG and F97TAG. Based on these findings, we conducted a series of characterizations, from the formation of curli proteins, to a series of characterizations with TCO-Cy5, and finally to the validation of the Click-to-release effect using TCO-Coumarin.
As a significant contribution to the scientific community and to facilitate the progress of future research endeavors, our team has meticulously compiled and made available a comprehensive set of resources for subsequent teams to build upon.
Experimental Protocols
We have meticulously documented all of our experimental protocols, which are essential for the replication and further exploration of Curli Fibers in bacteria. Understanding and studying Curli Fibers is a complex and delicate process that requires precision and a deep understanding of microbiology. Our team has encountered numerous challenges and setbacks during our experiments, which has led to the development of a robust set of protocols.
These protocols are not merely a collection of procedures but a testament to our trial-and-error process, encapsulating the lessons learned from each failure. We have organized this document in a user-friendly manner, ensuring that it is accessible and practical for future teams. It includes detailed step-by-step instructions, safety precautions, and troubleshooting tips that we have found to be critical in the successful execution of such experiments.
This document has been placed in the engineering section of our shared resources, where it can be easily accessed by those who are interested in continuing our work or exploring new avenues within the field of bacterial Curli Fiber research.
Parts Registration
We have also registered two key parts with the iGEM Registry of Standard Biological Parts: BBa_K5231000 and BBa_K5231001. These parts are not just simple components; they represent the culmination of our research and the distilled essence of our findings.
Each part registration includes a thorough characterization, detailing the properties, behaviors, and interactions of the Curli Fiber components we have studied. This characterization is vital for other teams as it provides a clear and concise understanding of our results. It allows them to quickly grasp the intricacies of our work and to consider how these findings can be integrated into their own research.
By including all our characterizations, we aim to accelerate the research process for other teams. They can use this information to make informed decisions about their own experimental designs, potentially saving them time and resources that would otherwise be spent on initial characterizations.
In summary, our contributions are designed to be a springboard for future research, offering a solid foundation upon which subsequent teams can build. We hope that by sharing our protocols and part characterizations, we can foster collaboration, innovation, and a deeper understanding of Curli Fibers in bacteria, ultimately advancing the field of synthetic biology.
In our human practices initiatives this year, we've been in close communication with industry experts and academic mentors to uncover the societal impact of our project and to incorporate feedback from stakeholders into our development process.
Through this endeavor, we've identified safety as a paramount concern. Recognizing that all applications, particularly in the realm of biotechnology, must be pursued with safety as a fundamental principle, we've partnered with several iGEM teams. Together, we've authored a white paper on our use of the EcN bacterial strain, as well as the ethical considerations surrounding synthetic biology applications. Our aim is to offer valuable insights to future teams as they navigate similar challenges.
2024 E.coli Nissle 1917 White Paper
This white paper, led primarily by PekingHSC, offers an exhaustive examination of E. coli Nissle 1917 (EcN). It details EcN's background, benefits, and its role in treating diseases like cancer and IBD. The paper also explores the treatment possibilities, industry potential and safety concerns of genetically engineered EcN, along with innovative iGEM projects that utilize them for biomedical applications.
The white paper is available in both Chinese and English.
Biosafety and Bioethics in Synthetic biology
We also participated in the creation of another white paper that detailed the biosafety and bioethics regulations and potential problems in synthetic biology as well as clever solutions current and past iGEM teams came up with to deal with them. We collaborated with over a dozen teams to conduct project analysis and case studies in multiple different fields such as bioremediation and agriculture, and we hope this guide can provide valuable insight to future iGEM teams when they encounter similar problems on their quest for innovation.
This year, we've strategically bolstered our design team with the aim of elevating the visual appeal and presentation of our projects. Their performance has been remarkable, surpassing our expectations and setting a new benchmark. Below, you'll find examples of our designers' work, which we hope will spark further inspiration for subsequent teams.
To maintain a cohesive theme throughout the project, we utilized a green color scheme across all design elements. At the start of our project, we considered our design to be akin to building a modular platform, like a game where components can be freely assembled and replaced—much like Tetris. This inspired us to use a pixel art style to emphasize this feature. The low-resolution pixel composition brings a minimalist style that highlights the “tool” aspect of our project. Meanwhile, pixel art's emphasis on simple design and clear contours allows complex information to be presented in an accessible and easily understandable manner, enabling visitors to quickly grasp the core content of the project. Moreover, pixel art is often associated with retro technology and video games, conveying a sense of experimentation and innovation that aligns with the cutting-edge and innovative nature of scientific and biotechnological projects.
Project Name
After finalizing our project name as "Curmino," we began working on the logo design. As medical students, we incorporated the typical symbol of medical schools—a "snake"—into the "C" of our project name. Additionally, since our team is from the School of Pharmacy, we integrated a pill as a minor element within the "i" to symbolize our project's focus on therapeutic applications.
First Version of the Logo
After finalizing our project name as "Curmino," we began working on the logo design. As medical students, we incorporated the typical symbol of medical schools—a "snake"—into the "C" of our project name. Additionally, since our team is from the School of Pharmacy, we integrated a pill as a minor element within the "i" to symbolize our project's focus on therapeutic applications.
Wiki
To carry on our team's design tradition from last year, we used a green color palette. This time, however, we assigned a unique color to each section of the wiki. This helps readers easily identify where they are on the page, and the color scheme will be consistent throughout the project, including in our presentations.
Final Version of the Logo
We refined our logo by assigning a unique color to each letter of "Curmino," reflecting the distinct colors used for each section of our wiki. The final version retains the core concept of the original design.
Summer Team Shirt Design
For our logo, we started with the first letter "C" from the project name. To make our project easily recognizable, we added a folded arrow in the middle of the "C," representing targeted therapy. Below the arrow, the shape of an "A" can be seen, symbolizing unnatural amino acids, while also representing click chemistry. As a team from a Chinese medical university, our logo subtly incorporates the Chinese character for "medicine"(医), conveying both the essence of our project and the unique identity of our team and culture.
On the back of the shirt, we used the "C" shape again to illustrate the project's workflow, including elements and reactions from our experiments. This allows people to easily grasp the essence of our project just by looking at the shirt. Finally, our team name "PekingHSC" is placed on the right sleeve, making it easy for us to introduce our team during interactions.
Project Promotion Video
The goal of promotion is to capture the attention of passersby, spark curiosity about our project, and leave a lasting impression. Synthetic biology is not just for university students but belongs to the world. Hence, we aimed to present our project in the simplest and most entertaining way possible. We adopted a pixel art style to show that synthetic biology is made up of small building blocks. During discussions and conferences, we realized that many people, including judges, found it difficult to understand our project. To address this, we designed characters for Curli fibers like CsgA and CsgB, inspired by the game Among Us, to represent Curmino. Additionally, we used the lock-and-key mechanism to explain click chemistry. The video's storyline is about a battle between our "army" and cancer cells, using engaging characters and vibrant colors. With Pokémon background music and sound effects, we presented our project in a fun, cartoonish way. Our goal is for everyone who watches the short video to gain a better understanding of our project and synthetic biology. If just one person becomes interested in synthetic biology after watching, the video will have served its purpose.
Presentation Video - Animation Production
In the presentation video, most animations were drawn using Adobe Illustrator and then animated in Microsoft PowerPoint. After the Wet Lab and presentation team designed the project flow and experimental mechanisms, we discussed and finalized the content that needed animation. The animations are designed with simple, fun illustrations and harmonious colors to help viewers easily grasp the project concepts.
Game
Given that previous peripheral products were all designed in a pixelated style, we decide to create our project as a pixel-art game like Mario. The game is set in the tumor microenvironment,, where CsgA and CsgB collaborate to kill tumor cells. Compared to the simple level-clearing mode of previous Mario games, our game is more complex. We changed the mode into Click-to-release mode. Our gamemode is a representation of the Click-to-Release reaction. Through this reaction process, active drug molecules are locally and efficiently released to kill tumors cells specifically. Through specific moves, players can successfully kill tumor cells.
In the game, the first objective is to anchor CsgB to the tumor site in a recon mission, so CsgA can locate cancer by first nucleating on CsgB. Then the baton is passed to CsgA as they carry their keys and embark on a search for the correct prodrug lock. If they match, it means that the Click-to-Release reaction was successful and the delivery of drugs is completed, empowering our CsgA to be able to eliminate cancer cells.
The player directly controls CsgA and CsgB through keyboard inputs.
By coding and designing this game, we hope that future teams can consider also adopting a more interactive artistic medium when designing their products since they are easier for people to understand and allows for greater artistic expression. We firmly believe that the most important part of engagement is the sense of involvement, in education, advertisement and so on.
Comic
When we were cooperating with Jilin University to promote synthetic biology, we used hand-drawn cartoons to re-characterize the application of bacterial therapy. We aim to shatter the stereotype that bacteria are disgusting and deadly and tell people that bacteria might one day help us defeat complicated and terminal diseases in an interesting way.
