Contributions
We noticed that iGEM currently lacks comprehensive guidelines for the use of AI, so we hope to contribute some of our thoughts to establish such standards. We conducted a social experiment to verify that the use of AI poses potential biosecurity risks. To mitigate these risks, we believe that AI usage needs to be standardized and traceable. Based on these two principles, we developed an AI Safety Policy for SynBio together with an AI Dialogue Record. The AI Safety Policy is designed to check the AI usage standards of iGEM teams, while the AI Dialogue Record serves as a log of AI usage. We hope to engage the iGEM community in discussions about AI usage and work together to establish more robust AI standards, fostering a culture of responsible innovation in AI. "We have taken the first step."
In addition, we made contributions to the iGEM community in the Parts section by submitting two innovative Composite Parts: BBa_K5461001 and BBa_K5461000. These two plasmids form the foundation of our "Bacterial Cellulose Modification Machine." BBa_K5461001 is a POI-SpyCatcher expression plasmid with a standardized interface, enabling bacterial cellulose to acquire different functionalities. BBa_K5461000 serves as an "scaffold," linking bacterial cellulose to the POI. It expresses Curlis Fiber that connect cellulose-Curlis Fiber-Spy system-POI. This system provides future iGEMers with a tool for bacterial cellulose modification, allowing for easier testing of new functions. Moreover, future iGEM teams can leverage this system to perform high-throughput screening of bacterial cellulose modifications.
We have selected the Part BBa_K1159200 to complement existing data by adding new test results. Using the Co-Immunoprecipitation (Co-IP) method, we successfully verified the strong binding between SpyCatcher and SpyTag by demonstrating the formation of a complex, which confirms their interaction under physiological conditions. This approach provides additional binding data for the SpyTag system and also validates the feasibility of this system from an immunological perspective. These findings are crucial for our project, especially in verifying the modification and binding of bacterial cellulose.
The SpyTag/SpyCatcher system is a technology for irreversible conjugation of recombinant proteins. The peptide SpyTag (13 amino acids) spontaneously reacts with the protein SpyCatcher (12.3 kDa) to form an intermolecular isopeptide bond between the pair[1]. DNA sequence encoding either SpyTag or SpyCatcher can be recombinantly introduced into the DNA sequence encoding a protein of interest, forming a fusion protein. These fusion proteins can be covalently linked when mixed in a reaction through the SpyTag/SpyCatcher system.
Using the Co-Immunoprecipitation (Co-IP) method, we successfully verified the strong binding between SpyCatcher and SpyTag by demonstrating the formation of a complex, which confirms their interaction under physiological conditions. This approach provides additional binding data for the SpyTag system and also validates the feasibility of this system from an immunological perspective. These findings are crucial for our project, especially in verifying the modification and binding of bacterial cellulose.
You can find more information through our Parts wiki page and part BBa_K1159200 on iGEM Registry.
On May 26, 2024, LCG-China held its first team meeting, marking the beginning of our iGEM journey. From day one, we have been contemplating what contributions we could make to the iGEM community. Our goal is to carry out pioneering, impactful work that can have long-term applications. During our brainstorming session, we turned our attention to the use of AI. It has been over two years since ChatGPT was widely available, and AI has deeply integrated into our daily lives. We began to question the impact of AI on synthetic biology and how AI development influences responsible innovation. We hope to explore these issues in collaboration with other iGEMers.
We conducted a social experiment in which we used ChatGPT to obtain viral sequences and directly submitted them to a DNA synthesis company. To our astonishment, this request did not trigger any safety warnings. This highlighted the significant gaps in biosecurity related to AI usage, indicating there is still much room for improvement.
Drawing from iGEM’s Safety Form and Notebook, which ensure project safety and traceability, we established an AI Safety Form and AI Dialogue Record, both based on AI safety principles. Our goal is to assist iGEM teams in using AI tools responsibly in their iGEM projects through this system.
You can view our work on AI Safety at the following pages: AI Safety Policy and AI Dialogue Record on our wiki.
In September 2024, Ginkgo Bioworks also launched its AI tools, marking the increasing frequency of AI applications in the SynBio field. Through our social experiments, iGEM projects, and tools, we hope to raise awareness among the next generation of iGEMers regarding responsible innovation in AI usage. Our ultimate goal is to foster a culture of responsible AI use within the iGEM community.
Based on the LCG-China iGEM project's bacterial cellulose modification machine, we successfully defined the two plasmids of the system as universal bacterial cellulose modification plasmids. These plasmids can effectively link bacterial cellulose, Curlis Fiber, and POI (protein of interest) through the SpyTag/SpyCatcher system and the properties of Curlis Fiber, enabling biological modification of bacterial cellulose. The two plasmids are BBa_K5461001 and BBa_K5461000.
The New Composite Part BBa_K5461001 functions to form a POI-SpyCatcher fusion protein for linking with the SpyTag, serving as the "Plug-and-Play Protein Assembly Module" of the bacterial cellulose modification machine. The structure of BBa_K5461001 is J23119-BBa_B0034-POI-SpyCatcher-BBa_B1006. We utilized commonly used iGEM promoter J23119, RBS BBa_B0034, and terminator BBa_B1006. Additionally, we designed standard BsaI interfaces (GGTCTCaGGTAtctagt - POI - GAGCtGAGACCa) on both sides of the POI, allowing for easy replacement of the POI. The POI standard interface in BBa_K5461001 implies the infinite potential for extending the functionalities of the bacterial cellulose modification machine. Future iGEMers can utilize this system to attempt various modifications of bacterial cellulose or even perform high-throughput screening by replacing the POI with a POI library.
We also submitted another New Composite Part, BBa_K5461000, named "T7p-RBS-GST-csgA-Spytag-T7t". Its function is to produce CsgA to form Curlis Fiber, and to incorporate the SpyTag into the Curlis Fiber to facilitate subsequent cellulose modification. This is the "scaffold module" of the bacterial cellulose modification system.
The combination of these two Composite Parts, BBa_K5461001 and BBa_K5461000, constitutes the bacterial cellulose modification machine for the LCG-China iGEM project. This system not only introduces an innovative structure for biological modification but also provides an expandable POI interface. We have defined standardized components while maintaining the potential for creative flexibility.
You can find more information in our Parts wiki page, and part: BBa_K5461001, and part: BBa_K5461000 on iGEM Registry.
[1] akeri, B., Fierer, J.O., Celik, E., Chittock, E.C., Schwarz-Linek, U., Moy, V.T. and Howarth, M. (2012). Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. Proceedings of the National Academy of Sciences of the United States of America, 109(12), pp. E690-E697. doi:10.1073/pnas.1115485109.
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