Designing smart gut bacteria: utilizing biological foundation models for genetic component engineering
Project Description
The gut microbiome plays a crucial role in human health and disease, presenting a highly promising frontier for synthetic biology interventions. Recent advancements in artificial intelligence, particularly biological foundation models, offer unprecedented capabilities to design novel proteins and genetic regulatory elements. This project aims to leverage these cutting-edge computational tools to engineer synthetic genetic circuits tailored specifically for human gut bacterial cells. By integrating AI-driven sequence generation with synthetic biology, we will create genetic components that can precisely control bacterial cell behaviors. The computationally designed components will then be physically constructed and rigorously validated in our laboratory using advanced molecular biology techniques. Ultimately, this interdisciplinary research paves the way for developing next-generation living therapeutics and programmable cellular models for gut health.
Supervisor
LAI, Yong
Quota
2
Course type
UROP1100
UROP2100
UROP3100
UROP3200
UROP4100
Applicant's Roles
The undergraduate students will be actively involved in both the computational design and experimental validation phases of the project. They will utilize biological foundation models to generate novel genetic sequences and predict their functions. Subsequently, the student will perform molecular cloning and cell culturing to construct these components in gut bacteria, assisting in assay execution, data collection, and result analysis.
Applicant's Learning Objectives
1. Foundations of synthetic biology: understand the fundamental concepts of synthetic biology, genetic engineering, and the manipulation of gut microbiota.
2. Computational biology skills: gain practical experience utilizing biological foundation models and bioinformatics tools to design and analyze genetic components.
3. Experimental techniques: develop hands-on proficiency in standard molecular biology laboratory skills, including PCR, molecular cloning, plasmid construction, and bacterial transformation.
4. Experimental design and execution: learn how to bridge in-silico design with in-vitro/in-vivo validation by designing, executing, and troubleshooting biological assays to test the engineered cell behaviors.
5. Scientific communication & analysis: enhance essential research skills by systematically documenting experimental data, critically analyzing results, and communicating scientific findings.
2. Computational biology skills: gain practical experience utilizing biological foundation models and bioinformatics tools to design and analyze genetic components.
3. Experimental techniques: develop hands-on proficiency in standard molecular biology laboratory skills, including PCR, molecular cloning, plasmid construction, and bacterial transformation.
4. Experimental design and execution: learn how to bridge in-silico design with in-vitro/in-vivo validation by designing, executing, and troubleshooting biological assays to test the engineered cell behaviors.
5. Scientific communication & analysis: enhance essential research skills by systematically documenting experimental data, critically analyzing results, and communicating scientific findings.
Complexity of the project
Challenging