Systems and Synthetic Biology

Student Learning Outcomes, Goals, Objectives:

Students successfully completing this course will be able to:

• Explain core principles of systems biology and synthetic biology and distinguish approaches used to understand biological systems from approaches used to design or re-engineer them.

• Design and critically evaluate DNA engineering strategies, including molecular cloning and DNA assembly, promoter and regulatory element selection, CRISPR-based genome editing, and strategies for validating engineered constructs.

• Interpret genomic and epigenomic information relevant to gene regulation, including promoter architecture, regulatory elements, chromatin state, and bioinformatic approaches used to analyze DNA-level regulation.

• Explain major approaches in RNA engineering and RNA-based therapeutics, including mRNA design and delivery, and interpret RNA-seq data in the context of biological systems.

• Apply protein engineering principles to structure-function relationships and therapeutic design, including computational protein-structure prediction.

• Analyze the design and behavior of synthetic genetic circuits and engineered cell systems, including feedback, logic, cell-cell communication, and therapeutic cell engineering such as CAR-T and related receptor-engineering strategies.

• Evaluate organism-level engineering strategies, including transgenic and genome-edited animal models, by linking molecular modifications to cellular, tissue, and whole organism phenotypes.

• Critically analyze primary research papers by evaluating the scientific question, experimental design, controls, data analysis, bioinformatic methods, interpretation, limitations, and significance of the work.

• Develop and communicate an original systems or synthetic biology project that integrates a biological question or engineering objective with an experimental design, computational or bioinformatic analysis plan, validation strategy, anticipated outcomes, limitations, and responsible research considerations.

Course Grading Information:

Activity/Performance Measure	Percentage/Points
Assignments	20%
Case Study Presentation	20%
Preparation, Attendance, and Discussion Participation	30%
Final Synthetic Biology Design Project	30%

Student performance will be assessed through case study assignments, a student-led research paper presentation, preparation and participation in discussion, and a final synthetic biology design project. The course emphasizes critical reading of primary literature, interpretation of experimental and computational data, and application of systems and synthetic biology principles to research design.

The final project will require students to develop an original systems or synthetic biology proposal that integrates molecular or cellular engineering with an appropriate experimental and/or bioinformatic analysis strategy.

Grading Scale

Percentage	Letter Grade
94-100%	A
90-93%	A-
87-89%	B+
84-86%	B
80-83%	B-
75-79%	C+
70-74%	C
Not used	C-
Not used	D+
Not used	D
Not used	D-
Below 70%	F

Attendance/Participation:

Active preparation and participation are central to this case study course and account for 30% of the final grade. Students are expected to complete assigned research papers before class and arrive prepared to discuss the scientific question, methods, figures, controls, computational or bioinformatic analyses, conclusions, limitations, and possible follow-up experiments. Participation will be evaluated based on preparation, consistency of engagement, quality of scientific reasoning, and constructive contribution to discussion.

Because much of the learning occurs through in-class paper analysis and discussion, regular attendance is expected. An absence reduces the opportunity to earn participation credit for that class. Students should communicate with the instructor about approved or documented absences and any appropriate alternative work in accordance with applicable university policies.

Course Materials Purchased by the Students:

No course materials are required to be purchased by the students. This course will use open access materials.