BME-455-davidlin-2026-09-16-01-46-47

Create simple metabolic models.

Lecture, in-class problem solving, writing assignments.

Writing assignments.

Find and apply appropriate analysis techniques to metabolic models.

Lecture, in-class problem solving, writing assignments.

Writing assignments, final project.

Use metabolic models to calculate yield of bioproducts.

Lecture, in-class problem solving, writing assignments.

Writing assignments, final project.

Discuss uncertainty around calculated bioproduct yield (through variability analysis and trade-off plots).

Lecture, in-class problem solving, writing assignments.

Writing assignments, final project.

Predict genetic manipulations to induce or increase bioproduction (knockouts, gene additions, overexpression targets, etc.).

Lecture, in-class problem solving, writing assignments.

Writing assignments, final project.

Use biochemical database to find biochemistry, build gene-protein-reaction links, and interpret metabolic model results.

Lecture, in-class problem solving, writing assignments.

Writing assignments.

Use metabolism visualization tools (like Escher maps and KEGG pathways) to aid in result interpretation and communication.

Lecture, in-class problem solving, writing assignments.

Writing assignments, final project.

Analyze feasibility of a proposed metabolic pathway using metabolic models and thermodynamic analysis techniques.

Lecture, in-class problem solving, writing assignments.

Writing assignments, final project.

Select appropriate control systems for gene expression.

Lecture, in-class problem solving, writing assignments.

Writing assignments, final project.

Select appropriate genetic engineering tools.

Lecture, in-class problem solving, writing assignments.

Writing assignments, final project.

Select appropriate genetic delivery systems.

Lecture, in-class problem solving, writing assignments.

Writing assignments, final project.

Propose metabolic engineering of E. coli for a new bioproduct. Report yield, uncertainty, and recombinant DNA technologies to use. Defend this design through pathway analysis.

Lecture, written assignments, final project.

Final project.

Week 1

Course introduction and overview. Definition, approaches, and history of metabolic engineering.

Lecture, reading (Chapter 1)

Written assignment: syllabus review. In-class quiz: definitions and terminology.  

Week 2

Metabolic models: structure, mathematic representation, assumptions, and reconstruction.

Lecture, reading (Chapter 2 of Metabolic Engineering), written assignment.

Written assignment: Develop a “toy” metabolic model.

Week 3

Metabolic models: flux balance analysis. Medium definition. Yield calculations.

Lecture, reading (provided), written assignment.

Written assignment: demonstrate each technique on “toy” metabolic model and E. coli model, iJO1366.

Week 4

Metabolic models: other fundamental analysis techniques: variability, coupling, parsimony, and trade-off plots.

Lecture, reading (Chapter 3 of optimization methods), written assignment.

Written assignment: demonstrate application of these techniques on “toy” model and iJO1366.

Week 5

Metabolic thermodynamic analysis. Futile vs. productive cycles.

Lecture, reading (Chapter 5 of Optimization Methods), written assignment.

Written assignment: Thermodynamic analysis of glycolysis.

Week 6

Thermodynamics of metabolic transport (chemical potential).

Lecture, reading (Chapter 7 of Metabolic Engineering), written assignment.

Written assignment: thermodynamic analysis of ATP synthase.

Week 7

Visualizing biochemical networks. Biochemical databases. Analysis of designed pathways.

Lecture, reading (Chapter 8 of Metabolic Engineering), written assignment.

Written assignment: Pathway visualization, mapping (p)FBA, FVA, and FCA results.

Week 8

Metabolic models: a survey of design tools.

Lecture, readings (provided)

Written assignment: identifying design tool to use in particular cases

Week 9

Omics: methods and datasets

Lecture, reading (Chapter 9 of Metabolic Engineering), written assignment.

Written assignment: analyzing pathway use through omics

Week 10

Overview of in vivo metabolic engineering techniques. Classic in vivo approaches.

Lecture, reading (Chapter 10 of Metabolic Engineering), written assignments

Written assignments: identify candidates for overexpression, propose where to change expression for bioproduction

Week 11

Design of gene systems through control: transcriptional, post-transcriptional, translational and codon, post translational, toggles

Lecture, reading (provided), written assignments

Written assignments: Suggest appropriate control system to use in various circumstances.

Week 12

Gene delivery systems: plasmids, viral vectors, Agrobacterium, bacteriophages

Lecture, readings (provided) written assignments

Written assignments: identify appropriate gene delivery systems

Week 13

The CRISPR systems: CRISPR-Cas, CRISPRa, CRISPRi

Lecture, readings (provided) written assignments

Written assignments: CRISPR system selection, design of sequences.

Week 14

Other gene editing techniques: TALENs, Zinc Finger Nucleases

Lecture, readings (provided), written assignments

Written assignments: selecting of appropriate gene editing techniques

Week 15

Case studies and successful applications: metabolic engineering of E. coli

Lecture, readings (Chapter 11), written assignments

Prepare final project report and presentation.

Writing assignments

60%

Class participation

10%

Final project

30%

Extra credit

5%

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