CHE.496/2008/Assignments

Assignment 1: Synthetic biology overview

1. Extreme genetic engineering: An introduction to synthetic biology
2. Intelligent Life
3. Synthetic Life
4. Engineering Life: Building a FAB for biology

Assignment 2: Foundational technologies

1. Foundations for engineering biology
2. A partnership between biology and engineering
3. Synthetic biology - putting engineering into biology

Assignment 3: Engineering principles

1. Synthetic biology: New engineering rules for an emerging discipline

Assignment 4: Practical applications

1. Advances in synthetic biology: on the path from prototypes to applications
2. Molecular switches for cellular sensors

Assignment 5: Biobricks and design overview

1. Idempotent vector design for standard assembly of biobricks
2. Designing biological systems
3. Biology by design: Reduction and synthesis of cellular components and behavior

Assignment 6: Genetic programming, Gene Designer, codon optimization

1. Genetic parts to program bacteria
2. Codon bias and heterologous protein expression
3. Programming and engineering biological networks
4. Modular approaches to expanding the functions of living matter
5. Synthetic biology: New engineering rules for an emerging discipline
6. Programming and engineering biological networks
7. Fast, cheap and somewhat in control

Assignment 7: Synthetic genes, biological machines, and minimal genomes

1. Global transposon mutagenesis and a minimal mycoplasma genome

Assignment 8: Case studies in synthetic biology

1. Environmentally controlled invasion of cancer cells by engineered bacteria
2. Production of isoprenoid pharmaceuticals by engineered microbes

Assignment 9: Final project

Assignment 10: Genetic circuit engineering

1. A synthetic oscillatory network of transcriptional regulators
2. Construction of a genetic toggle switch in Escherichia coli
3. Engineered gene circuits

Assignment 11: Metabolic pathway engineering

1. Bioengineering novel in vitro metabolic pathways using synthetic biology

Assignment 12: Protein engineering

Assignment 13: Bioinformatics and online databases

Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information

Assignment 14: Systems biology and the omic sciences

Systems biology as a foundation for genome-scale synthetic biology

Assignment 15: Mathematical biology

Assignment 16: Genome-scale metabolic models

Assignment 17: Modeling genetic regulatory networks

Assignment 18: Systems biotechnology and CellDesigner

Assignment 19: Biological safety and security

1. DNA synthesis and biological security
2. Characterization of the reconstructed 1918 Spanish influenza pandemic virus

Assignment 20: Bioethics

1. The promises and perils of synthetic biology
2. Synthetic biology: Navigating the challenges ahead

Assignment 21: Ownership and sharing

Assignment 22: Bio-business

1. Economics of synthetic biology
2. Synthetic biology: Caught between property rights, the public domain, & the commons