CHE.496/2008/Assignments

Assignment 1: Synthetic biology overview

1. Extreme genetic engineering: An introduction to synthetic biology
2. Intelligent Life

Assignment 2: Foundational technologies

1. Foundations for engineering biology
2. A partnership between biology and engineering

Assignment 3: Engineering principles

1. Synthetic biology - putting engineering into biology
2. 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

1. Genetic parts to program bacteria
2. Codon bias and heterologous protein expression
3. 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

1. Description of 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: Biological network engineering

1. Programming and engineering biological networks
2. Modular approaches to expanding the functions of living matter

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

1. Synthetic biology: Caught between property rights, the public domain, & the commons

Assignment 22: Bio-business

1. Economics of synthetic biology