CHE.496/2008/Assignments

Assigned Readings

Assignment 1: Synthetic biology overview

1. Intelligent Design link
2. Extreme genetic engineering: an introduction to synthetic biology link

Assignment 2: Foundational technologies

1. Foundations for engineering biology link
2. Synthetic biology: promises and challenges link
3. The iGEM competition: building with biology link

Assignment 3: Engineering principles

1. Synthetic biology - putting engineering into biology link
2. Synthetic biology: new engineering rules for an emerging discipline link

Assignment 4: Genetic programming

1. Idempotent vector design for standard assembly of biobricks link
2. Genetic parts to program bacteria link

Assignment 5: Natural biological parts

1. Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information link
2. Codon bias and heterologous protein expression link

Assignment 6: Practical applications

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

Assignment 7: Social implications

1. The promises and perils of synthetic biology link
2. DNA synthesis and biological security link

Assignment 8: Engineering biology

1. A partnership between biology and engineering link
2. Fast, cheap and somewhat in control link

Assignment 9: Biological machines

1. Designing biological systems link
2. Biology by design: Reduction and synthesis of cellular components and behavior link

Assignment 10: Minimal genomes

1. Essential genes of a minimal bacterium link
2. Leaner and meaner genomes in E. coli link

Assignment 11: Minimal cells

1. Toward synthesis of a minimal cell link
2. Rebuilding microbial genomes link

Assignment 12: Genetic circuit engineering

1. A synthetic oscillatory network of transcriptional regulators link
2. Construction of a genetic toggle switch in Escherichia coli link

Assignment 13: Genetic circuit engineering

1. Environmentally controlled invasion of cancer cells by engineered bacteria link
2. Environmental signal integration by a modular AND gate link

Assignment 14: Metabolic pathway engineering

1. Bioengineering novel in vitro metabolic pathways using synthetic biology link
2. Production of the antimalarial drug precursor artemisinic acid in engineered yeast link

Assignment 15: Systems biology

1. The evolution of molecular biology into systems biology link
2. Integrating 'omic information: A bridge between genomics and systems biology link

Assignment 16: Systems biology and synthetic biology

1. Systems biology as a foundation for genome-scale synthetic biology link
2. From systems biology to synthetic biology
3. Modular approaches to expanding the functions of living matter

Assignment 17: Computational Biology

1. Modelling cellular behaviour
2. Bioinformatics analysis for genome design and synthetic biology

Assignment 18: Biological networks

1. Biological networks
2. Programming and engineering biological networks

Assignment 19: Metabolic modeling

1. Use of genome-scale microbial models for metabolic engineering
2. Microbial regulatory and metabolic networks

Assignment 20: RNA synthetic biology

1. RNA synthetic biology
2. RNA and RNP as new molecular parts in synthetic biology

Assignment 21: The future of synthetic biology

1. Synthetic biology: Navigating the challenges ahead
2. Economics of synthetic biology link