CHE.496/2008/Assignments

Assigned Readings

Assignment 1: Synthetic biology overview

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

Assignment 2: Foundational technologies

1. Foundations for engineering biology
2. Economics of synthetic biology

Assignment 3: Engineering principles

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

Assignment 4: Genetic programming

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

Assignment 5: Natural biological parts

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

Assignment 6: Practical applications

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

Assignment 7: Social implications

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

Assignment 8: Engineering biology

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

Assignment 9: Biological machines

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

Assignment 10: Minimal genomes

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

Assignment 11: Minimal cells

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

Assignment 12: Genetic circuit engineering

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

Assignment 13: Genetic circuit engineering

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

Assignment 14: Metabolic pathway engineering

1. Production of isoprenoid pharmaceuticals by engineered microbes
2. Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli

Assignment 15: Systems biology

1. The evolution of molecular biology into systems biology
2. Integrating 'omic information: A bridge between genomics and systems biology
3. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

Assignment 16: Systems biology and synthetic biology

1. Systems biology as a foundation for genome-scale synthetic biology
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. Global physiological understanding and metabolic engineering of microorganisms based on omics studies
3. 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. Synthetic biology through the prism of scenarios