CHE.496/2008/Assignments

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CHE.496: Biological Systems Design Seminar

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Assigned Readings

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. 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: Biological machines

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

Assignment 9: RNA synthetic biology

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

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

Assignment 16: Systems biology and synthetic biology

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

Assignment 17: Systems biology and synthetic biology

  1. Systems biology as a foundation for genome-scale synthetic biology
  2. From systems biology to synthetic biology

Assignment 18: Systems biology and synthetic biology

  1. Biological networks
  2. Programming and engineering biological networks

Assignment 19: Computational Biology

  1. From molecular to modular cell biology
  2. Modelling cellular behaviour

Assignment 20: Computational biology

  1. Bioinformatics analysis for genome design and synthetic biology
  2. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
  3. Use of genome-scale microbial models for metabolic engineering
  4. Global physiological understanding and metabolic engineering of microorganisms based on omics studies
  5. Microbial regulatory and metabolic networks
  6. Modular approaches to expanding the functions of living matter

Assignment 21: Systems biotechnology

  1. Synthetic biology: Navigating the challenges ahead
  2. Synthetic biology through the prism of scenarios

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