CHE.496/2008/Projects/2/Group 2

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CHE.496: Biological Systems Design Seminar

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Group 2's project overview and part design

List of initial ideas

  • Foundational
    • Parts for genetic circuits
      • New light sensor (i.e., new wavelength)
    • New chassis (e.g., yeast)
      • Standardized plasmids
      • Standardized restriction sites
    • Optimizing existing parts (e.g., inverter)
    • Compartmentalization/insulation
      • Molecular screens (filters) that enable signal isolation and insulation (inside the cells and in between cells)
  • Computational
    • modeling of biotech-relevant microorganisms
  • Synthetic Biology Tools
    • Quality characterization techniques
    • Ways to insulate biological signals
  • Genetic Circuit Engineering
    • Light-based repressilator
    • Light switch
  • Biosensing
    • Ethylene biosensor
    • Algae that sense light and displays permanent memory
  • Metabolic Engineering
    • Polysaccharide synthesis (for food)
    • Bioplastic production
    • Chemical degradation (toxin breakdown)
      • Oil
      • CO2
      • Plastics

List of top two project ideas

  • Biological production of plastic
    • Polyhydroxyalkanoates (PHAs) are naturally synthesized polyesters in Ralstonia eutropha
    • These PHAs are used for energy storage
    • Polyhydroxybutyrate (PHB) is a PHA and could possible replace polypropylene
    • Biologically-produced plastics represent a sustainable chemical industry that is not dependent on petroleum
    • Three genes necessary for PHB synthesis: PhaA, PhaB and PhaC (from Pohlmann et al., 2006)
    • Pathway: 2 acetyl-CoA are condensed into acetoacetyl-CoA by PhaA. Then, PhaB (NADPH-dependent) reduces this to (R)-3-hydroxybutyryl-CoA. Finally, this is polymerized into PHB by PhaC.
    • PhaA (code for acetyl-CoA acetyltransferase) Nucleotide sequence
    • Possible use in tissue engineering applications (PHB is found in blood plasma)
    • Chassis: E. coli
  • Biological degradation of plastic
    • Biodegradation of natural plastics
      • PHAs are biodegradable.
      • Ralstonia eutropha breaks down PHB using PhaZ1, PhaZ2 and PhaY1.
    • Biodegradation of synthetic plastics
      • Streptomyces, a gram-positive bacteria, can naturally break down polyethylene
      • Phanerochaete chrysosporium manganese peroxidase breaks down polyethylene Nucleotide sequence