CHE.496/2009/Schedule/Oral presentations of part design/Group 1

Group 1

• Members: Patrick Gildea & Thaddeus Webb

Parts

=Part 1=: Multiple input AND gate

• Description:
  • The genetic circuit would function as a standard AND gate with the exception that it does not function on binary input but ternary and possibly quaternary input if we can make it possible. While it is possible to build a circuit that can encode multiple inputs by linking a series of AND gates in a cascade as has been done in electronic circuits and VLSI design. However, in a biological system there are stoichastic effects that can interfere with a large biological network. Another consideration is that for such a network of multiple binary AND gates in a biological organism, the inputs would have to be different from each other because otherwise it would defeat the purpose of the genetic circuits. Having an AND gate with multiple inputs would eliminate the issues listed above and would be far more efficient and faster. The AND gate could be constructed of genes or possibly orthogonal Ribosomes.
• Source & References
  • Programming and engineering biological networks
  • Mining logic gates in prokaryotic transcriptional regulation networks

=Part 2=: Repressilator (different design)

• Description:
  • to be added
• Source:

A synthetic oscillatory network of transcriptional regulators

=Part 3=:AND-OR gate

• Description:
  • to be added
• Source:
  • Mining logic gates in prokaryotic transcriptional regulation networks

=Part 4=: Protein-Purification by way of Thermophile polymerase

• Description:
  • to be added
• Source:

Microbiology in Yellowstone Analysis of Nanoarchaeum equitans genome and proteome composition: indications for hyperthermophilic and parasitic adaptation

=Part 5=: Production of GBA glucosidase in E. Coli

• Purpose:
  • to be added
• Description of how the part would work:
  • to be added
• Sources:

GBA glucosidase, beta Nucleotide sequence PDB

=Part 6=: Iron absorption by E. Coli 

• Purpose:
  • To enable E. Coli to absorb iron from the environment and survive. This could be useful both in the extraction of iron and in cleanup of a contaminated area.
• Description of how the part would work:
  • This part would be based primarily on two genes VIT1 and ferretin. VIT1 is a transporter protein used by arabidopsis to uptake iron from the soil. Over expression of this single gene in arabidopsis has been shown to increase iron uptake by several hundred percent. Proper expression of this gene would require correct localization in the cell, specifically we would need to localize expression to the cell membrane. Plants and animals both use the protein ferritin to safely store iron in the cytoplasm. If ferritin could be properly expressed in bacteria it should allow them to survive with high intracellular concentrations of iron. This part would probably need to by used in conjunction with a motility part or another mechanism for collecting the cells.
• Sources:
  • Description of iron transport[1]
  • Storage of iron by ferritin[2]
  • Iron transport and signalling in plants[3]

=Part 6=: Arsenic absorption by E. Coli

• Purpose:
  • to be added
• Description of how the part would work:
  • to be added
• Sources:
  • to be added