IGEM:Stanford/2009/Groups/Team Isis

Members

• Ariana
• Leon
• Isis

Questions

Biofuels

• Can a chemostat be used to culture biofuel producing organisms?
• How are biofuels transported out the cells and how can this be improved?
• What genes can be pared away/controlled so the cell uses the maximizes energy usage for fuel output?
• Can light adsorption range be improved by expressing other photosensitive pigments?

Plastic Degredation

• How do fungi degrade stuff?
• How are fungi cultured/are they genetically tractable?
• What are the degradation products of plastics?
• How can degradation be controlled? Riboswitches? A kill switch?
• Other iGEM projects:
  • Hopkins 2008 - This team considered making bioplastics as their project and on this page they talk a little bit about D. radiodurans being able to degrade styrene. - Isis
  • styrene degradation pathways - Well apparently a lot of organisms can degrade styrene.. I guess what we're interested in is poly-sytrene - Isis

Other Stuff

• What is the mechanism of quorum sensing?
  • From wikipedia: "Bacteria that use quorum sensing constantly produce and secrete certain signaling molecules (called autoinducers or pheromones). These bacteria also have a receptor that can specifically detect the signaling molecule (inducer). When the inducer binds the receptor, it activates transcription of certain genes, including those for inducer synthesis. There is a low likelihood of a bacterium detecting its own secreted inducer. Thus, in order for gene transcription to be activated, the cell must encounter signaling molecules secreted by other cells in its environment. When only a few other bacteria of the same kind are in the vicinity, diffusion reduces the concentration of the inducer in the surrounding medium to almost zero, so the bacteria produce little inducer. However, as the population grows the concentration of the inducer passes a threshold, causing more inducer to be synthesized. This forms a positive feedback loop, and the receptor becomes fully activated. Activation of the receptor induces the up regulation of other specific genes, causing all of the cells to begin transcription at approximately the same time. This coordinated behavior of bacterial cells can be useful in a variety of situations. For instance, the bioluminescent luciferase produced by V. fischeri would not be visible if it were produced by a single cell. By using quorum sensing to limit the production of luciferase to situations when cell populations are large, V. fischeri cells are able to avoid wasting energy on the production of useless products."

Past Meetings

• What is the natural function of hammerhead ribozymes?
  • They are found in viroids, which are plant viruses that have a naked RNA genome (no protein coat). To protect the genome from degradation by ribonucleases it is packed very tightly until it enters the host. Once it gets in, the hammerhead ribozyme part is activated to cleave the genome open so it an be translated.
• Next meeting: Thursday at 5pm. Location TBD.
  • Agenda: Discuss RNA paper.

• Things to think about/research:
  • How to read/write DNA
  • Using cells as sensors? How to Input/Output information? How to control behavior?

Storing info in DNA

• Here's an article about storing "It's a small world" in DNA which Ariana mentioned at our meeting.
  • Deinococcus radiodurans