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From 2010.igem.org

Contents 1 Session 8 1.1 1. Oil removal 1.1.1 Hydrocarbon degradation 1.1.2 Salt tolerance 1.1.3 Overcoming mass transfer 1.1.4 Extra features 1.1.5 Other points 1.2 2. Algae bloom /nitrate reduction 1.3 3. Appetite inhibitor 1.4 4. Circadian Clocks / oscillators

Session 8

Now it’s not if we like the idea anymore (otherwise it wouldn’t be a chosen idea), but how could we accomplish it? How feasible is it? What BioBricks do we expect to make with this?

1. Oil removal

• Hydrocarbon degradation
• Oil sand processing gives wastewater with allot of oil (bitumen) => Convert this wastewater into something valuable
• Salinity, pH, mass transfer problems

Split into 3 teams:

Hydrocarbon degradation

• Genes for enzymes that degrade various aromatic compounds are known
• Maybe start with Benzoic acid & Alkenes?
• Probably the most work of all the teams, but others could help once they are done
• Most likely an aerobic process (most likely none of the enzymes are oxygen sensitive)
• Be careful whether the intermediates may be toxic
• Sugar metabolism is no longer necessary in E.coli

Salt tolerance

• Give the other team a strain of E.coli that can handle salt.
• Article: gene that helps in salt resistance (sea levels, NaCl) but function isn’t really understood
• Biobrick 2009; not clear whether it works or not?

Overcoming mass transfer

• Adding an emulsifier to make the oil soluble?
• Peptide production made of Leucine & Glutamic acid (paper) with an export mechanism
• Production of hydrophilic/hydrophobic peptide

Extra features

• We are making allot of acetyl CoA, so why not produce something useful?
• Biofuel? Propanol/ethanol/biodiesel? There are some biobricks for this… but no Exporter? (Biobrick)
• PHA/PHB
• What about working at higher temperatures? Ethanol vaporization

Other points

• Money / many biobricks / lot of literature
• Is E.coli the bug to go with?
• We don’t necessarily have to put all 4 projects into one strain, but we can start with 4 and maybe if we have time we could try to.
• Good project that represents Delft (mass transfer etc.)
• There are no biobricks for hydrocarbon degradation!

Vote: Yes (8/8)

2. Algae bloom /nitrate reduction

• Fumarate reductase is the only difference between the aerobic and anaerobic paths?
• A mutated FNR can induce the nitrate consumption under aerobic conditions
• But there is also an E.coli strain that can reduce nitrite & nitrate under aerobic conditions
• Biobrick for nitrite sensor
• E.coli would probably be outcompeted by the algae? Depends on the carbon source
• Appealing idea to switch on and off the aerobic/anaerobic pathways…
• Some enzymes will be inhibited by oxygen

Vote: No (0/8)

3. Appetite inhibitor

• Caerulein
• Combination with circadian clock for times of production and non-production?
• Combination with cell differentiation for part of the MOs to produce (and maybe die), while the others don’t produce the peptide.
• Regulation is definitely necessary
• Couple it to blood sugar levels? Not really possible to sensor something in the blood from within the gut?

Vote: No (3/8)

4. Circadian Clocks / oscillators

• Oscillations are easy to come by
• Maybe too simple as a project on its own?
• Tool for another project?
• Hard to accurately predict the actual frequency; could only occur through true labwork
• Frequency would be dependent on the concentrations of the compounds as well as the growth rates for these also determine the degradation etc.
• How could you change affinity constants? (Kai system)
• Biobrick for Kai is already available, but how can you influence the frequency without trial-and-error?
• There is literature that could help make a model…

Vote: No (3/8)