Team:TU Delft/Brainstorming

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Revision as of 12:25, 12 July 2010

Brainstorming

Brainstorming method

We have tried to set up our brainstorming sessions in such a way that creativity was stimulated and no important areas where missed:

  • First we enumerated problems which might be solvable by synthetic biology, then we gathered as many ways to solve them as possible. It's important to allow any idea to be mentioned here, without any cricital judging of team members yet.
  • In later rounds, we voted on which ideas to work out, split up in teams and assessed the ideas in terms of feasibility, cost, coolness and how useful they could be for synthetic biology.
  • We ended with 3 detailed project ideas and voted on them, and oil degradation was chosen!

Bacterial buffers

Yeast/bacteria that resist change in their environment (such as pH, temperature, pressure; looking at extremophiles) Possibilities:

  • Temperature could be difficult, because we would have to change the temperature externally. Cooling down of an organism can have allot of problems.
  • Metabolite production for endothermic reactions extracellular
  • Antifreeze proteins (bind to ice)
  • pH; this has never been done before
  • Metal sequestering
  • Many different biobricks; differentiation into different possible effects.
  • Using characteristics of extremophiles

Bacterial eye

Coupling sensing of light to any output (electrical signal/ color/ growth/ etc etc)

Motility in yeast

Flagellum production in yeast.
  • Would mean that you have to stir less hard in a fermentor (less cell death)
  • Maybe yeast cell could move towards food when it has a flagellum, or would it just randomly move around?

Plastic soup in ocean

Substrate level measurement

High concentrations; low sensitivity Low concentrations; highly sensitive cellular systems necessary We would need a highly quantitative system What would the output be? In vivo metabolite measurements would be ideal, but how could this be possible?

Bacterial solar clock

sense light intensity and given an output Light sensor genes, production of a colorful reaction We already have a “biological clock”: the sun

Circadian clock/rhythm

Regulation for feast famine regime without needing to vary the actual substrate levels? This way you could use the organisms in which this is needed in combination with others in which other

Biofims / clusters / granules of bacteria

Improvement of DSP; avoid centrifugation etc Not all the time, but after a signal at the end of a process making it easy to remove the cells from the solution This could also occur using adhesion Fast growing biofilms

Yeast mating factors

One cell that can produce both factors so we can have a homozygote Used to avoid losing genes

Strain wars

Biological random generator

For cell differentiation? Difference between spontaneous and radiation mutations You can’t prove it’s truly random

Bacterial battery

Riboswitches

Can be used for any project we chose (method, not an idea) Or could we make a number of biobricks for this? Testing it is very difficult Applicable for future iGEM teams Too difficult? Challenge!

Calcium removal from water

Calcium accumulating bacteria? Is this even possible? Polymer production with negative charge?

Algae bloom

Consumption of algae? Protozoa? Stop or kill algae growth by MOs… Degradation of algae to let go of biofuel?? (Shell sponsor?)

Sea water desalination

There are so many different salts in seawater Remove those that are most abundant

Polymer production

Is being done at the TU right now

Cloning tool

Already been done..

Hydrogen sulfide removal

Algae that use H2S instead of oxygen, maybe we can use this?

Removal of Indool (toilet odor)

Convert it too a nice smelling compound? Indool as a signal to produce “good” odor Jasmine smell?

Bacteria that can melt ice on roads/ train rails

Anti-freeze proteins?

Trash color coding

Useful for trash sorting and recycling.

Biological filter

Sticky bacteria that catch all remains that go through the drain Wouldn’t this clog up the drain even more? Biofilm that filters

Lamp of bacteria

Fish have bacteria that illuminate (think of practical)

Fish have bacteria that illuminate (think of practical)

Diagnostic Gas detection

Measure levels of substances in patients exhaled breath to determine what the disease is What would the signal be? Nitrate, hormones? When the input signal is a small molecule this could be used What diseases could you detect in some ones breath? (cationic bodies as well)

Remove/detect medicines in (waste) water

Penicillin (Small) Hormones Bacteria that can find and sense medicines (resistant to antibiotics)

Fire retarders

Consumption of all the oxygen Fire retardation chemicals? You would need allot of MO’s

Fire retarders

Consumption of all the oxygen Fire retardation chemicals? You would need allot of MO’s

Hugo's Risk Scale

Our own standard for project risk assessment. Risk is represented with a value from 0 (no risk) to 10 (very risky)

  • 0: Lac operon (or other piece of cake) + our biobrick
  • 1: Less than 5 genes or biobricks (copy-paste) + our biobrick
  • 2: Less than 10 genes or biobricks (copy-paste) + our biobrick
  • 3: Biobrick engineering <5, improvement of things already done
  • 4: Multi biobrick engineering >5, improvement of things already done
  • 5: Site directed mutagenesis of several genes, results unknown a priori
  • 6: Evolutionary engineering involved = sequencing
  • 7: Protein engineering involved, results unknown a priori
  • 8: A lot of genes and/or biobricks (>20), known genes in other species and characterized. Stress, social friction
  • 9: A lot of genes and/or biobricks (>20), Known genes in other species, not fully characterized. Start a project one-eyed = stress, social friction, high chances of collapse
  • 10: A lot of genes (>20), Unknown genes= characterization + sequencing + cloning. Start a project from nothing or partially blind, team-member losses + obituraries. Good side: paper in Nature or Nobel
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