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Team:TU Delft/Brainstorming
From 2010.igem.org
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!
Ideas
This is still work in progress...
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)
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 a lot of MO’s
Asbestos
Sensor for allergens
Mutagenic compounds/radiation detection
Detect different wavelengths
Change Rhodopsin so it can sense the different wavelengths
Intelligent sunscreen
UV detection
Should we use directed evolution as a method?
Parasites/mosquitoes
Attracts mosquitoes/kill mosquitoes
Bacteria is water pools => blocks malaria/ parasites (save the mosquitoes)
Lot's of research already being done in this area.
Mold detection (indoor) /prevention
Skin tanner/pigment producer
Hair growth
Bodily odors
Cortisol (stress hormone) sensor
Heart attack prediction
Teeth plaque
Done before? (2 years ago)
Vaccination
Oral vaccination?
E.coli that is your immune system? That will degrade any pathogens/viruses
Antigen presenting E.coli
Bacteria that introduces the antigen to the immune system
Peptide production (milk companies)
Bacteria that can form blood clots
Blood loss (in cases of an emergency) could be reduced by bacteria that can react on thrombin by producing fibrin fibers.
Sensing a molecule that is in the blood
Include a suicide gene
Denmark group: bacteria in Band-Aid
Delivery mechanism for MOs to your gut
There are many projects that have MO’s that work in your gut, but how do you get them there?
In your gut starts producing anything (medicine etc)
Has to survive stomach etc
Blood group detection
Rhesus factor determination
Appetite inhibitor
The solution to obesity?
Peptide Caerulein from the Australian green treefrog
200x more potent in inhibition of food intakethan equivalent dose of CCK-8 given IP
Patented (here in Delft, Verheart)
Polymer production
Bacteria that overproduce polymers (for example starch) and contain a time-bomb to kill itself. First the bacteria make a lot of polymers and after a certain time, the bacteria lyse themselves and the polymers come into the environment. These bacteria can be injected for example in dykes or sand dune for firmness
Is being done at the TU right now
Reinforcement of any kind by MOs
Biomass concentration sensor
Cell-cell interactions
Sensor for population control
Cell differentiation
Cell that has motility, and has the possibilities to use many different substrates. It measures a chemical gradient of a susbtrate, and will loose motility and start making a biofilm
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
