Team:TU Delft/Brainstorming

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{{:Team:TU_Delft/Header}}
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__NOTOC__
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= 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!
-
= Brainstorming =
 
-
Work in progress...
+
== Ideas ==
 +
 
 +
This is still work in progress...
 +
 
 +
 
 +
<html>
 +
 
 +
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 +
 
 +
 
 +
 
 +
<style>
 +
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 +
  display: inline;
 +
  width: 200px;
 +
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 +
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 +
 
 +
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 +
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 +
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 +
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 +
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 +
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 +
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 +
 
 +
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 +
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 +
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 +
<div id="idea_list">
 +
 
 +
<div class="idea">
 +
<h3 class="idea_title">Bacterial buffers</h3>
 +
<div class="idea_desc">
 +
</html>
 +
 
 +
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
 +
<html>
 +
</div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Bacterial eye</h3>
 +
  <div class="idea_desc">
 +
  Coupling sensing of light to any output (electrical signal/ color/ growth/ etc etc)
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Motility in yeast</h3>
 +
  <div class="idea_desc">
 +
    Flagellum production in yeast.
 +
    <ul>
 +
    <li>Would mean that you have to stir less hard in a fermentor (less cell death)</li>
 +
    <li>Maybe yeast cell could move towards food when it has a flagellum, or would it just randomly move around?</li>
 +
    </ul>
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Plastic soup in ocean</h3>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Substrate level measurement</h3>
 +
 
 +
  <div class="idea_desc">
 +
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?
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Bacterial solar clock</h3>
 +
  <div class="idea_desc">
 +
sense light intensity and given an output
 +
Light sensor genes, production of a colorful reaction
 +
We already have a “biological clock”: the sun
 +
  </div> 
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Circadian clock/rhythm</h3>
 +
  <div class="idea_desc">
 +
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
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Biofims / clusters / granules of bacteria</h3>
 +
  <div class="idea_desc">
 +
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
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Yeast mating factors</h3>
 +
  <div class="idea_desc">
 +
One cell that can produce both factors so we can have a homozygote
 +
Used to avoid losing genes
 +
  </div>
 +
</div>
 +
 
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Strain wars</h3>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Biological random generator</h3>
 +
  <div class="idea_desc">
 +
For cell differentiation?
 +
Difference between spontaneous and radiation mutations
 +
You can’t prove it’s truly random
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Bacterial battery</h3>
 +
  <div class="idea_desc">
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Riboswitches</h3>
 +
  <div class="idea_desc">
 +
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!
 +
  </div>
 +
</div>
 +
 
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Calcium removal from water</h3>
 +
  <div class="idea_desc">
 +
Calcium accumulating bacteria? Is this even possible?
 +
Polymer production with negative charge?
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Algae bloom</h3>
 +
  <div class="idea_desc">
 +
Consumption of algae? Protozoa?
 +
Stop or kill algae growth by MOs…
 +
Degradation of algae to let go of biofuel?? (Shell sponsor?)
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Sea water desalination</h3>
 +
  <div class="idea_desc">
 +
There are so many different salts in seawater
 +
Remove those that are most abundant
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Polymer production</h3>
 +
  <div class="idea_desc">
 +
Is being done at the TU right now
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Cloning tool</h3>
 +
  <div class="idea_desc">
 +
Already been done..
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Hydrogen sulfide removal</h3>
 +
  <div class="idea_desc">
 +
Algae that use H2S instead of oxygen, maybe we can use this?
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Removal of Indool (toilet odor)</h3>
 +
  <div class="idea_desc">
 +
Convert it too a nice smelling compound?
 +
Indool as a signal to produce “good” odor
 +
Jasmine smell?
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Bacteria that can melt ice on roads/ train rails</h3>
 +
  <div class="idea_desc">
 +
Anti-freeze proteins?
 +
  </div>
 +
</div>
 +
 
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Trash color coding</h3>
 +
  <div class="idea_desc">
 +
Useful for trash sorting and recycling.
 +
  </div>
 +
</div>
 +
 
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Biological filter</h3>
 +
  <div class="idea_desc">
 +
Sticky bacteria that catch all remains that go through the drain
 +
Wouldn’t this clog up the drain even more?
 +
Biofilm that filters
 +
  </div>
 +
</div>
 +
 
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Lamp of bacteria</h3>
 +
  <div class="idea_desc">
 +
Fish have bacteria that illuminate (think of practical)
 +
  </div>
 +
</div>
 +
 
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Diagnostic Gas detection</h3>
 +
  <div class="idea_desc">
 +
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)
 +
  </div>
 +
</div>
 +
 
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Remove/detect medicines in (waste) water</h3>
 +
  <div class="idea_desc">
 +
Penicillin
 +
(Small) Hormones
 +
Bacteria that can find and sense medicines (resistant to antibiotics)
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Fire retarders</h3>
 +
  <div class="idea_desc">
 +
Consumption of all the oxygen
 +
Fire retardation chemicals?
 +
You would need a lot of MO’s
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Asbestos</h3>
 +
  <div class="idea_desc">   
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Sensor for allergens</h3>
 +
  <div class="idea_desc">   
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Mutagenic compounds/radiation detection</h3>
 +
  <div class="idea_desc">   
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Detect different wavelengths</h3>
 +
  <div class="idea_desc">   
 +
Change Rhodopsin so it can sense the different wavelengths
 +
Intelligent sunscreen
 +
UV detection
 +
Should we use directed evolution as a method?
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Parasites/mosquitoes</h3>
 +
  <div class="idea_desc">   
 +
Attracts mosquitoes/kill mosquitoes
 +
Bacteria is water pools => blocks malaria/ parasites (save the mosquitoes)
 +
Lot's of research already being done in this area.
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Mold detection (indoor) /prevention</h3>
 +
  <div class="idea_desc">
 +
  </div>
 +
</div>
 +
<div class="idea">
 +
  <h3 class="idea_title">Skin tanner/pigment producer</h3>
 +
  <div class="idea_desc">   
 +
  </div>
 +
</div>
 +
<div class="idea">
 +
  <h3 class="idea_title">Hair growth</h3>
 +
  <div class="idea_desc">   
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Bodily odors</h3>
 +
  <div class="idea_desc">   
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Cortisol (stress hormone) sensor</h3>
 +
  <div class="idea_desc">   
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Heart attack prediction</h3>
 +
  <div class="idea_desc">   
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Teeth plaque </h3>
 +
  <div class="idea_desc">   
 +
    Done before? (2 years ago)
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Vaccination</h3>
 +
  <div class="idea_desc"> 
 +
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)
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Bacteria that can form blood clots</h3>
 +
  <div class="idea_desc">   
 +
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
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Delivery mechanism for MOs to your gut</h3>
 +
  <div class="idea_desc">
 +
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
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Blood group detection</h3>
 +
  <div class="idea_desc">
 +
Rhesus factor determination
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Appetite inhibitor</h3>
 +
  <div class="idea_desc">
 +
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)
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Polymer production</h3>
 +
  <div class="idea_desc">
 +
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
 +
  </div>
 +
</div>
 +
 
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Biomass concentration sensor</h3>
 +
  <div class="idea_desc">
 +
Cell-cell interactions
 +
Sensor for population control
 +
  </div>
 +
</div>
 +
 
 +
<div class="idea">
 +
  <h3 class="idea_title">Cell differentiation</h3>
 +
  <div class="idea_desc">
 +
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
 +
  </div>
 +
</div>
 +
 
 +
</div>
 +
 
 +
<script type="text/javascript">
 +
$(function() {
 +
  $("#idea_list > *").each(function() {
 +
    var content = $(".idea_desc", this).html();
 +
    $(this).simpletip({
 +
      content: content
 +
    });
 +
  });
 +
});
 +
</script>
-
One of our team members has developed a most useful risk scale for assessing project risks,
+
</html>
-
including chance of team member casualties!
+
{{:Team:TU_Delft/Brainstorming/HRS_content}}
{{:Team:TU_Delft/Brainstorming/HRS_content}}

Latest revision as of 13:44, 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!


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
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