Team:KULeuven/8 July 2009

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=Stand van zaken=
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Currently there are 2 projects being worked on. Friday (10th of July at 12.45 in lokaal LAND 00.210.) we make a definite decission for which project we will do. So tomorow (thursday) will be used to find solutions for the problems/questions (challenges?) in both projects. Below is a short summary of the progress and questions in both projects.
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=Progress of the project=
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Currently we work on 2 projects simultaneously. Friday (10th of July at 12.45h in room LAND 00.210.) we make a definite decision for which project we will choose. So tomorrow (thursday) will be used to find solutions for the problems/questions (challenges?) still pending. Below is a short summary of the progress and questions in both projects.
==Regulation bacteria==
==Regulation bacteria==
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The main idea is to develop a bacteria that regulates the concentration of a molecule 'X' and keeps it constant by a dynamical equilibrium (see presentation). This is being done by simultaneous synthesis and degradation (with 1 or 2 being dependant on concentration), a dynamical equilibrium exists when the synthesis equals the degradation. This dynamical equilibrium can be set by using light sensor, the light intensity would then be proportional to the concentration for the equilibrium.
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The main idea is to develop a bacterium that regulates the concentration of a molecule 'X' and keeps it constant by a dynamical equilibrium (see presentation). This occurs when the synthesis equals the degradation. This dynamical equilibrium can be set by using a light sensor. The light intensity would then be proportional to the equilibrium concentration.
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For the lightsensor we found a biobrick plus a paper from nature in which the light intensity is related to the expression of 'black output'
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As a light sensor, we found a biobrick plus a paper from Nature in which the light intensity is related to the expression of 'black output'
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*[http://partsregistry.org/Part:BBa_S03417 BBa_S03417]
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*{{kulpart|BBa_S03417}}
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*[http://partsregistry.org/wiki/index.php/Part:BBa_M30109 BBa_M30109]
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*{{kulpart|BBa_M30109}}
*[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html Nature artikel from Levskaya]
*[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html Nature artikel from Levskaya]
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By example we chose the amino acid Leucine for molecule 'X' (see presentation). Leucine is an essential amino acid for eukaryotes and might be regulatable (by the way an additional problem if we would use this in humans is that we can't just radiate red light the entire day on them)
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By example we chose the amino acid Leucine for molecule 'X' (see presentation). Leucine is an essential amino acid for eukaryotes and could be regulated. Remark: if we would use this in humans, an additional problem is that we can't just irradiate them with red light the entire day.
[https://2009.igem.org/Image:Voorsteling_project_regel-bacterie.pdf Presentation of the regulation bacteria]
[https://2009.igem.org/Image:Voorsteling_project_regel-bacterie.pdf Presentation of the regulation bacteria]
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This concept has currently 2 problems, namely:
This concept has currently 2 problems, namely:
#The current proposal for the dynamical equilibrium (see presentation) will not result in a controlling equilibrium because the external synthesis or degradation would shift the equilibrium to another concentration, which is exactly what we are trying to prevent.
#The current proposal for the dynamical equilibrium (see presentation) will not result in a controlling equilibrium because the external synthesis or degradation would shift the equilibrium to another concentration, which is exactly what we are trying to prevent.
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#* Solution (yea we got one ^^), use of a desired value instead of the amount of protein synthesized. The desired value is set by the light intensity and results in a concentration of a reference molecule. The concentration of molecule 'X' is compared to this reference after which it is decided to synthesize or degrade more of molecule 'X'.
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#* Solution (yeah we got one ^^): use of a desired value instead of the amount of protein synthesized. The desired value is set by the light intensity and results in a concentration of a reference molecule. The concentration of molecule 'X' is compared to this reference. Afterwards, the decision to synthesize or degrade more of molecule 'X' is made.
# FIND OUR MAGICAL MOLECULE 'X' (replacement of Leucine). It is important to know where we will use it (ideas: aquaria, plants, bioreactor) and what this molecule adds for use (nutrient/vitamine/food/etc..?). The demands for magical molecule 'X' are:
# FIND OUR MAGICAL MOLECULE 'X' (replacement of Leucine). It is important to know where we will use it (ideas: aquaria, plants, bioreactor) and what this molecule adds for use (nutrient/vitamine/food/etc..?). The demands for magical molecule 'X' are:
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#*usefelness for the system, regulation of the concentration of the substance should not be regulated by another chemical/physical way because then it is not interesting to develop in a bacteria.
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#*Usefulness to the biological system: regulation of the concentration of the substance should not be under control by another chemical/physical way.
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#* Active transport inside AND outisde the cell
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#* Active transport inside AND outside the cell
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#** It might be possible to modify the molecule during transport OR transport something (inside the cell) that is proportional to the concentration of the molecule 'X' outisde the cell.
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#** It might be possible to modify the molecule during transport OR transport something (inside the cell) that is proportional to the concentration of the molecule 'X' outside the cell.
#* Possibility to synthesize the molecule by the bacteria.
#* Possibility to synthesize the molecule by the bacteria.
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==The blue lagoon==
==The blue lagoon==
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The plan is to create a bacterium that's able to remove phosphates and nitrogens from contaminated ponds. When put into a pond, the bacteria will start to replicate and after a set amount of time will start taking up those phosphates and nitrogens. Simultaneously, the bacterium will start to take up iron from the water.
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Storage of nitrogen in the cell would be done by our new molecule Lagonine. A molecule that would contain a lot of K, R and Q.
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The uptake of iron is done by increased synthesis of enterocholin, a siderophore, and ferritin, a molecule that is used to store iron in the cell. The accumulation of iron causes the bacterium to become slightly magnetic, which should allow us to remove it from the pond by the use of a magnet.
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Our bacteria would be deficient in a vital substance, which allows us to start the growth of the bacteria by the addition of that substance and kill off all bacteria in the pond by just stopping the addition.
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[[https://2009.igem.org/Image:The_blue_lagoon.pdf Presentation of the blue lagoon]]
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=== Problems / questions ===
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# Can we get Lagonine inside an inclusion body?
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# ''E. coli'' minicells?
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# Can ''E. coli'' grow in low temperature conditions? And in pond?
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# Is ''E. coli'' toxic for pond life?
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# Does ''E. coli'' take too much iron out of the pond?
==Others==
==Others==
On thursday we expect some koffiekoeke
On thursday we expect some koffiekoeke
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Latest revision as of 08:33, 10 September 2009


Contents

Progress of the project

Currently we work on 2 projects simultaneously. Friday (10th of July at 12.45h in room LAND 00.210.) we make a definite decision for which project we will choose. So tomorrow (thursday) will be used to find solutions for the problems/questions (challenges?) still pending. Below is a short summary of the progress and questions in both projects.

Regulation bacteria

The main idea is to develop a bacterium that regulates the concentration of a molecule 'X' and keeps it constant by a dynamical equilibrium (see presentation). This occurs when the synthesis equals the degradation. This dynamical equilibrium can be set by using a light sensor. The light intensity would then be proportional to the equilibrium concentration.

As a light sensor, we found a biobrick plus a paper from Nature in which the light intensity is related to the expression of 'black output'

  • [http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html Nature artikel from Levskaya]

By example we chose the amino acid Leucine for molecule 'X' (see presentation). Leucine is an essential amino acid for eukaryotes and could be regulated. Remark: if we would use this in humans, an additional problem is that we can't just irradiate them with red light the entire day.

Presentation of the regulation bacteria

Problems/questions(/challenges?)

This concept has currently 2 problems, namely:

  1. The current proposal for the dynamical equilibrium (see presentation) will not result in a controlling equilibrium because the external synthesis or degradation would shift the equilibrium to another concentration, which is exactly what we are trying to prevent.
    • Solution (yeah we got one ^^): use of a desired value instead of the amount of protein synthesized. The desired value is set by the light intensity and results in a concentration of a reference molecule. The concentration of molecule 'X' is compared to this reference. Afterwards, the decision to synthesize or degrade more of molecule 'X' is made.
  2. FIND OUR MAGICAL MOLECULE 'X' (replacement of Leucine). It is important to know where we will use it (ideas: aquaria, plants, bioreactor) and what this molecule adds for use (nutrient/vitamine/food/etc..?). The demands for magical molecule 'X' are:
    • Usefulness to the biological system: regulation of the concentration of the substance should not be under control by another chemical/physical way.
    • Active transport inside AND outside the cell
      • It might be possible to modify the molecule during transport OR transport something (inside the cell) that is proportional to the concentration of the molecule 'X' outside the cell.
    • Possibility to synthesize the molecule by the bacteria.

Especially problem 2 is an important problem, help is appreciated ^^

The blue lagoon

The plan is to create a bacterium that's able to remove phosphates and nitrogens from contaminated ponds. When put into a pond, the bacteria will start to replicate and after a set amount of time will start taking up those phosphates and nitrogens. Simultaneously, the bacterium will start to take up iron from the water.

Storage of nitrogen in the cell would be done by our new molecule Lagonine. A molecule that would contain a lot of K, R and Q.

The uptake of iron is done by increased synthesis of enterocholin, a siderophore, and ferritin, a molecule that is used to store iron in the cell. The accumulation of iron causes the bacterium to become slightly magnetic, which should allow us to remove it from the pond by the use of a magnet.

Our bacteria would be deficient in a vital substance, which allows us to start the growth of the bacteria by the addition of that substance and kill off all bacteria in the pond by just stopping the addition.

[Presentation of the blue lagoon]

Problems / questions

  1. Can we get Lagonine inside an inclusion body?
  2. E. coli minicells?
  3. Can E. coli grow in low temperature conditions? And in pond?
  4. Is E. coli toxic for pond life?
  5. Does E. coli take too much iron out of the pond?

Others

On thursday we expect some koffiekoeke

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