Team:KULeuven/8 July 2009

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=Stand van zaken=
 
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Er zijn 2 projecten uitgewerkt en voorgesteld.
 
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Het idee is om op vrijdag (10 juli om 12u45 in lokaal LAND 00.210.) een definitieve beslissing te maken welk project uit te voeren. Morgen (donderdag) wordt dan gebruikt om problemen met beide projecten porberen op te lossen. Hieronder een korte samenvatting van de stand van zaken en op te lossen problemen van beide projecten.
 
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==Regel bacterie==
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=Progress of the project=
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Het principe is om een bacterie te creëeren die de concentratie van een bepaalde molecuul 'X' constant houd door middel van een dynamische evenwicht. Tegelijkertijd synthese en afbraak van deze molecule zorgt voor een evenwicht als 1 van de 2 afhankelijk is van de concentratie (zie presentatie). Dit evenwichtspunt kan dan ingesteld worden door gebruik te maken van een lichtsensor. De lichtintensiteit is dan evenredig met het evenwichtspunt.
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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.
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Voor de lichtsensor hebben we een biobrick gevonden plus een paper uit nature waarin de lichtintensiteit gerelateerd werd aan de expressie van een 'black output'
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==Regulation bacteria==
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*[http://partsregistry.org/Part:BBa_S03417 BBa_S03417]]
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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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*[http://partsregistry.org/wiki/index.php/Part:BBa_M30109 BBa_M30109]
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*Synthetic biology: engineering Escherichia coli to see light, Anselm Levskaya et al. Nature, Vol. 438, No. 7067. (Nov 2005), pp. 441-2.
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Als voorbeeld is kort het principe van Leucine gekozen als te regelen factoor 'X' (zie presentatie). Leucine is een essentieel aminozuur voor eukaryote en zou daarom evt te regelen zijn (probleem, mensen met licht bestralen heel de dag is niet erg handig)
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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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*{{kulpart|BBa_S03417}}
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*{{kulpart|BBa_M30109}}
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*[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html Nature artikel from Levskaya]
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[https://2009.igem.org/Image:Voorsteling_project_regel-bacterie.pdf Presentatie van het project regel bacterie]
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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.
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===probleem===
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Het concept heeft 2 problemen op het moment, namelijk
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# Het huidige voorstel voor het dynamisch evenwicht zorgt niet voor een te controlleren evenwicht omdat externe synthese of afbraak een ander evenwicht veroorzaken en er daardoor schommelingen ontstaan die we juist tegen willen gaan
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#* oplossing, gebruik van een gewenste waarde afhankelijk van de lichtintensiteit waartegen de concentratie wordt vergeleken en wat bepaald hoeveel er wordt gesynthetiseerd of afgebroken. Dit moet alleen nog in het biologische systeem omgezet worden
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# Vinden van de magische molecuul 'X'. Waar gaan we het in gebruiken (in een aquarium?) en wat doet de molecule (voedingsstof/vitamine/etc..?). De eisen voor magisch molecuul 'X' zijn:
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#* Nut voor het systeem waar we het insteken (als op een andere manier de concentratie makkelijk te regelen is of de concentratie is niet interessant dan is het een nutteloze oplossing)
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#* actief te transporteren naar binnen EN buiten de cel
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#** Mogelijkheid is ook om de molecuul te modificeren tijdens het transport OF iets te transporteren wat evenredig is aan de concentratie van de te transporteren molecuul.
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[https://2009.igem.org/Image:Voorsteling_project_regel-bacterie.pdf Presentation of the regulation bacteria]
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===Problems/questions(/challenges?)===
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This concept has currently 2 problems, namely:
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#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 (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.
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# 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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#*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 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' outside the cell.
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#* Possibility to synthesize the molecule by the bacteria.
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Especially problem 2 is an important problem, help is appreciated ^^
==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?
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==Others==
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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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