Latest revision as of 08:33, 10 September 2009

Notebook

Progress

Regulation bacteria

The focus was on finding the magical molecule 'X'. Ideas that gathered the most attention:

Ideas concerning aquaria (nutrients for fish):
- Essential amino acids (Methionine/Leucine/etc..)
- Vitamines (Vitamine K/Thiamin/Choline)
Odour bacteria (Manage the concentration of odour that is synthesized and transported)
- Vanilla odour
- biobricks for odour:
  - [http://partsregistry.org/Odor Odor bricks]
    - (Banana odour generator)
    - (Wintergreen odour generator)
    - (Feruloyl-CoA hydratase for vanillin biosynthesis protein generator) <-- no experience/DNA available (yet)
    - (Synthetic periplasmic binding protein that docks a vanillin molecule) Receptor molecule
  - Experience from [http://openwetware.org/wiki/IGEM:MIT/2006/Blurb iGEM 2006 MIT group] wintergreen and banana odor generator
  - Experience from [http://www.igem.upv.es/igem06/index.php?title=Main_Page Igem 2006 valencia group] Vanillin detector system

Problem: Vanillin receptor and light receptor use the same ompr-p molecule. So, either find a different receptor for vanillin/other receptor or use a different regulator system, such as chemical receptors or others...

The system for measuring the difference between desired value (light) and the vanillin concentration would be competitive binding of repressor and activator. However, if both systems utilize the same receptor protein, no competitive binding of repressor and activator occurs. Therefore a different receptor is required. In that way the light receptor (desired value) can express A (activator) and the odour receptor can express B (inhibitor).

The blue lagoon

Today was about finding answers to the questions posed yesterday.

We searched for information about the optimal growth temperature for E. coli and temperature profiles for ponds in summer. We found that E. coli can grow in temperatures as low as 7,5 °C, while ponds should be well above 18°C. So, temperature should not be a problem.

We also continued working on the refinement of the ideas for our Blue Lagoon. After a short talk with Inge, we started looking for suitable cyanobacteria to replace E. coli, since it would solve a lot of the problems we were still facing with E. coli.

Our preferred cyanobacterium will be a strain from P. marinus, it will either by the SS120 strain or the MIT9313 (?) strain. Both strains have desirable properties, but we will have to make adjustments to the biobricks if we want to use these.

Tomorrow will be about further searching for information about P. marinus and it's possible use.

Drylab

Wiki

Created main stylesheet
Included common header in all pages
Daynavigator code, included in default notebook template

Remarks

Quote of the day

Bart van Parys over muggepotjes:

"ik mag dat niet gebruiken van mijn mama. Ze heeft dat ooit afgepakt van mij"

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 ==Regulation bacteria==
 The focus was on finding the magical molecule 'X'. Ideas that gathered the most attention:
-#Ideas for in aquarium (nutrients for fish):
+#Ideas concerning aquaria (nutrients for fish):
 #*Essential amino acids (Methionine/Leucine/etc..)
 #*Vitamines (Vitamine K/Thiamin/Choline)
-#Odor bacteria (Manage the concentration of odor that is synthesized and transported)
+#Odour bacteria (Manage the concentration of odour that is synthesized and transported)
-#*Vanille odor
+#*Vanilla odour
-#*biobricks for odor:
+#*biobricks for odour:
 #**[http://partsregistry.org/Odor Odor bricks]
-#***{{kulpart|BBa_J45200}} (Banana odor generator)
+#***{{kulpart|BBa_J45200}} (Banana odour generator)
-#***{{kulpart|BBa_J45120}} (Wintergreen odor generator)
+#***{{kulpart|BBa_J45120}} (Wintergreen odour generator)
 #***{{kulpart|BBa_I769103}} (Feruloyl-CoA hydratase for vanillin biosynthesis protein generator) <-- no experience/DNA available (yet)
 #***{{kulpart|BBa_J58105}}  (Synthetic periplasmic binding protein that docks a vanillin molecule) Receptor molecule
@@ Line 22: / Line 22: @@
 '''Problem:'''
-Vanillin receptor and light receptor use the same ompr-p molecule, either find a different receptor for vanillin/other receptor
+Vanillin receptor and light receptor use the same ompr-p molecule. So, either find a different receptor for vanillin/other receptor or use a different regulator system, such as chemical receptors or others...
-or use a different regulator system, such as chemical receptors or others...
-The system for measuring the difference between desired value (light) and the concentration vanillin would be competitive binding of repressor and activator. However if both systems utilize the same receptor protein then there can be no competitive binding of repressor and activator, so therefore a different receptor is required. Then the light receptor (desired value) can express A (activator) and the odor receptor can express B (inhibitor).
+The system for measuring the difference between desired value (light) and the vanillin concentration would be competitive binding of repressor and activator. However, if both systems utilize the same receptor protein, no competitive binding of repressor and activator occurs. Therefore a different receptor is required. In that way the light receptor (desired value) can express A (activator) and the odour receptor can express B (inhibitor).
 ==The blue lagoon==
@@ Line 31: / Line 30: @@
 Today was about finding answers to the questions posed yesterday.
-We searched for information about the optimal growth temperature for ''E. coli'' and temperature profiles for ponds in summer. We found that ''E. coli'' can grow in temperatures as low as 7,5 °C, but temperatures in ponds should be well above 18 °C, so temperature should not be a problem.
+We searched for information about the optimal growth temperature for ''E. coli'' and temperature profiles for ponds in summer. We found that ''E. coli'' can grow in temperatures as low as 7,5 °C, while ponds should be well above 18°C. So, temperature should not be a problem.
-We also continued on working on the refinement of the ideas for our Blue Lagoon. After a short talk with Inge, we started looking for a suitable cyanobacteria to replace ''E. coli'', since it would solve a lot of the problems we were still facing with ''E. coli''.
+We also continued working on the refinement of the ideas for our Blue Lagoon. After a short talk with Inge, we started looking for suitable cyanobacteria to replace ''E. coli'', since it would solve a lot of the problems we were still facing with ''E. coli''.
-Our preferred cyanobacteria will be a strain from ''P. marinus'', it will either by the SS120 strain or the MIT9313 (?) strain. Both strain have desirable properties, but we will have to make adjustments to the biobricks if we want to use these.
+Our preferred cyanobacterium will be a strain from ''P. marinus'', it will either by the SS120 strain or the MIT9313 (?) strain. Both strains have desirable properties, but we will have to make adjustments to the biobricks if we want to use these.
 Tomorrow will be about further searching for information about ''P. marinus'' and it's possible use.
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Team:KULeuven/9 July 2009

From 2009.igem.org