Team:KU Leuven/Journal

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Revision as of 10:28, 10 July 2013

Secret garden

Congratulations! You've found our secret garden! Follow the instructions below and win a great prize at the World jamboree!

A video shows that two of our team members are having great fun at our favourite company. Do you know the name of the second member that appears in the video?
For one of our models we had to do very extensive computations. To prevent our own computers from overheating and to keep the temperature in our iGEM room at a normal level, we used a supercomputer. Which centre maintains this supercomputer? (Dutch abbreviation)
We organised a symposium with a debate, some seminars and 2 iGEM project presentations. An iGEM team came all the way from the Netherlands to present their project. What is the name of their city?

Now put all of these in this URL:https://2013.igem.org/Team:KU_Leuven/(firstname)(abbreviation)(city), (loose the brackets and put everything in lowercase) and follow the very last instruction to get your special jamboree prize!

Modeling

01/07

We installed Matlab, took a look at some presentations about modeling. We are also investigating SimBiology.

02/07

We watched some webinars about SimBiology. In the afternoon we had an appointment with professor Bernaerts of the division of (bio)chemical procestechnology. It was very useful, as she gave some good ideas on how to get started. We will have to design a way of expressing the enzyme(s) in a cyclic manner. We could achieve this by expressing it during a short pulse, activated by the presence of a signal from other cells.

03/07

During the morning we brainstormed about some possible networks with oscillating behavior. We have to keep in mind that the colony has to be and stay synchronized. This could be achieved by a rapid (protein-protein interaction) feedback which is proportional to the phase difference.

We had a meeting with the wetlab team and discussed our main focus for the upcoming weeks: figuring out an oscillating construct and simulating the behaviour of the methyl salicylate BioBrick.

04/07

Bert and Sander are working on simulating the Mortier Oscillator in SimBiology.

Tina and Tomas are modeling the network to produce methyl salicylate.

BSMT1 is the enzyme that catalyzes the reaction from salicylate to methyl salicylate.

pchA and pchB catalyze the reactions from chorismate to isochorismate to salicylate.

Tomas and Sander are looking on how to use the COBRA toolbox for our purpose. We would need to check the constraints on reaction rates and add our new reactions. Bert made contact with professors Suykens of the department of electrical engineering and professor Degrève of the division of (bio)chemical procestechnology in order to have an idea of how to analyse the MO, we apparently need bifurcation analysis, which Bert started looking up about.

05/07

Knock-out/complementary RNA of genes responsible for chorismate mutase and chorismate lyase as a strategy to optimize methyl salicylate production? Tomas started the development of another oscillator, while Sander and Tina are looking deeper into metabolic network modeling.

07/07

We are in touch with professor Roose of the applied mathematics division, who suggested the use of MatCont for the analysis of our oscillator.

08/07

We’re investigating the AutoBioCAD software and looking for a better model to our quorum sensing system using PDEs.

09/07

We started investigation of literature of ecology. We chose our model species (aphid and crop). We’ll try to model aphid reproduction and the influence of bèta-farnesene and methylsalicylate on life cycle and movement. We’ll have to make an estimation of the damage/loss of crops due to a certain population of aphids. Bert added spatial heterogeneity in his Mortier Oscillator to see what happens on a population level.

@@ Line 15: / Line 15: @@
 '''03/07'''
-During the morning we brainstormed about some possible networks with oscillating behavior. We have to keep in mind that the colony has to be and stay synchronized. This could be achieved by a rapid (protein-protein interaction) feedback which is proportional to the phase difference.
+During the morning we brainstormed about some possible '''networks with oscillating behavior'''. We have to keep in mind that the colony has to be and stay '''synchronized'''. This could be achieved by a rapid (protein-protein interaction) feedback which is proportional to the phase difference.
 We had a meeting with the wetlab team and discussed our main focus for the upcoming weeks: figuring out an oscillating construct and simulating the behaviour of the methyl salicylate BioBrick.
@@ Line 21: / Line 22: @@
 '''04/07'''
-Bert and Sander are working on simulating the Mortier Oscillator in SimBiology.
+:Bert and Sander are working on simulating the Mortier Oscillator in SimBiology.
-Tina and Tomas are modeling the network to produce methyl salicylate.
-BSMT1 is the enzyme that catalyzes the reaction from salicylate to methyl salicylate.
+:Tina and Tomas are modeling the network to produce methyl salicylate.
-pchA and pchB catalyze the reactions from chorismate to isochorismate to salicylate.
+'''BSMT1''' is the enzyme that catalyzes the reaction from salicylate to methyl salicylate.
+'''pchA''' and '''pchB''' catalyze the reactions from chorismate to isochorismate to salicylate.
 Tomas and Sander are looking on how to use the [http://opencobra.sourceforge.net/openCOBRA/Welcome.html COBRA toolbox] for our purpose. We would need to check the constraints on reaction rates and add our new reactions.
 Bert made contact with professors Suykens of the [http://www.esat.kuleuven.be/scd/ department of electrical engineering] and professor Degrève of the division of (bio)chemical procestechnology in order to have an idea of how to analyse the MO, we apparently need bifurcation analysis, which Bert started looking up about.