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-	{{:Team:KU Leuven/Template:Menu}}	+	==Wetlab==
		+	'''26/06'''
		+	Some of us have already finished their exams so we started working in the lab. For now we just made the antibiotics solutions that we will have to use this summer.
-	== Modeling ==
-	'''01/07'''
-	We installed '''Matlab''', took a look at some presentations about modeling. We are also investigating [http://www.mathworks.nl/products/simbiology/ SimBiology].	+	'''27/06'''
		+	Today we poured the agar plates with and without the antibiotics.
-	'''02/07'''
-	We watched some [http://www.mathworks.nl/products/simbiology/webinars.html 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.	+	'''28/06'''
		+	Just one thing to do today: make the FSB buffer. Easy job, but we have to recover from the exams, and it is almost weekend ofcourse.
-	'''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.	+	'''01/07'''
-	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.	+	As the first day of July, our job today wasn't too heavy. We started making the competent cells. The main task was to inoculate Top10 and DH5alpha strains from agar plate into the medium, herein we use tips to transfer both the strains into 3ml LB medium under laminar flow, two times for each strain. Then incubate them overnight.
-	'''04/07'''	+	'''02/07'''
-	Bert and Sander are working on simulating the '''″Mortier Oscillator″''' in SimBiology.	+	In the morning we continued yesterday's job, working with competent cells and in the afternoon we tried the transformation efficiency kit. Fingers crossed!
-	Tina and Tomas are modeling the network to produce methyl salicylate.
-	:'''pchA''' and '''pchB''' catalyze the reactions from '''chorismate''' to '''isochorismate''' to '''salicylate'''.	+	'''03/07'''
-	:'''BSMT1''' is the enzyme that catalyzes the reaction from '''salicylate''' to '''methyl salicylate'''.	+	We checked the plates that grew under 37°C overnight, and surprisingly no colony appear in any of them! Now we have to figure out what went wrong. Possible reasons are:
		+	*Bad competent cells (please not!)
		+	*We didn't use enough recovery time for the cells.
		+	*The cells need more time to grow.
-	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.	+	To examine what went wrong we did the experiment over again, but this time we used our own pUC 19-vector and let the cells recover for 2 hours instead of one.
-	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 '''[http://en.wikipedia.org/wiki/Bifurcation_theory bifurcation analysis]''', which Bert started looking up about.	+
		+	We also prepared the SOC-medium for future use.
-	'''05/07'''
-	Tomas started the development of another oscillator, while Sander and Tina are looking deeper into metabolic network modeling.	+	'''04/07'''
		+	Hurray! This time we do have cell growth, so we counted the cells and calculated the transform efficiency. This was still quite low though...
		+	We prepared the GTE-buffer for future use and prepared agar medium.
		+	in the afternoon, we found out that the medium in the autoclave spilled out everywhere in the autoclave, possibly due to the pressure in the autoclave. Lukas was the lucky guy who got to clean out the autoclave.
-	'''07/07'''
-	We are in touch with professor Roose of the [http://wms.cs.kuleuven.be/groups/natw/index.html applied mathematics division], who suggested the use of '''[http://www.matcont.ugent.be/ MatCont]''' for the analysis of our oscillator.	+	'''05/07'''
-		+
-		+
-	'''08/07'''	+
-		+
-	We’re investigating the [http://pubs.acs.org/doi/abs/10.1021/sb300084h 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.	+
-		+
-	==Wetlab==	+
-	'''01/07'''	+
-		+
-	As the first day of July, our job today wasn't heavy.The main task was to inoculate Top10 and DH5alpha strains from agar plate into the medium, herein we use tips to transfer both the strains into 3ml LB medium under larmillar, two times for each strain. Then incubate them overnight.	+
-	Moreover, we also transferred 100ml LB medium into an erlenmeyer for the use of tomorrow.	+
-		+
-		+
-	'''02/07'''	+
-		+
-	In the morning we continued working with competent cells and in the afternoon we tried the transformation efficiency kit.	+

---

Revision as of 13:20, 10 July 2013

Wetlab

26/06

Some of us have already finished their exams so we started working in the lab. For now we just made the antibiotics solutions that we will have to use this summer.

27/06

Today we poured the agar plates with and without the antibiotics.

28/06

Just one thing to do today: make the FSB buffer. Easy job, but we have to recover from the exams, and it is almost weekend ofcourse.

01/07

As the first day of July, our job today wasn't too heavy. We started making the competent cells. The main task was to inoculate Top10 and DH5alpha strains from agar plate into the medium, herein we use tips to transfer both the strains into 3ml LB medium under laminar flow, two times for each strain. Then incubate them overnight.

02/07

In the morning we continued yesterday's job, working with competent cells and in the afternoon we tried the transformation efficiency kit. Fingers crossed!

03/07

We checked the plates that grew under 37°C overnight, and surprisingly no colony appear in any of them! Now we have to figure out what went wrong. Possible reasons are:

• Bad competent cells (please not!)
• We didn't use enough recovery time for the cells.
• The cells need more time to grow.

To examine what went wrong we did the experiment over again, but this time we used our own pUC 19-vector and let the cells recover for 2 hours instead of one.

We also prepared the SOC-medium for future use.

04/07

Hurray! This time we do have cell growth, so we counted the cells and calculated the transform efficiency. This was still quite low though... We prepared the GTE-buffer for future use and prepared agar medium. in the afternoon, we found out that the medium in the autoclave spilled out everywhere in the autoclave, possibly due to the pressure in the autoclave. Lukas was the lucky guy who got to clean out the autoclave.

05/07