Team:KU Leuven/Journal

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== Team ==
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'''11/07'''
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We decided to take advantage of the nice weather and had a BBQ. The morning after the iGEM-room was pretty empty, which might had something to do with the beers...
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[[File:BBQjuly11.JPG|200px|caption]]
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== Modeling ==
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'''01/07'''
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We installed '''Matlab''', took a look at some presentations about modeling. We are also investigating [http://www.mathworks.nl/products/simbiology/ SimBiology].
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'''02/07'''
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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.
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'''03/07'''
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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.
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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.
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'''04/07'''
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Bert and Sander are working on simulating the '''&Prime;Mortier Oscillator&Prime;''' in SimBiology.
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Tina and Tomas are modeling the network to produce methyl salicylate.
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:'''pchA''' and '''pchB''' catalyze the reactions from '''chorismate''' to '''isochorismate''' to '''salicylate'''.
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:'''BSMT1''' is the enzyme that catalyzes the reaction from '''salicylate''' to '''methyl salicylate'''.
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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.
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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.
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'''05/07'''
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Tomas started the development of another oscillator, while Sander and Tina are looking deeper into metabolic network modeling.
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'''07/07'''
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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.
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'''08/07'''
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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.
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'''09/07'''
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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.
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Bert added spatial heterogeneity in his Mortier Oscillator to see what happens on a population level.
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'''10/07'''
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We had a meeting Jonas Demeulemeester, member of the [https://2008.igem.org/Team:KULeuven KULeuven iGEM team of 2008], who explained us the methods their modeling team used. It was a lot of help to us and now we are at a new start!
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'''11/07'''
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Today was a Flemish holiday and we couldn't make use of our HQ, so we decided to work at Agora, the KU Leuven study centre.
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==Wetlab==
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'''26/06'''
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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.
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'''27/06'''
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Today we poured the agar plates with and without the antibiotics.
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'''28/06'''
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Just one thing to do today: make the [[Team:KU_Leuven/Protocols#Chemically competent E.coli cells: CaCl2 method |''' FSB buffer''']] to make competent cells. Easy job, but we have to recover from the exams, and it is almost weekend.
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'''01/07'''
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As the first day of July, our job today wasn't too heavy. We started making the [[Team:KU_Leuven/Protocols#Chemically competent E.coli cells: CaCl2 method | '''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.
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'''02/07'''
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In the morning we continued yesterday's job, working with [[Team:KU_Leuven/Protocols#Chemically competent E.coli cells: CaCl2 method | '''competent cells''']] and in the afternoon we tried the '''transformation efficiency kit'''. Fingers crossed!
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'''03/07'''
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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:
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*Bad competent cells (please not!)
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*We didn't use enough recovery time for the cells.
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*The cells need more time to grow.
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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.
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We also prepared the SOC-medium for future use.
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'''04/07'''
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Hurray! This time we do have '''cell growth''', so we counted the cells and calculated the transform efficiency. This was still quite low though...
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We prepared the [[Team:KU_Leuven/Protocols#Plasmid DNA isolation | '''GTE-buffer''']] for future use and prepared agar medium.
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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.
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'''05/07'''
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We selected 16 parts to work with further
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{| class = "wikitable"
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! align="left"| Plate 1
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! Plate 2
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! Plate 3
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! Plate 4
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! Plate 5
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|-
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|1C [http://parts.igem.org/Part:BBa_K398326 BBa_K398326]
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|1I [http://parts.igem.org/Part:BBa_B0032 BBa_B0032]
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|5E [http://parts.igem.org/Part:BBa_R0040 BBa_R0040]
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|6I [http://parts.igem.org/Part:BBa_J45199 BBa_J45199]
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|1H [http://parts.igem.org/Part:BBa_B0030 BBa_B0030]
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|-
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|1G [http://parts.igem.org/Part:BBa_K314100 BBa_K314100]
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|7E [http://parts.igem.org/Part:BBa_K808000 BBa_K808000]
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|20O [http://parts.igem.org/Part:BBa_I13453 BBa_I13453]
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|19K [http://parts.igem.org/Part:BBa_J45014 BBa_J45014]
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|2M [http://parts.igem.org/Part:BBa_B0034 BBa_B0034]
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|3D [http://parts.igem.org/Part:BBa_K823017 BBa_K823017]
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|15N [http://parts.igem.org/Part:BBa_I719005 BBa_I719005]
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|3O [http://parts.igem.org/Part:BBa_K608002 BBa_K608002]
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|4D [http://parts.igem.org/Part:BBa_K314103 BBa_K314103]
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|5E [http://parts.igem.org/Part:BBa_K608006 BBa_K608006]
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|17D [http://parts.igem.org/Part:BBa_K864600 BBa_K864600]
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During the '''heat shock''' the heat automatically turned off after one round, wicht we didnt realize at first. So for the bricks from plate 2 and 3, the heat shock temperature is a bit lower (around 37°C). Hence during the plating we used 50µl of transformed competent cells instead of 20µl for the tubes from plates 2 & 3.
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We also inoculated '''methyl salicylate producing cells''' (received from iGEM) on both Amp & Kan plates.
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'''08/07'''
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Unpatient as we were, we first checked the plates of the transformed competent cells and found out that '''only 4 petri dishes''' have small amount of colonies (7E2 top10, 5E3 top10, 1G1top10, 5E3 DH5alpha). Interestingly, cells plated on plates 2 and 3 (the ones where we used 50µl cells instead of 20µl), were most succesful, which means that the lack of colony may be caused by low amount of cells put on the petri dishes. This in turn also proves that the '''transforming efficiency is quite low'''. We should repeat this step with 50µl or more cells today.
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  <div class="visible-desktop span3 bg-yellow">
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    <a href="https://2013.igem.org/Team:KU_Leuven/Journal" title="Team:KU_leuven">
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    <i class="livicon activeicon" data-name="calendar" data-color="white"></i></div>
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  <div class="span7 icon-text">
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    <h3>Journals</h3>
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    </a>
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    <p>You are here!</p>
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  </div>
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  </div>
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</div>
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In the mean time, we also prepared LB agar medium and LB chloramphenicol agar medium to pour the plates.
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    <a href="https://2013.igem.org/Team:KU_Leuven/Protocols">
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    <i class="livicon activeicon" data-name="magic" data-color="white"></i></div>
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  <div class="span7 icon-text">
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    <h3>Protocols</h3> </a>
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    <p>No magic involved - unfortunately</p>
 +
  </div>
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  </div>
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</div>
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In the afternoon we inoculated the methyl salicilate strains with medium containing both ampicilline and kanamycin for each AB medium, the volume is 3ml per tube, and we repeated 3 tubes for each AB medium.
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    <a href="https://2013.igem.org/Team:KU_Leuven/Safety">
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    <i class="livicon activeicon" data-name="biohazard" data-color="white"></i>
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    </div>
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  <div class="span7 icon-text">
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    <h3>Safety</h3>
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    </a>
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    <p>Be careful!</p>
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  </div>
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  </div>
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</div>
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Moreover, we transformed the unsuccessful biobricks again into the competent cells.
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</div>
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'''09/07'''
 
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We made methyl salicylate producing cell stocks from the inoculation of yesterday and tried to isolate their plasmid.
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<!-- Modelling -->
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    <a href = "https://2013.igem.org/Team:KU_Leuven/Journal/Modelling">
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  <div class="span10 icon-text ">
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    <h3>Modelling</h3> </a>
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    <div class="row-fluid">
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    <div class="span12">
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      <p align="justify">This summer, three dedicated male engineers spent a whole summer modelling our systems. <br/>However, without the help of a girl, Tina, this would have been a rather "nerdy" journal. Luckily, Tina was always there when the modelling team sought a balance between awful jokes and work efficiency. Nevertheless, without Sander's work tempo, Bert’s criticism and Tomas' factotum mind, the modelling would not have been as thorough as now.<br/>
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In this journal, you can read how they started modelling from scratch up to being modelling specialists, using Matlab, SimBiology, COBRA and even qPCR.</p>
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    </div>
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We also tried to make competent TOP10 and DH5alpha cells using the [[Team:KU_Leuven/Protocols#Chemically competent E.coli cells: Inoue method | '''Inoue method''']] .
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<!-- E. coligy -->
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<div class="span12 icon-small white">
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  <div class="span2 bg-journals visible-desktop">
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    <a href = "https://2013.igem.org/Team:KU_Leuven/Journal/Ecology">
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    <i class="livicon activeicon" data-name="tree" data-onparent="true" data-color="white"></i>
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    <h3><i>E. coligy</i></h3> </a>
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    <div class="row-fluid">
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      <p align="justify">We worked together with two research groups, Biobest and pcfruit. Both offer a whole series of parasitoids and predators against aphids for the purpose of biological pest control and investigate the relationship between plant and aphid in search of a method to protect plants from this pest. Here, you can read more about the experiments Aurelie and Flore (Biobest) and Tina and Tomas (pcfruit) performed to test our model on aphids and ladybugs.</p>
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    </div>
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'''10/07'''
 
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We had a busy lab day today, with 3 main experiments running parallel, so all hands on deck!
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<!-- EBF-biobrick -->
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    <a href="https://2013.igem.org/Team:KU_Leuven/Journal/EBF/wetlab">
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    <h3>E-β-Farnesene</h3></a>
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      <p align="justify">Here we present the work on the <a href="Http://2013.igem.org/Team:KU Leuven/Project/Glucosemodel/EBF">EBF-biobrick</a>, a part of the glucose model, week by week. The contributors are Lukas and Su, which formed a very tight team that already started with lab work even during the exams in June. Lukas’ multitasking skills and Su’s precise work, combined with their cute smiles, made sure everyone regretted not being part of this team. <br/> You can read all about the extensive work the EBF guys have done in this part.</p>
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In the morning, we first made the gel to separate the plasmid that we extracted yesterday. The gel looked good, the separation is very clear.
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<!-- FLL -->
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[[File:Gel10 July.JPG|200px|caption]]
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    <a href = "https://2013.igem.org/Team:KU_Leuven/Journal/FFL/wetlab">
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    <i class="livicon activeicon" data-name="gears" data-onparent="true" data-color="white"></i>
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  <div class="span10 icon-text ">
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    <h3>Feed forward loop</h3> </a>
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    <div class="row-fluid">
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    <div class="span12">
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      <p align="justify">Long team discussions and Bert’s persistence resulted this summer in a ‘proof of concept’ wetlab version of Bert Mortier’s oscillator, called the ‘feed forward loop’. <br/>
 +
Pieter and Sylvie were immediately up to form a subteam and started working in order to create a part of the <a href="https://2013.igem.org/Team:KU_Leuven/Project/Oscillator">oscillator</a>.<br/>
 +
In this part, you can read all about their big UP in the beginning, going to a down after a while and the eventual steady state with troubleshooting in the end.<br/>
 +
Nevertheless, this feed forward loop is only the beginning to create Bert’s oscillator.</p>
 +
    </div>
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    </div>
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  </div>
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  </div>
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Afterwards, we extracted the plasmid from the gel by using the gel extraction kit and measured the amount of DNA with nanodrop.
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<a href="https://2013.igem.org/Team:KU_Leuven/Journal/MeS/wetlab">
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    <i class="livicon activeicon" data-name="lab" data-onparent="lab" data-color="white"></i>
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    <h3>Methyl Salicylate</h3> </a>
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    <div class="row-fluid">
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    <div class="span12">
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      <p align="justify">The Methyl Salicylate team or ‘MeS boys’, in normal life called Robbert and Laurens, worked on the improvement of the methyl salicylate brick round the clock almost whole summer.  The journal can be found here. More information on the MeS biobrick can be found on <a href="https://2013.igem.org/Team:KU_Leuven/Project/Glucosemodel/MeS"> this page</a>.</p>
 +
    </div>
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    </div>
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  </div>
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  </div>
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</div>
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</div>
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We also finished with the '''Inoue method''' to make competent cells.
 
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We wanted to do a '''colony PCR''' on Streptomyces, so first we prepared the primer stocks for our PCR.
 
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Ingmar extracted the genome from Streptomyces at IMPG using 4 different methods (as Streptomyces is gram negative, it is a bit difficult to extract the genome)
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<!-- Wetlab -->
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*microwave Streptomyces for 4mins
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*Streptomyces in water and 0.2%SDS, 4min microwave
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*Streptomyces in water and 1% SDS, 4min microwave
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*Streptomyces in TE buffer, 0.2% SDS, 4min microwave
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<a href="https://2013.igem.org/Team:KU_Leuven/Journal/MeS/qPCR">
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    <i class="livicon activeicon" data-name="spinner-six" data-onparent="true" data-color="white"></i>
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    <h3>qPCR</h3> </a>
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      <p align="justify">The modelling team also performed a qPCR, a new and appeasing way to characterise and to find data for our <a href="https://2013.igem.org/Team:KU_Leuven/Project/qPCR">computer model</a>. In this part, you can read how to properly manage with troubles and how to search for promising directions.</p>
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We ran a colony PCR for all these streptomyces + a negative control.
 
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In the afternoon, we also performed the plasmid extraction of all the successfully transformed biobricks.
 
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'''11/07'''
 
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Today is a Flemish holiday so the lab was closed unfortunately.
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Latest revision as of 10:27, 3 January 2014

iGem

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!

tree ladybugcartoon

Journals

You are here!

Protocols

No magic involved - unfortunately

Safety

Be careful!

Modelling

This summer, three dedicated male engineers spent a whole summer modelling our systems.
However, without the help of a girl, Tina, this would have been a rather "nerdy" journal. Luckily, Tina was always there when the modelling team sought a balance between awful jokes and work efficiency. Nevertheless, without Sander's work tempo, Bert’s criticism and Tomas' factotum mind, the modelling would not have been as thorough as now.
In this journal, you can read how they started modelling from scratch up to being modelling specialists, using Matlab, SimBiology, COBRA and even qPCR.

E. coligy

We worked together with two research groups, Biobest and pcfruit. Both offer a whole series of parasitoids and predators against aphids for the purpose of biological pest control and investigate the relationship between plant and aphid in search of a method to protect plants from this pest. Here, you can read more about the experiments Aurelie and Flore (Biobest) and Tina and Tomas (pcfruit) performed to test our model on aphids and ladybugs.

E-β-Farnesene

Here we present the work on the EBF-biobrick, a part of the glucose model, week by week. The contributors are Lukas and Su, which formed a very tight team that already started with lab work even during the exams in June. Lukas’ multitasking skills and Su’s precise work, combined with their cute smiles, made sure everyone regretted not being part of this team.
You can read all about the extensive work the EBF guys have done in this part.

Feed forward loop

Long team discussions and Bert’s persistence resulted this summer in a ‘proof of concept’ wetlab version of Bert Mortier’s oscillator, called the ‘feed forward loop’.
Pieter and Sylvie were immediately up to form a subteam and started working in order to create a part of the oscillator.
In this part, you can read all about their big UP in the beginning, going to a down after a while and the eventual steady state with troubleshooting in the end.
Nevertheless, this feed forward loop is only the beginning to create Bert’s oscillator.

Methyl Salicylate

The Methyl Salicylate team or ‘MeS boys’, in normal life called Robbert and Laurens, worked on the improvement of the methyl salicylate brick round the clock almost whole summer. The journal can be found here. More information on the MeS biobrick can be found on this page.

qPCR

The modelling team also performed a qPCR, a new and appeasing way to characterise and to find data for our computer model. In this part, you can read how to properly manage with troubles and how to search for promising directions.

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