Team:KU Leuven/Journal/Ecology

From 2013.igem.org

(Difference between revisions)
(Created page with "{{:Team:KU Leuven/Template:Header}} {{:Team:KU Leuven/Template:Style}} {{:Team:KU Leuven/Template:Menu}} <html> <body> <div class="row-fluid"> <div class="span12 timeline"> <ul c...")
Line 10: Line 10:
  <li>
  <li>
-
   <time class="cbp_tmtime"><span></span> <span>01/07 – 07/07</span></time>
+
   <time class="cbp_tmtime"><span></span> <span>05/08 – 08/08</span></time>
-
   <div class="cbp_tmicon cbp_tmicon-phone"><i class="livicon activeicon" data-name="rocket" data-size="23" data-onparent="true" data-color="white"></i></div>
+
   <div class="cbp_tmicon cbp_tmicon-phone"><i class="livicon activeicon" data-name="caret-right" data-size="23" data-onparent="true" data-color="white"></i></div>
   <div class="cbp_tmlabel">
   <div class="cbp_tmlabel">
-
     <h3>Week 1: The modelling team is on fire!</h3>
+
     <h3>Week 5:</h3>
     <div class="content">
     <div class="content">
-
     <p align="justify">The modelling team is ready to rock Matlab after watching some tutorials and webinars about modelling and <a href="http://www.mathworks.nl/products/simbiology/webinars.html">Symbiology</a><br/>
+
     <p align="justify">After reading a lot of articles about MeS attracting of ladybugs, we wanted to test it ourselves. At Biobest, we could perform preference experiments with two-spotted ladybugs, therefore we made a special platform. We made different dilutions of MeS in ethanol and used pure ethanol as a control in our experiments. All our experiments were performed in a chemical safety cabinet to avoid distribution of the volatile MeS and ethanol.<br/>
-
We are excited to get our modelling  team going and therefore we had an appointment with professor <a href="http://www.kuleuven.be/optec/people/74-Prof-Kristel-Bernaerts">Kristel Bernaerts</a>. 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 and a possible way to achieve this would be by expressing it during a short pulse, stimulated by the presence of a signal from other cells.<br/>
+
-
And to tackle this problem we also started brainstorming about some possible networks with oscillating behaviour. Here we have to keep in mind that the bacterial colonies have to get and stay synchronized and this might be achieved by a rapid (protein-protein interaction) feedback which is proportional to the phase difference.
+
-
In an attempt to collaborate with the wetlab team we discussed our main focus for the upcoming weeks: figuring out an oscillating construct and simulating the behaviour of the methyl salicylate BioBrick.<br/>
+
-
And since organization comes after thought Bert and Sander started  working on simulating the Mortier Oscillator (as Bert likes to call it) in SimBiology, while Tina and Tomas started modelling the network to produce methyl salicylate by looking at BSMT1(the enzyme that catalyzes the reaction from salicylate to methyl salicylate) and at pchA and pchB which catalyze the reactions from chorismate to isochorismate to salicylate.<br/>
+
-
Later this week Tina had a look on how to use the COBRA toolbox for our purpose and we would have to check the constraints on reaction rates and add our new reactions.<br/>
+
-
Bert contacted professor <a href="http://www.kuleuven.be/wieiswie/en/person/u0015385">Johan Suykens</a> and professor <a href="http://www.kuleuven.be/wieiswie/nl/person/00005764">Jan Degrève</a> to get an idea of how to analyse the MO. He gave the advice towards a bifurcation analysis, on which Bert will have a closer look.<br/>Tomas on the other hand started on the development of another oscillator and contacted professor <a href="http://www.kuleuven.be/wieiswie/en/person/u0006989">Dirk Roose</a> of mathematical engineering, who suggested the use of MatCont.Furthermore we are also considering a strategy of a knock-out/knock-down of genes responsible for chorismate mutase and chorismate lyase to optimize methyl salicylate production.<br/>
+
</p> </div>
</p> </div>
   </div>
   </div>
   </li>
   </li>
 +
<li>
 +
  <time class="cbp_tmtime"><span></span> <span>05/08 – 08/08</span></time>
 +
  <div class="cbp_tmicon cbp_tmicon-phone"><i class="livicon activeicon" data-name="caret-right" data-size="23" data-onparent="true" data-color="white"></i></div>
 +
  <div class="cbp_tmlabel">
 +
    <h3>Week 5:</h3>
 +
    <div class="content">
 +
    <p align="justify">After reading a lot of articles about MeS attracting of ladybugs, we wanted to test it ourselves. At Biobest, we could perform preference experiments with two-spotted ladybugs, therefore we made a special platform. We made different dilutions of MeS in ethanol and used pure ethanol as a control in our experiments. All our experiments were performed in a chemical safety cabinet to avoid distribution of the volatile MeS and ethanol.<br/>
 +
</p> </div>
 +
  </div>
 +
  </li>
 +
 +
 +
<li>
 +
  <time class="cbp_tmtime"><span></span> <span>26/08 – 30/08</span></time>
 +
  <div class="cbp_tmicon cbp_tmicon-phone"><i class="livicon activeicon" data-name="caret-right" data-size="23" data-onparent="true" data-color="white"></i></div>
 +
  <div class="cbp_tmlabel">
 +
    <h3>Week 8:</h3>
 +
    <div class="content">
 +
    <p align="justify">After the disappointing results of our insect experiments at BioBest, we wanted to find out the cause of the random movement of the ladybugs. We thought about different concentrations and solvents,  a different set-up and so on. After talking to Tim Belien of pcfruit, he offered us their Y-tube olfactometer and their lab, to perform some more experiments in different conditions. After reading some articles, we contacted the authors for some help. With some great information over the solvent and concentrations, we begun our experiments at pcfruit. <br/>
 +
We started the first day by making different dilutions of methyl salicylate in hexane. We compared the behaviour of adult ladybugs on these concentrations with a control, pure hexane, in a Y-tube olfactometer. The next day, we tried to dilute the methyl salicylate in paraffin oil. This was not easy, because of the viscosity. We compared again all the MeS concentrations with the control in a Y-tube olfactometer.
 +
</p> </div>
 +
  </div>
 +
  </li>
 +
 +
<li>
 +
  <time class="cbp_tmtime"><span></span> <span>09/09 – 13/09</span></time>
 +
  <div class="cbp_tmicon cbp_tmicon-phone"><i class="livicon activeicon" data-name="caret-right" data-size="23" data-onparent="true" data-color="white"></i></div>
 +
  <div class="cbp_tmlabel">
 +
    <h3>Week 10:</h3>
 +
    <div class="content">
 +
    <p align="justify">We examined the amount of aphids and the distribution of these aphids 3 and 7 days after putting them on the plants. After this last aphid count, we used the plants for a cafeteria experiment with predators. We wanted to examine the effect of the different MeS inductions on the predator preference. In this experiment we used Macrolophus, a recently identified natural enemy of the aphids. A plant of every MeS concentration and a control were put in a circle and the predators were released in the middle of the circle. The amount of predators on every plant was counted after 45 min. Afterwards, the predators were shaken off the plant. This was repeated twice. To determine the effect on a longer time span, we counted the aphids also after 24h.
 +
</p> </div>
 +
  </div>
 +
  </li>
 +
 +
<li>
 +
  <time class="cbp_tmtime"><span></span> <span>16/09 – 20/09</span></time>
 +
  <div class="cbp_tmicon cbp_tmicon-phone"><i class="livicon activeicon" data-name="caret-right" data-size="23" data-onparent="true" data-color="white"></i></div>
 +
  <div class="cbp_tmlabel">
 +
    <h3>Week 11:</h3>
 +
    <div class="content">
 +
    <p align="justify">After the cafeteria experiment, we also wanted to determine the effect of MeS on the root growth. Therefore, we washed all the roots and measured the most important parameters: the primary root, the width of the top of the primary root and the longest secondary root.
 +
</p> </div>
 +
  </div>
 +
  </li>
</ul>
</ul>

Revision as of 12:32, 4 October 2013

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

  • Week 5:

    After reading a lot of articles about MeS attracting of ladybugs, we wanted to test it ourselves. At Biobest, we could perform preference experiments with two-spotted ladybugs, therefore we made a special platform. We made different dilutions of MeS in ethanol and used pure ethanol as a control in our experiments. All our experiments were performed in a chemical safety cabinet to avoid distribution of the volatile MeS and ethanol.

  • Week 5:

    After reading a lot of articles about MeS attracting of ladybugs, we wanted to test it ourselves. At Biobest, we could perform preference experiments with two-spotted ladybugs, therefore we made a special platform. We made different dilutions of MeS in ethanol and used pure ethanol as a control in our experiments. All our experiments were performed in a chemical safety cabinet to avoid distribution of the volatile MeS and ethanol.

  • Week 8:

    After the disappointing results of our insect experiments at BioBest, we wanted to find out the cause of the random movement of the ladybugs. We thought about different concentrations and solvents, a different set-up and so on. After talking to Tim Belien of pcfruit, he offered us their Y-tube olfactometer and their lab, to perform some more experiments in different conditions. After reading some articles, we contacted the authors for some help. With some great information over the solvent and concentrations, we begun our experiments at pcfruit.
    We started the first day by making different dilutions of methyl salicylate in hexane. We compared the behaviour of adult ladybugs on these concentrations with a control, pure hexane, in a Y-tube olfactometer. The next day, we tried to dilute the methyl salicylate in paraffin oil. This was not easy, because of the viscosity. We compared again all the MeS concentrations with the control in a Y-tube olfactometer.

  • Week 10:

    We examined the amount of aphids and the distribution of these aphids 3 and 7 days after putting them on the plants. After this last aphid count, we used the plants for a cafeteria experiment with predators. We wanted to examine the effect of the different MeS inductions on the predator preference. In this experiment we used Macrolophus, a recently identified natural enemy of the aphids. A plant of every MeS concentration and a control were put in a circle and the predators were released in the middle of the circle. The amount of predators on every plant was counted after 45 min. Afterwards, the predators were shaken off the plant. This was repeated twice. To determine the effect on a longer time span, we counted the aphids also after 24h.

  • Week 11:

    After the cafeteria experiment, we also wanted to determine the effect of MeS on the root growth. Therefore, we washed all the roots and measured the most important parameters: the primary root, the width of the top of the primary root and the longest secondary root.

Retrieved from "http://2013.igem.org/Team:KU_Leuven/Journal/Ecology"