Team:Wageningen UR/Collaborations

From 2013.igem.org

(Difference between revisions)
 
(12 intermediate revisions not shown)
Line 3: Line 3:
<!--- Navigation Template --->
<!--- Navigation Template --->
{{:Team:Wageningen_UR/Templates/Navigation}}
{{:Team:Wageningen_UR/Templates/Navigation}}
-
 
<html>
<html>
-
<div class="pagina-titel">
+
<script type="text/javascript">
-
<h2>iGEM team Cornell University</h2>
+
$(window).scroll(function(){
-
      
+
 
 +
    var windowPos = $(window).scrollTop(); // get the offset of the window from the top of page
 +
    var windowHeight = $(window).height(); // get the height of the window
 +
    var docHeight = $(document).height();
 +
    var docAction = (docHeight -60) - windowHeight;
 +
 
 +
    if( windowPos >= docAction ){
 +
        $('.tournavleft, .tournavright').addClass('mar');
 +
    } else {
 +
        $('.tournavleft, .tournavright').removeClass('mar');
 +
    }
 +
});
 +
</script>
 +
<div class="projectheader">
 +
<img src="https://static.igem.org/mediawiki/2013/f/f8/Humanheader.jpg">
 +
<div class="content collaborations">
 +
<h1>Collaborations</h1>
 +
<h2></h2>
 +
</div>
 +
</div>
 +
 
 +
<div id="wrapper">
 +
     <div id="humantabs">
 +
        <ul>
 +
            <li><a href="https://2013.igem.org/Team:Wageningen_UR/Masterclass">Masterclass</a></li>
 +
            <li><a href="https://2013.igem.org/Team:Wageningen_UR/Science_cafe">Science cafe</a></li>
 +
            <li><a href="https://2013.igem.org/Team:Wageningen_UR/IgemNL">iGEM Netherlands</a></li>
 +
            <li class="active"><span>Collaborations</span></li>
 +
            <li><a href="https://2013.igem.org/Team:Wageningen_UR/Conference">Conference</a></li>
 +
            <li><a href="https://2013.igem.org/Team:Wageningen_UR/Vitruvian_man">Vitruvian man</a></li>
 +
        </ul>
 +
    </div>
 +
</div>
<div id="pagewrapper">
<div id="pagewrapper">
 +
</html>
 +
==iGEM team Cornell University==
 +
<html>
 +
<h3>Introduction</h3>
<p>
<p>
-
The iGEM team of Cornell is one of the iGEM teams that is, as well as we are, working on a fungus. They are working on <i>basidiomycetes</i> and are making a toolkit for this unknown chassis. For the collaboration between iGEM Cornell and us we exchanged biobricks. This would be a pki promoter and terminator from our site and we got a cre-recombinase and two resistance genes (geneticin and hygomycin) from them to be tested in <i>A. niger</i>. For the geneticin resistance markers <i>A. niger</i> was transformed with the construct and at different geneticin the growth of a negative control and the transformants are checked. It appeared that 60µg/mL is not enough geneticin to inhibit the growth of <i>A. niger</i> without the resistance gene. Another growth experience was done with a concentration of 220µg/mL.  
+
Filamentous fungi are only rarely used in iGEM. This is partly because genetic modifications take a lot more time, but also because there are few (if any) parts available in the iGEM registry. Fortunately, we found that the <a href="https://2013.igem.org/Team:Cornell" target="_blank">2013 Cornell team</a> has selected a fungus as organism of choice. They are working on <i>Basidiomycetes</i> and are making a toolkit for this chassis that has not been used in iGEM before. We decided that, since Cornell is making selection markers for filamentous fungi, we would use their constructs and validate them in our organism of choice: <i>Aspergillus niger</i>. These constructs encoded antibiotic resistance cassettes against hygromycin and geneticin. In addition a pki promoter was send to the iGEM team of Cornell.  
</p>
</p>
 +
<h3>Aim</h3>
 +
<p>
 +
The goal was to test the geneticin resistance gene in <i>A. niger</i>. Cornell was kind enough to provide us with pure geneticin to perform the experiment. As hygromycin could not be sent via standard shipping as it is considered a hazardous material, we only worked with the geneticin resistance construct.
 +
</p>
 +
<h3>Approach</h3>
 +
<p>
 +
The construct we received from the iGEM team from Cornell University was present in <i>E. coli</i> and the organization of the construct was as followed: promoter, the geneticin resistence gene and a terminator. The first step was to isolate the plasmid from <i>E. coli</i>, and after obtaining sufficient quantities of the vector it was used to transform <i>A. niger</i>. The transformants were grown on two different concentrations of geneticin and one controle plate for a period of 3-4 days at 30°C. One plate contained a control and no geneticin was present in the agar. The other two plates contained different concentration of geneticin: 60µg/mL and 220µg/mL.
 +
</p>
 +
<h3>Results</h3>
 +
<p>
 +
Transformation of <i>A. niger</i> requires the generation of protoplasts, which is a delicate process, and somewhat more cumbersome than the making of competent <i>E. coli</i> cells. After transformation the protoplasts take 3-4 days to grow. Interestingly, we observed growth on all the plates, including the negative controls, in which untransformed protoplasts were left to grow on plates containing high doses of geneticin.
 +
</p>
 +
<img src="https://static.igem.org/mediawiki/2013/9/98/Marit_WUR_Geneticin.jpg" />
 +
<p class="caption"> On the left two plates with 60µg/mL geneticin and on the rigth two plates with 220µg/mL geneticin are shown. The control plates are also included on the right side of the two pictures.</p>
 +
<h3>Discussion</h3>
 +
<p>
 +
In literature study it was mentioned that geneticin has an inhibitory concentration between 60 µg/mL and 200 µg/mL for <i>Trichoderma atroviride</i>. For this reason we selected the concentrations mentioned above. We conclude that our <i>A. niger</i> strain, which is closely related to the standard (<a href="http://www.ncbi.nlm.nih.gov/pubmed/17259976" target="_blank">and fully sequenced CBS strain</a>), is not sensitive to geneticin. Though it is possible that the geneticin resistance gene works properly in other Eukaryotes, we conclude that it is unsuited as a selection marker for Aspergillus niger. 
 +
</p>
</div>
</div>
-
</html>
 
-
 
-
 
-
<div class="pagina-titel">
 
-
<h2>Samples for NRP UEA Norwich</h2>
 
-
   
 
<div id="pagewrapper">
<div id="pagewrapper">
-
 
+
</html>
 +
==Samples for NRP UEA Norwich==
 +
<html>
<p>
<p>
The iGEM team of NRP UEA Norwich is working on a biosensor to be able to detect antimycins, an anti-fungal compound produced by <i>Streptomyces</i>. For the quality of their project they asked different iGEM teams to send them soil samples from different places in their hometown. Of course we grabbed our bikes, played in the mud and collected samples to help out the iGEM team of Norwich.</p>
The iGEM team of NRP UEA Norwich is working on a biosensor to be able to detect antimycins, an anti-fungal compound produced by <i>Streptomyces</i>. For the quality of their project they asked different iGEM teams to send them soil samples from different places in their hometown. Of course we grabbed our bikes, played in the mud and collected samples to help out the iGEM team of Norwich.</p>
Line 34: Line 83:
<img src="https://static.igem.org/mediawiki/2013/f/f5/Marit_WUR_Soil_samples_Norwich.jpg" style="width:80%;height:80%;"/>
<img src="https://static.igem.org/mediawiki/2013/f/f5/Marit_WUR_Soil_samples_Norwich.jpg" style="width:80%;height:80%;"/>
<p class="caption">Soil samples in Greiner tubes </p>
<p class="caption">Soil samples in Greiner tubes </p>
-
<html>
 
</div>
</div>
-
</html>
 
-
<html>
 
-
<div class="pagina-titel">
 
-
<h2>Protocols for TU Delft iGEM team</h2>
 
-
   
 
<div id="pagewrapper">
<div id="pagewrapper">
-
 
+
</html>
 +
==Protocols for TU Delft iGEM team==
 +
<html>
<p>
<p>
Gel extraction and DNA purification kits are expensive to come by for most iGEM teams. Few of our team members found a cheaper and effective alternative for the same. These are homemade silica spin columns which have made it into the Elseiver journal, Analytical biochemistry. We sent this protocol to the iGEM team of TU Delft as they had problems with gel extraction and buying expensive kits.
Gel extraction and DNA purification kits are expensive to come by for most iGEM teams. Few of our team members found a cheaper and effective alternative for the same. These are homemade silica spin columns which have made it into the Elseiver journal, Analytical biochemistry. We sent this protocol to the iGEM team of TU Delft as they had problems with gel extraction and buying expensive kits.
</p>
</p>
-
 
</div>
</div>
-
</html>
 
 +
<div id="pagewrapper">
 +
</html>
 +
==Questionnaire for iGEM Purdue==
<html>
<html>
-
<div class="pagina-titel">
 
-
<h2>Questionnaire for iGEM Purdue</h2>
 
-
   
 
-
 
-
<div id="pagewrapper">
 
-
 
-
 
<p>
<p>
The iGEM team of Purdue asked iGEM teams to fill in a questionnaire about the standardization of the data sheet of the biobricks. They asked more than 50 teams around the world about their opinion and iGEM Wageningen was one of them. Of course we were happy to fill in this questionnaire and help them. Especially because it will help us and future iGEM teams in submitting their parts and search for other interesting parts.  
The iGEM team of Purdue asked iGEM teams to fill in a questionnaire about the standardization of the data sheet of the biobricks. They asked more than 50 teams around the world about their opinion and iGEM Wageningen was one of them. Of course we were happy to fill in this questionnaire and help them. Especially because it will help us and future iGEM teams in submitting their parts and search for other interesting parts.  
</p>
</p>
-
 
</div>
</div>
-
</html>
 
-
 
-
<html>
 
-
<div class="pagina-titel">
 
-
<h2>Survey about your peronal motivation from iGEM Paris</h2>
 
-
   
 
<div id="pagewrapper">
<div id="pagewrapper">
-
 
+
</html>
-
 
+
==Survey about your peronal motivation from iGEM Paris==
 +
<html>
<p>
<p>
Why are you joining the iGEM and what experiences do you want to get and actually get? This is something the iGEM team Paris was wondering about and that is why they sent around a survey we were happy to fill in. Every team member was asked to do it separately as it was a survey about your motivation.   
Why are you joining the iGEM and what experiences do you want to get and actually get? This is something the iGEM team Paris was wondering about and that is why they sent around a survey we were happy to fill in. Every team member was asked to do it separately as it was a survey about your motivation.   
</p>
</p>
-
 
</div>
</div>
 +
<div class="tournavleft">
 +
<a href="https://2013.igem.org/Team:Wageningen_UR/Science_cafe" class="tourprev"><span class="prev">Previous</span><span class="tourr">Tour Page</span></a>
 +
</div>
 +
<div class="tournavright">
 +
<a href="https://2013.igem.org/Team:Wageningen_UR/Achievements" class="tournext"><span class="prev">Next</span><span class="tourr">Tour Page</span></a>
 +
</div>
 +
</html>
</html>

Latest revision as of 03:55, 5 October 2013

Collaborations

iGEM team Cornell University

Introduction

Filamentous fungi are only rarely used in iGEM. This is partly because genetic modifications take a lot more time, but also because there are few (if any) parts available in the iGEM registry. Fortunately, we found that the 2013 Cornell team has selected a fungus as organism of choice. They are working on Basidiomycetes and are making a toolkit for this chassis that has not been used in iGEM before. We decided that, since Cornell is making selection markers for filamentous fungi, we would use their constructs and validate them in our organism of choice: Aspergillus niger. These constructs encoded antibiotic resistance cassettes against hygromycin and geneticin. In addition a pki promoter was send to the iGEM team of Cornell.

Aim

The goal was to test the geneticin resistance gene in A. niger. Cornell was kind enough to provide us with pure geneticin to perform the experiment. As hygromycin could not be sent via standard shipping as it is considered a hazardous material, we only worked with the geneticin resistance construct.

Approach

The construct we received from the iGEM team from Cornell University was present in E. coli and the organization of the construct was as followed: promoter, the geneticin resistence gene and a terminator. The first step was to isolate the plasmid from E. coli, and after obtaining sufficient quantities of the vector it was used to transform A. niger. The transformants were grown on two different concentrations of geneticin and one controle plate for a period of 3-4 days at 30°C. One plate contained a control and no geneticin was present in the agar. The other two plates contained different concentration of geneticin: 60µg/mL and 220µg/mL.

Results

Transformation of A. niger requires the generation of protoplasts, which is a delicate process, and somewhat more cumbersome than the making of competent E. coli cells. After transformation the protoplasts take 3-4 days to grow. Interestingly, we observed growth on all the plates, including the negative controls, in which untransformed protoplasts were left to grow on plates containing high doses of geneticin.

On the left two plates with 60µg/mL geneticin and on the rigth two plates with 220µg/mL geneticin are shown. The control plates are also included on the right side of the two pictures.

Discussion

In literature study it was mentioned that geneticin has an inhibitory concentration between 60 µg/mL and 200 µg/mL for Trichoderma atroviride. For this reason we selected the concentrations mentioned above. We conclude that our A. niger strain, which is closely related to the standard (and fully sequenced CBS strain), is not sensitive to geneticin. Though it is possible that the geneticin resistance gene works properly in other Eukaryotes, we conclude that it is unsuited as a selection marker for Aspergillus niger.

Samples for NRP UEA Norwich

The iGEM team of NRP UEA Norwich is working on a biosensor to be able to detect antimycins, an anti-fungal compound produced by Streptomyces. For the quality of their project they asked different iGEM teams to send them soil samples from different places in their hometown. Of course we grabbed our bikes, played in the mud and collected samples to help out the iGEM team of Norwich.

Soil samples in Greiner tubes

Protocols for TU Delft iGEM team

Gel extraction and DNA purification kits are expensive to come by for most iGEM teams. Few of our team members found a cheaper and effective alternative for the same. These are homemade silica spin columns which have made it into the Elseiver journal, Analytical biochemistry. We sent this protocol to the iGEM team of TU Delft as they had problems with gel extraction and buying expensive kits.

Questionnaire for iGEM Purdue

The iGEM team of Purdue asked iGEM teams to fill in a questionnaire about the standardization of the data sheet of the biobricks. They asked more than 50 teams around the world about their opinion and iGEM Wageningen was one of them. Of course we were happy to fill in this questionnaire and help them. Especially because it will help us and future iGEM teams in submitting their parts and search for other interesting parts.

Survey about your peronal motivation from iGEM Paris

Why are you joining the iGEM and what experiences do you want to get and actually get? This is something the iGEM team Paris was wondering about and that is why they sent around a survey we were happy to fill in. Every team member was asked to do it separately as it was a survey about your motivation.

PreviousTour Page
NextTour Page


Retrieved from "http://2013.igem.org/Team:Wageningen_UR/Collaborations"