Difference between revisions of "Team:Aalto-Helsinki/Parts"

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<div class="row">
 
<div class="row">
  
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<div class="col-xs-12 col-sm-6">
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<h2>Propane 1</h2>
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<h2>Propane 1 / BBa_K1655000</h2>
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<figure style="float:right">
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  <img src="https://static.igem.org/mediawiki/2015/7/7c/Aalto-Helsinki_plasmid_propane1_for_white_bckgr.png" style="width:230px;"/>
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  <figcaption><b><center>Figure 1.</b> Propane 1</center></figcaption>
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</figure>
  
 
<p>Our Propane 1 includes 4 of the 10 required genes to produce propane in <i>E. coli</i>. The plasmid has been assembled from IDT's gBlocks with NEBuilder assembly, similar to Gibson Assembly.</p>
 
<p>Our Propane 1 includes 4 of the 10 required genes to produce propane in <i>E. coli</i>. The plasmid has been assembled from IDT's gBlocks with NEBuilder assembly, similar to Gibson Assembly.</p>
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<p><b>Validation:</b> We restricted our Propane 1 and ran the insert on an agarose gel. From the picture we can tell that the insert is the correct size. <span style="color:red">Onko tähän jotain muuta? Sekvenssidataa tms?</span></p>  
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<p><b>Validation:</b> We restricted our Propane 1 and ran the insert on an agarose gel. From the picture we can tell that the insert is the correct size. The result can be seen in <a href="https://static.igem.org/mediawiki/2015/3/3a/Aalto-Helsinki_car_submittedparts.png">Figure 2.</a><br/>
 +
Additionally, we did a colony PCR with VR and our primer P001. The VR primer attaches to our plasmid's backbone while P001 anneals with the very beginning of our construct. With this colony PCR we were able to show that the insert is present and it is indeed in the pSB1C3 backbone. See <a href="https://static.igem.org/mediawiki/2015/d/d1/Aalto-Helsinki_submittedparts_colony_pcr_validation.png">figure 3</a> for results, where the product in wells 1, and 5-10 is of the right size.</p>
 +
<p>The colony which produced the product seen in figure 3, well 10 was sent to the registry under the name <b><a href="http://parts.igem.org/Part:BBa_K1655000">BBa_K1655000</a></b>.</p>
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<p>Click <a href="">here</a> to download the full sequence of Propane 1 in pSB1C3 backbone.</p>
  
 
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<div class="col-xs-12 col-sm-6">
 
  
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<figure style="margin-bottom:2%;margin-top:-4%;">
 
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  <img src="https://static.igem.org/mediawiki/2015/7/7c/Aalto-Helsinki_plasmid_propane1_for_white_bckgr.png" style="width:230px;"/>
 
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  <figcaption><b>Figure 1.</b> Propane 1</figcaption>
 
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</figure>
 
  
  
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<figure >
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<!-- row -->
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  <img src="https://static.igem.org/mediawiki/2015/3/3a/Aalto-Helsinki_car_submittedparts.png" style="width:280px;"/>
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  <figcaption><b>Figure 2.</b> Propane 1 insert on gel</figcaption>
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</figure>
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</div>
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</div><!-- row -->
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</section>
 
</section>
  
 
<section id="gfp" class="active" data-anchor="gfp">
 
<section id="gfp" class="active" data-anchor="gfp">
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<h2>Fusable GFP</h2>
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<h2>Fusable GFP / BBa_K1655001</h2>
  
 
<figure  style="float:right">
 
<figure  style="float:right">
 
   <img src="https://static.igem.org/mediawiki/2015/1/1d/Aalto-Helsinki_gfp_plasmid_with_text.png" style="width:150px;"/>
 
   <img src="https://static.igem.org/mediawiki/2015/1/1d/Aalto-Helsinki_gfp_plasmid_with_text.png" style="width:150px;"/>
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   <figcaption><b>Figure 3.</b> GFP Brick</figcaption>
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   <figcaption><center><b>Figure 4.</b> GFP Brick</center></figcaption>
 
</figure>
 
</figure>
  
 
<p>We built a GFP biobrick which can be fused to any protein's aminoterminal end with the standard BioBrick assembly enzymes. We have added an extra nucleotide prior to the brick's suffix to maintain the reading frame after fusion, which is typically lost when the restriction enzyme assembly is used. </p>
 
<p>We built a GFP biobrick which can be fused to any protein's aminoterminal end with the standard BioBrick assembly enzymes. We have added an extra nucleotide prior to the brick's suffix to maintain the reading frame after fusion, which is typically lost when the restriction enzyme assembly is used. </p>
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<p><b>Validation:</b> Our GFP brick has been fully sequenced, and the sequencing results were as expected. We have also been able to express the GFP after fusing it with an amphiphilic brick. This construct functioned under K608003, a strong constitutive promoter and a medium RBS. HS Slovenia Team also helped us validate this brick. They gained positive results of their construct with the GFP through colony PCR and analytical restrictions, but were unable to detect the fluerescence under UV light or functionality of the fused protein.</p>
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<p><b>Validation:</b> Our GFP brick has been fully sequenced, and the sequencing results were as expected. We have also been able to express the GFP after fusing it with an amphiphilic brick. This construct functioned under <a href="http://parts.igem.org/Part:BBa_K608003">BBa_K608003</a>, a strong constitutive promoter and a medium RBS. HS Slovenia Team also helped us validate this brick. They gained positive results of their construct with the GFP through colony PCR and analytical restrictions, but were unable to detect the fluerescence under UV light or functionality of the fused protein.</p>
 +
<p style="color:red">The colony which produced the product seen in figure 3, well 10 was sent to the registry under the name <b><a href="http://parts.igem.org/Part:BBa_K1655001">BBa_K1655001</a></b>.</p>
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<p>Click <a href="">here</a> to download the full sequence of our Fusable GFP in pSB1C3 backbone.</p>
  
 
</section>
 
</section>
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<section id="amph" class="active" data-anchor="amph">
 
<section id="amph" class="active" data-anchor="amph">
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<h2>Amphiphilic</h2>
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<h2>Amphiphilic / BBa_K1655002</h2>
  
 
<figure  style="float:right">
 
<figure  style="float:right">
 
   <img src="https://static.igem.org/mediawiki/2015/f/f7/Aalto-Helsinki_amph_plasmid_with_text.png" style="width:150px;"/>
 
   <img src="https://static.igem.org/mediawiki/2015/f/f7/Aalto-Helsinki_amph_plasmid_with_text.png" style="width:150px;"/>
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   <figcaption><b>Figure 4.</b> Amphiphilic Brick</figcaption>
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   <figcaption><center><b>Figure 5.</b> Amphiphilic Brick</center></figcaption>
 
</figure>
 
</figure>
  
 
<p>We submitted a sole amphiphilic brick, containing only the coding region of the ampihphilic protein. This brick can be used to produce intracellular micelles or vesicles under any chosen expression system.</p>
 
<p>We submitted a sole amphiphilic brick, containing only the coding region of the ampihphilic protein. This brick can be used to produce intracellular micelles or vesicles under any chosen expression system.</p>
 
<p><b>Validation:</b> Our amphiphilic brick's sequencing results were unclear, as the brick is mainly built of short repeats. <span style="color:red">Microscope pictures!</span></p>
 
<p><b>Validation:</b> Our amphiphilic brick's sequencing results were unclear, as the brick is mainly built of short repeats. <span style="color:red">Microscope pictures!</span></p>
 +
<p style="color:red">The colony which produced the product seen in figure 3, well 10 was sent to the registry under the name <b><a href="http://parts.igem.org/Part:BBa_K1655002">BBa_K1655002</a></b>.</p>
 +
<p>Click <a href="">here</a> to download the full sequence of the Amphiphilic Brick in pSB1C3 backbone.</p>
  
  
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<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
 
<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
 
<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.</p>
 
<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.</p>
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<div class="highlightBox">
 
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<h4>Note</h4>
 
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<p>Note that parts must be documented on the <a href="http://parts.igem.org/Main_Page"> Registry</a>. This page serves to <i>showcase</i> the parts you have made. Future teams and other users and are much more likely to find parts by looking in the Registry than by looking at your team wiki.</p>
 
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<h4>Adding parts to the registry</h4>
 
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<p>You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry">Add a Part to the Registry</a> link.</p>
 
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<p>We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
 
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<h4>What information do I need to start putting my parts on the Registry?</h4>
 
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<p>The information needed to initially create a part on the Registry is:</p>
 
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<ul>
 
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<li>Part Name</li>
 
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<li>Part type</li>
 
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<li>Creator</li>
 
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<li>Sequence</li>
 
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<li>Short Description (60 characters on what the DNA does)</li>
 
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<li>Long Description (Longer description of what the DNA does)</li>
 
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<li>Design considerations</li>
 
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</ul>
 
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<p>
 
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. </p>
 
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<h4>Inspiration</h4>
 
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<p>We have a created  a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started.</p>
 
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<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
 
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<ul>
 
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<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
 
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<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
 
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
 
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</ul>
 
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<h4>Part Table </h4>
 
<h4>Part Table </h4>

Revision as of 08:00, 15 September 2015

Submitted Parts

Propane 1 / BBa_K1655000

Figure 1. Propane 1

Our Propane 1 includes 4 of the 10 required genes to produce propane in E. coli. The plasmid has been assembled from IDT's gBlocks with NEBuilder assembly, similar to Gibson Assembly.

Validation: We restricted our Propane 1 and ran the insert on an agarose gel. From the picture we can tell that the insert is the correct size. The result can be seen in Figure 2.
Additionally, we did a colony PCR with VR and our primer P001. The VR primer attaches to our plasmid's backbone while P001 anneals with the very beginning of our construct. With this colony PCR we were able to show that the insert is present and it is indeed in the pSB1C3 backbone. See figure 3 for results, where the product in wells 1, and 5-10 is of the right size.

The colony which produced the product seen in figure 3, well 10 was sent to the registry under the name BBa_K1655000.

Click here to download the full sequence of Propane 1 in pSB1C3 backbone.

Fusable GFP / BBa_K1655001

Figure 4. GFP Brick

We built a GFP biobrick which can be fused to any protein's aminoterminal end with the standard BioBrick assembly enzymes. We have added an extra nucleotide prior to the brick's suffix to maintain the reading frame after fusion, which is typically lost when the restriction enzyme assembly is used.

Validation: Our GFP brick has been fully sequenced, and the sequencing results were as expected. We have also been able to express the GFP after fusing it with an amphiphilic brick. This construct functioned under BBa_K608003, a strong constitutive promoter and a medium RBS. HS Slovenia Team also helped us validate this brick. They gained positive results of their construct with the GFP through colony PCR and analytical restrictions, but were unable to detect the fluerescence under UV light or functionality of the fused protein.

The colony which produced the product seen in figure 3, well 10 was sent to the registry under the name BBa_K1655001.

Click here to download the full sequence of our Fusable GFP in pSB1C3 backbone.

Amphiphilic / BBa_K1655002

Figure 5. Amphiphilic Brick

We submitted a sole amphiphilic brick, containing only the coding region of the ampihphilic protein. This brick can be used to produce intracellular micelles or vesicles under any chosen expression system.

Validation: Our amphiphilic brick's sequencing results were unclear, as the brick is mainly built of short repeats. Microscope pictures!

The colony which produced the product seen in figure 3, well 10 was sent to the registry under the name BBa_K1655002.

Click here to download the full sequence of the Amphiphilic Brick in pSB1C3 backbone.

Part Documentation

Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <groupparts> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.

Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.

Part Table

<groupparts>iGEM015 Example</groupparts>