Difference between revisions of "Team:BioIQS-Barcelona/Parts"

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<h1>Parts</h1>
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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>
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<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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<h3>Note</h3>
 
<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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<h3>Adding parts to the registry</h3>
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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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<a href="http://parts.igem.org/Add_a_Part_to_the_Registry">
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<h3>Inspiration</h3>
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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>
+
  
<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
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    #groupparts{
<ul>
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        margin:auto
<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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<h3>What information do I need to start putting my parts on the Registry?</h3>
 
<p>The information needed to initially create a part on the Registry is:</p>
 
<ul>
 
<li>Part Name</li>
 
<li>Part type</li>
 
<li>Creator</li>
 
<li>Sequence</li>
 
<li>Short Description (60 characters on what the DNA does)</li>
 
<li>Long Description (Longer description of what the DNA does)</li>
 
<li>Design considerations</li>
 
</ul>
 
  
<p>
 
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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                        <h1 class="mb-5">Wet Lab | Parts</h1>
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                        <a href="https://2018.igem.org/Team:BioIQS-Barcelona/Parts#cl-description" class="btn btn-outline btn-xl js-scroll-trigger">Have a look!</a>
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<h3>Part Table </h3>
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                                <h2 class="section-heading orange">Basic Parts</h2>
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                                    <p class="book orange-medium">Our basic parts consist of the alpha and beta chains of the HLA-DQ protein. Both chains can be obtained from genomic DNA of any celiac patient by PCR following the protocol that we designed in our <a href="https://2018.igem.org/Team:BioIQS-Barcelona/Basic_Part" target="_blank">basic parts page</a>.</p>
 +
                                    <p class="book orange-medium">However, to get and submit the parts, we synthetized them after performing a codon optimization of the sequence for expression in <i>E. coli</i>. The aminoacidic sequence was obtained from the genomic sequence of a celiac patient. The parts were then amplified by PCR and cloned into the pSB1C3 vector.</p>
 +
                                </div>
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                                <h4 class="section-heading orange">BBa_K2879666: HLA-DQA:</h4>
 +
                            </div>
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                                    <p class="book orange-medium">This biobrick corresponds to the HLA-DQA1*05:01 gene variant. Thus, when coupled to the protein encoded by the HLA-DQB1*02:01 gene variant (BBa_K2879800) it will form the HLA haplotype DQ2. This part only contains the exons 2 and 3 of the protein (which encode the extracellular domains of the protein), for more information see the design tab. Therefore, this part (HLA-DQA1) can be used in combination with part BBa_K2879800 (HLA-DQB) to form a variant of the HLA-DQ complex which recognizes the deaminated gliadin peptide, which plays a central role in celiac disease.</p>
 +
                                    <p class="book orange-medium">Note that this biobrick has been synthetized de novo and it has been codon optimized to be expressed in E. coli BL21. See the detailed information of this biobrick for more information on how to form the complex HLA-DQ by expressing this part in combination with part BBa_K2879800 in E. coli. See the design tab to see how the sequence has been obtained and codon optimized.</p>
 +
                                </div>
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 +
                                <h4 class="section-heading orange">BBa_K2879800: HLA-DQB:</h4>
 +
                            </div>
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                                <div class="col-md-12">
 +
                                    <p class="book orange-medium">This biobrick corresponds to the HLA-DQB1*02:01 gene variant. Thus, when coupled to the protein encoded by the HLA-DQA1*05:01 gene variant (BBa_K2879666) it will form the HLA haplotype DQ2. This part only contains the exons 2 and 3 of the protein (which encode the extracellular domains of the protein), for more information see the design tab. Therefore, this part (HLA-DQB1) can be used in combination with part BBa_K2879666 (HLA-DQA1) to form a variant of the HLA-DQ complex which recognizes the deaminated gliadin peptide, which plays a central role in celiac disease.</p>
 +
                                    <p class="book orange-medium">Note that this biobrick has been synthetized de novo and it has been codon optimized to be expressed in E. coli BL21. See the detailed information of this biobrick for more information on how to form the complex HLA-DQ by expressing this part in combination with part BBa_K2879666 in E. coli. See the design tab to see how the sequence has been obtained and codon optimized.</p>
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        </div>
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    </section>
  
<p>Please include a table of all the parts your team has made during your project on this page. Remember part characterization and measurement data must go on your team part pages on the Registry. </p>
 
  
</html>
 
<groupparts>iGEM18 BioIQS-Barcelona</groupparts>
 
<html>
 
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                                <h2 class="section-heading white center" style="text-align:center">Composite Parts</h2>
 +
                            </div>
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                                    <p class="book white">We have created several functional units made from the combination of the HLA-DQ basic parts. The objective of our composite parts is to find a suitable expression system for the HLA-DQ protein, which is the basis of our sensor.</p>
 +
                                </div>
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                                <h4 class="section-heading white">BBa_K2879100: HLA-DQ a+b polycistronic</h4>
 +
                            </div>
 +
                        </div>
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                        <div class="col-md-10 right">
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                                    <p class="book white">This composite is formed by the &alpha; and &beta; chain of the human HLA-DQ flanked by the restriction enzymes <i>NdeI</i> and <i>SacI/SalI</i>. Each chain is separated by an intergenic regions containing a RBS for translation.</p>
 +
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                                <h4 class="section-heading white" id="cuttheword">BBa_K2879102: LZipper+HLADQA+HLADQB+NdeISacI</h4>
 +
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                                    <p class="book white">This composite encodes for the &alpha; and &beta; chains of the human HLA-DQ. Each chain is linked to a Fos/Jun domain for protein stability. Both chains are separated by an intergenic region that contains a RBS. The entire construct is flanked by the restriction enzymes <i>NdeI</i> and <i>SacI/SalI</i>. A Strep Tag is placed after the &alpha; chain.</p>
 +
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                            <h3 class="orange-intense">Submitted parts</h3>
 +
                            <p class="book orange">Below you can see a table of all the parts that our team has characterized and submitted to the registry.</p>
 +
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    </section> <!-- below we close /html because the table is automatically inserted when detects the tag <groupparts> which is for mediawiki, not for HTML. -->
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<groupparts>iGEM2018 BioIQS-Barcelona</groupparts>
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Latest revision as of 23:20, 17 December 2018

BIO IQS

Wet Lab | Parts

Have a look!

Basic Parts

Our basic parts consist of the alpha and beta chains of the HLA-DQ protein. Both chains can be obtained from genomic DNA of any celiac patient by PCR following the protocol that we designed in our basic parts page.

However, to get and submit the parts, we synthetized them after performing a codon optimization of the sequence for expression in E. coli. The aminoacidic sequence was obtained from the genomic sequence of a celiac patient. The parts were then amplified by PCR and cloned into the pSB1C3 vector.

BBa_K2879666: HLA-DQA:

This biobrick corresponds to the HLA-DQA1*05:01 gene variant. Thus, when coupled to the protein encoded by the HLA-DQB1*02:01 gene variant (BBa_K2879800) it will form the HLA haplotype DQ2. This part only contains the exons 2 and 3 of the protein (which encode the extracellular domains of the protein), for more information see the design tab. Therefore, this part (HLA-DQA1) can be used in combination with part BBa_K2879800 (HLA-DQB) to form a variant of the HLA-DQ complex which recognizes the deaminated gliadin peptide, which plays a central role in celiac disease.

Note that this biobrick has been synthetized de novo and it has been codon optimized to be expressed in E. coli BL21. See the detailed information of this biobrick for more information on how to form the complex HLA-DQ by expressing this part in combination with part BBa_K2879800 in E. coli. See the design tab to see how the sequence has been obtained and codon optimized.

BBa_K2879800: HLA-DQB:

This biobrick corresponds to the HLA-DQB1*02:01 gene variant. Thus, when coupled to the protein encoded by the HLA-DQA1*05:01 gene variant (BBa_K2879666) it will form the HLA haplotype DQ2. This part only contains the exons 2 and 3 of the protein (which encode the extracellular domains of the protein), for more information see the design tab. Therefore, this part (HLA-DQB1) can be used in combination with part BBa_K2879666 (HLA-DQA1) to form a variant of the HLA-DQ complex which recognizes the deaminated gliadin peptide, which plays a central role in celiac disease.

Note that this biobrick has been synthetized de novo and it has been codon optimized to be expressed in E. coli BL21. See the detailed information of this biobrick for more information on how to form the complex HLA-DQ by expressing this part in combination with part BBa_K2879666 in E. coli. See the design tab to see how the sequence has been obtained and codon optimized.

Composite Parts

We have created several functional units made from the combination of the HLA-DQ basic parts. The objective of our composite parts is to find a suitable expression system for the HLA-DQ protein, which is the basis of our sensor.

BBa_K2879100: HLA-DQ a+b polycistronic

This composite is formed by the α and β chain of the human HLA-DQ flanked by the restriction enzymes NdeI and SacI/SalI. Each chain is separated by an intergenic regions containing a RBS for translation.

BBa_K2879102: LZipper+HLADQA+HLADQB+NdeISacI

This composite encodes for the α and β chains of the human HLA-DQ. Each chain is linked to a Fos/Jun domain for protein stability. Both chains are separated by an intergenic region that contains a RBS. The entire construct is flanked by the restriction enzymes NdeI and SacI/SalI. A Strep Tag is placed after the α chain.

Submitted parts

Below you can see a table of all the parts that our team has characterized and submitted to the registry.

<groupparts>iGEM2018 BioIQS-Barcelona</groupparts>