Difference between revisions of "Team:TecCEM/Parts"

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{{TecCEM}}
 
{{TecCEM}}
 
<html>
 
<html>
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<style>
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    div.parts-div a:vistied,
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    div.parts-div a:hover {
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        color: #333333 !important;
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        text-decoration: none !important;
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    }
  
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    div.parts-div a:hover {
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        font-weight: 500;
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    }
  
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<div class="column full_size">
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    div.parts-div a {
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<h1>Parts</h1>
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        color: #ff9d33;
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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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    }
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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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</style>
 +
<div id="gif-title" class="text-parts">
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    <img src="https://static.igem.org/mediawiki/2018/e/ec/T--TecCEM--Cells--Parts.gif" alt="Cell Gif">
 +
    <h1>Parts Overview</h1>
 
</div>
 
</div>
 +
<div class="wrapper">
 +
    <nav class="sidebar-index d-none d-md-block">
 +
        <div class="sidebar-header">
 +
            <h3>Parts/ Overview</h3>
 +
        </div>
 +
        <a href="#partsSubmenu" data-toggle="collapse" aria-expanded="false" data-offset="100" data-change="sidemenu">
 +
            <span data-change="el" class="d-inline-block open"></span>
 +
            Index
 +
        </a>
 +
        <ul class="collapse list-unstyled" id="partsSubmenu">
 +
            <li>
 +
                <a data-target="#overview">Overview</a>
 +
            </li>
 +
            <li>
 +
                <a data-target="#collagen">Collagen Biobrick</a>
 +
            </li>
 +
            <li>
 +
                <a data-target="#tenascin">Tenascin Biobrick</a>
 +
            </li>
 +
            <li>
 +
                <a data-target="#leptin">Leptin Biobrick</a>
 +
            </li>
 +
        </ul>
 +
    </nav>
 +
    <div class="content parts-div">
 +
        <div class="container">
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            <div class="row">
 +
                <div class="col">
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                    <h1 id="overview"> Overview </h1>
 +
                    <p> The main aim for our project was to produce recombinant proteins that would compose our
 +
                        scaffold to improve cell proliferation. Throughout our literary research, we came across
 +
                        scaffolds, which were the ideal support that would improve cell-cell interaction, cell
 +
                        migration, proliferation and differentiation. We approached the scaffold design with three
 +
                        different proteins, each with properties to achieve better tissue regeneration and could
 +
                        interact with each other. This meant we needed a way to produce protein overexpression in <i>E.
 +
                        coli</i> vectors. </p>
 +
                    <p> In this section the description of the constructs and background behind the constructs is
 +
                        explained. </p>
  
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<div class="column full_size">
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                    <h2 id="collagen"> Collagen Biobrick</h2>
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<div class="highlight decoration_background">
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                    <ol>
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<h3>Note</h3>
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                        <li>A collagen-like synthetic gene comprising heparin binding site of collagen type V (HepV)
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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>
+
                            was employed. The synthetic gene for COL5A1 was optimized for codon usage in <i>E. coli</i>
−
</div>
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                            Rosetta 2 (DE3), whereas illegal sequences were removed.</li>
−
</div>
+
                        <li>The nucleotide sequence of collagen is optimized for <i>E. coli</i> Rosetta 2 (DE3) and cloned
 +
                            into the backbone pSB1C3 that consists of a chloramphenicol resistant gene using EcoRI and
 +
                            PstI restriction sites, with an inducible T7-lac promoter for the construction of the
 +
                            BioBrick. The T7-lac promoter is extracted from plasmid pET-DEST42.</li>
 +
                        <li>A nucleotide sequence encoding Red Fluorescent Protein (RFP) was retrieved from iGEM
 +
                            database (BBa_K1323009) and cloned into pSB1C3 under an Anderson constitutive promoter
 +
                            (BBa_K823005) using an RFC[10] with restriction enzymes: EcoRI and PstI and used a double
 +
                            TAATAA stop codon. The resulting plasmid is referred to as pSB1C3-RFP-COLlikeHepV. To
 +
                            determine whether the sequence of the resulting gene would produce the same protein a
 +
                            simulation of the protein was done with I-Tasser.</li>
 +
                    </ol>
 +
<div class="text-center">
 +
                                <figure class="figure text-center">
 +
                                    <img style="max-height: 70vh;" src="https://static.igem.org/mediawiki/2018/b/bc/T--TecCEM--Colageno.jpg"
 +
                                        class="figure-img img-fluid rounded" alt="IMP-1">
 +
                                    <figcaption class="figure-caption"><strong>Figure 1. Collagen construct pSB1C3 </strong></figcaption>
 +
                                </figure>
 +
                            </div>  
  
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<div class="clear extra_space"></div>
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                    <h2 id="tenascin">Tenascin Biobrick </h2>
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<div class="line_divider"></div>
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                    <ol>
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<div class="clear extra_space"></div>
+
                        <li>The TNC domain of fibronectin type III-like repeats (TNCIII), specifically the subdomain
−
 
+
                            TNCIII5 has the responsibility of the binding with heparin. This binding between heparin
−
 
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                            and tenascin is involved in affinity with many growth factors, specifically with Fibroblast
−
 
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                            Growth Factor (FGF). </li>
−
 
+
                        <li>The nucleotide sequence of TNCIII5 is optimized for <i>E. coli</i> BL21 DE3 and cloned into the
−
 
+
                            backbone (pSB1C3) using EcoRI and PstI restriction sites, with an inducible T7-lac promoter
−
<div class="column two_thirds_size">
+
                            and rrnB-T1 terminator using RFC[10]. The domain was expressed by bacterial expression as
−
<div class="highlight decoration_B_full">
+
                            GST fusion protein and use C-terminal HIS tag. The fusion protein GST was used for the
−
 
+
                            stability of the domain.</li>
−
<h3>Adding parts to the registry</h3>
+
                        <li>A polyproline linker was used between the TCDIII5 domain and GST in order to conserve the
−
<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>
+
                            three-dimensional structure of the full protein and then a protein simulation was done
−
 
+
                            using I-Tasser simulator. </li>
−
<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>
+
                    </ol>
−
<div class="button_link">
+
<div class="text-center">
−
<a href="http://parts.igem.org/Add_a_Part_to_the_Registry">
+
                                <figure class="figure text-center">
−
ADD PARTS
+
                                    <img style="max-height: 70vh;" src="https://static.igem.org/mediawiki/2018/2/2b/T--TecCEM--TNCGST.png "
−
</a>
+
                                        class="figure-img img-fluid rounded" alt="IMP-1">
 +
                                    <figcaption class="figure-caption"><strong>Figure 2. Tenascin-GST construct pSB1C3 </strong></figcaption>
 +
                                </figure>
 +
                            </div>
 +
                    <h2 id="leptin">Leptin Biobrick </h2>
 +
                    <ol>
 +
                        <li>Leptin is a growth factor and is the main protein that helps in this project for skin
 +
                            regeneration. This is going to be encapsulated by chitosan and bound to the scaffold
 +
                            composed by Tenascin, collagen, and heparin. Leptin protein is the product of the ob gene
 +
                            and it is found in adipocytes cells. </li>
 +
                        <li>The coding sequence is optimized for <i>Escherichia coli</i> BL21 (DE3) and cloned in a pSB1C3
 +
                            plasmid. To get the cloned sequence is necessary the implementation of EcoRI and PstI
 +
                            restriction sites, that they are located in the prefix and suffix, respectively, previously
 +
                            sintetized for the coding leptin sequence. In addition, the sequence part has an inducible
 +
                            T7-lac promoter (BBa_R0184 → BBa_K2406020) and a double terminator (B0010-B0012 →
 +
                            BBa_B0015) rrnBT1-T7TE from <i>E. coli</i> using RFC[10]. For its purification was used a
 +
                            C-terminal HIS tag. </li>
 +
                        <li>A simulation in I-Tasser was used to prove the stability of the protein and also, to
 +
                            observe the interaction of Leptin with chitosan, was necessary the implementation of the
 +
                            math model created by the iGEM-TEC CEM team. </li>
 +
                    </ol>
 +
<div class="text-center">
 +
                                <figure class="figure text-center">
 +
                                    <img style="max-height: 70vh;" src="https://static.igem.org/mediawiki/2018/7/72/T--TecCEM--LeptinParts.png"
 +
                                        class="figure-img img-fluid rounded" alt="IMP-1">
 +
                                    <figcaption class="figure-caption"><strong>Figure 3. Leptin construct pSB1C3 </strong></figcaption>
 +
                                </figure>
 +
                            </div>
 +
                </div>
 +
            </div>
 +
            <div class="row">
 +
                <div class="col">
 +
                    <table class="table">
 +
                        <thead>
 +
                            <tr>
 +
                                <th>Name</th>
 +
                                <th>Type</th>
 +
                                <th>Description</th>
 +
                                <th>Designers</th>
 +
                            </tr>
 +
                        </thead>
 +
                        <tbody>
 +
                            <tr>
 +
                                <td><a href="http://parts.igem.org/Part:BBa_K2719000">BBa_K2719000</a></td>
 +
                                <td>Tag</td>
 +
                                <td>GST</td>
 +
                                <td>Karla Soto Blas</td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><a href="http://parts.igem.org/Part:BBa_K2719001">BBa_K2719001</a></td>
 +
                                <td>Coding</td>
 +
                                <td>Tenascin Domain V</td>
 +
                                <td>Karla Soto Blas</td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><a href="http://parts.igem.org/Part:BBa_K2719002">BBa_K2719002</a></td>
 +
                                <td>Coding</td>
 +
                                <td>GST + Tenascin Domain V</td>
 +
                                <td>Karla Soto Blas</td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><a href="http://parts.igem.org/Part:BBa_K2719003">BBa_K2719003</a></td>
 +
                                <td>Tag</td>
 +
                                <td>GST (Optimized for <i>E.coli</i> BL21)</td>
 +
                                <td>Karla Soto Blas</td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><a href="http://parts.igem.org/Part:BBa_K2719004">BBa_K2719004</a></td>
 +
                                <td>Coding</td>
 +
                                <td>Tenascin Fibronectin Domains (I-V)</td>
 +
                                <td>Karla Soto Blas</td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><a href="http://parts.igem.org/Part:BBa_K2719005">BBa_K2719005</a></td>
 +
                                <td>Device</td>
 +
                                <td>Tenascin Domain V Expression Device</td>
 +
                                <td>Karla Soto Blas</td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><a href="http://parts.igem.org/Part:BBa_K2719006">BBa_K2719006</a></td>
 +
                                <td>Coding</td>
 +
                                <td>Collagen V - Like</td>
 +
                                <td>Armando Cortés Reséndiz & María José Ugarte Orozco</td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><a href="http://parts.igem.org/Part:BBa_K2719007">BBa_K2719007</a></td>
 +
                                <td>Device</td>
 +
                                <td>Collagen V - Like Expression Device.</td>
 +
                                <td>Armando Cortés Reséndiz & María José Ugarte Orozco</td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><a href="http://parts.igem.org/Part:BBa_K2719008">BBa_K2719008</a></td>
 +
                                <td>Coding</td>
 +
                                <td>Leptin</td>
 +
                                <td>Andrea Pamela Jimenez Tapia & Rodrigo Valencia Ocampo</td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><a href="http://parts.igem.org/Part:BBa_K2719009">BBa_K2719009</a></td>
 +
                                <td>Device</td>
 +
                                <td>Leptin Coding Device</td>
 +
                                <td>Andrea Pamela Jimenez Tapia & Rodrigo Valencia Ocampo</td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><a href="http://parts.igem.org/Part:BBa_K2719010">BBa_K2719010</a></td>
 +
                                <td>Coding</td>
 +
                                <td>Leptin codiNg device with blue chromoprotein</td>
 +
                                <td>Juan Carlos Rueda Silva & Arantxa Karam Coppola</td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><a href="http://parts.igem.org/Part:BBa_K2719011">BBa_K2719011</a></td>
 +
                                <td>Coding</td>
 +
                                <td>Collagen coding device with blue chromoprotein</td>
 +
                                <td>Juan Carlos Rueda Silva & Arantxa Karam Coppola</td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><a href="http://parts.igem.org/Part:BBa_K2719012">BBa_K2719012</a></td>
 +
                                <td>Coding</td>
 +
                                <td>TCD5 coding device with blue chromoprotein</td>
 +
                                <td>Juan Carlos Rueda Silva & Arantxa Karam Coppola</td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td><a href="http://parts.igem.org/Part:BBa_K2719013">BBa_K2719013</a></td>
 +
                                <td>Device</td>
 +
                                <td>Blue Chromoprotein and RFP combined reporter</td>
 +
                                <td>Juan Carlos Rueda Silva & Arantxa Karam Coppola</td>
 +
                            </tr>
 +
                        </tbody>
 +
                    </table>
 +
                </div>
 +
            </div>
 +
        </div>
 +
    </div>
 
</div>
 
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<div class="highlight decoration_A_full">
 
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<h3>Inspiration</h3>
 
−
<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>
 
−
<ul>
 
−
<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
 
−
<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
 
−
<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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Latest revision as of 01:13, 18 October 2018

Cell Gif

Parts Overview

Overview

The main aim for our project was to produce recombinant proteins that would compose our scaffold to improve cell proliferation. Throughout our literary research, we came across scaffolds, which were the ideal support that would improve cell-cell interaction, cell migration, proliferation and differentiation. We approached the scaffold design with three different proteins, each with properties to achieve better tissue regeneration and could interact with each other. This meant we needed a way to produce protein overexpression in E. coli vectors.

In this section the description of the constructs and background behind the constructs is explained.

Collagen Biobrick

  1. A collagen-like synthetic gene comprising heparin binding site of collagen type V (HepV) was employed. The synthetic gene for COL5A1 was optimized for codon usage in E. coli Rosetta 2 (DE3), whereas illegal sequences were removed.
  2. The nucleotide sequence of collagen is optimized for E. coli Rosetta 2 (DE3) and cloned into the backbone pSB1C3 that consists of a chloramphenicol resistant gene using EcoRI and PstI restriction sites, with an inducible T7-lac promoter for the construction of the BioBrick. The T7-lac promoter is extracted from plasmid pET-DEST42.
  3. A nucleotide sequence encoding Red Fluorescent Protein (RFP) was retrieved from iGEM database (BBa_K1323009) and cloned into pSB1C3 under an Anderson constitutive promoter (BBa_K823005) using an RFC[10] with restriction enzymes: EcoRI and PstI and used a double TAATAA stop codon. The resulting plasmid is referred to as pSB1C3-RFP-COLlikeHepV. To determine whether the sequence of the resulting gene would produce the same protein a simulation of the protein was done with I-Tasser.
IMP-1
Figure 1. Collagen construct pSB1C3

Tenascin Biobrick

  1. The TNC domain of fibronectin type III-like repeats (TNCIII), specifically the subdomain TNCIII5 has the responsibility of the binding with heparin. This binding between heparin and tenascin is involved in affinity with many growth factors, specifically with Fibroblast Growth Factor (FGF).
  2. The nucleotide sequence of TNCIII5 is optimized for E. coli BL21 DE3 and cloned into the backbone (pSB1C3) using EcoRI and PstI restriction sites, with an inducible T7-lac promoter and rrnB-T1 terminator using RFC[10]. The domain was expressed by bacterial expression as GST fusion protein and use C-terminal HIS tag. The fusion protein GST was used for the stability of the domain.
  3. A polyproline linker was used between the TCDIII5 domain and GST in order to conserve the three-dimensional structure of the full protein and then a protein simulation was done using I-Tasser simulator.
IMP-1
Figure 2. Tenascin-GST construct pSB1C3

Leptin Biobrick

  1. Leptin is a growth factor and is the main protein that helps in this project for skin regeneration. This is going to be encapsulated by chitosan and bound to the scaffold composed by Tenascin, collagen, and heparin. Leptin protein is the product of the ob gene and it is found in adipocytes cells.
  2. The coding sequence is optimized for Escherichia coli BL21 (DE3) and cloned in a pSB1C3 plasmid. To get the cloned sequence is necessary the implementation of EcoRI and PstI restriction sites, that they are located in the prefix and suffix, respectively, previously sintetized for the coding leptin sequence. In addition, the sequence part has an inducible T7-lac promoter (BBa_R0184 → BBa_K2406020) and a double terminator (B0010-B0012 → BBa_B0015) rrnBT1-T7TE from E. coli using RFC[10]. For its purification was used a C-terminal HIS tag.
  3. A simulation in I-Tasser was used to prove the stability of the protein and also, to observe the interaction of Leptin with chitosan, was necessary the implementation of the math model created by the iGEM-TEC CEM team.
IMP-1
Figure 3. Leptin construct pSB1C3
Name Type Description Designers
BBa_K2719000 Tag GST Karla Soto Blas
BBa_K2719001 Coding Tenascin Domain V Karla Soto Blas
BBa_K2719002 Coding GST + Tenascin Domain V Karla Soto Blas
BBa_K2719003 Tag GST (Optimized for E.coli BL21) Karla Soto Blas
BBa_K2719004 Coding Tenascin Fibronectin Domains (I-V) Karla Soto Blas
BBa_K2719005 Device Tenascin Domain V Expression Device Karla Soto Blas
BBa_K2719006 Coding Collagen V - Like Armando Cortés Reséndiz & María José Ugarte Orozco
BBa_K2719007 Device Collagen V - Like Expression Device. Armando Cortés Reséndiz & María José Ugarte Orozco
BBa_K2719008 Coding Leptin Andrea Pamela Jimenez Tapia & Rodrigo Valencia Ocampo
BBa_K2719009 Device Leptin Coding Device Andrea Pamela Jimenez Tapia & Rodrigo Valencia Ocampo
BBa_K2719010 Coding Leptin codiNg device with blue chromoprotein Juan Carlos Rueda Silva & Arantxa Karam Coppola
BBa_K2719011 Coding Collagen coding device with blue chromoprotein Juan Carlos Rueda Silva & Arantxa Karam Coppola
BBa_K2719012 Coding TCD5 coding device with blue chromoprotein Juan Carlos Rueda Silva & Arantxa Karam Coppola
BBa_K2719013 Device Blue Chromoprotein and RFP combined reporter Juan Carlos Rueda Silva & Arantxa Karam Coppola