Difference between revisions of "Team:IISER-Kolkata/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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<div id="logo"><a href="https://2018.igem.org/Team:IISER-Kolkata"><img src="https://static.igem.org/mediawiki/2018/c/cd/T--IISER-Kolkata--bacman.jpg"/></a></div>
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<div class="pagelink" id="homeMenu"><a href="https://2018.igem.org/Team:IISER-Kolkata">Home</a></div>
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<div class="pagelink" id="projectMenu"><a href="https://2018.igem.org/Team:IISER-Kolkata/Problem">Project</a></div>
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<div class="pagelink" id="labMenu"><a href="https://2018.igem.org/Team:IISER-Kolkata/Deletion">Lab</a></div>
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<div class="pagelink" id="achieveMenu"><a href="https://2018.igem.org/Team:IISER-Kolkata/Results">Achievements</a></div>
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<div class="pagelink" id="humanityMenu"><a href="https://2018.igem.org/Team:IISER-Kolkata/Human_Practices">Humanity</a></div>
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<div class="subtab" id="deletionTab"><p><a href='https://2018.igem.org/Team:IISER-Kolkata/Deletion'>Deletion</a></p></div>
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<div class="subtab" id="assemblyTab"><p><a href='https://2018.igem.org/Team:IISER-Kolkata/Assembly'>Assembly</a></p></div>
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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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<div class="subtab" id="partsTab" style="background-color: black;"><p><a href='https://2018.igem.org/Team:IISER-Kolkata/Parts' style='color:white;'>Parts</a></p></div>
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<section class="intropic" style="background: url('https://static.igem.org/mediawiki/2018/4/48/T--IISER-Kolkata--Parts_Header.jpg') no-repeat; background-size: cover;"></section>
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<h1 class="subheading">Parts</h1>
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<p>Team IISER Kolkata’s contribution to this year’s 2018 iGEM registry are the following parts:</p>
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<tr><th>Part Number</th><th>Part Type</th><th>Sequence</th><th>Experience</th></tr>
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<tr><td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2773000" target="_blank">Bba_K2773000</a></td><td>Composite</td><td>Confirmed</td><td>Will work, requires testing</td></tr>
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<p><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2773000" target="_blank">Bba_K2773000</a> is a composite biobrick part designed by Mr. Diptatanu Das and Miss. Hrishika Rai. The part comprises of an Arsenic responsive promoter and autorepressor unit (Bba_J33201) upstream of a strong ribosome binding site (Bba_B0030).</p>
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<img class="subimage" src="https://static.igem.org/mediawiki/2018/1/1a/T--IISER-Kolkata--K2773000.png" style="width: 30vw;"/>
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<p>When cloned upstream of a reporter or any other protein coding gene, the part will cause strong expression of the protein in response to arsenate and/or arsenite ions. As per characterization by team Edinburgh 2006, the threshold for derepression of the promoter is 1μM of arsenate or arsenite salts in the external growth media of the chassis organism.</p>
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                                <p>In an ideal scenario the best way to characterize this part would have been to clone a reporter biobrick such as RFP or a chromoprotein downstream to it and quantify expression upon induction with increasing concentrations of arsenate or arsenite salts. However, despite several trials, such a characterizable clone could not be obtained. The basic parts used from the registry to produce this composite clone are both very well characterized and used by several iGEM teams in different iGEM seasons before. As a result, we very strongly believe that this part is most likely to work as expected. Nonetheless, as a part of its characterization, we could show the expression of ArsR regulatory protein from the biobrick part indicating that cloning an additional RBS downstream does not affect the ArsR expression, which can be considered as an additional testimony that this biobrick is expected to work.</p>
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                                <img class="subimage" src="https://static.igem.org/mediawiki/2018/2/21/T--IISER-Kolkata--Part_Characterize.png" style=""/>
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                                <p> The above SDS PAGE image shows expression of ArsR regulatory protein with induction by arsenate salts. The characterization is not full proof yet, but can be considered as satisfactory to the conviction, that the part works.</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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<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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<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>
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<p>The information needed to initially create a part on the Registry is:</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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<h3>Part Table </h3>
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<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>
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<groupparts>iGEM18 IISER-Kolkata</groupparts>
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Latest revision as of 01:43, 18 October 2018

Parts

Team IISER Kolkata’s contribution to this year’s 2018 iGEM registry are the following parts:

Part NumberPart TypeSequenceExperience
Bba_K2773000CompositeConfirmedWill work, requires testing

Bba_K2773000 is a composite biobrick part designed by Mr. Diptatanu Das and Miss. Hrishika Rai. The part comprises of an Arsenic responsive promoter and autorepressor unit (Bba_J33201) upstream of a strong ribosome binding site (Bba_B0030).

When cloned upstream of a reporter or any other protein coding gene, the part will cause strong expression of the protein in response to arsenate and/or arsenite ions. As per characterization by team Edinburgh 2006, the threshold for derepression of the promoter is 1μM of arsenate or arsenite salts in the external growth media of the chassis organism.

In an ideal scenario the best way to characterize this part would have been to clone a reporter biobrick such as RFP or a chromoprotein downstream to it and quantify expression upon induction with increasing concentrations of arsenate or arsenite salts. However, despite several trials, such a characterizable clone could not be obtained. The basic parts used from the registry to produce this composite clone are both very well characterized and used by several iGEM teams in different iGEM seasons before. As a result, we very strongly believe that this part is most likely to work as expected. Nonetheless, as a part of its characterization, we could show the expression of ArsR regulatory protein from the biobrick part indicating that cloning an additional RBS downstream does not affect the ArsR expression, which can be considered as an additional testimony that this biobrick is expected to work.

The above SDS PAGE image shows expression of ArsR regulatory protein with induction by arsenate salts. The characterization is not full proof yet, but can be considered as satisfactory to the conviction, that the part works.