Difference between revisions of "Team:MSU-Michigan/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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<p>The parts were taken from the Shewanella oneidensis MR-1 genome by finding a regulator on <a href="http://regprecise.lbl.gov/RegPrecise/">RegPrecise.</a> Then the consensus sequence was located at the appropriate distance from a gene and DNA upstream from the gene was taken, which included the consensus sequence. This ensured that the ribosomal binding site would be in the sequence we took as well as any other necessary machinery for the following gene to be regulated by the promoter that we extracted.  All of the promoters were then amplified using PCR and inserted into the prL814 plasmid in place of the T7A1 promoter.
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<h5>Note</h5>
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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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Each part that the MSU iGEM team constructed, was taken from the Shewanella oneidensis MR-1 genome by finding a regulator for each desired part on http://regprecise.lbl.gov/RegPrecise/. These parts were all built to detect contaminants. A provided consensus sequence was then taken at the appropriate distance from a gene and included with the DNA that is upstream from that gene. This selection process ensured that the ribosomal binding site would be in the sequence taken, as well as any other necessary machinery for the following gene to be regulated by the promoter that was extracted. All of the promoters were then amplified using PCR and inserted into the prL814 plasmid in place of the T7A1 promoter. From the nine parts created ( part numbers listed below) Paraquat was the main part that the MSU team chose to pursue for GFP experiments, and proof of concept, due to no metabolic relevance to the cell.
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<h2>Part Table </h2>
  
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<h5>Adding parts to the registry</h5>
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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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<img src="https://static.igem.org/mediawiki/2017/f/ff/MSU-Michigan_Part_Insertion.png">
  
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<img src="https://static.igem.org/mediawiki/2017/thumb/4/45/MSU-Michigan_Biobrick_confirmation.jpeg/800px-MSU-Michigan_Biobrick_confirmation.jpeg.png" alt="Biobricks" label="Confirmation of promoters induced by <em>(from left to right)</em> Blue light, Paraquat, Nitrate (NO3), and Copper"/>
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<p>"Confirmation of promoters induced by <em>(from left to right)</em> Blue light, Paraquat, Nitrate (NO3), and Copper"</p>
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<groupparts>iGEM17 MSU-Michigan</groupparts>
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<h5>What information do I need to start putting my parts on the Registry?</h5>
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<p>The information needed to initially create a part on the Registry is:</p>
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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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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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<h5>Inspiration</h5>
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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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<h5>Part Table </h5>
 
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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>iGEM17 MSU-Michigan</groupparts>
 
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Latest revision as of 03:24, 2 November 2017

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Parts

The parts were taken from the Shewanella oneidensis MR-1 genome by finding a regulator on RegPrecise. Then the consensus sequence was located at the appropriate distance from a gene and DNA upstream from the gene was taken, which included the consensus sequence. This ensured that the ribosomal binding site would be in the sequence we took as well as any other necessary machinery for the following gene to be regulated by the promoter that we extracted. All of the promoters were then amplified using PCR and inserted into the prL814 plasmid in place of the T7A1 promoter.

Each part that the MSU iGEM team constructed, was taken from the Shewanella oneidensis MR-1 genome by finding a regulator for each desired part on http://regprecise.lbl.gov/RegPrecise/. These parts were all built to detect contaminants. A provided consensus sequence was then taken at the appropriate distance from a gene and included with the DNA that is upstream from that gene. This selection process ensured that the ribosomal binding site would be in the sequence taken, as well as any other necessary machinery for the following gene to be regulated by the promoter that was extracted. All of the promoters were then amplified using PCR and inserted into the prL814 plasmid in place of the T7A1 promoter. From the nine parts created ( part numbers listed below) Paraquat was the main part that the MSU team chose to pursue for GFP experiments, and proof of concept, due to no metabolic relevance to the cell.

Part Table

Biobricks

"Confirmation of promoters induced by (from left to right) Blue light, Paraquat, Nitrate (NO3), and Copper"

<groupparts>iGEM17 MSU-Michigan</groupparts>

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