Difference between revisions of "Team:SZMS 15 Shenzhen/Parts"

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                <li class="nav-li"><a href="https://2015.igem.org/Team:SZMS_15_Shenzhen">Homepage</a></li>
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        <div class="heading">
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                <div class="heading-text-title">Part Description</div>
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                <div class="heading-text-content">&nbsp;&nbsp;&nbsp;&nbsp;Parts documented and tested in lab:
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                <img src="https://static.igem.org/mediawiki/2015/8/83/SZMS2015_ptd-1.png">
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                <div class="content1-text-title"></div>
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                <div class="content1-text-content">&nbsp;&nbsp;&nbsp;&nbsp;Here we quote our previous project below:<br><br>
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EC 1.7.7.2 is able to catalyze the reactions:<br><br>
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Nitrite + H2O + oxidized ferredoxin ⇄ nitrate + reduced ferredoxin + 2H+
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HNO2 + NH3 = N2↑+ 2H2O<br><br>
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Obviously as suggested above, the first reaction is a reversible one; the heat we need is actually from the second reaction since the first one is basically to convert nitrate provided by our special LB into nitrite. On the other hand, the warmth released by the first reaction is so little that it has nearly no effect on the result. Consequently, we make only the math models for the second reaction, whose substrate is nitrate. As calculated, the general warmth that would be released is 334.55 KJ/mole, which is a theoretical datum.
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                <div class="content1-text-title">New Basic Parts</div>
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                <div class="content1-text-content">&nbsp;&nbsp;&nbsp;&nbsp;1. EC 1.7.7.2 Generator (BBa_K1687000)<br><br>
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EC 1.7.7.2 is a ferredoxin-nitrate reductase that catalyzes an oxidation reaction that shifts nitrite into nitrate. According to the change in enthalpy, it produces heat as well. Used by our previous team as plant-sitter, this enzyme is proved effective.<br><br>
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In order to assess the efficiency of our E.coli babysitter, we have made math models for the core system in it, EC 1.7.7.2, which functions as to heat up the environment to provide a more suitable temperature for the plant.<br><br>
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                <div class="content2-text-title"></div>
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                <div class="content2-text-content">However, considering the fact that we do not have adequate data to carry out our math models, we finally decide to use proportionality instead of accurate data. Both of the following charts are established by Excel.<br><br>
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The first one is a model under the condition that purely only EC 1.7.7.2 is functioning, which means, the concentration of it remains unchanged: (grey line → temperature inside the system)
  
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<h2> Part Documentation</h2>
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                <img src="https://2015.igem.org/File:SZMS2015_ptd-2.png">
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                <img src="https://2015.igem.org/File:SZMS2015_ptd-3.png">
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                </div>
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                <div class="content1-text-title"></div>
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                <div class="content1-text-content">The second one is a model under the condition that RNA Thermometer in the first part of our entire plasmid is functioning to start the heating-up system which is mostly EC 1.7.7.2 in certain extent of external temperature (&#60;27℃). Since it is being manipulated by the other system, the concentration of EC 1.7.7.2 can no long remain unchanged, but changed over time: (black line → temperature inside the system)<br><br>
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                    General information about EC 1.7.7.2 can be found in the following link: http://www.genome.jp/dbget-bin/www_bget?ec:1.7.7.2.
  
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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 class="content2-text-title">New Composite parts</div>
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                <div class="content2-text-content">
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1. BBa_K1687002 is a composite part combining a EC 1.7.7.2<br><br>
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This part, submitted to the Registry, is used in our story “Houyi shoots down sun” in order to simulate the suns, which in our project produce heat and light but is later suppressed. We proudly use this part in our plasmid and are pleasing to report that it really worked. As time goes through, the molarity of nitrite and oxidized ferredoxins reduced like a bow-shaped curve.<br><br>
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Consisting of BBa_K1687000, an RBS (BBa_B0034), a GFP coding sequence and a double terminator (BBa_B0015), this part is able to produce both light and heat, just as the sun functions in the real world.
  
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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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        <font class="buttom-intro" color="#555555">Part description Team:SZMS_15_Shenzhen</font>
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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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<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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<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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<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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<h4>Part Table </h4>
 
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<groupparts>iGEM015 Example</groupparts>
 
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Revision as of 23:36, 17 September 2015

Title

Part Description
    Parts documented and tested in lab:
    Here we quote our previous project below:

EC 1.7.7.2 is able to catalyze the reactions:

Nitrite + H2O + oxidized ferredoxin ⇄ nitrate + reduced ferredoxin + 2H+ HNO2 + NH3 = N2↑+ 2H2O

Obviously as suggested above, the first reaction is a reversible one; the heat we need is actually from the second reaction since the first one is basically to convert nitrate provided by our special LB into nitrite. On the other hand, the warmth released by the first reaction is so little that it has nearly no effect on the result. Consequently, we make only the math models for the second reaction, whose substrate is nitrate. As calculated, the general warmth that would be released is 334.55 KJ/mole, which is a theoretical datum.
New Basic Parts
    1. EC 1.7.7.2 Generator (BBa_K1687000)

EC 1.7.7.2 is a ferredoxin-nitrate reductase that catalyzes an oxidation reaction that shifts nitrite into nitrate. According to the change in enthalpy, it produces heat as well. Used by our previous team as plant-sitter, this enzyme is proved effective.

In order to assess the efficiency of our E.coli babysitter, we have made math models for the core system in it, EC 1.7.7.2, which functions as to heat up the environment to provide a more suitable temperature for the plant.

However, considering the fact that we do not have adequate data to carry out our math models, we finally decide to use proportionality instead of accurate data. Both of the following charts are established by Excel.

The first one is a model under the condition that purely only EC 1.7.7.2 is functioning, which means, the concentration of it remains unchanged: (grey line → temperature inside the system)
The second one is a model under the condition that RNA Thermometer in the first part of our entire plasmid is functioning to start the heating-up system which is mostly EC 1.7.7.2 in certain extent of external temperature (<27℃). Since it is being manipulated by the other system, the concentration of EC 1.7.7.2 can no long remain unchanged, but changed over time: (black line → temperature inside the system)

General information about EC 1.7.7.2 can be found in the following link: http://www.genome.jp/dbget-bin/www_bget?ec:1.7.7.2.
New Composite parts
1. BBa_K1687002 is a composite part combining a EC 1.7.7.2

This part, submitted to the Registry, is used in our story “Houyi shoots down sun” in order to simulate the suns, which in our project produce heat and light but is later suppressed. We proudly use this part in our plasmid and are pleasing to report that it really worked. As time goes through, the molarity of nitrite and oxidized ferredoxins reduced like a bow-shaped curve.

Consisting of BBa_K1687000, an RBS (BBa_B0034), a GFP coding sequence and a double terminator (BBa_B0015), this part is able to produce both light and heat, just as the sun functions in the real world.
Part description Team:SZMS_15_Shenzhen