Difference between revisions of "Team:Tec-Chihuahua/Parts"

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            <h1>Parts</h1>
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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>Basic Parts</h3>
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<b>Promoter T7 and RBS (BBa_K525998)</b>
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<p align="justify">This unregulated T7 promoter has high levels of transcription when the T7 RNA polymerase is present; thus, in order to express BioBricks™ under the control of this T7 promoter, a bacteria carrying a T7 polymerase gene has to be used.
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For our proof of concept, we needed to always express our enzymes in large quantities. Escherichia coli BL21(DE3) and Erwinia amylovora, the two bacteria used to test the three enzymes, both contain the T7 polymerase gene
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</p>
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<b>RBS (Elowitz 1999) -- defines RBS efficiency (BBa_B0034)</b>
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<p align="justify">A Ribosome Binding Site (RBS) is an RNA sequence found in mRNA to which ribosomes can bind and initiate translation. This RBS is based on the Elowitz repressilator.
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As one of our final BioBricks™ contains the three genes coding for our three enzymes, we added RBS sequences between each to increase translation efficiency.
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</p>
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<b>Autoinducer inactivation enzyme from Bacillus; hydrolyzes acetyl homoserine lactone (BBa_C0060)</b>
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<p align="justify">This gene encodes for the aiiA enzyme, which catalyzes the degradation of N-acyl-homoserine lactones (AHLs), quorum sensing autoinducers.
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The lack of communication that will result from the decrement of AHLs will result in the inability to sense population density and coordinate the expression of target genes, which in the case of several Gram-negative bacteria, include virulence factors.
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</p>
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<b>YhjH Gene From E.coli str. K12 (BBa_K861090)</b>
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<p align="justify">This gene encodes for the yhjH enzyme, which contains a EAL domain that catalyzes the reaction of c-di-GMP into GMP.
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C-di-GMP can serve as a second messenger to inhibit motility and increase biofilm formation and adhesion of bacteria, thus, the expression of this gene can make the bacteria more motile.
  
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</p>
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<b>EpsE Molecular Clutch Gene of B. subtilis (BBa_K143032)</b>
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<p align="justify">This gene encodes for the epsE enzyme, which has been suggested to function in a manner similar to a molecular clutch. If expressed inside a cell it will disengage the flagellum from the motor proteins in the cell membrane, causing the cell to no longer be able to swim effectively.
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EpsE could potentially be used as a controller of bacterial movement, promoting biofilm formation and inhibiting motility.
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</p>
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<b>T1 from E. coli rrnB (BBa_B0010)</b>
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<p align="justify">A transcriptional terminator consisting of a 64 bp stem-loop.
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For the construction of our genetic circuitry, an efficient and reliable terminator was needed.
  
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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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<img src="https://static.igem.org/mediawiki/2017/e/e0/T--Tec-Chihuahua--Biobrick.png" align="middle">
  
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<h3>Composite Pats</h3>
  
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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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<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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<ul>
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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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<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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<ul>
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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 Tec-Chihuahua</groupparts>
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Revision as of 22:10, 23 October 2017

Erwinions

Parts

Basic Parts


Promoter T7 and RBS (BBa_K525998)

This unregulated T7 promoter has high levels of transcription when the T7 RNA polymerase is present; thus, in order to express BioBricks™ under the control of this T7 promoter, a bacteria carrying a T7 polymerase gene has to be used. For our proof of concept, we needed to always express our enzymes in large quantities. Escherichia coli BL21(DE3) and Erwinia amylovora, the two bacteria used to test the three enzymes, both contain the T7 polymerase gene

RBS (Elowitz 1999) -- defines RBS efficiency (BBa_B0034)

A Ribosome Binding Site (RBS) is an RNA sequence found in mRNA to which ribosomes can bind and initiate translation. This RBS is based on the Elowitz repressilator. As one of our final BioBricks™ contains the three genes coding for our three enzymes, we added RBS sequences between each to increase translation efficiency.

Autoinducer inactivation enzyme from Bacillus; hydrolyzes acetyl homoserine lactone (BBa_C0060)

This gene encodes for the aiiA enzyme, which catalyzes the degradation of N-acyl-homoserine lactones (AHLs), quorum sensing autoinducers. The lack of communication that will result from the decrement of AHLs will result in the inability to sense population density and coordinate the expression of target genes, which in the case of several Gram-negative bacteria, include virulence factors.

YhjH Gene From E.coli str. K12 (BBa_K861090)

This gene encodes for the yhjH enzyme, which contains a EAL domain that catalyzes the reaction of c-di-GMP into GMP. C-di-GMP can serve as a second messenger to inhibit motility and increase biofilm formation and adhesion of bacteria, thus, the expression of this gene can make the bacteria more motile.

EpsE Molecular Clutch Gene of B. subtilis (BBa_K143032)

This gene encodes for the epsE enzyme, which has been suggested to function in a manner similar to a molecular clutch. If expressed inside a cell it will disengage the flagellum from the motor proteins in the cell membrane, causing the cell to no longer be able to swim effectively. EpsE could potentially be used as a controller of bacterial movement, promoting biofilm formation and inhibiting motility.

T1 from E. coli rrnB (BBa_B0010)

A transcriptional terminator consisting of a 64 bp stem-loop. For the construction of our genetic circuitry, an efficient and reliable terminator was needed.

Composite Pats

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