Team:Oxford/Parts

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<h1 >WELCOME TO iGEM 2014! </h1>
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<p>Your team has been approved and you are ready to start the iGEM season!
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<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
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<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:Oxford/Parts&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
 
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<a href="https://2014.igem.org/Team:Oxford"style="color:#000000">Home </a> </td>
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<h1>Oxford iGEM has submitted three parts to the registry, which are described on the relevant registry pages. </h1>
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<a href="https://2014.igem.org/Team:Oxford/Team"style="color:#000000"> Team </a> </td>
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<br><br>
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<a href="http://parts.igem.org/Part:BBa_K1446001">
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<u>Part no. 1 (BBa_K1446001)</u></a> is the gene coding for DcmA with an N-terminal pdu-microcompartment tag.
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<img src="https://static.igem.org/mediawiki/parts/c/c0/BBa_k1446001.jpg" style="float:left;position:relative; width:90%; margin-right:75%;margin-bottom:2%;" />
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<br><br>
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<a href="http://parts.igem.org/Part:BBa_K1446002">
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<u>Part no. 2 (BBa_K1446002)</u></a> is a superfolder GFP-gene with the N-terminal pdu-microcompartment tag. We have included a ribosome binding site upstream of the coding region as well as a his-tag at the C-terminus. This part has been used for fluorescent image analysis to show that the targeting mechanism of the N-terminal microcompartment tag works as expected.
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<img src="https://static.igem.org/mediawiki/parts/1/1d/BBa_k1446002.jpg" style="float:left;position:relative; width:90%; margin-right:75%;margin-bottom:2%;" />
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<a href="http://parts.igem.org/Part:BBa_K1446003">
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<u>Part no. 3 (BBa_K1446003)</u></a> is the dcmR gene with a tetR promoter. We have used this part to get fluorescence data for our model described <a href="https://2014.igem.org/Team:Oxford/biosensor_characterisation#show2">
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<u>here</u></a> and showed that mCherry expression increased at higher ATC (anhydrous tetracycline) concentration, as expected.
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<img src="https://static.igem.org/mediawiki/parts/8/80/BBa_k1446003.jpg" style="float:left;position:relative; width:90%; margin-right:75%;margin-bottom:2%;" />
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<a href="https://igem.org/Team.cgi?year=2014&team_name=Oxford"style="color:#000000"> Official Team Profile </a></td>
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Parts no. 1 and 2 belong to our bioremediation subproject and part 3 to our biosensor subproject.
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<a href="https://2014.igem.org/Team:Oxford/Project"style="color:#000000"> Project</a></td>
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<a href="https://2014.igem.org/Team:Oxford/Parts"style="color:#000000"> Parts</a></td>
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<h1>Oxford iGEM have also constructed further parts but were not fully in a BioBrick compatible plasmid thus were not sent before the deadline but will be on the registry in the near future</h1>
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<a href="https://2014.igem.org/Team:Oxford/Modeling"style="color:#000000"> Modeling</a></td>
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The following two constructs are based on the intergenic region shown below from the native DCM-degrading bacterium (Methylobacterium extorquens DM4):
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<img src="https://static.igem.org/mediawiki/2014/7/7f/Oxford_charac3.png" style="float:right;position:relative; width:80%; margin-right:10%;margin-bottom:2%;margin-left:10%;" />
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<h1>PdcmA-sfGFP</h1>
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<a href="https://2014.igem.org/Team:Oxford/Notebook"style="color:#000000"> Notebook</a></td>
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<img src="https://static.igem.org/mediawiki/2014/e/e8/Oxfordigem_pdcma.jpg" style="float:left;position:relative; width:90%; margin-right:75%;margin-bottom:2%;" />
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This construct involves the bidirectional promoter that has been characterised as a new tool for molecular biologists. In this construct sfGFP is placed under control in the PdcmA direction.
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Click <a href="https://2014.igem.org/Team:Oxford/biosensor_characterisation#show11">
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<u>here</u></a> to see characterisation on this part in plasmid PJ404.
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<br><br>
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<h1>PdcmR-sfGFP</h1>
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<img src="https://static.igem.org/mediawiki/2014/b/ba/Oxfordigem_pdcmR.jpg" style="float:left;position:relative; width:90%; margin-right:75%;margin-bottom:2%;" />
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Similar to the construct above, this involves the same bidirectional promoter with sfGFP in placed in the opposite direction under control of PdcmR.  
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Click <a href="https://2014.igem.org/Team:Oxford/biosensor_characterisation#show11">
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<u>here</u></a> to see characterisation on this part in plasmid PJ404.  
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<br>
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<h1>dcmA-sfGFP</h1>
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<img src="https://static.igem.org/mediawiki/parts/9/93/DcmA-sfGFP.jpg" style="float:left;position:relative; width:90%; margin-right:75%;margin-bottom:2%;" />
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For the <a href="https://2014.igem.org/Team:Oxford/codon_optimisation#show14">
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<u>analysis</u></a> of dcmA-expression we have used dcmA-fused to sfGFP in the pRSFDuet vector, which has a T7-promoter that is under lac-control.
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<a href="https://2014.igem.org/Team:Oxford/Safety"style=" color:#000000"> Safety </a></td>
 
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<a href="https://2014.igem.org/Team:Oxford/Attributions"style="color:#000000"> Attributions </a></td>
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<td > <h3>What information do I need to start putting my parts on the Registry? </h3></td>
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An important aspect of the iGEM competition is the use and creation of standard  biological parts. Each team will make new parts during iGEM and will submit them to the <a href="http://partsregistry.org"> Registry of Standard Biological Parts</a>. The iGEM software provides an easy way to present the parts your team has created. The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. 
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<strong>Note that if you want to document a part you need to document it on the <a href="http://partsregistry.org Registry"> Registry</a>, not on your team wiki.</strong> Future teams and other users and are much more likely to find parts on the Registry than on your team wiki.
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Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without a need 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.
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<h3>When should you put parts into the Registry?</h3>
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As soon as possible! 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 recall you will have of all details surrounding your parts. Remember you don't need to send us the DNA to create an entry for a part on the Registry. However, you must send us the sample/DNA before the Jamboree. Only parts for which you have sent us samples/DNA are eligible for awards and medal requirements.
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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. Check out part <a href="http://parts.igem.org/Part:BBa_K404003">BBa_K404003</a> for an excellent example of a highly characterized part.
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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.
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<tr><td colspan="3" > <h3> Parts Table</h3></td></tr>
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Any parts your team has created will appear in this table below:</td></tr>
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<groupparts>iGEM013 Oxford</groupparts>
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Latest revision as of 03:47, 18 October 2014


Parts


Oxford iGEM has submitted three parts to the registry, which are described on the relevant registry pages.



Part no. 1 (BBa_K1446001) is the gene coding for DcmA with an N-terminal pdu-microcompartment tag.

Part no. 2 (BBa_K1446002) is a superfolder GFP-gene with the N-terminal pdu-microcompartment tag. We have included a ribosome binding site upstream of the coding region as well as a his-tag at the C-terminus. This part has been used for fluorescent image analysis to show that the targeting mechanism of the N-terminal microcompartment tag works as expected.

Part no. 3 (BBa_K1446003) is the dcmR gene with a tetR promoter. We have used this part to get fluorescence data for our model described here and showed that mCherry expression increased at higher ATC (anhydrous tetracycline) concentration, as expected.

Parts no. 1 and 2 belong to our bioremediation subproject and part 3 to our biosensor subproject.





Oxford iGEM have also constructed further parts but were not fully in a BioBrick compatible plasmid thus were not sent before the deadline but will be on the registry in the near future


The following two constructs are based on the intergenic region shown below from the native DCM-degrading bacterium (Methylobacterium extorquens DM4):

PdcmA-sfGFP


This construct involves the bidirectional promoter that has been characterised as a new tool for molecular biologists. In this construct sfGFP is placed under control in the PdcmA direction. Click here to see characterisation on this part in plasmid PJ404.


PdcmR-sfGFP


Similar to the construct above, this involves the same bidirectional promoter with sfGFP in placed in the opposite direction under control of PdcmR. Click here to see characterisation on this part in plasmid PJ404.

dcmA-sfGFP


For the analysis of dcmA-expression we have used dcmA-fused to sfGFP in the pRSFDuet vector, which has a T7-promoter that is under lac-control.


Retrieved from "http://2014.igem.org/Team:Oxford/Parts"