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<font face="trebuchet ms" style="color:#FFFFFF" size="5">'''iGEM 2009 - Imperial College London Team'''</font><br>
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<center><font face="trebuchet ms" style="color:#FFFFFF" size="3">''Work in progress ...''</font><br></center>
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<h1> The E.ncapsulator </h1>


==ToDo & Deadlines==
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<b><i>Click on the bubble to expand so you can see all the text in each calendar entry</i></b>
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==Contents==
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<b>*[[IGEM:IMPERIAL/2009/Main |Main page - Navigate through modules]]</b><br>
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*[[IGEM:IMPERIAL/2009/Weekly_Aims |Weekly Aims]]<br>
<td id="Table" width="52%" bgcolor=#6e92e3>
*[[IGEM:IMPERIAL/2009/Feedback_&_Debriefs |Feedback & Debriefs]]<br>
<div id="Title">The E.ncapsulator: the disease killer</div>
*[[IGEM:IMPERIAL/2009/Encapsulation | Encapsulation project overview]]<br>
<img src="http://openwetware.org/images/e/e8/II09_Encapsulator.png" width="50%" align="right">
**[[IGEM:IMPERIAL/2009/NAAAME |Module 1 : Compound Production]]<br>
**[[IGEM:IMPERIAL/2009/Encapsulation/Phase2 |Module 2 : Encapsulation and Trehalose Production]]<br>
**[[IGEM:IMPERIAL/2009/Encapsulation/Module3 |Module 3 : Genomic Neutralisation]]<br>
**[[IGEM:IMPERIAL/2009/Encapsulation/Quality_Control |Quality Control]]<br>
<br>
*[[IGEM:IMPERIAL/2009/Dry_Lab|Dry Lab]]
**[[IGEM:IMPERIAL/2009/Encapsulation/Modelling |Modelling]]<br>
*[[IGEM:IMPERIAL/2009/Wet_Lab |Wet Lab]]<br>
<br>
*[[IGEM:IMPERIAL/2009/Assays_Protocols |Assay Protocols and Cloning Strategies]]<br>
** [[IGEM:IMPERIAL/2009/Assays_Protocols/WetLab_Plan |Up to Date WetLab Plan and Cloning Strategies]]
**[[IGEM:IMPERIAL/2009/Assays_Protocols/Testing_Constructs |Testing Constructs]]
** [[IGEM:IMPERIAL/2009/Assays_Protocols/Shopping |List of Assays]]
** [[IGEM:IMPERIAL/2009/Assays_Protocols/Shopping_List |Shopping List]]
*[[IGEM:IMPERIAL/2009/Encapsulation/Biobricks |BioBrick Designs]]<br>
*[[IGEM:IMPERIAL/2009/Encapsulation_Parts |Schematics and Parts]]<br>
**[[IGEM:IMPERIAL/2009/Encapsulation/Timers | Timer]] <br>
*[[IGEM:IMPERIAL/2009/Primers |Primers for PCR]]<br>
*[[IGEM:IMPERIAL/2009/Specifications |Specifications by Module]]<br><br>
*[[IGEM:IMPERIAL/2009/Past_Presentations| Past Presentations]]<br>
**[[IGEM:IMPERIAL/2009/Past_Presentations/Journal_Clubs| Journal Clubs]]<br>
**[[IGEM:IMPERIAL/2009/Past_Presentations/Tutorials| Tutorials]]<br>
*[[IGEM:IMPERIAL/2009/Brainstormings | Brainstorming]]<br>
** [[IGEM:IMPERIAL/2009/Brainstormings | Initial Ideas]]<br>
**[[IGEM:IMPERIAL/2009/Application_Analysis | Possible Encapsulation Applications]]<br>
**[[IGEM:IMPERIAL/2009/Encapsulation/Applications |Drug Delivery Applications - Details]]<br>
**[[IGEM:IMPERIAL/2009/Encapsulation/Applications | Applications Page]]
<br><br>
<br><br>


==Useful Links==
<div id="Paragraph">A major, yet unsolved, challenge in the pharmaceutical industry involves overcoming the harsh acidic environment of the stomach in order to deliver proteins to the gut. This year the Imperial College iGEM team has decided to tackle this problem by developing an innovative, self-contained drug fabrication and delivery system. In our 'E.ncapsulator', Escherichia coli will be engineered not only to efficiently manufacure important biopharmaceuticals, but also to coat and protect protein based drugs until release in the small intestine.<br><br>
*[http://2009.igem.org/Team:Imperial_College_London Imperial iGEM 2009 Official Wiki]
Furthermore, in order to create E.ncapsulator tablets for oral delivery, there has been much focus on designing and engineering a number of modules for implementation in E.coli. The modularity that is central to our project will be evident in the areas of protein drug production, self-encapsulation and genomic neutralisation. Utilising the E.coli bacterium, we are creating a re-usable chassis that will allow the development of a range of biopharmaceuticals to be delivered to the gut. Our E.ncapsulator is therefore intended as an elegant solution to, not one, but a range of human ailments and conditions, which cannot currently be successfully treated by oral drugs.<br><br>
*[http://2009.igem.org/Main_Page iGEM 2009 Main Page]
The first module involves engineering E.coli to synthesise the protein drug of interest to a tuneable threshold. Once accomplished, activation of module two initiates the encapsulation phase, in which E.coli coats itself in a protective layer of colanic acid to form the E.ncapsulator. This protective capsule is what shields the biopharmaceutical against the harsh acidic environment of the stomach. The third module, genomic neutralisation, is composed of a ‘suicide trigger’ mechanism that destroys the genetic material of the bacteria. Finally, once in the small intestine, the capsule will be degraded, thereby releasing the designed biopharmaceutical to the gut micro biota where it can carry out its intended function.<br><br>
*[http://www.partsregistry.org/Main_Page BioBrick Registry]
The self-encapsulation of a synthetic biology chassis is new to iGEM and represents a completely novel and innovative approach to biopharmaceutical design, manufacture and delivery. Throughout the project we have followed an engineering approach that incorporates modular design, detailed modelling and simulation as well as systematic integration. Using such an approach, we are hopeful that the E.ncapsulator will be coming soon to a Pharmacy near you!</div>
*[http://www.ecoliwiki.net/colipedia/index.php/Welcome_to_EcoliWiki  Ecoli wiki]<br>
<br>
 
==Team Roles==
<i>Change your role when applicable</i><br>
<br>
<b>Charles</b> - M1/Wiki<br>
<b>Dave</b> - M2<br>
<b>Dineka</b> - M3/Wet lab<br>
<b>James</b> -  M2/Wet lab<br>
<b>Kun</b> - M3<br>
<b>Nuri</b> - M2<br>
<b>Royah</b> - Wet lab/ Primer design for In-Fusion SLIC<br>
<b>Tianyi</b> - M1<br>
<br>
<b><i>Please write what you have accomplished each day. Click the link for the day, this will take you to a page where you can give a brief summary of what you have been doing.</i></b>
 
'''[[User:Vincent Rouilly|Vincent]] 04:55, 15 August 2009 (EDT):'''The calendar is not part of the Imperial/2009 sub-domain. It should be under IGEM:IMPERIAL/2009. Change name=Calendar:TeamProgress to name=IGEM:IMPERIAL/2009/Calendar:TeamProgress. And, copy the existing pages.<br>
<b>[[User:Royah Vaezi|Royah Vaezi]] 11:50, 15 August 2009 (EDT)</b>:Sorry about that; I've made the necessary changes.
 
<calendar>
name=Calendar:IGEM:IMPERIAL/2009/Calendar:TeamProgress
view=threemonths
format=%name/%year-%month-%day
weekstart=7
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==Wiki Updates==
{{Special:Recentchanges/b=IGEM:IMPERIAL&limit=50}}
<br>
 
==Synthetic Biology @ Imperial==
 
* [http://www3.imperial.ac.uk/systemsbiology Institute of Systems and Synthetic Biology]
* Center of Synthetic Biology ([http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/newssummary/news_22-12-2008-13-10-50?newsid=52514 press release])
* [[Imperial_College/Courses/Spring2008/Synthetic_Biology/Syllabus | Synthetic Biology Course @ Imperial]]<br><br>
 
==iGEM resources==
 
* [http://igem.org iGEM website at MIT]
* [http://parts.igem.org Registry of BioBricks]<br>
* [[IGEM:IMPERIAL/2009/IGEMUPDATES | iGEM updates]]<br>
 
== Advisor Contributions ==
 
Schumann lab from Uni. Beyreuth, DE have done [http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652005000100009&lng=en&nrm=iso&tlng=en some interesting work] on using spores to direct antigens to the gut - to act as vaccines. Sporulation guys might also be interested in [http://mmbr.asm.org/cgi/content/abstract/63/1/1 this paper], describing the ''B. sub'' coat protein (and how it's hilariously complex but not all required). Oh, and ''subtilis'' spores [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2519260 will] [http://aem.asm.org/cgi/content/abstract/67/9/3819 germinate] in the gut (probably), justifying using the killswitch!
 
Killswitch guys, I think perhaps looking into recombinases as opposed to restriction enzymes would be useful as they won't act on host DNA. [http://aem.asm.org/cgi/content/full/72/4/2520 Xer and Dif sites] will recombine with themselves in presence of the required enzyme, excising any genes between them - you could flank genes with them, then express the enzyme to chop your construct up. Sites are required to be within ≈5kb of each other, I think, so random ones on host DNA shouldn't be affected. It might take a while to work so look into the time; could be useful as a fallback, anyway.


Biobrick images you can use if you need (advisors like named/labelled circuit diagrams!): [[Image:P.png]] [[Image:R.png]] [[Image:G.png]] [[Image:T.png]]
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~ [[User:Tom Adie|Tom Adie]] 15:44, 20 July 2009 (EDT)
</table>
 
Killing guys, things to keep in mind for the restriction enzymes...
 
1. Restriction enzyme:
** Cuts at short sequences; makes it easier to insert (see next point) and will cut in the genome and plasmid more often by chance
** Restriction sites be inserted by codon changes; GeneArt optimise constructs to remove restriction sites all the time, so putting them in should be OK
** Is not native; if it's expressed somehow by the cell, it'll suicide on its own
2. Regulation of expression:
** Needs to be near 100% off when off; even a low level of expression will destroy your cells long before any product is produced
** You may want to look for a less-efficient enzyme so small leakage wouldn't be that bad; or an enzyme that is degraded relatively quickly
** Bistable switch with no leakage might be good; or flippase regulation! My pet idea for the bioremediation project last year =P
 
You can also insert sites after the transcription terminators in all your genes to ensure full destruction of the construct, and maybe add your sites into normal bricks (terminators etc.) and put them up as variants.
 
~ [[User:Tom Adie|Tom Adie]] 11:41, 23 July 2009 (EDT)
 
 
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Revision as of 10:26, 16 August 2009

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<ul> <li class="menu_header"><img src="http://2009.igem.org/wiki/images/c/c1/II09_Thumb_m1.png" width="15%" align="left"> Module 1: Protein production</li> <li><a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2009/M1"> Overview</a></li> <li><a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2009/M1/Genetic"> Genetic circuit</a></li> <li><a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2009/M1/Results"> Results</a></li> <li><a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2009/M1/Modelling"> Modelling</a></li> </ul>

<ul> <li class="menu_header"><img src="http://2009.igem.org/wiki/images/d/df/II09_Thumb_m2.png" width="15%" align="left">Module 2: Encapsulation &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</li> <li><a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2009/M2"> Overview</a></li> <li><a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2009/M2/Genetic"> Genetic circuit</a></li> <li><a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2009/M2/Results"> Results</a></li> <li><a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2009/M2/Modelling"> Modelling</a></li> <li><a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2009/M2/Pictures"> Picture gallery</a></li> </ul>

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<td id="Table" width="52%" bgcolor=#6e92e3> <div id="Title">The E.ncapsulator: the disease killer</div> <img src="http://openwetware.org/images/e/e8/II09_Encapsulator.png" width="50%" align="right"> <br><br>

<div id="Paragraph">A major, yet unsolved, challenge in the pharmaceutical industry involves overcoming the harsh acidic environment of the stomach in order to deliver proteins to the gut. This year the Imperial College iGEM team has decided to tackle this problem by developing an innovative, self-contained drug fabrication and delivery system. In our 'E.ncapsulator', Escherichia coli will be engineered not only to efficiently manufacure important biopharmaceuticals, but also to coat and protect protein based drugs until release in the small intestine.<br><br> Furthermore, in order to create E.ncapsulator tablets for oral delivery, there has been much focus on designing and engineering a number of modules for implementation in E.coli. The modularity that is central to our project will be evident in the areas of protein drug production, self-encapsulation and genomic neutralisation. Utilising the E.coli bacterium, we are creating a re-usable chassis that will allow the development of a range of biopharmaceuticals to be delivered to the gut. Our E.ncapsulator is therefore intended as an elegant solution to, not one, but a range of human ailments and conditions, which cannot currently be successfully treated by oral drugs.<br><br> The first module involves engineering E.coli to synthesise the protein drug of interest to a tuneable threshold. Once accomplished, activation of module two initiates the encapsulation phase, in which E.coli coats itself in a protective layer of colanic acid to form the E.ncapsulator. This protective capsule is what shields the biopharmaceutical against the harsh acidic environment of the stomach. The third module, genomic neutralisation, is composed of a ‘suicide trigger’ mechanism that destroys the genetic material of the bacteria. Finally, once in the small intestine, the capsule will be degraded, thereby releasing the designed biopharmaceutical to the gut micro biota where it can carry out its intended function.<br><br> The self-encapsulation of a synthetic biology chassis is new to iGEM and represents a completely novel and innovative approach to biopharmaceutical design, manufacture and delivery. Throughout the project we have followed an engineering approach that incorporates modular design, detailed modelling and simulation as well as systematic integration. Using such an approach, we are hopeful that the E.ncapsulator will be coming soon to a Pharmacy near you!</div>

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